The explicative video is available at [[YouTube]](https://youtu.be/6YIkDhN4SaY) ## One-Sentence Summary Our work presents an ant-inspired Mushroom Body model on a compact, low-cost robotic platform, achieving continuous, efficient, and adaptable navigation in real-world environments with minimal computational resources. ![Insert a preview image here](antcar_and_ant.jpg) ## Abstract Solitary foraging ants excel at route following using minimal neural resources, Robots don't. Recent biological studies proposed lateralized, nest-centric memories to explain ants' direct visual homing but did not address how ants follow curved visual routes away from their nest. We present a biologically inspired neuromorphic model for one-shot panoramic route learning and continuous route following, implemented on a compact car-like robot, Antcar. We demonstrate that route-centric lateralized memories, inspired by the insect mushroom body, enable Antcar to achieve bi-directional route-following, with motivation-driven recognition of route extremities and familiarity-based velocity control. With rigorous Lyapunov-based stability analysis and an empirical memory scalability evaluation, the model was tested over 1.6 km across 113 challenging real-world trials. The system achieves less than 25 cm median lateral error using minimal resources (800-pixel input, 300 MB RAM, 500 mW power, and 18.75 kB memory per 50 m route), offering insights into insect cognition and advancing autonomous robotics under strict resource constraints. ## Project Setup and Environment Preparation Just run the run.sh file and it will run every code, it will put the results in results folder, you can see the figures generated in the results/figure folder. You will find the generated Jupyter notebooks as well and the mapping folders for different oscillations amplitude of learning. ## Citation If this work is helpful, please cite as: *** Upon Publication*** The code used in the AntCar robot for real-time learning and route following is available upon request. ## Acknowledgments G.G. was supported by a doctoral fellowship grant from Aix Marseille University and the French Ministry of Defense (AID - Agence Innovation D\'{e}fense, agreement \#A01D22020549 ARM/DGA /AID). G.G., J.R.S. and F.R. were also supported by Aix Marseille University and the CNRS (Life Science, Information Science, and Engineering and Science \& technology Institutes). The facilities for the experimental tests has been mainly provided by ROBOTEX 2.0 (Grants ROBOTEX ANR-10-EQPX-44-01 and TIRREX ANR-21-ESRE-0015). ## Contact gabriel.gattaux_at_univ-amu.fr ## License [License]"> The explicative video is available at [[YouTube]](https://youtu.be/6YIkDhN4SaY) ## One-Sentence Summary Our work presents an ant-inspired Mushroom Body model on a compact, low-cost robotic platform, achieving continuous, efficient, and adaptable navigation in real-world environments with minimal computational resources. ![Insert a preview image here](antcar_and_ant.jpg) ## Abstract Solitary foraging ants excel at route following using minimal neural resources, Robots don't. Recent biological studies proposed lateralized, nest-centric memories to explain ants' direct visual homing but did not address how ants follow curved visual routes away from their nest. We present a biologically inspired neuromorphic model for one-shot panoramic route learning and continuous route following, implemented on a compact car-like robot, Antcar. We demonstrate that route-centric lateralized memories, inspired by the insect mushroom body, enable Antcar to achieve bi-directional route-following, with motivation-driven recognition of route extremities and familiarity-based velocity control. With rigorous Lyapunov-based stability analysis and an empirical memory scalability evaluation, the model was tested over 1.6 km across 113 challenging real-world trials. The system achieves less than 25 cm median lateral error using minimal resources (800-pixel input, 300 MB RAM, 500 mW power, and 18.75 kB memory per 50 m route), offering insights into insect cognition and advancing autonomous robotics under strict resource constraints. ## Project Setup and Environment Preparation Just run the run.sh file and it will run every code, it will put the results in results folder, you can see the figures generated in the results/figure folder. You will find the generated Jupyter notebooks as well and the mapping folders for different oscillations amplitude of learning. ## Citation If this work is helpful, please cite as: *** Upon Publication*** The code used in the AntCar robot for real-time learning and route following is available upon request. ## Acknowledgments G.G. was supported by a doctoral fellowship grant from Aix Marseille University and the French Ministry of Defense (AID - Agence Innovation D\'{e}fense, agreement \#A01D22020549 ARM/DGA /AID). G.G., J.R.S. and F.R. were also supported by Aix Marseille University and the CNRS (Life Science, Information Science, and Engineering and Science \& technology Institutes). The facilities for the experimental tests has been mainly provided by ROBOTEX 2.0 (Grants ROBOTEX ANR-10-EQPX-44-01 and TIRREX ANR-21-ESRE-0015). ## Contact gabriel.gattaux_at_univ-amu.fr ## License [License]">

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  1. [Genomics (Duplex Sequencing)]\ \
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[Earth Sciences\ \ 5 | Mar | 2026\ \ Desert dust exerts twice the longwave radiative heating estimated by climate models\ \ This code obtains the DustCOMM data set, including a calculation of the longwave direct radiative effect of desert dust. The main function to run DustCOMM is main_constrain_modern_dust_cycle.m. This function takes the following inputs: \ \ • The number of desired bootstrap iterations (e.g., ~50 for quick results; 1000 iterations are normally used for results used in a publication) \ \ • The model # to use (this should almost always be zero) \ \ • A spare variable that can be used for various purposes (this should almost always be zero) \ \ • The year for which to run the code. This should be 0 to run the code for the standard 2004-2008 climatology obtained in Kok et al. (2021a, b). \ \ The main_constrain_modern_dust_cycle.m code performs the following actions: \ \

  • It initializes variables and settings. Some of this is done in the sub-scripts load_data_and_pars_modern_dust_cycle.m and initialize_variables.m \ \
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  • Copy\ \
It then calculates the various attributes of the global dust cycle, including the LW direct radiative effect (in the function calc_LW_rad_forcing.m, which is called by the script calc_results_modern_dust_cycle.m)\\
```\\
\\
- The processing of the results of each bootstrap iteration occurs in process\_results\_modern\_dust\_cycle \\
\\
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The abstract of the corresponding article, titled " **Desert dust exerts twice the longwave radiative heating estimated by climate models**", is as follows: \\
\\
Although desert dust is the most abundant atmospheric aerosol by mass, its longwave radiative effects remain unclear, obscuring the impacts of dust on weather and climate. Using a data-driven analytical model constrained by observations, we show that scattering and absorption of longwave radiation by dust heats the planet by +0.25 ± 0.06 W m⁻² (90% confidence). This is nearly twice the value simulated by current climate models, which omit longwave scattering and underrepresent super coarse dust (diameter > 10 μm). These omissions bias modeled surface energy fluxes, cloud responses, precipitation, and atmospheric circulation. At the global scale, the sign and magnitude of the net dust direct radiative effect remain uncertain, with additional work needed to constrain shortwave cooling effects. These findings show that improving the representation of dust interactions with longwave radiation can improve weather forecasting and is essential to resolve the role of dust in climate change.\\
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A nutrient bottleneck controls antibiotic efficacy in structured bacterial populations](/content/explore/63ec11bb-168c-45fc-9e02-7962e9320a40?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[The included code includes MATLAB function lines.m and script runsim\_codeocean.m for simulations reported in the manuscript “A nutrient bottleneck controls antibiotic efficacy in structured bacterial populations” by Anna M. Hancock, Arabella S. Dill-Macky, Jenna A. Moore, Catherine Day, Mohamed S. Donia, and Sujit S. Datta, submitted for consideration as an article in Nature Communications.\\
\\
Antibiotic resistance is a growing global health threat. Although antibiotic activity is well studied at the single cell level, many infections are caused by spatially structured multicellular populations where consumption of scarce nutrients establishes strong spatial variations in their abundance. These nutrient variations have long been hypothesized to help bacterial populations tolerate antibiotics, since single-cell studies link antibiotic tolerance to metabolic activity, and thus, local nutrient availability. Here, we test this hypothesis by visualizing cell death in structured \\textit{Escherichia coli} populations exposed to nutrient (glucose) and antibiotic (fosfomycin). We find that nutrient availability acts as a bottleneck to antibiotic killing, causing death to propagate through the population as a traveling front. By integrating our measurements with biophysical theory and simulations (sample code included here), we establish quantitative principles that explain how collective nutrient consumption can limit the progression of this \`\`death front,'' protecting a population from a nominally deadly antibiotic dose. While increasing nutrient supply can overcome this bottleneck, in some cases, excess nutrient unexpectedly \\emph{promotes} the regrowth of resistant cells. Altogether, this work provides a key step toward predicting and controlling antibiotic treatment of spatially structured bacterial populations, yielding biophysical insights into collective behavior and guiding strategies for effective antibiotic stewardship.\\
\\
The parameters in runsim\_codeocean.m, the code run in this demo, recreate data reported in Fig. 3E-G. By changing the input parameters within the script, this same code, which calls the function lines.m to evaluate the model reported in the manuscript, can generate simulation results reported elsewhere in the manuscript.](/content/explore/63ec11bb-168c-45fc-9e02-7962e9320a40?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[All code was demo’ed on MATLAB 2024a, which can be installed following directions found here:](/content/explore/63ec11bb-168c-45fc-9e02-7962e9320a40?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [https://www.mathworks.com/help/install/index.html](https://www.mathworks.com/help/install/index.html)

Please contact Anna Hancock ( [annahancock@princeton.edu](mailto:annahancock@princeton.edu)) with questions.

Anna M. Hancock et al.

[Open Capsule](/content/capsule/9055864/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Chemistry\\
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1 \| Jun \| 2026\\
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Machine-learning enhanced simulations predict graphene is microscopically hydrophobic and not wetting transparent](/content/explore/474d0963-5cbe-4037-890d-218e0acab15d?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[This script is primarily used to analyze the water orientation in our graphene/water systems. To run the script, using the command "julia angle\_orientation.jl >> angle.txt 2>&1 &"](/content/explore/474d0963-5cbe-4037-890d-218e0acab15d?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[If you use the script in your work, please cite the associated publication:](/content/explore/474d0963-5cbe-4037-890d-218e0acab15d?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [https://doi.org/10.1038/s41467-026-71053-3](https://doi.org/10.1038/s41467-026-71053-3)

Dianwei Hou

[Open Capsule](/content/capsule/6138159/tree/v2/index.html)

[Associated article](https://doi.org/10.1038/s41467-026-71053-3) published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
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2 \| Feb \| 2026\\
\\
Physical limits of sea-level rise adaptation in global river deltas: code instruction\\
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Abstract: Sea-level rise threatens deltas worldwide, requiring adaptation to flood risks. Delta adaptation is typically presented as a choice between five strategies: advance, protect-closed, protect-open, accommodate, and retreat. However, a full assessment of the physical feasibility of these strategies across deltas remains limited. We present a first-order assessment of the physical solution space for adaptation to sea-level rise for nearly 800 deltas globally. We find that current technologies, resources, and space provide at least one physically feasible delta-wide strategy for every delta to adapt by 2100. This number may increase in the future through technical innovation or collaboration between deltas. The type and number of physically feasible strategies are mostly determined by delta’s physical characteristics, whereby, large, urbanized, or frequently flooded deltas have fewer options than small, rural, or infrequently flooded deltas. Our analysis highlights the risk of resource limitations as global deltas will need to adapt simultaneously to future flood risks.\\
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This capsule contains the code and datasets used to map the physical solution space of global deltas by 2100 under a number of climate scenarios. The workflow combines data preprocessing, modelling and visualizations. The model determines the physical feasibility of adaptation by assessing the physical characteristics of each delta and applying three thresholds to assess whether measures can be implemented. The visualization scripts include the physical solution space figures for individual and global deltas, and the material requirements for each strategy.\\
\\
Kiara Lasch, Jaap Nienhuis, Gundula Winter & Marjolijn Haasnoot](/content/explore/06e6320f-9b17-4f3f-b5e6-05f1364720b1?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8754340/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Chemistry\\
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30 \| Jan \| 2026\\
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Structural defects in amyloid-β fibrils drive secondary nucleation\\
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Uses standard Python packages to fit a simple quadratic ligand binding model to FCS data on Brichos binding to Ab40 fibrils.\\
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Jing Hu](/content/explore/995ddf4e-bed5-438b-b91b-4bcabf8ac37e?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9535526/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
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29 \| Jan \| 2026\\
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Engineering non-exponential proliferation in Escherichia coli using functionalized protein aggregates\\
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Individual based model for the manuscript Engineering non-exponential proliferation in Escherichia coli using functionalized protein aggregates\\
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Ronald Van Eyken et al.](/content/explore/5454fa10-9bfa-4f72-b755-0bf2a76b6ab7?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/1884928/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
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2 \| Mar \| 2026\\
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Tropical cyclone rainfall extends inland\\
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This capsule is for you who want to reproduce the plots in the article "Tropical cyclone rainfall extends inland in a warming and urbanising world". All required packages are installed, and you can click run to plot all results.\\
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E Deng et al.](/content/explore/747ff3c8-2378-4e24-ac03-4a968bdedb52?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/0568189/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
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28 \| Jan \| 2026\\
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eQTL in diseased colon tissue identifies novel potential target genes associated with IBD\\
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IBD colon eQTL\\
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Nina Nishiyama](/content/explore/3d8a6465-6614-4043-887f-b4788af18316?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/1077277/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
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28 \| Jan \| 2026\\
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code for "Emergent giant topological Hall effect in twisted Fe3GeTe2 metallic system"\\
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Code for "Emergent giant topological Hall effect in twisted Fe3GeTe2 metallic system"\\
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Yuhang Li](/content/explore/04a765dd-c0ff-4e52-9a25-a010f95df4bd?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2336028/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
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24 \| Jan \| 2026\\
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Early Diagnosis of Pancreatic Ductal Adenocarcinoma by Signal-Enhanced Lateral Flow Immunoassay: SELFI\\
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Pancreatic ductal adenocarcinoma (PDAC) is linked to high incidence and mortality rates because it is often detected in later stages, when the prognosis is poor. However, the current state-of-the-art methods for diagnosing early PDAC tend to be invasive, time-consuming, and unreliable, primarily due to the difficulties associated with the early detection of pancreatic cancers. Here, we report a quick and sensitive method for the early diagnosis of PDAC using a signal-enhanced lateral flow immunoassay called SELFI. We developed SELFI, which can generate a strong colorimetric signal through multiple hotspots formed by plasmonic gold nanoparticles (AuNPs) assembled on a silica bead. Our SELFI assay achieved a 28-fold increase in the limit of detection compared to conventional lateral flow immunoassays using 20 nm AuNPs, providing results within 15 min. We demonstrated that SELFI can be utilized for the early diagnosis of PDAC, as indicated by a receiver operating characteristic curve and a larger area under the curve compared to the enzyme-linked immunosorbent assay (\*\*\*\*P < 0.0001). SELFI's effective diagnostic features could enhance the timely identification of PDAC and may also serve in the early diagnosis of a range of other diseases.\\
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Sohyeon Jang et al.](/content/explore/90b34f8d-18fa-4897-8b02-23aa9be23c04?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/7919487/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
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23 \| Jan \| 2026\\
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Continuously trapped matter-wave interferometry in magic Floquet-Bloch band structures](/content/explore/1713a82a-f0aa-4dda-b94a-a58936debc26?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[This capsule provides the calculations of magic Floquet-Bloch band structures. It is based on a package we developed named](/content/explore/1713a82a-f0aa-4dda-b94a-a58936debc26?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [MuscleMuseum](https://github.com/XiaoCasd/MuscleMuseum) which computes the lattice properties. Simply run `main.m` to test the functionality.

The `plotFloquetBand` script computes and plots the Floquet-Bloch P-D hybridized bands, corresponding to Figure 1 of the main text. The produced figure is saved in `/results`

The `findMagicDepthStatic` and `findMagicDepthDressed` scripts compute magic band structures assuming static and dressed bands, respectively. They produce `.mat` files saved in `/results`. Each `.mat` contains variables including:

- loopSizeTheory: loop size in 2ℏkL2\\hbar k\_L2ℏkL​
- magicDepthTheory: magic depth in ERE\_RER​
- modDepth: relative modulation depth
- Frequency: modulation frequency in Hz
- fringeFrequency: fringe frequency in Hz

`findMagicDepthDressed` computes two extra quantities:

- toleranceTheory: tolerance against depth fluctuations, in ERE\_RER​
- toleranceTheoryRelative : relative tolerance again depth fluctuations

Note: in `findMagicDepthStatic` and `findMagicDepthDressed`, the variable `nl` can be modified to set how fine we scan across the loop size range. The `divisor` parameter can be changed to modify the applied force, given by F=Mg/divisorF=Mg/divisorF=Mg/divisor.

Xiao Chai et al.

[Open Capsule](/content/capsule/8593166/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Chemistry\\
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21 \| Jan \| 2026\\
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Realistic atomic model for amorphous nanoporous carbons\\
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Amorphous porous carbons have been widely used as electrodes for energy storage. However, due to their structural heterogeneity and complex pore topology, the absence of reliable atomic carbon models hinders understanding energy storage mechanisms through molecular simulations. Here, we developed a modelling approach capturing the rich experimental information of small angle X-ray scattering, gas adsorption for three-dimensional morphology (mGRF) construction\\
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Guang Feng & Jiaxing Peng](/content/explore/937a22fe-dcf2-40e0-9c24-a474c46e8d43?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/5025667/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
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20 \| Jan \| 2026\\
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SpatiotemporalMotifs.jl: Analyzing nested spatiotemporal waves in mouse Neuropixels data\\
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Julia code for reproducing the results of " _Nested spatiotemporal theta-gamma waves organize hierarchical visual processing_".\\
In this work, we analyzed mouse Neuropixels data to reveal a cross-scale principle of spatiotemporal dynamics involving low-frequency θ, high-frequency γ, and neuronal spiking that coordinate translaminar and hierarchical visual processing.\\
Detailed instructions for reproducing calculations and figures can be found in `code/SpatiotemporalMotifs.jl/README.md`.\\
\\
Brendan Harris & Pulin Gong](/content/explore/91bf4eb6-2352-4bcb-931f-e801c05176dd?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/4585157/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Chemistry\\
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20 \| Jan \| 2026\\
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Catalytic Proximal Protein Oligomerization (CaPPO) as a Novel Anti-Tumor Strategy Targeting WDR5\\
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Code for extracting Peak Current and Dwell Time from every events of nanopore sensing in the article of "Catalytic Proximal Protein Oligomerization (CaPPO) as a Novel Anti-Tumor Strategy Targeting WDR5".\\
\\
Yizheng Fang et al.](/content/explore/59a8cfcc-fa95-4b9e-a6e5-6e9e1d92f4d5?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/3397769/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Chemistry\\
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19 \| Mar \| 2026\\
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Gallium in Liquid State Shows Nuclease-Mimicking Activity\\
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This repository contains all code and data necessary to reproduce the ONT DNA sequencing results presented in the paper titled "Gallium in Liquid State Shows Nuclease-Mimicking Activity".\\
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Li Liu](/content/explore/4a7421e5-5288-4550-bb35-992d43c44caa?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/0837350/tree/v3/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
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19 \| Jan \| 2026\\
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Bioinspired spiking architecture enables energy constrained touch encoding\\
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This capsule enables the reproduction of the main results presented in the paper: "Bioinspired Spiking Architecture Enables Energy-Constrained Touch Encoding".\\
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Andrea Ortone et al.](/content/explore/88147aef-99a1-438f-b659-e093da9b9277?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/1018585/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
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12 \| Jan \| 2026\\
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Benchmarking PRS methods for risk prediction of 36 complex traits in UK Biobank by establishment of a large-scale PRS computation platform PRS-hub](/content/explore/cac63269-145b-4733-b1ff-5a82dfd52987?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[**PRS-hub\_offline** \\
PRS-hub is a platform for batch offline calculation of various Polygenic Risk Score (PRS) methods, built on WDL, allowing for local or server-based execution. Below are detailed instructions for installation, dependencies, and usage.\\
**Installation**\\
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1. Clone this repository:\\
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bash\\
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Copy\\
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```bash\\
git clone https://github.com/yourusername/PRS-hub.git\\
```\\
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2. Set the `PRSHUB_PATH` environment variable in your `.bashrc` file to quickly call scripts from the installation path:\\
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\\
\\
bash\\
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Copy\\
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```bash\\
export PRSHUB_PATH=`pwd`/PRS-hub_offline\\
```\\
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3. Save and source the `.bashrc` file to apply changes:\\
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bash\\
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Copy\\
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```bash\\
source ~/.bashrc\\
```\\
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If the installation path changes, simply update the `PRSHUB_PATH` value accordingly.\\
**Dependencies** \\
To ensure the platform runs correctly, please install the following software and dependencies:](/content/explore/cac63269-145b-4733-b1ff-5a82dfd52987?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

2. [**Cromwell**: This platform is based on WDL (Workflow Description Language), so Cromwell is required to execute WDL scripts. You can download Cromwell and refer to the installation instructions on the](/content/explore/cac63269-145b-4733-b1ff-5a82dfd52987?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Cromwell GitHub page](https://github.com/broadinstitute/cromwell).

[**R and Python**:\\
\\
   - **R** and **Python** need to be included in the `PATH` to allow direct usage of the `Rscript` and `python` commands. If not installed, they can be added via Conda, and the Conda environment path can be appended to `.bashrc`.\\
     \\
     For example, install R and Python using Conda:\\
     \\
     \\
     \\
     bash\\
     \\
     Copy\\
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     ```bash\\
     conda install -c conda-forge r-base python\\
     ```\\
**R Packages**: Install the following R packages to ensure compatibility with the environment.\\
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   - Use the following command to install the required R packages:\\
     \\
     \\
     \\
     R\\
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     Copy\\
     \\
     ```r\\
     install.packages(c("pacman", "dplyr", "docopt", "rio", "data.table", "magrittr", "bigsnpr"))\\
     ```](/content/explore/cac63269-145b-4733-b1ff-5a82dfd52987?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) 4. [**Python Packages**:](/content/explore/cac63269-145b-4733-b1ff-5a82dfd52987?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

- [**scipy**: Required for scientific computing. For details, refer to the](/content/explore/cac63269-145b-4733-b1ff-5a82dfd52987?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Scipy official website](https://www.scipy.org/).
   - **h5py**: Needed for handling HDF5 file formats. For details, refer to the [H5py official website](https://www.h5py.org/).

Install the Python packages with:

bash

Copy

```bash
pip install scipy h5py

Usage

  1. To execute a specific algorithm WDL file using Cromwell, use the following command, replacing <algorithm_name> with the name of the desired algorithm:

bash

Copy

java -jar /path/to/cromwell.jar run $PRSHUB_PATH/wdl/<algorithmname>.wdl --inputs /path/to/config_file
  • /path/to/cromwell.jar is the path to the Cromwell JAR file.
    • $PRSHUB_PATH/wdl/<algorithm_name>.wdl is the path to the WDL file for the chosen algorithm.
    • --inputs /path/to/config_file specifies the path to the configuration file, which contains the parameter settings for the algorithm.
  1. Each algorithm's supported configuration file parameters can be found in the config_example folder. Adjust the parameters in the configuration file according to the requirements of each algorithm.

Thank you for using PRS-hub!

Xingyu Chen & Fei Wang

Open Capsule

published in Nature Communications

Engineering\ \ 9 | Jan | 2026\ \ China’s offshore wind power potential revisited: a realistic appraisal sug-gests substantially lower estimates than precedent studies\ \ This repository contains code for assessing offshore wind energy potential at the farm level scale for China. The workflow requires running the scripts in the following order: AEP-Wake loss.py, Main-calculate.py, and Farm-LCOE.py. See the readme.md file for a detailed description.\ \ Shiwei Xu Open Capsule

published in Nature Communications

Earth Sciences\ \ 9 | Jan | 2026\ \ European forest carbon and biodiversity policies have a limited win-win potential\ \ Data associated to the study "European forest carbon and biodiversity policies have a limited win-win potential"\ \ Lorenzo Balducci Open Capsule

published in Nature Communications

Physics\ \ 3 | Jan | 2026\ \ Frozen atom analysis in "Cooperative atomic motion during shear deformation in metallic glass"

[Frozen atom analysis \ This page has been prepared for the peer review of the manuscript titled "Cooperative Atomic Motion During Shear Deformation in Metallic Glass" submitted to Nature Communications.\ It provides access to the short Python script implementing the core algorithm of the manuscript— frozen atom analysis—allowing reviewers or readers to examine the algorithm and perform test runs as part of the review process.\ Contents\ \

  • code/frozen_atom_analysis.py Python script to run the frozen atom analysis\
  • data/1e09_002/xy_m/m445 Subdirectories including LAMMPS dump files to reproduce the histogram in figure 1c of the manuscript\
  • results/displacement_histogram.png Histogram shown in Figure 1c of the manuscript\
  • results/displacement_norms.csv CSV file including D_f parameter for each atom\ \ Usage](/content/explore/4e582ef1-bd41-4dfe-81db-778c4587cee3?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

Reproducible run - Check the figure in results/displacement_histogram.png. This should be the same as Figure 1c in the manuscript ( https://arxiv.org/pdf/2503.14903). The atomic group with small DfD_\text{f}Df​ is the STZ core detected in the frozen atom analysis.

To prepare input files

This code requires LAMMPS dump files that record atomic configurations before and after relaxation, in order to calculate the DfD_\text{f}Df​ parameter in the manuscript. Since preparing a complete input file set can be time-consuming, an example dataset is provided in the directory data/1e09_002/xy_m/m445 for convenience.

The procedure for generating these input files is outlined below (for further details, please refer to the manuscript):

  1. Perform an AQS (Athermal Quasi-Static) shear deformation simulation using LAMMPS. Examine the resulting stress–strain curve, and extract atomic configurations just before each stress drop event. In this example, we use a particular event labeled m445.
  2. For each atom in the configuration, create a separate directory named after its atom ID. See data/1e09_002/xy_m/m445 for an example, and proceed to the next step.
  3. Using the configuration from step 1, perform a LAMMPS relaxation calculation in each directory. In each calculation, the atom corresponding to the directory name (i.e., the atom ID) is frozen.

A sample LAMMPS input file for this purpose is provided as misc/frozen.inp. 4. After completing the above preparation for each event, run frozen_atom_analysis.py. This script analyzes the resulting atomic displacements and computes the $D_\text{f} parameter.

Reference and citing

https://arxiv.org/pdf/2503.14903

Author

Yoshinori Shiihara, Toyota Technological Institute

Contact

shiihara[at]toyota-ti.ac.jp

Yoshinori Shiihara et al.

Open Capsule

published in Nature Communications

[Bioinformatics\ \ 3 | Jan | 2026\ \ Biologically-informed integration of drug representations for breast cancer treatment using deep learning\ \ Project introduction \ \ Approximately 50% of breast cancer patients receiving neoadjuvant therapy do not achieve pathological complete response (pCR). Accurately predicting treatment response and selecting the optimal therapeutic strategy are unmet major challenges. To build a model with such functions, learning the interactions between tumor and treatments is necessary. Previous efforts to build response predictors have not incorporated this knowledge. Here, on the basis of data from 4,371 breast cancer patients undergoing neoadjuvant therapy across 31 datasets with transcriptomic and treatment information, we developed GDnet, an interpretable deep learning model integrating drug representations and tumor transcriptome profiles—functioning as a digital organoid—to predict the response to neoadjuvant therapy in breast cancer patients and aid in the selection of optimal treatment strategies. We demonstrate that GDnet (area under the curve (AUC) = 0.725) significantly outperforms transcriptome-only model (AUC = 0.683) in predicting treatment response. Then we conducted two series of in-silico simulated clinical trials based on I-SPY2 trial and external validation datasets respectively and showed that GDnet can optimize treatment selection and significantly increase the pCR rate in all trials. Moreover, the odds ratios (OR) for pCR increase from 1.6 to 2.5 linearly as optimization intensifies. Overall, biologically informed deep learning integrating drug representations and biological omics profiles can function as a digital organoid to optimize breast cancer neoadjuvant treatment selection and may have broader applications across various treatment settings and cancer types.\ \ Code description\ \

  • "main.py" file:\
    • This file mainly contain the codes to train GDnet in "3_model_construction_and_training.ipynb". Note: training of Gnetens and GNNetens are not performed give their high demand of cumputing resource.\
    • Because the environment seems do not contain R packages, codes written in R are not included in the main script.\
  • Other "*.ipynb" files:\
    • Codes are written in jupyter notebooks with R and python kernel separately. \
    • The notebook files are ordered by the prefixal number (start from 1, end with 9).\ \ Data description\ \
  • "Cleaned_data": the patient transcriptome and clinical information\
  • "GDSC_and_CTRP_data": GDSC and CTRP transcriptome and drug sensitivity data\
  • "Reactome": original data downloaded from Reactome website\
  • "Masks_with_prior_knowledge": generated masks containing the prior knowledge in Reactome\
  • "Model_performance": the model performance saved for "4_model_performance_comparason.ipynb"\
  • Trained_models: the trained models and the model predictions saved for "4_model_performance_comparason.ipynb" and "7_trial_group_aggignment_and_pCR_calculation_and_regimen_interpretation.ipynb"\ \ To train the model\ \
  • run "main.py" script\
  • trained models and model performance will be saved in "results"\ \ If you have any other questions, please feel free to let us know.\ \ Hewei Ge](/content/explore/b76d702f-e144-4149-ba36-377d20b20525?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) Open Capsule

published in Nature Communications

Engineering\ \ 1 | Jan | 2026\ \ Machine Learning–Driven Design of Engineered Cilia Enables Hybrid Operations in Acoustic Microrobots\ \ The code include the ML model to predict cilia resonance peak features and compared to FEA results.\ \ Yun Ling et al. Open Capsule

published in Nature Communications

Biology\ \ 24 | Feb | 2026\ \ Selective control of prefrontal neural timescales by parietal cortex\ \ Intrinsic neural timescales quantify how long spontaneous neuronal activity patterns persist, reflecting dynamics of endogenous fluctuations. We measured intrinsic timescales of frontal eye field (FEF) neurons in rhesus macaques and examined their changes during posterior parietal cortex (PPC) inactivation. We observed two distinct classes of FEF neurons based on their intrinsic timescales: short-timescale neurons (25 ms) and long-timescale neurons (100 ms). Short-timescale neurons showed stronger transient visual responses, suggesting their role in rapid visual processing. In contrast, long-timescale neurons exhibited stronger sustained salience representation, suggesting a role in spatiotemporal integration for maintaining stimulus-driven attention. During PPC inactivation, intrinsic timescales increased in both neuron types, with a significantly larger effect in short-timescale neurons. In addition, PPC inactivation disrupted salience computation, particularly in long-timescale neurons. Here, our findings provide the first causal evidence linking intrinsic local neural timescales to long-range inter-area communications and show the presence of at least two distinct network motifs that support different neuronal dynamics and functional computations within the FEF.\ \ Orhan Soyuhos, Marc Zirnsak, Rishidev Chaudhuri & Xiaomo Chen Open Capsule

published in Nature Communications

Engineering\ \ 30 | Dec | 2025\ \ Explainable mechanism for production process anomalies based on digital twin\ \ In the manufacturing sector, abnormal production (AP) can disrupt production schedules, leading to significant economic and reputational losses for manufacturers. To address this issue, in this study, we present an explainable mechanism for production process anomalies (EM2PA) designed to clarify the complex coupling relationships among various manufacturing factors, analyze the impact of these factors on the production process, identify AP, provide explanations for its causes, and enable trace-back analysis. EM2PA consists of three modules: the data augmenter (DAr), the influence factor recognizer (IFRr), and the causal interpreter (CIr). Specifically, the DAr generates small sample data of AP, the IFRr decouples the complex coupling relationships and identifies the factors influencing AP, and the CIr provides causal explanations. Furthermore, through a case study based on the actual production process of a discrete manufacturing workshop, we demonstrate the effectiveness of EM2PA in identifying the root causes of problems, while highlighting the importance of explainability and causal analysis of production process anomalies.\ \ Weiwei Qian et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 29 | Dec | 2025\ \ CARMSeD: Multi-Task Learning for Synergy Class and Signal Prediction\ \ This capsule implements the CARMSeD model pipeline described in the manuscript "AI-Guided CAR Designs and AKT3 Degradation Synergize to Enhance Bispecific and Trispecific CAR T Cell Persistence and Overcome Antigen Escape." It includes scripts for functional signal labeling, synergy class assignment (CARMSeD), multi-task model training, and inference on new CAR sequences. Sample data and trained model outputs are provided to enable full reproducibility.\ \ Nisha Chaudhary Open Capsule

published in Nature Communications

Biology\ \ 23 | Dec | 2025\ \ Comprehensive identification of cis-regulatory enhancers and promoters provides insights into tissue-specific gene regulation in the sheep reference genome\ \ We systematically characterized 274,682 enhancers and 25,975 promoters across 24 tissues in sheep using six high-resolution assays: ChIP-seq, ATAC-seq, CAGE-seq, RRBS, WGBS, and RNA-seq. The study provides a robust framework for exploring cis-regulatory mechanisms and tissue-specific regulation, advancing the functional annotation of the sheep reference genome. This capsule provides the analysis code for this study.\ \ Shangqian Xie Open Capsule

published in Nature Communications

Biology\ \ 18 | Dec | 2025\ \ Time-dependent deployment of medial prefrontal cortical representations in male mice

The code is organized in a way that allows user to generate all the figures for the manuscript “Time-dependent deployment of medial prefrontal cortical representations in mice”.\ Matlab scripts that start with Plot… will generate the respective plots for the figures in the MS. In order to run those scripts, you need first to initialize the database for 4 different groups of animals. These databases are FreeChoiceMClust.mat (VI task without delay manipulation, spikes sorted using MClust tool), FreeChoiceMaria.mat (VI task without delay manipulation spikes sorted using DSort), FreeChoiceDelay (VI task with delay manipulation), FreeChoiceBaitManip.mat (VI and VR task with short delay). For how to initialize these databases please see https://github.com/hangyabalazs/CellBase. Each cellbase stores precomputed features for each neuron, like average firing rate, spike width and so on. These features are organized in columns for each neuron per row. Since Cellbase already stores precomputed features if you want to load these features instead of computing from the scratch first you change the name of the CellBase.mat file to something else (for example CellBaseTemp.mat) and then run initcb function. After CellBase is initialized then delete the CellBase.mat file and revert the name of the CellBaseTemp.mat file to CellBase,mat file. Do it for each cellbase folder (FreeChoiceMClust, FreeChoiceMaria and etc). After you finish the initialization, Plot… scripts will generate the respective plots from the MS.

Junior Samuel Lopez-Yepez1, Anna Barta, Juliane Martin, Maria Moltessen, Tsz-Fung Woo, Oliver Hulme, Ebru Demir, Duda Kvitsiani

Open Capsule

published in Nature Communications

Medical Sciences\ \ 18 | Dec | 2025\ \ Longitudinal metabolome profiling from pregnancy through childhood and risk of neurodevelopmental disorders at age 10\ \ The capsule includes the code regarding manuscript NCOMMS-25-17954\ \ Tingting Wang Open Capsule

published in Nature Communications

Earth Sciences\ \ 16 | Dec | 2025\ \ Extreme temperature events reshuffle the ecological landscape of the Southern Ocean\ \ This code is associated with the manuscript “Extreme temperature events reshuffle the ecological landscape of the Southern Ocean”.\ It includes the detection of MHWs and MCSs in the Southern Ocean, as well as the calculation of phytoplankton of different size classes across different seasons.\ \ Zhimin Bai et al. Open Capsule

published in Nature Communications

Physics\ \ 12 | Dec | 2025\ \ Deep learning and superoscillatory speckles empowered multimode fiber probe for in situ nano-displacement detection and micro-imaging\ \ This dataset contains raw speckle data collected by the multimode fiber nano-displacement detection system and codes of MMF displacement detection neural network.\ \ Lele Wang, Qirong Xiao & Yiwei Zhang Open Capsule

published in Nature Communications

Bioinformatics\ \ 12 | Dec | 2025\ \ cfGWAS reveal genetic basis of cell-free DNA end motifs

This repository serves as a dedicated space for housing the codebase used in our publication for cfGWAS reveal genetic basis of cell-free DNA motifs. It is intended to provide researchers with access to the methodologies and algorithms employed in our study, facilitating further research and analysis in the field of genetic.

github: https://github.com/zhuhuanhuan20220519/cfGWAS

Note:

  1. Due to the complex external data required for analysis, some analyses cannot be run directly.
  2. Since the genotype data and individual-level phenotypes (motif frequencies) involved in this study are sensitive human-derived data, and in accordance with the requirements for the management of human genetic resources in China, they cannot be publicly provided.

Huanhuan Zhu

Open Capsule

published in Nature Communications

Bioinformatics\ \ 11 | Dec | 2025\ \ SamplingDesign: RNA Design via Continuous Optimization with Coupled Variables and Monte-Carlo Sampling\ \ RNA design aims to find an RNA sequence that can fold into a given target structure, which enables the creation of artificial RNA molecules with\ specific function, and has numerous applications in medicine. Computationally, it is particularly challenging due to two levels of combinatorial explosion:\ the exponentially large design space and the exponentially many competing structures for each design. As a result, heuristic methods such as local\ search have been popular for this task, but they cannot keep up with the combinatorial explosion. We instead borrow two techniques from machine learning,\ continuous relaxation and Monte-Carlo sampling, to the RNA design problem. We formulate RNA design as continuous optimization, which starts with\ a distribution over all valid candidate sequences, and uses gradient descent to improve the expectation of an arbitrary objective function. We define\ novel sequence distributions using coupled variables to model the correlation between nucleotides. To make it universally applicable to any objective\ function, we use sampling to approximate the expected objective function, to estimate the gradient, and to select the final candidate. Compared to\ the state-of-the-art methods, our work consistently outperforms them in key metrics such as Boltzmann probability, ensemble defect, and energy gap,\ especially on long and hard-to-design puzzles in the Eterna100 benchmark.\ \ Wei Yu Tang et al. Open Capsule

published in Nature Communications

Medical Sciences\ \ 9 | Dec | 2025\ \ Integrated computational and experimental immunoengineering of Adeno-associated virus capsid T cell epitopes in mice\ \ The Epitope Modification and MHC Prediction (EMMP) tool systematically evaluates amino acid substitutions for their predicted effects on MHC binding. The EMMP tool was used to identify, via insilico methods, a beneficial modification of a CD4⁺ T-cell epitope in the adeno-associated virus 9 (AAV9) capsid as a proof of concept. This approach for optimizing AAV vector design has potential applications for improvement of the safety and efficacy of gene therapy.\ \ Various approaches have been taken to limit AAV immunogenicity. This tool provides the capability to explore targeted modification of T-cell epitopes within the AAV capsid to prevent T-cell recognition while maintaining the structural integrity and biological function of the protein. The EMMP tool automates this task to reduce errors and the computational burden of evaluating every possible amino acid substitution/deletion/modification within and epitope and across multiple MHC alleles.\ \ Sojin Bing et al. Open Capsule

published in Nature Communications

[Earth Sciences\ \ 8 | Dec | 2025\ \ Shifting dominant periods in extreme climate impacts under global warming\ \ This capsule contains all scripts and data to produce the main results of the linked manuscript.\ \ To produce the results you need to run the following scripts in order:\ \

  1. bash run_main_N25.sb\
  2. bash run_result_averaging.sh\ \ The resulting dominant periods are then found in "results/original" for the non-detrended results and in "results/detrended" for the detrended ones. The total affected areas are found in "results/event_counts".\ \ Abstract of the related paper:\ Spatio-temporal patterns of extreme climate events have been extensively studied, yet two questions remain underexplored: Do such events occur regularly, and how do regularity patterns change under global warming? We address these questions by investigating dominant periods in crop failure, heatwave, and wildfire data.\ Here, we show that under pre-industrial conditions dominant periods emerge in 28% of cropland exposed to crop failure and 10% of wildfire-affected areas, likely related to climatic oscillations such as the El Niño-Southern Oscillation, while heatwaves occur irregularly. The number of dominant periods increases by 2-13% during the transition from the pre-industrial era to the anthropocene.\ In the anthropocene, the occurrence of extreme events shifts towards monotonic growth, replacing previous natural regularity patterns. Linearly de-trended projections reveal an additional shift towards smaller dominant periods due to climate change. These shifts in regularity are crucial for adaptation planning, and our method offers an additional approach for studying extreme events.\ \ Karim Zantout](/content/explore/5903570d-7157-4e17-8ab8-afbdd79fbac3?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) Open Capsule

published in Nature Communications

Computer Science\ \ 4 | Dec | 2025\ \ Single cell spatial transcriptomics integration deciphers the morphological heterogeneity of atherosclerotic carotid arteries\ \ The process of arterial atherosclerosis is characterised by accumulation of lipids and fibrous material with accompanying inflammation. As plaques progress, they restrict blood flow and cause rupture, which results in life threatening organ ischemia and dysfunction. Although extensively studied, a clear understanding of plaque heterogeneity and mechanisms that trigger their destabilization remains elusive. Our study reveals the molecular microarchitecture of human carotid artery plaques, using bulk and single-cell RNA sequencing combined with single-cell spatial transcriptomics, for which we present optimized cell segmentation algorithms. We identified distinct plaque morphologies linked to different cell type compositions, impacting early and advanced lesion formation, as well as destabilization. Spatial transcriptomics enabled us to further determine an inflammatory smooth muscle cell subtype, localize regions of neovascularization, and assign hotspots for macrophage activity within distinct cellular neighbourhoods across lesions. For different macrophage substates, we propose gradual and locally contained transdifferentiation of subluminal inflammatory HMOX1+ macrophages into a lipid-handling TREM2+ phenotype within border zones of the fibrous cap and necrotic core. Our findings provide insight into the complex heterogeneity of human atherosclerosis by unravelling location and proximity of different mural and immune cell substates involved in plaque progression and vulnerability.\ \ Jessica Pauli et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 23 | Jan | 2026\ \ Assessing Conformation Validity and Rationality of Deep Learning-Generated 3D Molecules\ \ Recent advancements in artificial intelligence (AI) have revolutionized the field of 3D molecule generation. However, the lack of effective evaluation methods for 3D conformations limits further improvements. Current techniques, in order to achieve the necessary speed for evaluating large number of AI-generated molecules, often rely on empirical geometric metrics that do not adequately capture various conformational anomalies, or on molecular mechanics (MM) energy metrics that exhibit low accuracy and lack atomic or torsional details. To address this gap, we propose a two-stage approach that achieves both high speed and quantum mechanical (QM) level accuracy. The first stage, termed the validity test, employs an AI-derived force field to identify atoms with elevated energy resulting from implausible neighboring environments. The tool developed for this purpose is named HEAD (high-energy atom detector). The second stage, known as the rationality test, utilizes a deep learning network trained on data with density functional theory (DFT) accuracy to detect rotatable bonds with high torsional energies. The tool developed for this purpose is named TED (torsional energy descriptor).\ \ Fan Fan et al. Open Capsule

published in Nature Communications

Social Sciences\ \ 2 | Dec | 2025\ \ Prevalence of plastic waste as a household fuel in low-income communities of the Global South (Stata Codes)\ \ Anecdotal evidence suggests that households burn plastics to manage waste and help satisfy their energy demand. To examine the prevalence, extent and reasons for use of plastic waste as household fuel, we conducted a survey with 1,018 key informants from cities in 26 countries in the Global South. Informants are purposively selected due to their familiarity with the living conditions in their communities. One-third of respondents reported being aware of plastic waste burning, with some reporting that their households engaged in this practice. Analyses of the data reveal significant correlations of plastic waste burning with both supply factors, such as , massive amount of plastic waste, and expensive clean fuels, and demand factors, including self-management of waste and energy needs. Expanding essential public waste management services and implementing programs that enhance the affordability of clean energy technologies, especially among marginalised and low-income communities, could reduce this health- and environment-damaging practice.\ \ Bishal Bharadwaj et al. Open Capsule

published in Nature Communications

Social Sciences\ \ 2 | Dec | 2025\ \ Prevalence of plastic waste as a household fuel in low-income communities of the Global South (R Script)\ \ Anecdotal evidence suggests that households burn plastics to manage waste and help satisfy their energy demand. To examine the prevalence, extent and reasons for use of plastic waste as household fuel, we conducted a survey with 1,018 key informants from cities in 26 countries in the Global South. Informants are purposively selected due to their familiarity with the living conditions in their communities. One-third of respondents reported being aware of plastic waste burning, with some reporting that their households engaged in this practice. Analyses of the data reveal significant correlations of plastic waste burning with both supply factors, such as , massive amount of plastic waste, and expensive clean fuels, and demand factors, including self-management of waste and energy needs. Expanding essential public waste management services and implementing programs that enhance the affordability of clean energy technologies, especially among marginalised and low-income communities, could reduce this health- and environment-damaging practice.\ \ Bishal Bharadwaj et al. Open Capsule

published in Nature Communications

Chemistry\ \ 25 | Feb | 2026\ \ Data-driven intelligent carbonization unifies diverse biomass into high-performance hard carbon negative electrodes\ \ You can run the MLP model using the data in 0704.csv to obtain a graph illustrating the structure-property relationship of hard carbon. Additionally, you can use extra data from input.csv or your own data to run the predictive model, enabling the rapid prediction of hard carbon performance based on its structural parameters.\ \ cui junfeng Open Capsule

published in Nature Communications

Bioinformatics\ \ 29 | Nov | 2025\ \ Genomics of rafting crustaceans in tropical oceans: adapting to marine climate change\ \ Genomics of rafting crustaceans in tropical oceans: adapting to marine climate change\ \ Hongguang Open Capsule

published in Nature Communications

Bioinformatics\ \ 27 | Nov | 2025\ \ Expression of antibody-drug conjugate targets in post-mortem samples of breast cancer metastases and normal tissue\ \ While many Antibody Drug Conjugates (ADCs) are investigated in solid tumors, their target expression and heterogeneity is poorly documented in metastatic breast cancer. Here, we perform RNA sequencing to investigate expression of 72 ADC targets in 909 samples from 30 female patients from our post-mortem tissue donation program UPTIDER (NCT04531696). We report that the highest median expression in metastases is seen for FN1, MUC1, LAMP1, HER3 and SLC39A6. TROP2 and HER2 have the 9th and 27th highest expression. We observe reduced expression in metastases as compared to primary untreated tumors for 15 targets but observe only limited differences in expression between metastases of different subtypes. We show that TROP2, VTCN1, NECTIN4, HER2 and HER3 are interesting targets as they have higher mRNA expression in tumor as compared to normal tissues. This is confirmed at the protein level by explorative immunohistochemistry. Correlations between targets can help guide design of bispecific ADCs. Taken together, the results of this study can help inform the design and prioritization of drugs for the treatment of patients with metastatic breast cancer.\ \ Kristien Borremans et al. Open Capsule

published in Nature Communications

Engineering\ \ 24 | Nov | 2025\ \ Tactile-integrated FlexiRay: Breaking Planar Limits by Harnessing Large Deformations for Flexible, Full-Coverage, Human-like Multimodal Sensing\ \ 'This is the demonstration code for the manuscript "Tactile-integrated FlexiRay: Breaking Planar Limits by Harnessing Large Deformations for Flexible, Full-Coverage, Human-like Multimodal Sensing."'\ \ Yanzhe Wang, Haotian Guo & Hao Wu Open Capsule

published in Nature Communications

Bioinformatics\ \ 20 | Nov | 2025\ \ A catalogue of early diverged contemporary human genome variation: new insights for ancestrally distinct KhoeSan populations\ \ Assembly-based Genome Analysis Toolkit\ \ Weerachai Jaratlerdsiri Open Capsule

published in Nature Communications

Medical Sciences\ \ 19 | Nov | 2025\ \ Single-neuron correlates of consciousness in human lateral occipital complex [Flash Suppression]\ \ This capsule preprocesses en analyzes the flash suppression experiment.\ \ Michaël Vanhoyland Open Capsule

published in Nature Communications

Medical Sciences\ \ 19 | Nov | 2025\ \ Single-neuron correlates of visual consciousness in human lateral occipital complex [Category]\ \ This capsule preprocesses and analyses the Category experiment.\ \ Michaël Vanhoyland Open Capsule

published in Nature Communications

Medical Sciences\ \ 19 | Nov | 2025\ \ Single-neuron correlates of visual consciousness in human lateral occipital complex [Binocular Rivalry]\ \ This capsule preprocesses and analyses the binocular rivalry experiment.\ \ Michael Vanhoyland Open Capsule

published in Nature Communications

Medical Sciences\ \ 19 | Nov | 2025\ \ Single-neuron correlates of consciousness in human lateral occipital complex [Non Scrambled vs Scrambled]\ \ This capsule preprocesses and analyses the non-scrambled vs scrambled experiment.\ \ Michaël Vanhoyland Open Capsule

published in Nature Communications

Biology\ \ 18 | Nov | 2025\ \ Decoding necrosome assembly: harmonizing signal amplification and attenuation for optimal RIP3 configuration\ \ Mathematical modeling of the TNF-induced cell death signaling\ \ Xiang Li Open Capsule

published in Nature Communications

Engineering\ \ 18 | Nov | 2025\ \ Contextual Conditions Define Maximum Energy-use Threshold in Low-Carbon Controlled Environment Agriculture for Agri-Food Transformation.\ \ This code calculates the maximum energy use-productivity that a controlled environment agricultural facility should operate under, in order to be emit lower carbon than imports. This takes into account where the facility is located, their existing import patterns, availability of clean energy today and in the future. It uses data from publicly available sources.\ \ Ng Shiwei Open Capsule

published in Nature Communications

Biology\ \ 13 | Nov | 2025\ \ Dynamic changes in mitochondria support phenotypic flexibility of microglia\ \ Analysis of time series datasets of mitochondria and microglia collected from leica stellaris two-photon microscope\ \ Katherine Espinoza et al. Open Capsule

published in Nature Communications

Medical Sciences\ \ 11 | Nov | 2025\ \ Impact of a community-based antiretroviral therapy delivery model for people living with HIV in Cambodia (Sensitivity Analysis)\ \ This Compute Capsule contains the sensitivity analyses conducted using RStudio (R 4.2.1) for the manuscript titled “Impact of a community-based antiretroviral therapy delivery model on treatment outcomes, mental health, and quality of life among people living with HIV in Cambodia: a quasi-experimental study.”\ \ The analyses assess the robustness of the main findings through multiple imputation techniques and marginal effect estimations, complementing the complete case analysis.\ \ Ziya Tian et al. Open Capsule

published in Nature Communications

Medical Sciences\ \ 11 | Nov | 2025\ \ Impact of a community-based antiretroviral therapy delivery model for people living with HIV in Cambodia (Complete-case Analysis)\ \ This Compute Capsule contains the complete case analysis conducted using Stata 18 BE for the manuscript titled “Impact of a community-based antiretroviral therapy delivery model on treatment outcomes, mental health, and quality of life among people living with HIV in Cambodia: a quasi-experimental study.”\ \ The analysis includes data management, model development, and statistical outputs focusing on treatment effectiveness, mental health outcomes, and quality of life indicators.\ \ All datasets have been de-identified, and the workflow is fully reproducible based on the provided .do scripts.\ \ Ziya Tian et al. Open Capsule

published in Nature Communications

Physics\ \ 11 | Nov | 2025\ \ Codes for Intelligent single-shot full-field characterization over femtosecond pulses\ \ Training codes and a sample dateset for Intelligent single-shot full-field characterization over femtosecond pulses\ \ Lilin Yi & Guoqing Pu Open Capsule

published in Nature Communications

Computer Science\ \ 10 | Nov | 2025\ \ Reshaping Reservoirs with Hebbian Plasticity:Unsupervised Adaptation that Works\ \ Code for Reshaping Reservoirs with Hebbian Plasticity:Unsupervised Adaptation that Works\ \ Tanguy CAZALETS Open Capsule

published in Nature Communications

Bioinformatics\ \ 10 | Nov | 2025\ \ Protein-protein interactions are a major source of epistasis in genetic interaction networks\ \ All scripts related to analyses and figures for the article "Protein-protein interaction is a major source of epistasis in genetic interaction networks"\ \ Xavier Castellanos-Girouard, Adrian WR Serohijos & Stephen W Michnick Open Capsule

published in Nature Communications

Medical Sciences\ \ 7 | Nov | 2025\ \ The AML cellular state space unveils NPM1 immune evasion subtypes with distinct clinical outcomes\ \ Code and data needed to recreate the analyses supporting the study "The cellular state space of AML unveils novel NPM1 subtypes with distinct clinical outcomes and immune evasion properties".\ \ Henrik Lilljebjörn, Rasmus Henningsson & Thoas Fioretos Open Capsule

published in Nature Communications

Physics\ \ 7 | Nov | 2025\ \ Homophily Withing and Across Groups\ \ Homophily -- the tendency of individuals to interact with similar others -- shapes how networks form and function. Yet existing approaches typically collapse homophily to a single scale, either one parameter for the whole network or one per community, thereby detaching it from other structural features. Here, we introduce a maximum-entropy random graph model that moves beyond these limits, capturing homophily across all social scales in the network, with parameters for each group size. The framework decomposes homophily into within- and across-group contributions, recovering the stochastic block model as a special case. As an exponential-family model, it fits empirical data and enables inference of group-level variation of homophily that aggregate metrics miss. The group-dependence of homophily substantially impacts network percolation thresholds, altering predictions for epidemic spread, information diffusion, and the effectiveness of interventions. Ignoring such heterogeneity risks systematically misjudging connectivity and dynamics in complex systems.\ \ Abbas K. Rizi, Riccardo Michielan, Clara Stegehuis & Mikko Kivelä Open Capsule

published in Nature Communications

Bioinformatics\ \ 6 | Nov | 2025\ \ Molecular Motif Learning\ \ Code and Data for the paper: Molecular Motif Learning\ \ Ziyang Liu et al. Open Capsule

published in Nature Communications

Chemistry\ \ 6 | Nov | 2025\ \ Real-space machine learning of correlation density functionals

This repository contains the python code for the generators of the MP2 correlation energy density and of the exact exchange energy density. They are taken from the github repository: https://github.com/vuckovic-lab/energy_densities.git

The derivation of the implemented formulas is based on the formulation in S. Vuckovic, T. J. P. Irons, A. Savin, A. M. Teale, and P. Gori-Giorgi, Journal of Chemical Theory and Computation 12, 2598 (2016). In the associated publication, the generator is employed for real-space machine learning of correlation energy functionals in density functional theory. The python-based implementation uses the JAX API with modern tensor libraries allowing platform agnostic evaluations for high performance computing.

Elias Polak, Heng Zhao & Stefan Vuckovic

Open Capsule

published in Nature Communications

Earth Sciences\ \ 4 | Nov | 2025\ \ CMIP6 models fail to capture long-term forced changes in the tropical Pacific zonal SST gradient - Review response\ \ Paper abstract \ \ The observed zonal sea surface temperature gradient in the tropical Pacific has strengthened over the last 150 years, but many CMIP6 models simulate a forced weakening of this gradient over the same period. This has spurred a multi-decade debate over whether models are correctly representing dynamics in the tropical Pacific and whether the observed strengthening is a forced response. We comprehensively assess all observed and modeled gradient trends of 20 years or longer from 1870-2024 across five observational datasets and 14 CMIP6 large ensembles and find that models are not able to match many long-term trends in the observed gradient, especially those that end more recently. Models that are able to match these trends do so through excessive internal variability that compensates for their gradient-weakening forced responses. We additionally find that trends in the observed gradient strengthen at an increasing rate with time, a forced response that is in contrast to the behavior of most models.\ \ Code description \ \ Investigation of all trends (20 years or longer) in the tropical Pacific zonal SST gradient between 1870 and 2024 in 5 observational datasets and 14 CMIP6 large ensembles.\ \ Hannah Byrne, Richard Seager & Jason Smerdon Open Capsule

published in Nature Communications

Bioinformatics\ \ 4 | Nov | 2025\ \ Personalized CRISPR Knock-In Cytokine Gene Therapy to Remodel the Tumor Microenvironment and Enhance CAR T Cell Therapy in Solid Tumors

CancerPAM is a pipeline for the identification of potential tumor-specific\ CRISPR cutting sites for homology-dependent repair (HDR) mediated knock-in. The\ pipeline offers the possibility to identify novel PAM sites based on various factors\ such as copy number, expression, or different scores that evaluate potential off-targets\ in the genome of interest and predict on-target activity. This multi-stage selection\ process can be used to evaluate promising CRISPR targets and to compare them within\ a data set.

Run time depends mainly on the number of novel PAM sites identified\ and the responsiveness of the CRISPOR website ( https://crispor.gi.ucsc.edu/). The minimalistic test dataset (6 PAMs in 32 SNPs derived from the SKNSH neuroblastoma cell line, DepMap23Q2 dataset) is processed in ~15 minutes. The Snakemake process is based on the rules defined in the Snakefile and obtains its information from the sample sheet and the config file. To run the pipeline with your own input data, these files must be modified accordingly.

Input:

The required files are specified in the sample sheet (sample_sheet.csv) and the config file (config_CancerPAM.yaml). The sample sheet coordinates different samples and ensures that the required reference genome is downloaded.

Sample sheet entry:

name;ref_genome;mode;raw_data_input

SKNSH;Hg19;DepMap;/data/depmap/cell_lines/DepMap_SKNSH_mutations.csv

Required datasets have to be uploaded to the directories specified in the config file. To configure samples, the user needs to edit the sample sheet and configure directories and feature data in the config file. Datasets must be provided in .csv format, organized and formatted analogously to the sample data provided for the test run.

raw_data: "/data/depmap/cell_lines/" Directory where the sample_data.csv (WGS/WES) specified in sample_sheet.csv is located

depmap_resources: "/data/depmap/" Directory where additional feature data .csv files are located

CRISPR_file: "CRISPR_DepMap_Public_23Q2+Score_Chronos_subsetted_renamed.csv" CRISPR screen dependency score data

merged_file: "dep_scores.csv" Mean dependency score data from CRISPR_file and rnai_file

rnai_file: "RNAi_Achilles+DRIVE+Marcotte_DEMETER2_subsetted_NAsdropped_renamed.csv" RNAi screen dependency score data

tpm_file: "OmicsExpressionProteinCodingGenesTPMLogp1_renamed.csv" Expression data

CN_file: "OmicsCNGene_renamed.csv" Gene copy number variation data

Output:

The pipeline produces a ranked list of CRISPR-targetable PAM-site mutations (e.g., SKNSH_final_score.csv) derived from processed mutation data, along with annotated intermediate files showing gene expression, copy number, dependency, and CRISPOR scores. The results are compiled into an interactive HTML report (SKNSH.html) that summarizes all annotated PAM candidates for the selected dataset.

GitHub repository:

The CodeOcean capsule is based on a GitHub repository: https://github.com/MichaelLaunspach/CancerPAM. This repository is currently private and will be made public upon publication. For more details, please see: /environment/README.md

Test data origin:

Test data are derived from the Cancer Dependency Map (DepMap) project.

Source: https://depmap.org

Data is licensed under CC BY 4.0 © Broad Institute.

DepMap, Broad (2023). DepMap 23Q2 Public. figshare. Dataset. https://doi.org/10.6084/m9.figshare.22765112.v4

Abstract:

The immunosuppressive tumor microenvironment (TME) remains a central barrier to effective immunotherapy in solid tumors. To address this, we developed a novel gene therapeutic strategy that enables localized remodeling of the TME via tumor-intrinsic cytokine expression. Central to this approach is CancerPAM, a multi-omics bioinformatics pipeline that identifies and ranks patient-specific, tumor-exclusive CRISPR-Cas9 knock-in sites with high specificity and integration efficiency.

Using neuroblastoma—a pediatric solid tumor with a suppressive TME—as a model, we applied CancerPAM to sequencing data from cell lines and patients to identify optimal integration sites for pro-inflammatory cytokines (CXCL10, CXCL11, IFNG). CRISPR-mediated CXCL10 knock-in into tumor cells significantly enhanced CAR T cell infiltration and antitumor efficacy both in vitro and in vivo. In vivo, CXCL10-expressing tumors showed significantly increased early CAR T cell infiltration and prolonged survival compared to controls.

CancerPAM rankings correlated strongly with target-site specificity and knock-in efficiency, validating its predictive performance. Our findings establish CancerPAM as a powerful tool for safe and effective CRISPR-based interventions and provide a conceptual framework for integrating cytokine-driven TME remodeling with cellular immunotherapies. This personalized strategy holds promise for enhancing CAR T cells and other immunotherapies across immune-refractory solid tumors.

Michael Launspach , Janik Hohmann, Marvin Jens & Marc Lucas Appis

Open Capsule

published in Nature Communications

Physics\ \ 4 | Nov | 2025\ \ vf_integral for SI of "Electronic dimensionality of UTe2"\ \ This capsule contains the python programs for calculating the integrated Fermi velocity (or the vf^2) over the symmetry-reduced domain of Fermi surface in one octant, which gives vf (or vf^2) along different axes for the discussion of anisotropy induced by Fermi surface geometry in the supplementary information of "Electronic dimensionality of UTe2"\ \ Ling Zhang Open Capsule

published in Nature Communications

Earth Sciences\ \ 4 | Nov | 2025\ \ Underestimated Accelerated Antarctic Phytoplankton NPP in Winter Over the Past Decade Revealed by Spaceborne LiDAR\ \ code and data for paper\ \ Peng Chen Open Capsule

published in Nature Communications

Physics\ \ 29 | Oct | 2025\ \ code for " Dimensional Transport Crossovers in Thermoelectrics Revealed by a Simple Transport Model"\ \ code for " Dimensional Transport Crossovers in Thermoelectrics Revealed by a Simple Transport Model"\ \ yue lin Open Capsule

published in Nature Communications

Engineering\ \ 28 | Oct | 2025\ \ Battery-Electric Trucks are Projected to Lower the Societal Cost of Long-Haul Freight in the United States\ \ Code for Porzio et al. in Nature Comms\ \ Jason Porzio Open Capsule

published in Nature Communications

Social Sciences\ \ 27 | Oct | 2025\ \ Mediators of the association between psychological distress and mortality in people living with and beyond cancer: A multicohort study\ \ This is a do file for the analyses in UK Biobank examining the mediators of the association between psychological distress and mortality in people living with and beyond cancer.\ \ Natalie Miller Open Capsule

published in Nature Communications

Chemistry\ \ 26 | Oct | 2025\ \ computational data Capsule for "Understanding Oxygen Transfer on Ceria with Pt Single Atoms for Surface Reaction" Jul 14, 2025 14:25\ \ This repository contains scripts for the preparation, simulation, and analysis of O2 uptake on Pt/CeO2-Al2O3 systems.\ The work employs neural network potential (NNP) models to study oxygen activation and lattice oxygen transfer dynamics across varying ceria domain sizes.\ \ Seokhyun Choung Open Capsule

published in Nature Communications

Earth Sciences\ \ 24 | Oct | 2025\ \ CMIP6 models fail to capture long-term forced changes in the tropical Pacific zonal SST gradient\ \ Paper abstract \ \ The observed zonal sea surface temperature gradient in the tropical Pacific has strengthened over the last 150 years, but many CMIP6 models simulate a forced weakening of this gradient over the same period. This has spurred a multi-decade debate over whether models are correctly representing dynamics in the tropical Pacific and whether the observed strengthening is a forced response. We comprehensively assess all observed and modeled gradient trends of 20 years or longer from 1870-2024 across five observational datasets and 14 CMIP6 large ensembles and find that models are not able to match many long-term trends in the observed gradient, especially those that end more recently. Models that are able to match these trends do so through excessive internal variability that compensates for their gradient-weakening forced responses. We additionally find that trends in the observed gradient strengthen at an increasing rate with time, a forced response that is in contrast to the behavior of most models.\ \ Code description \ \ Investigation of all trends (20 years or longer) in the tropical Pacific zonal SST gradient between 1870 and 2024 in 5 observational datasets and 14 CMIP6 large ensembles.\ \ Hannah Byrne, Richard Seager & Jason Smerdon Open Capsule

published in Nature Communications

Bioinformatics\ \ 23 | Oct | 2025\ \ ctDNA detectability and representativeness in seven body liquids from female patients with metastatic breast cancer\ \ Liquid biopsies enable non-invasive monitoring and characterization of metastatic cancer, primarily through circulating tumor DNA (ctDNA) in blood. The representativeness of all metastatic sites in these liquid biopsies and the clinical relevance of other body fluids remain uncertain. We performed low-pass whole genome sequencing on 216 liquid and 745 metastatic tissue samples from 20 autopsied women with metastatic breast cancer to assess ctDNA detection, fraction, and site representativeness in seven body fluids (blood, ascites, cerebrospinal fluid, pericardial fluid, pleural fluid, saliva, and urine). Complementarily, whole exome sequencing on 86 liquid samples from 11 patients explored mutational information. ctDNA was detected in all fluids, but most frequently in blood, followed by ascites, pleural fluid, and cerebrospinal fluid. Phylogenetic reconstruction indicated that site representativeness varies by fluid type. Mutational and gene-level copy number analyses revealed clinically relevant information unique to non-blood fluids. These findings suggest a multi-fluid approach could enhance metastatic cancer monitoring and characterization.\ \ François Richard et al. Open Capsule

published in Nature Communications

Engineering\ \ 20 | Oct | 2025\ \ Layer-Resolved Connective Fields from Ultrafast fMRI Decode Feedforward and Feedback Information Flow during Spontaneous Activity

This capsule contains raw data, metadata, sample data and the scripts to replicate the results shown in : Joana Carvalho, Francisca F. Fernandes, Mafalda Valente, Koen V. Haak, and Noam Shemesh\ Layer connective fields from ultrafast resting-state fMRI differentiate feedforward from feedback signaling\ Under Review\ \ Commented Matlab scripts are provided to allow quickly testing the application of the layer Connective Field model in other datasets.\ \ The package includes folderers with preprocessed fMRI data and with pre estimated connective fields to allow to replicate the manuscript Figures. Scripts were tested in MATLAB R2021a.

Scripts written by Joana Carvalho, contact: joana.carvalho@fpce.uc.pt

Code: Matlab scripts for: Area-to-layer Connective field model Layer-to-layer Connective field model To compute the Figures 2,3,4 and 5 of the manuscript

Fig2 requires the area-to-layer connective fields (CF) between LGN and LP (source areas) to all the layers of the visual cortex (VC) and higher visual areas (HVA). In the data associated to Fig2 already estimated CFs are available.

Fig3 requires the layer-to-layer CFs between V1 and HVA during stimulation and resting state conditions. In the data associated to Fig3 already estimated layer-to-layer CFs are available.

Fig4 requires area-to-layer and layer-to-layer CFs between VPL, SMI and M1 and M2. In the data associated to Fig4 already estimated area-to-layer and layer-to-layer CFs are available.

Fig 5b requires area-to-layer CFs estimated between between LGN and LP (source areas) to all the layers of the VC and HVA for lesioned and control animals

Joana Carvalho

Open Capsule

published in Nature Communications

Physics\ \ 17 | Oct | 2025\ \ Measuring the locations and properties of VHF sources emitted from an aircraft flying through high clouds\ \ Code to generate the results pictures with source positions and polarization directions for the planes seen in lightning flash 19A-1 as well as for the one in 20A-8\ As output a the plots are generated showing the locations and polarization info of the sources on the plane discussed in the main portion of the paper as well as those for the plane in the supplementary information.\ \ Olaf Scholten Open Capsule

published in Nature Communications

Physics\ \ 17 | Oct | 2025\ \ Measuring VHF source locations from an aircraft flying through high clouds\ \ Code to generate the results pictures with source positions and polarization directions\ \ Olaf Scholten Open Capsule

published in Nature Communications

Biology\ \ 17 | Oct | 2025\ \ Neural Correlates of Trial Outcome Monitoring during Long-term Learning in Primate Posterior Parietal Cortex\ \ This is a repository for a manuscript under review, titled "Neural Correlates of Trial Outcome Monitoring during Long-term Learning in Primate Posterior Parietal Cortex ". This is an unpublished work. The contents may change during the revision.\ \ Ziang Liu & Zhuangyi Jiang Open Capsule

published in Nature Communications

Engineering\ \ 16 | Oct | 2025\ \ Considering distributive justice as a planning principle helps navigate a diversity of future energy infrastructure designs\ \ Input data and code supporting the article, "Considering justice as a planning principle helps navigate a diversity of future energy infrastructure designs."\ Policymakers have signalled that the low-carbon energy transition should also deliver a more just distribution of energy-related burdens and benefits. However, achieving more just systems in practice is complicated by contested interpretations of justice, conflicting system impacts, and overarching technical system constraints. To resolve these challenges, we develop a set of indicators for distributive justice based on justice theory and current European policy to assess a set of low-carbon and low-cost European energy system designs. We find that accounting for distributive justice can help narrow the field of technically viable system design choices without introducing substantive cost trade-offs. Considering public opinion to create a balanced approach to distributive justice produces more consistent continental-level technology capacity recommendations than provided by theory alone, showing the value of considering public opinion in systems-level energy planning.\ \ Katherine Emma Lonergan & Giovanni Sansavini Open Capsule

published in Nature Communications

Physics\ \ 13 | Oct | 2025\ \ Hydrodynamic Spin-Pairing and Active Polymerization of Oppositely Spinning Rotors\ \ This code simulates counter-rotating particles interacting hydrodynamically and sterically in a viscous fluid where inertia is a perturbation\ \ Naomi Oppenheimer & Yahav Lavie Open Capsule

published in Nature Communications

Biology\ \ 10 | Oct | 2025\ \ Extracellular matrix remodeling during aging aligns with synapse, microglia, and cognitive status\ \ This code accesses putative contact between signal in different fluorescence channels in a microscopy image. The application it was designed for was to analyze contact between extracellular matrix molecules, neurons, and glial cells.\ \ Daniel T. Gray Open Capsule

published in Nature Communications

Biology\ \ 10 | Oct | 2025\ \ Frequency-dependent photic modulation of wakeful consolidation in visual learning\ \ Consolidation of encoded information during both sleep and wakefulness is crucial for learning, yet wakeful consolidation remains largely uncharted. Here, we demonstrate frequency-dependent modulation of the wakeful consolidation of visual learning by repetitive visual stimulation (RVS). Participants were trained on an orientation discrimination task and then exposed to flickering gratings at different temporal frequencies to modulate consolidation. We found that the 10-Hz grating RVS improved subsequent discrimination performance, while the 1-Hz grating RVS impaired it. These modulatory effects disappeared when gratings were replaced with uniform disks in RVS or when training was omitted, suggesting that such effects rely on early-stage sensory processing and reflect the modulation of consolidation, rather than being a direct consequence of RVS itself. Using event-related potentials (ERPs) and magnetic resonance spectroscopy (MRS), we showed that the RVS-facilitated wakeful consolidation manifested as enhanced N1 and increased glutamate/GABA (excitation/inhibition) ratio in the early visual cortex, implying a role of LTP-like plasticity in the modulation. These findings introduce a new photic stimulation method for modulating wakeful consolidation, distinct from behavioral interventions and electrical/magnetic stimulations, and offer new insights into the neural mechanisms underlying wakeful consolidation, a long-overlooked stage in learning.\ \ Xin-Yue Yang et al. Open Capsule

published in Nature Communications

Physics\ \ 9 | Oct | 2025\ \ Classically studied coherent structures only paint a partial picture of wall-bounded turbulence\ \ For the last 140 years, the mechanisms of transport and dissipation of energy in a turbulent flow have not been completely understood due to the complexity of this phenomenon. The dissipation of energy due to turbulence is significative, and understanding turbulence physics is crucial for fighting the present climate emergency. Previous research has focused on analyzing the so-called coherent structures of the flow (Q events, streaks, and vortices), which are regions of high turbulence transport, high/low streamwise fluctuation, and rotation, respectively. However, the connection between these classically studied structures and the flow development is still uncertain. To fill this gap, here we show a data-driven methodology for objectively identifying high-importance regions in a turbulent flow. A deep-learning model is trained to predict a future state of a turbulent channel flow and the gradient-SHAP explainability algorithm is used to calculate the importance of each grid point for such a prediction. Finally, high-importance regions are computed using the SHAP data, analyzing and comparing their characteristics with those of the other coherent structures. The SHAP analysis provides an objective way to identify the regions of highest importance in the turbulent flow, which exhibit different levels of agreement with the classically studied structures.\ \ Andrés Cremades, Sergio Hoyas & Ricardo Vinuesa Open Capsule

published in Nature Communications

Engineering\ \ 9 | Oct | 2025\ \ The Tymbal of a Cicada: Nature's Sound Generating Metastructure (Spectrogram) v2.0\ \ This code is used to plot the spectrogram of the time domain simulations stored in the file solution1. txt. Users should upload a new solution file if any changes in parameter are made in the time domain simulation code.\ \ Pritam Ghoshal & James Gibert Open Capsule

published in Nature Communications

Engineering\ \ 9 | Oct | 2025\ \ The Tymbal of a Cicada: Nature’s Sound Generating Metastructure Consolidated (Pritam Ghoshal and James Gibert)\ \ Complete MATLAB code to reproduce analyses and figures, including spectrogram computation.\ \ James Gibert Open Capsule

published in Nature Communications

Engineering\ \ 9 | Oct | 2025\ \ The Tymbal of a Cicada: Nature's Sound Generating Metastructure (Time Domain Simulations) v2.0\ \ This code is used to for the time domain simulations of the governing equations for the sound generation mechanism in cicadas.\ \ Pritam Ghoshal & James Gibert Open Capsule

published in Nature Communications

Engineering\ \ 7 | Oct | 2025\ \ Unlocking vehicle-to-grid potential of load shifting in China’s megacities considering comprehensive real-world behaviors: Code instruction

Please see metadata/readme.md to help you get started more quickly. Raw data of the figures in the manuscript are uploaded in Figshare: https://figshare.com/s/5cf7c0d5ce275a7083b8.

Kaisan Li

Open Capsule

published in Nature Communications

Earth Sciences\ \ 7 | Oct | 2025\ \ Interannual Wave-Driven Shoreline Change on the California Coast\ \ The important role of wave climate variability in driving shoreline evolution has been demonstrated recently with increasing satellite imagery, wave buoy records, and wave hindcast models. While severe beach erosion with extreme El Niño waves is well documented on Pacific coastlines, less clear is the broader link between interannual wave energy and shoreline response. Here, we show half of California's interannual Landsat shoreline change is a coherent response to wave power anomalies originating from a specific central North Pacific swell generation region, which in turn is only weakly correlated with the Niño3.4 index. Positive wave power anomalies (beach narrowing) are strongly associated with El Niños, but the negative anomalies (beach widening) are not similarly tied to La Niñas. The North Pacific wave climate modulation of beach width retreat and recovery over interannual to multi-decadal time scales has implications for long-term coastal resilience planning.\ \ William C. O'Reilly et al. Open Capsule

published in Nature Communications

Mathematics\ \ 6 | Oct | 2025\ \ Thermochromic Hydrogels for Synergistic Mechano-Optical Properties and Global Energy Saving Potential\ \ Transmittance integral calculation\ \ Bowen Yang Open Capsule

published in Nature Communications

Engineering\ \ 6 | Oct | 2025\ \ Global distribution of energy savings and carbon reduction achieved by PDH hydrogels\ \ This MATLAB code is used to calculate and plot the global distribution of energy savings and carbon reduction achieved by PDH hydrogels.\ \ Bowen Yang Open Capsule

published in Nature Communications

Biology\ \ 3 | Oct | 2025\ \ Phylogenomic profile of exon-intron organization across angiosperms, their relationships with protein domains, and functional implications

Here we provide our bioinformatics tool, ExonEvo, along with example data, so that it can be tested on the cloudstation. Conserved exons shared by homologous genes can be detected using ExonEvo. See additional information in the GitHub page https://github.com/TaikuiZhang/ExonEvo.

Taikui Zhang

Open Capsule

published in Nature Communications

Computer Science\ \ 21 | Nov | 2025\ \ Class Structure for Boosting Reservoir Computing with Brain-inspired Adaptive Dynamics\ \ Reservoir computers (RCs) provide a computationally efficient alternative to deep learning while also offering a framework for incorporating brain-inspired computational principles. By using an internal neural network with random, fixed connections—the 'reservoir'—and training only the output weights, RCs simplify the training process but remain sensitive to the choice of hyperparameters that govern activation functions and network architecture. Moreover, typical RC implementations overlook a critical aspect of neuronal dynamics: the balance between excitatory and inhibitory (E-I) signals, which is essential for robust brain function. Our results indicate that high performance in RCs consistently arises in balanced or slightly over-inhibited regimes, rather than in excitation-dominated ones. To reduce the need for precise hyperparameter tuning, we introduce a self-adapting mechanism that locally adjusts E/I balance to achieve target neuronal firing rates, improving performance by up to 130% in tasks like memory capacity and time series prediction compared with globally tuned RCs. Incorporating brain-inspired heterogeneity in target neuronal firing rates further reduces the need for fine-tuning hyperparameters and enables RCs to excel across linear and non-linear tasks. These results support a shift from static optimization to dynamic adaptation in reservoir design, demonstrating how brain-inspired mechanisms improve RC performance and robustness while deepening our understanding of neural computation.\ \ Keshav Srinivasan, Dietmar Plenz & Michelle Girvan Open Capsule

published in Nature Communications

Biology\ \ 30 | Sep | 2025\ \ Code for Distinctive Roles of Left and Right Entorhinal Cortex in Path Integrations a Non-invasive Stimulation Study\ \ Corresponding article: Distinctive Roles of Left and Right Entorhinal Cortex in Path Integration via Non-invasive Stimulation\ \ This study investigated the differential roles of the left and right entorhinal cortex (EC) in spatial cognition. Temporal interference (TI) stimulation was applied separately to the left and right EC to observe the resulting changes in participants' cognitive performance. The provided code includes partial electric field simulations and analyses of resting-state fMRI data, aimed at understanding how non-invasive stimulation impacts brain function and connectivity in the EC regions. Also, the supplymentary data for the comparison between two different sham conditions were also provided.\ \ N/A Open Capsule

published in Nature Communications

Physics\ \ 9 | Dec | 2025\ \ Codes for "Momentum-Space AC Josephson Effect and Intervalley Coherence in Multilayer Graphene"\ \ Code and data for manuscript entitled “Momentum-Space AC Josephson Effect and Intervalley Coherence in Multilayer Graphene”. In this manuscript, we explored the emergence of a novel phase-coherent dynamics in the intervalley coherent (IVC) state of rhombohedral multilayer graphene.\ We demonstrated that a static magnetic field can induce an oscillating orbital magnetization in the IVC state, leading to an AC Hall effect, which serves as a direct experimental signature of intervalley coherence. Using a detailed microscopic model of rhombohedral trilayer graphene (RTG), we computed the key parameters of the phase-number free energy and discussed the analogy between the IVC dynamics and the AC Josephson effect in superconductors. Furthermore, we highlighted the role of three-body Umklapp scattering in maintaining phase coherence and discussed potential extensions to other 2D materials, such as twisted transition metal dichalcogenides. To support the numerical results presented in the manuscript, we provide two Jupyter notebook files (Python environment): 1. RTG.ipynb: This notebook computes the band structure and energy of the intervalley coherent (IVC) phase in rhombohedral trilayer graphene using the self-consistent Fock approximation. The calculations extract important quantities such as the total energy and the orbital magnetization as a function of Lagrange multiplier.\ 2. IVC_res.ipynb: This notebook solves the coupled dynamical equations (Eqs. (6) and (7) in the manuscript) for the evolution of magnetization and phase as a function of time under a static magnetic field. It reveals the emergence of the oscillating orbital magnetization response characteristic of the momentum-space AC Josephson effect.\ The notebooks utilize standard scientific Python libraries (NumPy, SciPy, matplotlib) and are intended to allow for full reproducibility of the numerical findings.\ \ Mainak Das & Chunli Huang Open Capsule

published in Nature Communications

Engineering\ \ 23 | Sep | 2025\ \ Code underlying the publication: Mining extreme properties from a large 2D truss metamaterial database

[Title \ Code and data underlying the publication: Mining extreme properties from a large 2D truss metamaterial database\ Guide \ Due to the involvement of storing CSV files and PNG files, we strongly recommend that you run the following codes locally and set up the environment in advance.\ \ The following codes can reproduce the generation of the architecture database in the MainManuscript. The performance database is calculated using a homogenization method, which is not entirely original to this study and thus is not included in this code capsule.\ Code names\ \

  • /code/main_plot_node_distribution.py: This code is designed to implement the uniform distribution of optional inside node positions for arbitrary-shaped building blocks, as described in the "Generating Architecture-property Database" of MainManuscript (also see Fig. S4, SI Appendix 3).\ \
  • /code/main_plot_RVE.py: This code is designed to implement the plot the RVE from /data/Dataset S1_Architecture database.csv.\ \
  • /code/main_example_architecture_pgg.py: This code is designed to generate the architecture database. This code takes group pgg with 4 struts as an example.\ \ \ Data names \ Dataset S1 (Dataset S1_Architecture database.csv). Entire architecture database of the designed metamaterials, including coordinates of flattened node-sets and elements of flattened adjacency matrices within building blocks.\ \ Dataset S2 (Dataset S2_Mechanical property database.csv). Mechanical property database including Young's moduli, Poisson's ratios, shear modulus, and isotropy index.\ \ Example with names (example.csv). List the names of metamaterials to be plotted before running the file '/code/main_plot_RVE.py'\ Other Files \ The five STL files are CAD models for additive manufacturing using Ultimaker S5, corresponding to the experimental verification section.\ Access information](/content/explore/891402a6-867d-44d2-aecc-ea56a65c5a29?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

The code has not been published elsewhere. \ More detailed data has been deposited in 4TU.ResearchData: Chen, Jiaxin; Wei, Kai (2024): Data underlying the publication: Mining extremal property from a large 2D truss metamaterial database. Version 2. 4TU.ResearchData. dataset. https://doi.org/10.4121/03961539-129b-43b6-9c55-cfd3f5d40a8d.v2 The dataset is intended for reviews of potential publication and should not be cited or used before public publication. The code and data are intended for reviews of potential publication and should not be cited or used before public publication.

Jiaxin Chen & Kai Wei

Open Capsule

published in Nature Communications

Physics\ \ 23 | Sep | 2025\ \ Selecting fitted models under epistemic uncertainty

Fitting models to data is an important part of the practice of science.\ Advances in machine learning have made it possible to fit more — and more complex — models, but have also exacerbated a problem: when multiple models fit the data equally well, which one(s) should we pick?\ The answer depends entirely on the modelling goal.\ In Selecting fitted models under epistemic uncertainty using a stochastic process on quantile functions, we argue that in the scientific context, the essential goal is replicability: if a model works well to describe one experiment, it should continue to do so when that experiment is replicated tomorrow, or in another laboratory. We therein develop a method to estimate replication uncertainty (associated to epistemic uncertainty) based on the discrepancy between observations and model predictions, which is packaged as emdcmp and available on PyPI.

These computational notebooks illustrate our method by reproducing the paper’s figures, as well as additional intermediate analyses. We use two example datasets:

  • UV is simple experiment comparing two statistical models (Planck & Rayleigh-Jeans) inspired by the ultraviolet catastrophe. The simplicity allows us to control the epistemic and aleatoric uncertainty almost independently, and thus perform a systematic study of the method in different regimes. Since the two candidate models are structurally different, we can also use this example to compare to other model comparison methods like AIC, MDL and Bayes’ factors.
  • Prinz2004 is more representative of the modern data-driven context, based on the neuron model studied in Similar network activity from disparate circuit parameters (Prinz et al., 2004). Here all candidates are structurally identical, so standard approaches like AIC, MDL or Bayes’ would either not work or give nonsensical results.

Using the UV model, these notebooks also include a systematic comparison to the following criteria:

  • BIC
  • model evidence (aka marginal likelihood)
  • MDL
  • AIC
  • elpd (expected log predictive density)

As part of this, we include an implementation which computes the MDL directly (via Monte Carlo) for the UV example.

The original code repository for these notebooks is found here: https://github.com/alcrene/emd-paper-notebooks

A preprint of the publication (currently under review) is found here: https://arxiv.org/abs/2408.13414

If you just want to browse the code, see also the "Notebooks" section of the paper’s HTML version: https://alcrene.github.io/emd-paper/

Alexandre René

Open Capsule

published in Nature Communications

Biology\ \ 22 | Sep | 2025\ \ Reference-based chemical-genetic interaction profiling to elucidate small molecule mechanism of action in Mycobacterium tuberculosis\ \ We previously reported an antibiotic discovery screening platform that identifies whole-cell active compounds with high sensitivity while simultaneously providing mechanistic insight, necessary for hit prioritization. Named PROSPECT, (PRimary screening Of Strains to Prioritize Expanded Chemistry and Targets), this platform measures chemical-genetic interactions between small molecules and pooled Mycobacterium tuberculosis mutants, each depleted of a different essential protein. Here, we introduce Perturbagen CLass (PCL) analysis, a computational method that infers a compound's mechanism-of-action (MOA) by comparing its chemical-genetic interaction profile to those of a curated reference set of 437 known molecules. In leave-one-out cross-validation, we correctly predict MOA with 70% sensitivity and 75% precision, and achieve comparable results (69% sensitivity, 87% precision) with a test set of 75 antitubercular compounds with known MOA previously reported by GlaxoSmithKline (GSK). From 98 additional GSK antitubercular compounds with unknown MOA, we predict 60 to act via a reference MOA and functionally validate 29 compounds predicted to target respiration. Finally, from a set of ~5,000 compounds from larger unbiased libraries, we identify a novel QcrB-targeting scaffold that initially lacked wild-type activity, experimentally confirming this prediction while chemically optimizing this scaffold. PCL analysis of PROSPECT data enables rapid MOA assignment and hit prioritization, streamlining antimicrobial discovery.\ \ Austin Nathaniel Bond et al. Open Capsule

published in Nature Communications

Biology\ \ 22 | Sep | 2025\ \ Codes and Data for 'Allocentric Flocking' by Mohammad Salahshour and Iain D. Couzin - Dec 17, 2024 10:34\ \ The code and data for 'Allocentric flocking' by Mohammad Salahshour and Iain D. Couzin.\ \ The code to produce the raw data for individual and collective motion are provided in the code folder. The main script can be used to run the functions and produces a figure and the data for the trajectory of the agent(s). Further documentation is provided in the functions.\ \ The data folder contains all the Matlab scripts and data used to produce figures in the main text. The script named 'Dataanalysis.m' script in this folder can be run on the raw data to produce the measures of collective movement used for analysis.\ \ Mohammad Salahshour & Iain D. Couzin Open Capsule

published in Nature Communications

Earth Sciences\ \ 19 | Sep | 2025\ \ Dual layered mantle lithosphere beneath southeastern Canadian Cordillera\ \ This capsule contains the supplementary codes and datasets for the manuscript titled “Dual-Layered Mantle Lithosphere Beneath the Southeastern Canadian Cordillera.”\ \ songyun huang, Stephen T Johnston & Jeffrey Gu Open Capsule

published in Nature Communications

Biology\ \ 17 | Sep | 2025\ \ Engineering wetware and software for the predictive design of compressed genetic circuits for higher-state decision-making\ \ This repository contains codes for algorithmic enumeration of 3-input transcriptional programming (T-Pro) circuits in our paper "Engineering wetware and software for the predictive design of compressed genetic circuits for higher-state decision-making".\ \ Brian D. Huang et al. Open Capsule

published in Nature Communications

Physics\ \ 17 | Sep | 2025\ \ Efficient Classical Sampling from Gaussian Boson Sampling Distributions on Unweighted Graphs\ \ Numerical Code for Efficient Classical Sampling from Gaussian Boson Sampling Distributions on Unweighted Graphs.\ \ Tongyang Li Open Capsule

published in Nature Communications

Medical Sciences\ \ 16 | Sep | 2025\ \ Categorical and Phenotypic Image Synthetic Learning (CATphishing): An Alternative to Federated Learning in Medical Imaging\ \ This repository contains the source code and supplementary resources for the manuscript: "CATegorical and PHenotypic Image SyntHetic LearnING (CATphishing): An Alternative to Federated Learning in Medical Imaging."\ \ CATphishing introduces a novel approach to multi-center collaborations in medical imaging by leveraging Latent Diffusion Models (LDMs) to generate synthetic multi-contrast 3D MRI data. This technique addresses critical privacy, scalability, and communication challenges in federated learning and centralized data sharing.\ \ Nghi Truong et al. Open Capsule

published in Nature Communications

Computer Science\ \ 15 | Sep | 2025\ \ A frugal Spiking Neural Network for unsupervised classification of continuous multivariate temporal data\ \ The present capsule contains the data and python source code necessary to reproduce the main analyses and figures of the manuscript "A frugal Spiking Neural Network for unsupervised classification of continuous multivariate temporal data".\ \ Launching the Code Ocean's Reproducible Run will reproduce the majority of the figures. For an exhaustive reproduction of the analyses, please refer to README.txt.\ \ POKALA Sai Deepesh Open Capsule

published in Nature Communications

Computer Science\ \ 15 | Sep | 2025\ \ A frugal Spiking Neural Network for unsupervised multivariate temporal pattern classification and multichannel spike sorting\ \ The present capsule contains the data and python source code necessary to reproduce the main analyses and figures of the manuscript "A frugal Spiking Neural Network for unsupervised multivariate temporal pattern classification and multichannel spike sorting".\ \ Launching the Code Ocean's Reproducible Run will reproduce the majority of the figures. For an exhaustive reproduction of the analyses, please refer to README.md\ \ POKALA Sai Deepesh Open Capsule

published in Nature Communications

Engineering\ \ 15 | Sep | 2025\ \ Static mechanical cloaking and camouflage from disorder\ \ This code is used for calculating the static cloaking and camouflage performance of the article " Static mechanical cloaking and camouflage from disorder"\ \ Zhou Yang Open Capsule

published in Nature Communications

Medical Sciences\ \ 12 | Sep | 2025\ \ Ambient heat stress, preconceptional thyrotropin abnormalities, and the risk of preterm birth: A nationwide Chinese cohort study\ \ The code was used to reproduce the environmental assessment and cohort study analysis\ \ Xinghou He Open Capsule

published in Nature Communications

Physics\ \ 6 | Oct | 2025\ \ Global Distribution of Energy-Saving Potential of PDH Smart Windows 2.0\ \ Global Distribution of Energy-Saving Potential of PDH Smart Windows\ \ Bowen Yang Open Capsule

published in Nature Communications

Biology\ \ 13 | Dec | 2025\ \ Historical depletion and future drought driven risks to Gulf of Mexico fisheries production\ \ This code reproduces Fig. 2a: Mississippi river basin PDSI temporal and spatial projections for the mid- and the end of the 21st century. To reproduces Fig. 2a, run the MATLAB code, the code uses the CMIP5 PDSI model projections data (Cook et al. 2014). Due to the large size of the PDSI data, running the code may take around one minute.\ \ Igal Berenshtein, Benjamin Kirtman, Kim de Mutsert & David D. Chagaris Open Capsule

published in Nature Communications

Biology\ \ 13 | Dec | 2025\ \ Historical depletion and future drought driven risks to Gulf of Mexico fisheries production\ \ To reproduce the manuscript plots, run the R code files in this capsule. The R scripts generate all figures but Fig. 2a, and the MATLAB code generates Fig. 2a in the second capsule. Code that produces results mentioned in manuscript are at the end of in each script file along with a commented description.\ \ Igal Berenshtein, Benjamin Kirtman, Kim de Mutsert & David D. Chagaris Open Capsule

published in Nature Communications

Biology\ \ 4 | Sep | 2025\ \ A global phylogeny and taxonomy of Artemisia: new insights from genome and morphology\ \ Discretization of 8 continuous characters in Artemisia. The source code and data associated with the paper entitled "A global phylogeny and taxonomy of Artemisia: new insights from genome and morphology".\ \ Bohan Jiao Open Capsule

published in Nature Communications

Physics\ \ 27 | Oct | 2025\ \ Multi-stage Power-to-water Battery Synergizes Flexible Energy Storage and Efficient Atmospheric Water Harvesting\ \ Calculation and validation of multi-stage atmospheric water harvesting\ \ LIN Haosheng Open Capsule

published in Nature Communications

Biology\ \ 3 | Sep | 2025\ \ Stabilizing a mammalian RNA thermometer confers neuroprotection in subarachnoid hemorrhage\ \ Code for reproducing results/figures in the RNA G4 splicing study.\ \ Min Zhang et al. Open Capsule

published in Nature Communications

[Engineering\ \ 22 | Feb | 2026\ \ Revealing the Intrinsic Ethical Vulnerability of Aligned Large Language Models\ \ Code Execution Constraints and Verification\ \ We provide core algorithmic code for transparency, though full experiment reproduction on Code Ocean is infeasible. This is due to: \ \

  • Hardware requirements for state-of-the-art LLMs exceeding platform limits \
  • Prohibited public distribution of proprietary model weights \
  • Irreplicable custom security-testing environments \
  • Ethical safeguards for jailbreak experiments unattainable in public settings\ \ Verification Pathway\ \ To enable validation:\ \ Upon reviewer request and Editorial Office approval, we will supply comprehensive step-by-step instructions covering: \ \
  • Environment configuration (dependencies) \
  • Compliant LLM access protocols \
  • Security controls and ethical replication guidelines \
  • Hardware specifications (GPU requirements)\ \ These instructions support independent validation under reviewer-managed conditions, balancing transparency with legal, ethical, and computational constraints.\ \ Jiawei Lian](/content/explore/5bd4e349-14ba-41d9-8a7b-49461eb25f09?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) Open Capsule

published in Nature Communications

Physics\ \ 29 | Aug | 2025\ \ Phase-probability shaping for speckle-free holographic lithography\ \ Optical holography has undergone rapid development since its invention in 1948, but the accompanying speckles with alternating dark and bright spots of randomly varying shapes are still untamed now due to the intrinsic fluctuations from irregular complex-field superposition. Despite spatial, temporal and spectral averages for speckle reduction, holographic images cannot yet meet the requirement for high-homogeneity, edge-sharp and shape-unlimited features in optical display and lithography. Here we report that holographic speckles can be removed by narrowing the probability density distribution of encoded phase to homogenize optical superposition. Guided by this physical insight, an Adam-gradient-descent probability-shaping (APS) method is developed to prohibit the fluctuations of intensity in a computer-generated hologram (CGH), which empowers the experimental reconstruction of irregular images with ultralow speckle contrast (C=0.08) and record-high edge sharpness (~1000 mm-1). These excellent performances unlock the technology of CGH lithography, which enables us to experimentally fabricate arbitrary-shape and edge-sharp patterns with spatial resolution of 0.54λ/NA.\ \ Dong Zhao Open Capsule

published in Nature Communications

Biology\ \ 28 | Aug | 2025\ \ Neural coding of choice and outcome are modulated by uncertainty in orbitofrontal cortex but not secondary motor cortex\ \ Orbitofrontal cortex (OFC) and secondary motor cortex (M2) are both implicated in flexible reward learning but the conditions that differentially recruit these regions are not fully understood. We imaged calcium activity from single neurons in OFC or M2 during de novo learning of uncertain reward probability schedules. Predictions of choice were decoded from M2 neurons with high accuracy under all certainty conditions, but were more accurately decoded from OFC neurons under greater uncertainty. In M2, the proportion of outcome-selective neurons decreased with uncertainty whereas this proportion remained stable in OFC, due to an increased recruitment of reward-selective neurons across levels of uncertainty. Decoding accuracy of both choice and outcome were predicted by indices of flexible strategy like Win-Stay and Lose-Shift in OFC, but not M2. When schedules were experienced in increasing and then decreasing uncertainty, chemogenetic perturbation of M2 and OFC neurons resulted in opposing roles in certain and uncertain conditions, respectively. Our results indicate that M2 neurons are causally involved in learning of more certain conditions, whereas OFC neurons preferentially encode choices and outcomes that foster greater reliance on adaptive strategies under conditions of uncertainty. This reveals a novel functional heterogeneity within frontal cortex in support of flexible learning.\ \ Juan Luis Romero-Sosa et al. Open Capsule

published in Nature Communications

Earth Sciences\ \ 28 | Aug | 2025\ \ Southern Ocean CO2 outgassing and nutrient load reduced by a well-ventilated glacial North Pacific\ \ Code accompanying manuscript "Southern Ocean CO2 outgassing and nutrient load reduced by a well-ventilated glacial North Pacific" submitted to Nature Communications\ \ Madison Shankle et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 21 | Aug | 2025\ \ MorphDiff: Prediction of cellular morphology change under perturbations with transcriptome-guided diffusion model\ \ MorphDiff is a diffusion-based framework conditioned with gene expression for morphological responses under genetic and chemical perturbations. We provide an integrated pipeline for morphological responses prediction, various morphological analysis and cell morphology-based drugs' MOA (Mechanism Of Action) retrieval in this repository.\ \ Xuesong Wang et al. Open Capsule

published in Nature Communications

Earth Sciences\ \ 3 | Sep | 2025\ \ Recent slowing of Arctic sea ice melt tied to multidecadal NAO variability (NC)\ \ This repository contains the source code utilized in the paper ‘Recent slowing of Arctic sea ice melt tied to multidecadal NAO variability’.\ \ Cen Wang Open Capsule

published in Nature Communications

Bioinformatics\ \ 21 | Aug | 2025\ \ Quantitative methylation reference datasets of Quartet DNA reference materials for benchmarking genome-wide epigenome sequencing

  1. The code related to figure generation can achieve a 'Reproducible Run'. This includes both the main figures and the supplementary figures. Figs. 1, 4A, S1, and S10A were created at https://BioRender.com. The adjustment of figure details, such as font size, color, and legend position, is done by editing the PDF file using Adobe Illustrator (2021).

The upstream analysis process involves a large amount of computing and storage resources. Only the code is provided here(/code/upstream/), and you need to download the raw data from GSA by yourself before you can run it. 4. The raw sequence data used in this paper have been deposited in the Genome Sequence Archive (GSA, accession number: PRJCA037414)，which can be accessed by the link: https://ngdc.cncb.ac.cn/gsa-human/s/zlvSm7V1.

  1. The raw sequence data, CpG call sets, and microarray IDATs are accessible in NODE ( https://www.biosino.org/node ) with the accession number OEP00004817 or through the following URL: https://www.biosino.org/node/project/detail/OEP00004817.

  2. All reference datasets can be accessed from the Quartet Data Portal ( https://chinese-quartet.org/) under the Administrative Regulations of the People’s Republic of China on Human Genetic Resources.

Xiaorou Guo

Open Capsule

published in Nature Communications

Bioinformatics\ \ 21 | Aug | 2025\ \ Molecular Motif Learning (initial release)\ \ Code and Data for the paper: Molecular Motif Learning\ \ Ziyang Liu et al. Open Capsule

published in Nature Communications

Physics\ \ 19 | Aug | 2025\ \ Strong coupling between a single photon and a photon pair\ \ The realization of strong nonlinear coupling between single photons has been a long-standing goal in quantum optics and quantum information science, promising wide impact applications, such as all-optical deterministic quantum logic and single-photon frequency conversion. Here, we report an experimental observation of the strong coupling between a single photon and a photon pair in an ultrastrongly-coupled circuit-QED system. This strong nonlinear interaction is realized by introducing a detuned flux qubit working as an effective coupler between two modes of a superconducting coplanar waveguide resonator. The ultrastrong light--matter interaction breaks the excitation number conservation, and an external flux bias breaks the parity conservation. The combined effect of the two enables the strong one--two-photon coupling. Quantum Rabi-like avoided crossing is resolved when tuning the two-photon resonance frequency of the first mode across the single-photon resonance frequency of the second mode. Within this new photonic regime, we observe the second harmonic generation for a mean photon number below one. Our results represent a key step towards a new regime of quantum nonlinear optics, where individual photons can deterministically and coherently interact with each other in the absence of any stimulating fields.\ \ Shuai-Peng Wang et al. Open Capsule

published in Nature Communications

Earth Sciences\ \ 18 | Aug | 2025\ \ Capsule_GEE-MEGAN(Improved modelling of biogenic emissions in human-disturbed forest edges and urban areas)\ \ This Capsule is designed to build the GEE-MEGAN code and provide reproducible execution.\ GEE-MEGAN extends MEGAN2.1 biogenic VOC model to Google Earth Engine (GEE).\ With dynamic, satellite-based land-cover and vegetation data, it generates near-real-time BVOC emissions at 10-30 m resolution, and can run continental-scale (500 m) or global (5 km) simulations.\ \ Yanli Zhang et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 18 | Aug | 2025\ \ Longitudinal liquid biopsy identifies an early predictive biomarker of immune checkpoint blockade response in head and neck squamous cell carcinoma

[Immune checkpoint blockade (ICB) therapy has shown promise for treating head and neck squamous cell carcinoma (HNSCC), but only a subset of patients exhibit a meaningful response. Hence, identifying predictive biomarkers of the ICB response remains a critical roadblock. Here, for the first time, we systematically characterize the dynamic changes in the blood during ICB treatment across four different time points in a mouse HNSCC model treated with anti-PD-1 ICB. We profile serial pre and on-treatment liquid biopsies, both by single cell (SC) and bulk RNA with tandem SC-TCR sequencing to identify liquid predictors of the ICB response.\ \ This study charts the host peripheral response to ICB therapy on an unprecedented scale. We observe significant differences in the clonal expansion and temporal dynamics of effector memory T cells (Tem) and B cells between responders and non-responder mice. These changes were most prominent in mice at an early on-treatment time point, highlighting this time point as optimal for assessing ICB efficacy. Remarkably, the resulting LiBIO score which integrates the Tem and B cell signatures, successfully predict ICB response in HNSCC patients across multiple tumor and blood cohorts, without any additional training. Its application using one fixed decision threshold yields a fairly high predictive odds ratio of response, which surpasses the predictive power of existing biomarkers, including a newly generated validation cohort of HNSCC patients treated with ICB.\ \ Collectively, our preclinical insights support the premise that peripheral immune events can serve as a foundation for biomarker discovery, offering a non-invasive, biologically grounded approach to monitor and predict immunotherapy outcomes with high fidelity in HNSCC patients. Finally, the approach presented lays a solid basis for developing similar biomarkers in other cancer indications.\ \ To perform the analysis and generate all figures:\ \

  1. Set main.sh as the File to Run.\
  2. Click Reproducible Run in the top right corner.](/content/explore/884ea1c9-e1a4-4123-be66-b66602539e92?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

This code has been uploaded to GitHub: https://github.com/wbb1813/Time_series_mouse_ICB.git For any questions or concerns about the code, please contact Binbin Wang at wangbinbintj@gmail.com.

Binbin Wang

Open Capsule

published in Nature Communications

Earth Sciences\ \ 16 | Aug | 2025\ \ Decadal trends in global grassland growth peaks and their drivers since the 1980s\ \ We use the "partial _correlation" code to analysis the partial correlation between the grassland growth peak and envrionment variables. The partial correlation analysis was conducted to isolate the influence of individual environmental factors on NDVI while controlling for the effects of other correlated variables.\ We use the "factorial_experiment_RF" code to do the factor experiment using machine learning method. The RF model was driven by all time-varying variables and supplemented with five factorial simulations (CLI, CO2, N, Cropland, and Rangeland), where each simulation held a single factor (climate, CO2, nitrogen deposition rate, cropland fraction, or rangeland fraction) constant at its initial level (first year of data) while allowing the other variables to vary with time. Climate includes precpitation, air temperature and radiation.\ The data contains the imput data including grassland peak growth (NDVI) data and environmental variables CO2, Cropland fraction, Nitrogen deposition rate, Precipitation (PPT), Radiation (Rad), Air temperature (TA).\ \ Cuihai You Open Capsule

published in Nature Communications

Biology\ \ 15 | Aug | 2025\ \ Many plants naturalized as aliens abroad have also become more common within their native regions (Second Revision)\ \ Our research has ten native regions, as our study regions (see methods for detail) and we replicate the same analysis for each region. Therefore, here you can find the complete code to reproduce the analysis for one region ( Austria as example). Then, you can use the same code for other regions by replacing the data sets corresponding to that particular region.\ \ Rashmi Paudel et al. Open Capsule

published in Nature Communications

Medical Sciences\ \ 15 | Sep | 2025\ \ A motif preferred adenine base editor with minimal bystander and off-targets editing\ \ This capsule provides scripts to analyze pathogenic single-nucleotide variants (SNVs) from the ClinVar database, with a focus on evaluating their correctability by various adenine base editors (ABEs).\ \ Qiuyu Cao Open Capsule

published in Nature Communications

Engineering\ \ 12 | Aug | 2025\ \ China's Urban EV Ultra-Fast Charging Exacerbates Regulated Price Signal Distortions and Elevates Risk to Grid Capacity and Flexibility\ \ This repository contains the Python code and the data to reproduce figures in "NCOMMS-25-08422-T".\ \ Qing Yu et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 11 | Aug | 2025\ \ DeMBA: A developmental atlas for navigating the mouse brain in space and time [Common Coordinate Framework Translator]

\ \ CCF translator (brainglobe-ccf-translator) is a tool for translating between common coordinate frameworks using deformation matrices. \ A longstanding problem in NeuroInformatics has been the inability to easily translate data between common coordinate frameworks. CCF translator aims to solve this. By connecting each new space to an existing one, we can construct a graph of deformations. This means that data can be translated as long as there is a route from one space to another, even if that route passes through multiple other spaces. Now, when new templates for new modalities, strains, or ages are released, users will not be subdivided into unrelated spaces. As long as they are connected to a space which exists in our network, they will be fully connected to all other spaces. \ \ CCF translator can also interpolate between spaces and create a new intermediate space. This is primarily useful for development, where, for instance, the midpoint between day 5 and day 7 can be taken and used as a postnatal day 6 reference. It could also be useful for making references of disease progression. \ \ \ Use Cases \ One way you can use CCF translator is to view data from one space, in another space. For instance the allen connectivity dataset shows projections from viral tracing studies in the adult brain. We can take any of these projection datasets and view them in the developing brain, for instance post natal day 9.\ \ Installation \ CCF translator can be installed by running \ \ Copy\ \

pip install brainglobe-ccf-translator\\
```\\
\\
**Currently supported spaces** \\
the name in CCF translator aims to copy the name of atlases in the brainglobe\_atlasapi when possible. \\
\\
| Framework Name | name in api | supported age range |\\
| --- | --- | --- |\\
| Allen mouse CCFv3 | allen\_mouse | 56 |\\
| Demba developmental mouse | demba\_dev\_mouse | 4-56 |\\
| Gubra lightsheet mouse | perens\_lsfm\_mouse | 56 |\\
| Gubra MRI mouse | perens\_mri\_mouse | 56 |\\
| Gubra STPT mouse | perens\_stpt\_mouse | 56 |\\
| Princeton lighsheet mouse | princeton\_mouse | 56 |\\
\\
**Usage** \\
**Transforming points**\\
To take a coordinate in one volume and find the equivalent coordinate in a second volume is quite simple in CCF translator. \\
\\
python\\
\\
Copy\\
\\
```python\\
import numpy as np\\
import brainglobe_ccf_translator\\
\\
points = np.array([(286,250,267), (414,247,452)])\\
pset = brainglobe_ccf_translator.PointSet(points, 'demba_dev_mouse', voxel_size_micron=20, age_PND=56)\\
pset.transform(target_age=56, target_space='allen_mouse')\\
print(f"new points are {pset.values}")\\
```\\
\\
Copy\\
\\
```\\
new points are [[267 250 286] [452 247 414]]\\
```\\
\\
**Transforming volumes**\\
\\
To run the volume examples you will want to install brainglobe-atlasapi using the following\\
\\
Copy\\
\\
```\\
pip install brainglobe-atlasapi\\
```\\
\\
Transforming a volume is equally simple, here we get the volume from the brainglobe api, but you can load it however you like. In the Demba space the valid ages are from 4 to 56, and all of these are valid targets for transformation. \\
\\
python\\
\\
Copy\\
\\
```python\\
from brainglobe_atlasapi.bg_atlas import BrainGlobeAtlas\\
import brainglobe_ccf_translator\\
\\
voxel_size_micron = 10\\
space_name = r"allen_mouse"\\
atlas = BrainGlobeAtlas("{space_name}_{voxel_size_micron}um")\\
source_age = 56\\
target_age= 32\\
\\
ccft_vol = brainglobe_ccf_translator.Volume(\\
    values = atlas.reference,\\
    space = 'allen_mouse',\\
    voxel_size_micron=voxel_size_micron,\\
    segmentation_file=False,\\
    age_PND = source_age\\
)\\
\\
ccft_vol.transform(target_age, 'demba_dev_mouse')\\
ccft_vol.save(rf"demo_data/P{target_age}_template_{voxel_size_micron}um.nii.gz")\\
```\\
\\
**Contributing** \\
If you would like to add a new space or connect an existing one, please create a deformation matrix and/or describe the required reorientation, flipping, cropping, and padding of the axis between this space and one that already exists in the network, and then open an issue in this repository. Ideally, choose a space which covers all the areas which are covered in your space. While the Allen CCFv3 is very popular, it is missing the anterior olfactory bulb and the caudal portion of the cerebellum and brain stem, so it is not the optimal choice. \\
**Citation**](/content/explore/95ec9128-78ad-4d9c-aaac-f25c36aa1eb0?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[CCF translator was first described in](/content/explore/95ec9128-78ad-4d9c-aaac-f25c36aa1eb0?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [DeMBA: a developmental atlas for navigating the mouse brain in space and time](https://www.biorxiv.org/content/10.1101/2024.06.14.598876v1). If you use CCF translator, please cite that paper.

Harry Carey et al.

[Open Capsule](/content/capsule/7816212/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
11 \| Aug \| 2025\\
\\
DeMBA: A developmental atlas for navigating the mouse brain in space and time \[Atlas creation and analysis\]](/content/explore/cec34bd4-a4cb-434e-9104-8d8545f9816f?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[**Project overview**](/content/explore/cec34bd4-a4cb-434e-9104-8d8545f9816f?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[The Developmental Mouse Brain Atlas (DeMBA) is a four-dimensional atlas encompassing each postnatal day from 4 to 56, with delineations that are fully compatible with the Allen Mouse brain Common Coordinate Framework (Allen CCF) delineations. The atlas was created by 3D-to-3D registration of the Allen CCF template](/content/explore/cec34bd4-a4cb-434e-9104-8d8545f9816f?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [(Wang and colleagues)](https://www.sciencedirect.com/science/article/pii/S0092867420304025?via%3Dihub) to templates of developing mouse brains (P4, P7, P14, P21 and P28) acquired by serial two photon microscopy and published by [Newmaster and colleagues](https://www.nature.com/articles/s41467-020-15659-1) and [Liwang and colleagues](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10690281/). The deformation of the templates is subsequently used to transform the delineations in the same way, providing Allen CCF delineations in the template space for each age group. The deformation matrices were further used to create interpolated models of what the template and segmentations would look like at intermediate ages.

### :page\_facing\_up: **For more information about the atlas and how it can be used, read our [preprint](https://www.biorxiv.org/content/biorxiv/early/2024/06/14/2024.06.14.598876.full.pdf).**

# Data availability

The templates used in the transformation and the resulting atlases are shared via the EBRAINS Knowledge Graph.

### DeMBA atlas with continuous coverage from P4-P56

- Carey, H., Ovsthus, M., Kleven, H., Yates, S. C., Csucs, G., Puchades, M. A., Bjaalie, J. G., Leergaard, T. B., & Bjerke, I. E. (2024). Developmental mouse brain atlas (DeMBA) with continuous coverage of postnatal day 4 to 56 (v1) \[Data set\]. EBRAINS. [https://doi.org/10.25493/PWDG-536](https://doi.org/10.25493/PWDG-536)

### DeMBA templates

The P7, P14, P21 and P28 templates were originally acquired and shared by [Newmaster and colleagues](https://www.nature.com/articles/s41467-020-15659-1) as .tif files with a (20 \* 20 \* 50 µm) voxel resolution. We resampled them to isotropic (20 \* 20 \* 20 µm) voxel resolution. The P4 template was shared by [Liwang and colleagues](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10690281/) and was already provided in isotropic (20 \* 20 \* 20 µm) resolution. All the templates were re-oriented and processed to optimize them for co-registration. The processed templates, as used in our registration workflow, can be found under the following datasets:

- Carey, H., Kleven, H., Leergaard, T. B., & Bjerke, I. E. (2024). Population-averaged 3D isotropic serial two-photon tomography reference data for the P4 mouse brain (v1) \[Data set\]. EBRAINS. [https://doi.org/10.25493/VNF6-E92](https://doi.org/10.25493/VNF6-E92)
- Carey, H., Kleven, H., Qu, H., Leergaard, T. B., & Bjerke, I. E. (2024). Population-averaged 3D isotropic serial two-photon tomography reference data for the P7 mouse brain (v2) \[Data set\]. EBRAINS. [https://doi.org/10.25493/JKBM-608](https://doi.org/10.25493/JKBM-608)
- Carey, H., Kleven, H., Qu, H., Leergaard, T. B., & Bjerke, I. E. (2024). Population-averaged 3D isotropic serial two-photon tomography reference data for the P14 mouse brain (v2) \[Data set\]. EBRAINS. [https://doi.org/10.25493/KAHK-14](https://doi.org/10.25493/KAHK-14)
- Carey, H., Kleven, H., Qu, H., Leergaard, T. B., & Bjerke, I. E. (2024). Population-averaged 3D isotropic serial two-photon tomography reference data for the P21 mouse brain (v2) \[Data set\]. EBRAINS. [https://doi.org/10.25493/2FMJ-152](https://doi.org/10.25493/2FMJ-152)
- Carey, H., Kleven, H., Qu, H., Leergaard, T. B., & Bjerke, I. E. (2024). Population-averaged 3D isotropic serial two-photon tomography reference data for the P28 mouse brain (v2) \[Data set\]. EBRAINS. [https://doi.org/10.25493/TG8Z-PER](https://doi.org/10.25493/TG8Z-PER)

### DeMBA annotation sets

The Allen CCF segmentations (2017 and 2022 versions) were transformed to fit the DeMBA templates, and the resulting segmentation volumes are shared under the following datasets:

- Carey, H., Ovsthus, M., Kleven, H., Leergaard, T. B., & Bjerke, I. E. (2024). Allen Mouse Brain CCFv3 segmentations transformed to P4 population-averaged serial two-photon tomography data (v1) \[Data set\]. EBRAINS. [https://doi.org/10.25493/QG9H-16Y](https://doi.org/10.25493/QG9H-16Y)
- Ovsthus, M., Carey, H., Kleven, H., Leergaard, T. B., & Bjerke, I. E. (2024). Allen Mouse Brain CCFv3 segmentations transformed to P7 population-averaged serial two-photon tomography data (v1) \[Data set\]. EBRAINS. [https://doi.org/10.25493/NAWP-ND2](https://doi.org/10.25493/NAWP-ND2)
- Ovsthus, M., Carey, H., Kleven, H., Leergaard, T. B., & Bjerke, I. E. (2024). Allen Mouse Brain CCFv3 segmentations transformed to P14 population-averaged serial two-photon tomography data (v1) \[Data set\]. EBRAINS. [https://doi.org/10.25493/SZSR-BFZ](https://doi.org/10.25493/SZSR-BFZ)
- Ovsthus, M., Carey, H., Kleven, H., Leergaard, T. B., & Bjerke, I. E. (2024). Allen Mouse Brain CCFv3 segmentations transformed to P21 population-averaged serial two-photon tomography data (v1) \[Data set\]. EBRAINS. [https://doi.org/10.25493/JZKH-XWK](https://doi.org/10.25493/JZKH-XWK)
- Ovsthus, M., Carey, H., Kleven, H., Leergaard, T. B., & Bjerke, I. E. (2024). Allen Mouse Brain CCFv3 segmentations transformed to P28 population-averaged serial two-photon tomography data (v1) \[Data set\]. EBRAINS. [https://doi.org/10.25493/GVT5-4K9](https://doi.org/10.25493/GVT5-4K9)

# Code

This repository contains all the code used for the 3D-to-3D registration underlying DeMBA. The scripts are sorted into three main folders:

### volume\_preprocessing\_pipeline

- **download\_original\_allen\_data.py** This script can be used to download the template and label files from the Allen Institute used in the current project.
- **reorient\_original\_allen\_data.py** This scripts reorients the Allen data to be in the same orientation as the DeMBA volumes, which is crucial for the use of corresponding points in the registration.
- **download\_reoriented\_dev\_templates.py** This script can be used to dowload the DeMBA templates from the EBRAINS Knowledge Graph.

### elastix\_transformation

- **DeMBA\_functions.py** This script contains the functions used for elastix transformation.
- **DeMBA\_runs.py** This script was used to run transformations in the project. It allows you to run transformations specified fixed and moving volumes and copies all resulting files to a unique run directory, making it easy to keep an overview of different runs and results.
- **DeMBA\_P\[X\].py** These scripts (with X indicating the postnatal day of the fixed age for the transform) are the exact scripts used in our registration, to produce the datasets listed under "DeMBA annotation sets".

### other

The scripts in this folder are not part of the preprocessing or transformation pipeline but might be useful when working with volumes:

- **make\_thumbnail\_flythrough.py** This script creates a flythrough video of a volume file, suitable for use as a preview image on the EBRAINS Knowledge Graph.
- **label\_annotationIDs\_sequential.py** This script converts all the IDs in the Allen annotation volumes to sequential IDs. This avoids rounding errors for large IDs when using elastix.
- **relabel\_annotationIDs\_Allen.py** This script converts all the sequential IDs back to IDs from the Allen Institute ontology.

The code used to interpolate the templates and segmentation to intermediate ages will be shared shortly.

# Useful tips

- We use the SimpleITK package for elastix. Be aware that there is another package called simpleITK. To make sure you import the right package, first pip install SimpleITK-SimpleElastix.

Harry Carey et al.

[Open Capsule](/content/capsule/7632843/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
\\
11 \| Aug \| 2025\\
\\
Nonreciprocal surface plasmonic neural network for decoupled bidirectional analogue computing\\
\\
Nonreciprocal surface plasmonic neural network for decoupled bidirectional analogue computing\\
\\
xiaomengli](/content/explore/4d0aa666-25e6-4970-859f-b2198709bb57?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/0698286/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
\\
7 \| Aug \| 2025\\
\\
Decoding Millennia Records of Hailstorm: Climate Impacts and Future Trends](/content/explore/46243fb6-3cde-4ab5-bd72-7d76a567a1da?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[**Introduction:** \\
Scripts and data used to generate the plots in main text\\
**References:**](/content/explore/46243fb6-3cde-4ab5-bd72-7d76a567a1da?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[CEEMDAN:](/content/explore/46243fb6-3cde-4ab5-bd72-7d76a567a1da?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [https://perso.ens-lyon.fr/patrick.flandrin/emd.html](https://perso.ens-lyon.fr/patrick.flandrin/emd.html)

PDO calculation: [https://github.com/ZijieZhaoMMHW/Cal\_CM](https://github.com/ZijieZhaoMMHW/Cal_CM)

## Python:

System requirements for running machine learning in Python:

- python3.7
- keras2.2.5
- tensorflow-cpu1.15

Copy

conda env create -f environment.yml -n new_env_name


## Notes:

All remaining analyses were performed in MATLAB R2023a.

Rumeng LI

[Open Capsule](/content/capsule/5969349/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
\\
7 \| Aug \| 2025\\
\\
Fit of time-dependent strain, and simulation of time-dependent strain profiles and X-ray diffraction curves\\
\\
Abstract.\\
\\
A fundamental understanding of the interplay between lattice structure, polarization and electrons is pivotal to the optical control of ferroelectrics. The interaction between light and matter enables the remote and wireless control of the ferroelectric polarization on the picosecond timescale, while inducing strain, i.e., lattice deformation. At equilibrium, the ferroelectric polarization is proportional to the strain, and is typically assumed to be so also out of equilibrium. \\
Decoupling the polarization from the strain would remove the constraint of sample design and provide an effective knob to manipulate the polarization by light. Here, upon an above-bandgap laser excitation of the prototypical ferroelectric BaTiO3, we induce and measure an ultrafast decoupling between polarization and strain that begins within 350 fs, by softening Ti-O bonds via charge transfer, and lasts for several tens of picoseconds. We show that the ferroelectric polarization out of equilibrium is mainly determined by photoexcited electrons, instead of the strain. This excited state could serve as a starting point to achieve stable and reversible polarization switching via THz light. Our results demonstrate a light-induced transient and reversible control of the ferroelectric polarization and offer a pathway to control by light both ferroelectric and magnetic degrees of freedom in multiferroics.\\
\\
In the following we describe the content of the capsule.\\
\\
The notebook '\_1\_Fit\_strain\_profile' fits the average strain data measured at incident pump fluences of 1.4 and 2.7 mJ/cm2.\\
\\
The notebooks '\_2\_Simulation\_2D\_strain\_map\_1.4mJ' and '\_6\_Simulation\_2D\_strain\_map\_2.7mJ' simulate the strain curves as a function of pump-probe delay (t) and distance from the thin film surface (z), at incident pump fluences of 1.4 and 2.7 mJ/cm2, respectively.\\
\\
The notebooks '\_3\_Simulation\_average\_strain\_curves\_1.4mJ' and '\_7\_Simulation\_average\_strain\_curves\_2.7mJ' simulates the average strain as a function of pump-probe delay, the thermoelastic contribution and the deformation potential contribution to the total average strain, at incident pump fluences of 1.4 and 2.7 mJ/cm2, respectively.\\
\\
The notebooks '\_4\_Simulation\_x\_ray\_diffraction\_curves\_1.4mJ' and '\_8\_Simulation\_x\_ray\_diffraction\_curves\_2.7mJ' simulate X-ray diffraction curves at the same fixed pump probe delays as in the experiments, at incident pump fluences of 1.4 and 2.7 mJ/cm2, respectively.\\
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The notebooks '\_5\_Simulation\_2D\_x\_ray\_diffraction\_1.4mJ' and '\_9\_Simulation\_2D\_x\_ray\_diffraction\_2.7mJ' simulate X-ray diffraction curves as a function of photon energy and pump probe delay, at incident pump fluences of 1.4 and 2.7 mJ/cm2, respectively.\\
\\
Le Phuong Hoang & Giuseppe Mercurio](/content/explore/89bd9592-b63e-4100-8d3c-b0531a8112b0?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/0075355/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
\\
6 \| Aug \| 2025\\
\\
Deep Learning-based approach for screening neonatal cerebral lesions on ultrasound images in China: a stepwise, multicenter, early-stage clinical validation study](/content/explore/b6eaa8a4-a26a-4b37-9510-92522921a7cf?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[Deep Learning-based approach for screening neonatal cerebral lesions on ultrasound images in China: a stepwise, multicenter, early-stage clinical validation study .\\
GitHub:](/content/explore/b6eaa8a4-a26a-4b37-9510-92522921a7cf?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [https://github.com/Je1zzz/Neonatal\_cerebral\_lesions\_screening\_NCLS](https://github.com/Je1zzz/Neonatal_cerebral_lesions_screening_NCLS)

Haoming Zhang

[Open Capsule](/content/capsule/7873714/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
5 \| Aug \| 2025\\
\\
Target-aware 3D Molecular Generation Based on Guided Equivariant Diffusion\\
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Molecule generation based on protein pocket\\
\\
Qiaoyu Hu et al.](/content/explore/41ef5f4f-128d-4db8-b236-f8251c5cf67d?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/5374355/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
1 \| Aug \| 2025\\
\\
Modeling integration site data for safety assessment with MELISSA\\
\\
Code to reproduce results of paper "Modeling integration site data for safety assessment with MELISSA". Authors: Tsai-Yu Lin, Giacomo Ceoldo, Kimberley House, Matthew Welty, Thao Thi Dang, Denise Klatt, Christian Brendel, Michael P. Murphy, Kenneth Cornetta, Danilo Pellin.\\
\\
Giacomo Ceoldo & Danilo Pellin](/content/explore/1b90b402-87a2-4a61-9bae-bd28b60597c1?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9448953/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
\\
1 \| Aug \| 2025\\
\\
Observing the dynamics of quantum states generated inside nonlinear optical cavities\\
\\
Code for reproducing the main figures in the manuscript: Observing the dynamics of quantum states generated inside nonlinear optical cavities.\\
\\
Seou Choi et al.](/content/explore/47911839-8b8e-494b-908e-1541536d3214?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8772078/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
31 \| Jul \| 2025\\
\\
Fibrous Network Nature of Plant Cell Walls Enables Tunable Mechanics for Development(five-beam model incremental loading)\\
\\
custom MATLAB code for the five-beam model under incremental loading condition\\
\\
SI Chen et al.](/content/explore/38e0b001-802c-4cf3-9beb-853b91437784?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2017118/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
31 \| Jul \| 2025\\
\\
Fibrous Network Nature of Plant Cell Walls Enables Tunable Mechanics for Development(affine\_model)\\
\\
Custom MATLAB code for affine isotropic network model\\
\\
Si Chen et al.](/content/explore/3d65ecd4-607f-48d8-9d49-3325aed01a8a?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2847637/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
31 \| Jul \| 2025\\
\\
Fibrous Network Nature of Plant Cell Walls Enables Tunable Mechanics for Development(five-beam model monotonic loading)\\
\\
custom MATLAB code for the five-beam model under monotonic loading condition\\
\\
SI Chen et al.](/content/explore/13b3b1d6-d68f-4671-bdbc-35bf52a553da?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/5659405/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
29 \| Jul \| 2025\\
\\
Single-molecule tweezers decoding hidden dimerization patterns of membrane proteins within lipid bilayers\\
\\
The codes were used for analysis in the following work.\\
\\
Title of paper : Single-molecule tweezers decoding hidden dimerization patterns of membrane proteins within lipid bilayers\\
\\
Victor Wedia Sadongo](/content/explore/7ccb902a-d7df-40ec-8b86-290b0ca752c1?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8599086/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
\\
29 \| Jul \| 2025\\
\\
Photoinduced non-reciprocal magnetism\\
\\
This is a code to calculate the magnetization dynamics of photo-activated layered ferromagnets.\\
\\
Ryo Hanai, Rina Tazai & Daiki Ootsuki](/content/explore/35369332-a5d7-4554-bc95-38502f46f30a?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/7836852/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
\\
29 \| Jul \| 2025\\
\\
AI-embodied multi-modal flexible electronic robots with programmable sensing, actuating and self-learning\\
\\
locomotion simulation of the unit\\
\\
Junfeng Li et al.](/content/explore/7f32fc34-d1b6-4457-9a01-3840e5c9aabd?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/1197438/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
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2 \| Sep \| 2025\\
\\
AI-Powered High-Throughput Digital Colony Picker Platform for Sorting Microbial Strains by Multi-modal Phenotypes\\
\\
The objective of this project is to create an integrated control and analysis software that fully automates the process of chip-based single cell culture, identification, and sorting. The software encompasses key functionalities such as image recognition and process control, enabling the identification of microchambers and detailed analysis of their internal images. By integrating with hardware control, it facilitates the precise location of microchambers on the chip, while an optical module supports the acquisition of target monoclonal cells. This comprehensive solution aims to streamline and enhance the efficiency of single cell manipulation and analysis.\\
\\
Diao Zhidian](/content/explore/9075004b-23e5-4e98-8f8c-1f65cb02671c?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/7644501/tree/v3/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
\\
28 \| Jul \| 2025\\
\\
Causal inference from cross-sectional earth system data with geographical convergent cross mapping\\
\\
This capsule stores code for analyzing the causal relationships between heavy‑metal concentrations and environmental variables, with the Geographical Convergent Cross Mapping (GCCM) method. It includes both R version developed by the authors and Python version developed by Katharina et al. To run it, right‑click the \*.R or \*.py file, select 【Set as File to Run】, then click the 【Reproducible Run】 button on the right side of the page. You may close the website tab while it’s running.\\
\\
Bingbo Gao & Ziyue Chen](/content/explore/404355c7-b4bf-4628-a28a-c7ec32d3c430?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8214586/tree/v2/index.html)

[Associated article](https://doi.org/10.1038/s41467-023-41619-6) published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
\\
25 \| Jul \| 2025\\
\\
Fully Printable Integrated Multifunctional Sensor Arrays for Intelligent Lithium-ion Batteries\\
\\
A data-driven deep-learning framework is developed with the combination of convolutional neural network (CNN) and long short-term memory (LSTM) base models to process the relevant features via machine learning approach for SOH estimation.\\
\\
Nuo Sun](/content/explore/d396d1cd-f847-40ee-9166-ab76c07a5623?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/3089142/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
\\
25 \| Jul \| 2025\\
\\
Chip-scale reconfigurable carbon nanotube physical unclonable functions\\
\\
With the rapid advancement of edge intelligence, ensuring the security of edge devices and protecting their data communications has become critical. Physical unclonable functions (PUFs), known as hardware fingerprints, are an emerging hardware security solution enabled with the physical entropy inherent in the hardware systems. To facilitate the widespread edge deployment of PUFs, here we represent chip-scale reconfigurable PUFs created fabricated using carbon nanotube charge-trapping transistors, where the charge-trapping memory and its dynamics are harnessed to render over 10^13 reconfigurable states with ideal physical unclonability, surpassing state-of-the-art reports. Arising from this, the PUFs prove robust resilience against advanced machine learning and AI attacking (limiting success to ~50-60%) as well as brute force cracking (requesting an estimated 10^16 years to crack). This performance, along with the scalability and ultralow-power operation as well as cryogenic temperature robustness, positions the PUFs an optimal solution for integration into edge intelligence systems to enhance hardware security. As a practical demonstration, we model self-driving in Central Hong Kong and prove secure vehicle authentication and communications using the PUFs.\\
\\
Yang Liu et al.](/content/explore/6cb9e482-b53b-4d89-a550-3fd8fb0a0d15?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/4214745/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
\\
24 \| Jul \| 2025\\
\\
Knowledge-Guided Self-Learning control Strategy for Mixed Vehicle Platoons with Delays\\
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Mixplatoon by Reinforcement Learning\\
\\
Jingyao Wang, Jinghua Guo & Xunrui Li](/content/explore/3b96e994-2460-4915-91a9-84165bec4f4a?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/4412851/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
\\
23 \| Jul \| 2025\\
\\
Powder Diffraction Crystal Structure Determination Using Generative Models\\
\\
(1) The pre-training XRD encoder (PXE) module: CL folder\\
(2) The crystal structure generation (CSG) modules: xrd2struc & xrd2cell folders\\
(3) The Rietveld refinement (RR) module: Rietveld folder\\
\\
Qi Li (1) et al.](/content/explore/75fac1ae-f64b-41ef-9680-ef896215fa3c?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/7727770/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
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22 \| Jul \| 2025\\
\\
Reconfigurable non-Abelian integrated photonics\\
\\
This capsule is used to reproduce the numerical results in our manuscript titled "Reconfigurable non-Abelian integrated photonics". In our work, the figures in Supplementary Fig. 3a-d are calculated by using home-generated MATLAB codes, which have been uploaded to Code Ocean. Other simulation results such as those in Fig. 2b,c,e,f are simulated using a commercial software RSOFT. To reproduce corresponding results, we have uploaded a source file, which models a two-mode braiding building block, to this platform as well.\\
\\
Shijie Sun et al.](/content/explore/6cbdb273-9362-439c-8bfe-ae8ede9f3a55?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2553738/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
\\
2 \| Dec \| 2025\\
\\
High-Dimensional One-Shot Optical Field Compressive Sensing of Structured Light\\
\\
The algorithm used to calculate the point-diffraction holograms.\\
\\
Yaodan Hu](/content/explore/5b89882e-4662-448e-bfe8-1940601f2947?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2085968/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
\\
17 \| Jul \| 2025\\
\\
Matlab Code -- Exploiting vacant urban residential buildings to promote carbon neutrality in China\\
\\
This capsule includes codes that have been used for the analysis reported in the maunuscript "Exploiting vacant urban residential buildings to promote carbon neutrality in China"\\
\\
* * *\\
\\
Descriptions of codes\\
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Calculate\_prediction.m : Codes for setting parameter values of scenarios and mitigation strategies and generating main results of pathway predictions\\
Calculate\_sensitivity.m : Codes for conducting a sensitivity analysis on the strategy parameters of vacant RB utilization\\
census\_sort.m : Codes for estimating the floor spaces (FSs) of urban and rural residential buildings (RBs), along with urban and rural populations, based on the data from censuses.\\
CI\_cal.m: Codes for generating the temporal variations of carbon intensity of RB construction during 2005-2100\\
Demolition\_estimator.m : Codes for calculating the over-demolition ratio for the traditional paradigm of China's urban construction, based on the FSs of annually demolished RBs during 1997-2011\\
FSPC\_U\_fitting.m : Codes for calibrating the changes of floor space per capita (FSPC) over time\\
fitting\_vintage.m : function for fitting the adjustment factor and mean service lifespan of annually completed RBs based on input data\\
Inflow\_fitting.m : Codes for calibrating FS and service lifespans of annually completed RBs\\
Inflow\_Known.m : Codes for inferring the recorded FSs of annually completed RBs based on China Statistical Yearbooks\\
Life\_Dura\_generator.m : Codes for generating the predicted mean maximum lifespans of annually completed RBs considering the impacts of climate change\\
Main : The main script to run the codes in sequence.\\
Plot\_Fig2ae.m: Codes for plotting Fig. 2(a) and Fig. 2(e) in the main text of the manuscript\\
Plot\_Fig2bcd.m: Codes for plotting Fig. 2(b), Fig. 2(c) and Fig. 2(d) in the main text of the manuscript\\
Plot\_Fig3abc.m: Codes for plotting Fig. 3(a), Fig. 3(b) and Fig. 3(c) in the main text of the manuscript\\
Plot\_Fig3de.m: Codes for plotting Fig. 3(d) and Fig. 3(e) in the main text of the manuscript\\
Plot\_Fig4.m: Codes for plotting Fig. 4 in the main text of the manuscript\\
Plot\_SI\_figures.m: Codes for plotting some figures in the Supplementary Information of the manuscript\\
Projection\_generator.m : Codes for stock-driven analysis to predict the pathways of construction and renovation under preset scenarios and mitigation strategies\\
StockRetire\_predict.m : Function for estimating the annual changes in RB stock, including the quantities of available RBs, retired RBs, obsolete RBs, reusable RBs, and demolished RBs\\
Underused\_proportion.m : Codes for estimating the underused proportions in available RB stock based on FSPC distributions from censuses, and plotting Fig. 1(c) in the main text of the manuscript\\
Vacancy\_estimator.m : Codes for inflow-driven analysis to estimate the status of existing RB stock and housing vacancy rates, and plotting Fig. 1(d) and Fig. 1(e) in the main text of the manuscript\\
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* * *\\
\\
Descriptions of other files\\
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data : Including all the data used in the code analysis, where the data that may influence the results are consistent with those displayed in the Supplementary Data of the manuscript\\
results/1 : Including main results for the vacant RB utilization strategies preset in Table 1 of the manuscript, without considering the service lifespan extension of RBs\\
results/2 : Including main results for the vacant RB utilization strategies preset in Table 1 of the manuscript, considering the service lifespan extension of RBs\\
results/3 : Including results for the sensitivity analysis on the strategy parameters for vacant RB utilization\\
results/Figures : Including all the figures generated by the codes, which are used in the main text or Supplementary Information of the manuscript\\
\\
Bing Xia](/content/explore/3d337eb8-a6a3-4aaa-902d-6113ccb04cbb?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/0932821/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
\\
16 \| Jul \| 2025\\
\\
Non-Equilibrium Anti-Stokes Raman Spectroscopy for Investigating Higgs Modes in Superconductors\\
\\
This Code calculates the A1g and B1g pair-breaking responses. It is used to fit the microscopic model to the experimental equilibrium data as discussed in SI S.2 and the main text (Figure 4a and b). Furthermore we calculate the A1g Higgs response as discussed in SI S.2 and Figure 4c. This code creates the panels a-c of Figure 4. For further details, see the caption of Figure 4, main text, and supporting information. All data used to generate the results presented in the paper are included here. No additional installation instructions are necessary, and the data files are directly called within the code. The expected outputs include the fitting parameters and the code reproduces Fig. 4a-c of the main text as .png files. No non-standard hardware is required. The estimated runtime for generating Fig. 4a-c on a standard desktop computer is under 60 seconds.\\
\\
Sida Tian et al.](/content/explore/8e68e463-56b6-4395-9f6c-bf5bf8df0eec?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/5878170/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
\\
18 \| Jul \| 2025\\
\\
Philippine Archipelago and South China Sea monsoon plus ocean cooling buffer Northwestern Pacific super typhoons\\
\\
This capsule provides a customized Python environment built with Conda for geospatial data visualization.\\
Key packages include xarray, dask, netCDF4, shapely, cartopy, proplot, matplotlib, tqdm, statsmodels.\\
\\
Tian Ma](/content/explore/32cd57b1-f998-45bf-bfee-3396ae7135db?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9053538/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
\\
14 \| Jul \| 2025\\
\\
Simulation code for "Complete vectorial optical mode converter using multi-layer metasurface"\\
\\
We provide simulation code for the adjoint optimization of metasurface parameters and the simulation results described in "Complete vectorial optical mode converter using multi-layer metasurface."\\
\\
Go Soma, Kento Komatsu, Yoshiaki Nakano & Takuo Tanemura](/content/explore/5e8962f1-6822-40f7-b839-a9ca4e754fc7?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8269027/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
\\
19 \| Nov \| 2025\\
\\
Single-neuron correlates of visual consciousness in human lateral occipital complex \[Backward Masking\]\\
\\
This capsule preprocesses and analyses the backward masking experiment. It is set up to load the preprocessed data, since loading the raw data from figshare leads to a network abuse error.\\
\\
Michael Vanhoyland](/content/explore/4fc41141-1cc4-4049-aa16-0357bef3d862?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6006649/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
\\
10 \| Jul \| 2025\\
\\
Lateral Melt Variations induce Shift in Io’s Peak Tidal Heating](/content/explore/ece4a76f-539c-4e25-9979-a2f4b6c5dff6?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[LOV3D is a Matlab package for obtaining the tidal response of viscoelastic self-gravitating bodies with lateral variations of interior properties. For a given interior structure and tidal load, the software solves the mass conservation, momentum conservation and Poisson equations and computes the tidal Love numbers. This is done in the spectral domain as detailed in](/content/explore/ece4a76f-539c-4e25-9979-a2f4b6c5dff6?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Rovira-Navarro et al. 2024](https://arxiv.org/abs/2311.15710)

We use LOV3D to model tidal dissipation in Io and explore the feedback that exists between tidal heating and interior properties.

**Context:** The innermost Galilean moon, Io, exhibits widespread tidally-driven volcanism. Monitoring of its volcanoes has revealed that they are not homogeneously distributed across its surface: volcanic activity is higher at low latitudes and peaks east of the sub- and anti-Jovian points. Dissipation in a radially symmetric solid body cannot explain the observed longitudinal shift but dissipation in a magma ocean can. However, recent observations show that Io does not have one. Here, we demonstrate that a longitudinal shift in the heating pattern naturally arises from the feedback between tidal heating and melt production.

**To use the code:** The code should run as is and tries to recreate Fig. 2 from the article. Unfortunately, to recreate it completely requires a significant amount of iterations. To showcase the method, the standard settings in the code only do 2 iterations. Download the code and alter the number on line 33 in _Main\_Compute\_Iteration\_uni\_start.m_ to 74 in order to recreate the important part of Fig. 2.

The directory also contains the code to create the data to make Fig. 3 as well as the code to generate the plot.

For more information and other use cases check:
[https://github.com/mroviranavarro/LOV3D\_multi](https://github.com/mroviranavarro/LOV3D_multi)

Allard Veenstra et al.

[Open Capsule](/content/capsule/7519248/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Chemistry\\
\\
9 \| Jul \| 2025\\
\\
ETC-ROP model for Dispersity-Controlled Ring Opening Polymerization of Epoxide\\
\\
This capsule is for publication of ETC-ROP model for Dispersity-Controlled Ring Opening Polymerization of Epoxide in nature communications. The users can model a editable chain transfer polymerization via this capsule, the parameters can be set in the ETC-ROP.c.\\
\\
Yubo Zhou, Junpeng Zhao & Guangzhao Zhang](/content/explore/ce4b919d-433d-43ef-8fb4-8949f2dca860?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9069546/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
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9 \| Jul \| 2025\\
\\
Mechanisms and interventions promoting healthy frontostriatal dynamics in obsessive-compulsive disorder\\
\\
Run the capsule using JupyterLab and open the notebook CodeOcean\_Reproducibility.ipynb\\
\\
Sebastien Naze](/content/explore/b0baa89b-f35d-445c-8fe9-d19a01daa5ca?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/1463279/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
\\
23 \| Jul \| 2025\\
\\
The HM-TARGET personalised real-time haemodynamic targets in critical care\\
\\
Effective hemodynamic management in critical care often relies on static, population-based targets that overlook individual variability and dynamic disease progression. The interplay between heart rate and blood pressure is complex, influences outcomes together, yet has not been adequately considered in prior studies. This study introduces a framework for personalized hemodynamic management using a time-dependent Cox model that integrates static and dynamic clinical data to predict real-time survival probabilities and define individualized heart rate and blood pressure targets. Developed and validated with multi-institutional datasets, the model demonstrated superior predictive accuracy, with personalized targets linked to reduced mortality compared to traditional guidelines. Dose-response and propensity score-matched analyses confirmed clinical relevance, and case studies illustrated feasibility in intensive care settings. By addressing the interdependent effects of heart rate and blood pressure, this approach advances precision medicine in critical care. Prospective trials are needed to validate and expand its clinical application.\\
\\
Yanhua Sun et al.](/content/explore/0feb1c77-b6f1-450f-8cf1-035a6d181f6c?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/3874868/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
\\
2 \| Jul \| 2025\\
\\
Knowledge-Guided Self-Learning Control Strategy for Mixed Vehicle Platoons with Delays\\
\\
As autonomous vehicles and traditional vehicles will coexist for several decades, how to efficiently manage the mixed traffic, while enhancing road throughput, fuel consumption and traffic stability becomes a challenge. This is due to the randomness and heterogeneity of traditional vehicles interspersed among autonomous vehicles. Moreover, communication delays arising from the shared wireless communication network substantially degrade the performance of platooning control for connected autonomous vehicles. To address these challenging problems, this paper proposes a knowledge-guided self-learning mixed platoon control strategy.\\
\\
WangJingyao, WangHuinian, SongJian & ChenXingyu](/content/explore/0bdfd8ad-6ce2-4911-a7fa-3534192ef2fd?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/7637528/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
\\
2 \| Jul \| 2025\\
\\
Radio-Frequency Actuation For Soft Robots\\
\\
Channel estimation and beamforming control for the wireless actuation. Channel estimation shows the channel estiamtion algorithm, and beamforming algorithm provides the optimal beamforming weight according to the estimated channel values. The program must be run in companion with the hardware platform.\\
\\
Yiwen Song](/content/explore/b6ef0568-12bf-4554-bf8d-011e4de650e4?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6909118/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
\\
27 \| Oct \| 2025\\
\\
Magnetic Reconnection in the Plasma Disk at 23 Jupiter Radii\\
\\
The data and plots associated with the paper entitled with "Magnetic Reconnection in the Plasma Disk at 23 Jupiter Radii"\\
\\
Jian-zhao Wang](/content/explore/73434ec1-468f-42d4-a27c-b6cb817b1395?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8477399/tree/v3/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
27 \| Aug \| 2025\\
\\
Molecular Cartography of the Human Down Syndrome and Trisomic Mouse Brain\\
\\
This repository contains the custom code for microenvironment analysis, aimed at quantifying changes in local cell type compositions between Down Syndrome (DS) and euploid samples. This repository also includes all relevant codes for the snRNA-seq, Slide-seq, and MERFISH data analyses from the associated publication: "Molecular Cartography of the Human Down Syndrome and Trisomic Mouse Brain".\\
\\
Min Yi Feng et al.](/content/explore/d0e6b8c6-2045-44dd-ad73-839285419235?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6060467/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
\\
30 \| Jun \| 2025\\
\\
Personalized risk stratification system in colorectal cancer: Multi-omics analysis to clinical implications\\
\\
In this project, we developed PIANOS using a pathway-based k-TSP algorithm combined with resampling and ensemble modeling methods.\\
\\
The model developed using the CIT cohort, offers prognostic risk stratification for individual colorectal cancer patients based on genetic sequencing data from any source. This model eliminates the constraints of pre-constructed cohorts and predefined cutoff values, providing a more flexible and precise approach to patient prognosis. The following figure describe the construction of PIANOS.\\
\\
Du Cai & Haoning Qi](/content/explore/b7ca3d4a-2f00-45b7-bae3-02761e50130b?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6627451/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
26 \| Jun \| 2025\\
\\
BERTPhylo: An Efficient Method to Accelerate Phylogenetic Updates Using a Pretrained DNA Language Model\\
\\
This is a demo code for paper BERTPhylo: An Efficient Method to Accelerate Phylogenetic Updates Using a Pretrained DNA Language Model. BERTPhylo is a novel method designed to accelerate phylogenetic tree updates by reducing the number and length of input sequences required for alignment and tree analysis. It achieves this by identifying the smallest taxonomic unit for newly collected sequences on a given phylogenetic tree and extracting the high-attention regions of sequences within that smallest taxonomic unit.\\
\\
Danruo Deng et al.](/content/explore/cb39e3d2-0a0c-4ffc-99df-29684818f890?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6543435/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
\\
25 \| Jun \| 2025\\
\\
Wearable wired thermal sensor for the continuous assessment of flow in vascular access\\
\\
Proprietary code for experimental data analysis (MATLAB) from two wearable thermal flow sensing devices, which rely on anemometry principle through heterogenous tissues. Conversion of measured voltages to resistance and temperature values.\\
\\
Abstract: Hemodialysis for chronic kidney disease (CKD) patients involves diverting blood via vascular access (VA) devices for osmotic external filtration and returning it to circulation. The success of this process relies on the patency of an arteriovenous fistula (AVF), synthetic arteriovenous graft (AVG), or a catheter to ensure sufficient blood flow. Nonetheless, unpredictable progressive vascular stenosis due to neointimal formation or complete occlusion from acute thrombosis within the lumen remains the primary cause of mature vascular access failure. Despite emergent surgical intervention efforts, the lack of a reliable early detection tool significantly reduces patient outcomes and survival rates. Herein, we present a soft, wearable, flexible device designed to continuously monitor blood flow changes for the early detection of VA failure. Integrated actuators and sensors noninvasively exploit thermal anemometry to measure blood flow changes within large vessels. Systematic validation with benchtop models for both AVF and AVG show good agreement with finite element analysis (FEA) simulations. Human and preclinical swine model testing highlights the device capability, sensitivity, and versatility in rapidly recording alterations in blood flow dynamics of target vessels. Ultimately, adaptation of this platform to a wireless technology represents a novel strategy for at-home VA blood flow monitoring between hemodialysis sessions, enabling the rapid detection of VA-related complications and improving survival rates in patients with CKD.\\
\\
Andrea S. Carlini](/content/explore/c08839af-c70b-4147-aaee-9aacf07d9913?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6214629/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
25 \| Jun \| 2025\\
\\
Orbitrap noise structure and method for noise unbiased multivariate analysis\\
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Code for reproducing analysis of Figures 4 - 6. Main script is "PCA\_Orbitrap\_Images\_NCOMMS2408259TR1.m"\\
\\
Gustavo F. Trindade, Michael R. Keenan & Ian S. Gilmore](/content/explore/d7129601-47d9-40a0-b0ca-a7d1ab3c36e5?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/3124936/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
25 \| Jun \| 2025\\
\\
A Dedicated Skin-to-Brain Circuit for Cool Sensation in Mice\\
\\
This MATLAB script was developed to analyze behavioral video recordings from a custom-built gradient temperature arena used to assess thermal preference in mice. The arena is divided into 18 calibrated temperature zones ranging from 5°C to 50°C. The script processes tracked position data of the mouse over time, quantifies time spent in each temperature-defined zone, and generates plots for downstream statistical analysis. This tool supports high-resolution behavioral profiling of thermosensory responses.\\
\\
Keywords:\\
MATLAB, thermal gradient, temperature preference, behavioral analysis, mouse, thermosensation\\
\\
Hankyu Lee et al.](/content/explore/b71a0f11-152e-4030-a22b-21e5311fe7cd?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/0236721/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Mathematics\\
\\
24 \| Jun \| 2025\\
\\
Low-dimensional compact states in 3D moir\\'e lattices\\
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Calculate the eigenmode and eigenvalue for Moire system by Reduced Projection Method.\\
\\
Zixuan Gao](/content/explore/83539a23-c05d-480a-856e-e55c9a591850?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6792548/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
23 \| Jun \| 2025\\
\\
Real data analysis of "Uncovering causal gene-tissue pairs and variants: A multivariable TWAS method controlling for infinitesimal effects"\\
\\
Tissue-Gene pair, direct causal Variants, and Infinitesimal effect Selector (TGVIS) is a multivariable TWAS method that can identify causal gene-tissue pairs and direct causal variants while incorporating infinitesimal effects. Methodologically, TGVIS employs sum of single effect (SuSiE) for fine-mapping causal gene-tissue pairs and direct causal variants, and uses restricted maximum likelihood (REML) to estimate the infinitesimal effects. For variables such as gene-tissue pairs or direct causal variants, TGVIS uses the posterior inclusion probability (PIP) to evaluate the significance level, and employs the Pratt index to measure predictive importance.\\
\\
Yihe Yang, Noah Lorincz-comi & Xiaofeng Zhu](/content/explore/8cd85477-2751-4bcc-bbe7-3842904fdced?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6600361/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Social Sciences\\
\\
19 \| Jun \| 2025\\
\\
Patterns of maternal, newborn, and child health interventions coverage, and associated socioeconomic disparities in sub-Saharan Africa: A machine learning cluster analysis.\\
\\
This capsule includes the code for performing for clustering analysis for the manuscript "Patterns of maternal, newborn, and child health interventions coverage, and associated socioeconomic disparities in sub-Saharan Africa: A machine learning cluster analysis."\\
\\
Claire Najjuuko](/content/explore/ba9f9ab6-a81b-4ff7-b84d-c516efc9fa09?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6430216/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
\\
18 \| Jun \| 2025\\
\\
A 4×256 Gbps Silicon Transmitter with On-Chip Adaptive Dispersion Compensation\\
\\
This code demonstrates the offline DSP processing of the acquired PAM-4 signals; the algorithms used include FFE and MLSE. The result of the code run contains BER and SNR.\\
\\
Shihuan Ran](/content/explore/7c046247-2d4d-44b5-b420-a733fedeb071?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/0298106/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
17 \| Jun \| 2025\\
\\
Code and demo data for main analysis in Does SARS-CoV-2 Infection Increase Risk of Neuropsychiatric and Related Conditions? Findings from Difference-in-Differences Analyses\\
\\
The COVID-19 pandemic has been associated with increased neuropsychiatric conditions in children and youths, with evidence suggesting that SARS-CoV-2 infection may contribute additional risks beyond pandemic stressors. This study aimed to assess the full spectrum of neuropsychiatric conditions in COVID-19 positive children (ages 5–12) and youths (ages 12–20) compared to a matched COVID-19 negative cohort, accounting for factors influencing infection risk. Using EHR data from 25 institutions in the RECOVER program, we conducted a retrospective analysis of 326,074 COVID-19 positive and 887,314 negative participants matched for risk factors and stratified by age. Neuropsychiatric outcomes were examined 28 to 179 days post-infection or negative test between March 2020 and December 2022. SARS-CoV-2 positivity was confirmed via PCR, serology, or antigen tests, while negativity required negative test results and no related diagnoses. Risk differences revealed higher frequencies of neuropsychiatric conditions in the COVID-19 positive cohort. Children faced increased risks for anxiety, OCD, ADHD, autism, and other conditions, while youths exhibited elevated risks for anxiety, suicidality, depression, and related symptoms. These findings highlight SARS-CoV-2 infection as a potential contributor to neuropsychiatric risks, emphasizing the importance of research into tailored treatments and preventive strategies for affected individuals.\\
\\
Yiwen Lu, jiayi tong & Dazheng Zhang](/content/explore/3133abc2-f8e3-454b-9bc0-14398508cdc5?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/5662713/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Economics\\
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17 \| Jun \| 2025\\
\\
Adaptive food price forecasting improves public information in times of rapid economic change\\
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Code for the tables and figures in "Adaptive food price forecasting improves public information in times of rapid economic change"\\
\\
Matthew MacLachlan](/content/explore/a3a1e2f5-2d7f-4787-8475-4adbac34478c?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6834269/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
16 \| Jun \| 2025\\
\\
Mast cells boost anti-tumor potency of MAIT cells via inflammasome activation\\
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The code and data of lung adenocarcinoma infiltrating MCs for the article “Mast cells boost anti-tumor potency of MAIT cells via inflammasome activation”\\
\\
Jun Wang](/content/explore/2f7d9555-bd52-44c0-af18-7c2dab221c18?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/7204774/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
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16 \| Jun \| 2025\\
\\
Public capsule of: Friedel oscillations and chiral superconductivity in monolayer NbSe2\\
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This is a time capsule for the entire tool chain used to generate the data underpinning our manuscript submitted to Nature Communications. It contains a demonstration script that executes all steps of the calculation in a limited manner to show the operability of each individual code.\\
\\
Julian Siegl, Magdalena Marganska & Anton Bleibaum](/content/explore/968ff47e-8417-4512-b07a-f40bb29a413b?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9651616/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
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13 \| Jun \| 2025\\
\\
MorphLink: Bridging Cell Morphological Behaviors and Molecular Dynamics in Multi-modal Spatial Omics](/content/explore/1fd4d675-24d5-4085-bf02-ad122435c931?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[MorphLink is a computational framework to systematically extract and link interpretable morphological features with molecular measurements in multi-model spatial omics analyses. The identified linkages provide a transparent depiction of cellular behaviors that drive transcriptomic heterogeneity and immune diversity across different regions within diseased tissues. Moreover, MorphLink is scalable and robust against cross-sample batch effects, making it an efficient method for integrating spatial omics data analysis across samples, cohorts, and modalities, and enhancing the interpretation of results for large-scale studies. MorphLink is applicable to various types of spatial omics data, including spatial transcriptomics (Spatial Transcriptomics, 10x Visium, 10x Xenium, and MERFISH), spatial proteomics (CODEX and IMS), and the simultaneous measurement of proteins and transcriptome (spatial CITE-seq and CosMx). \\
For more info, please refer to:](/content/explore/1fd4d675-24d5-4085-bf02-ad122435c931?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [https://github.com/jianhuupenn/MorphLink](https://github.com/jianhuupenn/MorphLink)

Jing Huang & Jian Hu

[Open Capsule](/content/capsule/3029371/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
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11 \| Jun \| 2025\\
\\
ADTnorm: Robust Integration of Single-cell Protein Measurement across CITE-seq Datasets](/content/explore/9383703f-3c9e-4db0-b665-529c4af02558?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[CITE-seq enables paired measurement of surface protein and mRNA expression in single cells using antibodies conjugated to oligonucleotide tags. Due to the high copy number of surface protein molecules, sequencing antibody-derived tags (ADTs) allows for robust protein detection, improving cell-type identification. However, variability in antibody staining leads to batch effects in the ADT expression, obscuring biological variation, reducing interpretability, and obstructing cross-study analyses. Here, we present ADTnorm (](/content/explore/9383703f-3c9e-4db0-b665-529c4af02558?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [https://github.com/yezhengSTAT/ADTnorm](https://github.com/yezhengSTAT/ADTnorm)), a normalization and integration method designed explicitly for ADT abundance. Benchmarking against 14 existing scaling and normalization methods, we show that ADTnorm accurately aligns populations with negative- and positive-expression of surface protein markers across 13 public datasets, effectively removing technical variation across batches and improving cell-type separation. ADTnorm enables efficient integration of public CITE-seq datasets, each with unique experimental designs, paving the way for atlas-level analyses. Beyond normalization, ADTnorm includes built-in utilities to aid in automated threshold-gating as well as assessment of antibody staining quality for titration optimization and antibody panel selection. Applying ADTnorm to a published COVID-19 CITE-seq dataset allowed for identifying previously undetected disease-associated markers, illustrating a broad utility in biological applications.

Ye Zheng et al.

[Open Capsule](/content/capsule/2163811/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
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10 \| Jun \| 2025\\
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Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell\\
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Apollo is a comprehensive simulation software for epidemics in a population complete with within-host dynamics. It is powered by CATE, our large-scale parallel processing architecture.\\
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Apollo is a stochastic evolutionary simulator for haploid viruses, designed to study the progression of a disease across a population. Apollo’s simulations move forward in time and aim to facilitate the design of highly dynamic and robust simulation models for studying within-host viral evolution and disease spread.\\
\\
Deshan Perera et al.](/content/explore/1fcdd50a-7fee-4cac-ba58-015618149415?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9213238/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
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6 \| Jun \| 2025\\
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Modeling heterogeneous signaling dynamics of macrophages reveals principles of information transmission in stimulus responses\\
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This is codes and dataset for instruction for running codes of Guo et. al. "Modeling heterogeneous signaling dynamics of macrophages reveals principles of information transmission in stimulus responses"\\
\\
Xiaolu Guo et al.](/content/explore/2eaf9ea8-395e-40c6-a2b0-e13ce7c81a44?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/1321332/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
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5 \| Jun \| 2025\\
\\
Friedel oscillations and chiral superconductivity in monolayer NbSe2](/content/explore/ddac41ef-2da6-48e5-9ecb-b5c40b4629c3?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[This is a time capsule for the entire tool chain used to generate the data underpinning our manuscript](/content/explore/ddac41ef-2da6-48e5-9ecb-b5c40b4629c3?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [https://arxiv.org/abs/2412.00273](https://arxiv.org/abs/2412.00273) . It contains a demonstration script that executes all steps of the calculation in a limited manner to show the operability of each individual code.

Julian Siegl, Magdalena Marganska & Anton Bleibaum

[Open Capsule](/content/capsule/2814802/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
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4 \| Jun \| 2025\\
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Pattern Finder to identify DNA microhomologies containing mismatches\\
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DNA polymerase theta (Pol θ) initiates repair of DNA double-strand breaks by pairing single strands at short “microhomologies”. It is important to understand microhomology selection, as some cancer cells rely on Pol θ for survival. We investigated end-joining by purified human Pol θ, employing DNA sequencing of products generated from oligonucleotide libraries having diverse 3′ ends. Pol θ overwhelmingly selected short internal microhomologies found within 15 nucleotides of the terminus of single stranded DNAs, restricting deletion size during end joining. Significantly, we find that the selected microhomologies are usually interrupted by mismatches and that base pairing within 6 nucleotides of the 3′ end is important for determining microhomology choice. Bidirectional synthesis is not necessary to initiate end joining. The preference for mismatched microhomologies suggests a revision of the definition of microhomology to account for the unique properties of Pol θ. This could advance the analysis of mutations in cancer genomes. This demo demonstrates the operation of PatternFinder in identifying and analyzing patterns sequences, using sample data. Full data generated by Next Generation Sequencing has been deposited to NCBI SRA database. BioProject: PRJNA1178638\\
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Yuzhen Li et al.](/content/explore/cbc9be46-c952-4ac8-b128-8dfb6f9c608c?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9102227/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
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4 \| Jun \| 2025\\
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Single Particle Fluorescence Imaging of Coupled Nucleation and Growth in Perovskite Nanocrystal Crystallization\\
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Free energy\\
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Lige Liu et al.](/content/explore/aef57cd8-c259-46d2-812f-4818ddfc1b6c?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/5935246/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
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10 \| Jun \| 2025\\
\\
CD137L promotes immune surveillance in melanoma via HLTF regulation\\
\\
Immune checkpoint blockers (ICBs) have demonstrated substantial efficacy across various malignancies, yet the benefits of ICBs are limited to a subset of patients. Therefore, it is essential to identify novel therapeutic targets. By integrating multi-omics data from cohorts of patients with melanoma treated with ICBs, a positive correlation was observed between tumor CD137L expression and the efficacy of PD-1 blockade. Functionally, CD137L induction in cancer cells significantly enhanced anti-tumor immunity by promoting CD8+ T cell survival, both in vivo and in vitro. Mechanistically, helicase-like transcription factor (HLTF) was identified as a pivotal transcriptional regulator of CD137L, controlling its expression through phosphorylation of serine at position 398. Therapeutically, the FDA-approved drug AICAR (acadesine) was identified as a CD137L-specific agonist, which exhibited synergistic effects with PD-1 or CTLA4 blockade. In summary, our findings elucidate an HLTF-mediated regulatory mechanism controlling CD137L expression, propose its potential as a predictor for PD-1 blockade efficacy, and highlight a promising combination therapy to enhance ICBs efficacy in melanoma.\\
\\
Guanxiong Zhang](/content/explore/e5ee5fc3-f234-422d-8eb6-62f114a4f6ac?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2891918/tree/v3/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
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3 \| Jun \| 2025\\
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Methods code for "Cholinergic Subgroups in Parkinson Disease: A Multicenter Longitudinal Study"\\
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Methods code for "Cholinergic Subgroups in Parkinson Disease: A Multicenter Longitudinal Study".\\
\\
Nicolaas I. Bohnen](/content/explore/36f21222-e083-43e1-aa89-f0e451667a90?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/3508354/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
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2 \| Jun \| 2025\\
\\
Polygenic architecture of brain structure and function, behaviors, and psychopathologies in children\\
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This capsule contains the code and data associated with the manuscript titled 'Polygenic architecture of brain structure and function, behaviors, and psychopathologies in children.' The code supports the following analyses: (1) heritability analysis to assess genetic influences on brain structure, function, and related traits; (2) canonical correlation analysis (CCA), including two-block and three-block CCA, to explore multivariate relationships among genetic, brain, and behavioral data; and (3) machine learning-based prediction to model and predict outcomes related to psychopathologies and cognitive ability. This capsule includes all preprocessing pipelines, statistical modeling scripts, and machine learning frameworks required to replicate the findings presented in the manuscript.\\
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Yoonjung Yoonie Joo et al.](/content/explore/c5e6c244-e136-46e1-85a1-fb7ae09b45d7?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2631739/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
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30 \| May \| 2025\\
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Boundary Complexity of (Sub-) Cortical Areas Predict Deep Brain Stimulation Outcomes in Parkinson's Disease\\
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**LASSO Feature Selection and Hypergraph Neural Network Classification** \\
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This project integrates **LASSO (Least Absolute Shrinkage and Selection Operator)** for feature selection with a **Hypergraph Neural Network (HGNN)** for classification tasks. The goal is to identify key clinical and imaging biomarkers using LASSO and leverage HGNN to classify outcomes, even in datasets with complex relationships and imbalanced classes.\\
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**Key Features**\\
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- **Feature Selection with LASSO**:\\
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Identifies the most important features (e.g., fractal dimensions of brain regions) that contribute to the outcome. These features reduce dimensionality and focus on clinically relevant predictors.\\
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- **Hypergraph Neural Network (HGNN)**:\\
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Models relationships between data points and higher-order interactions using hypergraphs. Clinical features, imaging features, and their combinations are integrated for robust classification.\\
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- **Class Imbalance Handling**:\\
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Applies weighted loss functions to address imbalanced datasets where one class is underrepresented.\\
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- **Model Comparison**:\\
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Builds and evaluates two models:\\
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1. **Model 1**: Uses clinical features only.\\
2. **Model 2**: Combines clinical and imaging features.\\
      Compares performance metrics such as accuracy, sensitivity, specificity, and additional variance explained by imaging features.\\
\\
Devin Schoen](/content/explore/62b6026d-02c0-4c39-85e5-2169cca9e4bb?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/0732329/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
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30 \| May \| 2025\\
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Phenotypic plasticity co-varies with the elevation range of Himalayan altitudinal migrants\\
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We investigate the contribution of gene and protein expression plasticity to variation in temperature and partial pressure of oxygen (PO2) in the two closely related bush-robin species in the Sino-Himalayan mountainous region, a biodiversity hotspot in Asia, to understand the impacts of phenotypic plasticity on the seasonal elevation distributions of altitudinal migrants\\
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Boning Xue et al.](/content/explore/497b5e7c-7081-4a52-9bee-729729fd3742?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9435638/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
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27 \| May \| 2025\\
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An improved reference library and method for accurate cell-type deconvolution of bulk-tissue miRNA data\\
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An R package for Cell Type Deconvolution using miRNA Expression Profiling Data\\
\\
Zhen Yang](/content/explore/db81ca2b-2de4-41cd-b9ea-b87bd3ae03e1?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6159054/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
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27 \| May \| 2025\\
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Climate change impacts on ocean light in Arctic ecosystems.\\
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Radiative Transfer Model used to calculate the amount of light reaching the ocean under different climate scenarios using different climate models from the Coupled Model Intercomparison Project Phase 6 (CMIP6) as input. The RTM model can be used to create the forcing files required prior to running the model for the light calculations.\\
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Trond Kristiansen et al.](/content/explore/675ea292-89f6-456f-ae61-7a6e9ceb7d2b?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/0694935/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
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26 \| May \| 2025\\
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BIGFAM - variance components analysis from relatives without genotype\\
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BIGFAM is a model that estimates heritability using relatives phenotype without genotype. This model does not require genotype information and uses only phenotype and familial relationship data as input.\\
\\
Jaeeun Jerry Lee](/content/explore/85e0a440-d4ff-401c-af58-e495b6dc52f7?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9403573/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
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27 \| Jun \| 2025\\
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Circular-polarization-selective perfect reflection from chiral superconductors\\
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Fortran and mathematical codes for generating numerical results. Generated data are also included.\\
\\
Junyeong Ahn & Ashvin Vishwanath](/content/explore/dc3dd637-4da6-492b-86cc-e067e18ce446?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/5146073/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
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23 \| May \| 2025\\
\\
AAV-based delivery of RNAi targeting Ataxin-2 improves survival, strength, and pathology in TDP-43 mice\\
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Analysis code for DESeq2 differential gene expression from transcriptome sequencing data.\\
\\
Ashley B. Robbins](/content/explore/02473a2f-e8dd-4bbb-bad6-ee467ef03c6e?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/4503125/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Computer Science\\
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23 \| May \| 2025\\
\\
Assessing and improving reliability of neighbor embedding methods: a map-continuity perspective\\
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We provide two diagnostic scores to assess and improve the reliability of neighbor embedding methods based on a map-continuity view. Our approach is flexible and works as a wrapper around many neighbor embedding algorithms. Please see `README.md` for a quick guide.\\
\\
Zhexuan Liu, Rong Ma & Yiqiao Zhong](/content/explore/188418d2-ad87-4dde-90b4-8679578f537a?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6906342/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Mathematics\\
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22 \| May \| 2025\\
\\
R code--Optimizing enzyme inhibition analysis: precise estimation with a single inhibitor concentration\\
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This is a R code for precise and efficient estimation of reversible enzyme inhibition constants from initial velocity data. Guideline of this package is in the file named 'README.md' in code file.\\
\\
Hyeong Jun Jang & Yun Min Song](/content/explore/0926e27a-a376-4871-982e-d6b43abe400d?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/0987082/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Mathematics\\
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22 \| May \| 2025\\
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MATLAB Code--Optimizing enzyme inhibition analysis: precise estimation with a single inhibitor concentration\\
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This is a MATLAB code for precise and efficient estimation of reversible enzyme inhibition constants from initial velocity data. Guideline of this package is in the file named 'README.md' in code file.\\
\\
Hyeong Jun Jang & Yun Min Song](/content/explore/bcaec65c-8d83-401a-af2c-c569777eeaa3?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2766317/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
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20 \| May \| 2025\\
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Unravelling the transcriptome of the human tuberculosis lesion and its clinical implications\\
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Supplementary code repository for: Unravelling the transcriptome of the human tuberculosis lesion and its clinical implications.\\
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Authors of the manuscript:\\
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Kaori L. Fonseca , Juan José Lozano, Albert Despuig, Dominic Habgood-Coote, Julia Sidorova, Lilibeth Arias, Álvaro Del RÌo-Álvarez, Juan Carrillo-Reixach,Aaron Goff, Leticia Muraro Wildner, Shota Gogishvili, Keti Nikolaishvili, Natalia Shubladze, Zaza Avaliani, Pere-Joan Cardona, Federico Martinón-Torres,Antonio Salas,Alberto Gómez-Carballa, Carolina Armengol, Simon J Waddell, Myrsini Kaforou, Anne O'Garra, Sergo Vashakidze, Cristina Vilaplana\\
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Juan José Lozano et al.](/content/explore/70e4a4c1-9fa7-4996-b42f-7367c6635031?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9294029/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
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19 \| May \| 2025\\
\\
Program for "Phase-Field Modeling for Practical Engineering Materials"\\
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You can conduct numerical tests in "Phase-Field Modeling for Practical Engineering Materials" by this capsule.\\
\\
Takumi Morino, Shoichi Hirosawa & Machiko Ode](/content/explore/e9a96b67-0096-40af-ac9a-828e19c16698?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/3744764/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
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19 \| May \| 2025\\
\\
Data and code: Giant Activity-Induced Elasticity in Entangled Polymer Solutions](/content/explore/3e59485b-de00-479e-8d86-f4d4ad191dcc?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[Data and code related to the publication "Giant Activity-Induced Stress Plateau in Entangled Polymer Solutions" (D. Breoni, C. Kurzthaler, B. Liebchen, H. Löwen, S. Mandal) are provided. We compile and run a simple script example of a short simulation with our modified LAMMPS code. For our study, we performed each simulation on a high-performance computer using at least 96 CPUs for a minimum of 48 hours. A description of the modified code can be found in the README\_modified\_lammps.txt file. The "data" folder contains the equilibrated configurations used, the Python scripts, and the data necessary to plot the figures for the publication. It also includes the Z1+ executable \[see](/content/explore/3e59485b-de00-479e-8d86-f4d4ad191dcc?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [https://doi.org/10.1016/j.cpc.2022.108567\]](https://doi.org/10.1016/j.cpc.2022.108567%5D), which was used to analyze the topology of our system. More detailed information can be found in the README\_data.txt file.

Breoni, Davide et al.

[Open Capsule](/content/capsule/7659820/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Chemistry\\
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19 \| May \| 2025\\
\\
Customization Design of Circularized Polarized Phosphorescent Materials Guided by Transfer Learning\\
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Official Code for paper "Customization Design of Circularized Polarized Phosphorescent Materials Guided by Transfer Learning"\\
\\
zhang yihan](/content/explore/ea030bce-4339-44e6-b0e7-d68d5f4baffb?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/3084761/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
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26 \| Sep \| 2025\\
\\
PGAP2: A Comprehensive Toolkit for Prokaryotic Pan-Genome Analysis Based on Fine-grained Feature Networks](/content/explore/2e0ca655-2bcb-4ff6-942c-090ccc406e41?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[PGAP2 (Pan-Genome Analysis Pipeline 2) is an ultra-fast and comprehensive toolkit for prokaryotic pan-genome analysis. Powered by a Fine-Grained Feature Network, PGAP2 can construct a pan-genome map from 1,000 genomes within 20 minutes while ensuring high accuracy. In addition, it offers a rich set of upstream quality control modules and downstream analysis tools to support common pan-genome analyses. Additional details can be found on the GitHub page](/content/explore/2e0ca655-2bcb-4ff6-942c-090ccc406e41?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [https://github.com/bucongfan/PGAP2](https://github.com/bucongfan/PGAP2).

Congfan Bu

[Open Capsule](/content/capsule/4012983/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
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15 \| May \| 2025\\
\\
Age-related constraints on the spatial geometry of the brain\\
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R code + data pertaining to our manuscript "Age-related constraints on the spatial geometry of the brain"\\
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Niels Janssen](/content/explore/1cf2acb2-88b8-4149-931b-bedf416639ce?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8432592/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
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15 \| May \| 2025\\
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Evidence for preferred propagating terrestrial heatwave pathways due to Rossby wave activity\\
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We develope a complex network method to detect spatial propagation patterns of heatwaves. The footprints of heatwaves are represented by the hot weather events in each network node, and the network connectivity analysis can help to reveal the frequent and recurrent propagation pathways of the heatwaves.\\
\\
Mingzhao Wang & Yu Huang](/content/explore/c7e4134e-25d5-49b4-a9c2-942e0b3f6ede?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/7919219/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
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12 \| May \| 2025\\
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Keypoint-Based Modeling Reveals Fine-Grained Body Pose Tuning in Superior Temporal Sulcus Neurons\\
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Body pose and orientation serve as vital visual signals in primate non-verbal social communication. Leveraging deep learning algorithms that extract body poses from videos of behaving monkeys, applied to a monkey avatar, we investigated neural tuning for pose and view, targeting fMRI-defined mid and anterior Superior Temporal Sulcus (STS) body patches. In this project, we modeled the pose and view selectivity of the units with keypoint-based principal component regression and applied model inversion as a key approach to identify effective body parts and views.\\
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Rajani Raman et al.](/content/explore/8d5af548-1620-4890-a863-4a6562db09ab?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2215416/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
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12 \| May \| 2025\\
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Deep Brain Stimulation of the Cortico-Basal Ganglia Network Enhances Cognitive Flexibility and Ameliorates Exploration Anomalies in a Primate Schizophrenia Model\\
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This capsule contains the code for the reinforcement learning algorithm used in the creation of the paper's Fig. 6. \\
The code generates three figures.\\
Fig. 1 The left subplot compares the NHPs’ recorded GPe FR (solid black) with the model’s alpha(t) value (dashed yellow) calculated based on the\\
NHPs’ choices. The middle subplot compares the model’s sGPe value calculated based on the NHPs’ naïve state choices (dashed yellow, as shown in the left plot) and PCP-state (dashed red) behavioral choices. The right subplot compares the model’s sGPe value calculated based on the NHPs’ naïve state (dashed yellow) and post-PCP state (dashed black) behavioral choices. Then, simulating the increase in GPe’s activity observed post-PCP by increasing sGPe’s modulator parameter (C). These subplots correspond to Fig. 6 subplots b,d, and f.\\
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Fig. 2 Comparing the model’s behavioral results and sGPe (alpha(t)) values to the NHPs’ data. Top - Comparing the NHP’s (solid black) and the simulation’s (dashed yellow) learning curves. Middle comparing the model's learning slope and alpha(t) value. Bottom comparing the model's switch probability and alpha(t) (sGPe) value. Corresponding to Fig. 6c. r and c values represent the correlation and corresponding Pvalues of the presented plots.\\
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Fig. 3 Simulating the effect of changing the model's parameters on its ability to perform the task. The left column shows the effect of increasing the temperature. Simulated parameters color graded from naïve values colored black to red as the temperature increases. Top – learning criterion Vs. temperature. Middle – sGPe value after an unsuccessful trial compared to the probability for directed exploration. Bottom – sGPe value after a successful trial compared to the probability for random exploration. Corresponding to the Fig 6e. The middle column shows the effect of increasing the value of the alpha modulator parameter (C). Corresponding to Fig. 6g. The right column simulates the effects of GPe stimulation (modulating the value of C) under PCP conditions (increased temperature) by increasing (graded blue) and decreasing (graded green) sGPe modulator parameter from its original values (red). Corresponding to Fig. 6h.\\
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Nir Asch](/content/explore/858365ed-80ce-49b0-b38e-975f4d66d2b1?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/0692162/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
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12 \| May \| 2025\\
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Single-cell reactive oxygen species regulome profiling reveals dynamic redox regulation in immune cells\\
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Utilize the scROP approach to predict immune cell types and map in vivo immune cell states to their corresponding in vitro models for training.\\
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Yi-Chuan Wang & Ming-Hang Yang](/content/explore/9170e18d-69bb-4a65-90b5-da126ff88163?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/3768382/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
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8 \| May \| 2025\\
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Lightweight, error-tolerant edge detection using memristor-enabled stochastic logics\\
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The demand for efficient edge vision has spurred the interest in developing stochastic computing approaches for performing image processing tasks. Memristors with inherent stochasticity readily introduce probability into the computations and thus enable stochastic image processing computations. Here, we present a stochastic computing approach for edge detection, a fundamental image processing technique, facilitated with memristor-enabled stochastic logics. Specifically, we integrate the memristors with logic circuits and harness the stochasticity from the memristors to realize compact stochastic logics for stochastic number encoding and processing. The stochastic numbers, exhibiting well-regulated probabilities and correlations, can be processed to perform logic operations with statistical probabilities. This can facilitate lightweight stochastic edge detection for edge visual scenarios characterized with high-level noise errors. As a practical demonstration, we implement a hardware stochastic Roberts cross operator using the stochastic logics, and prove its exceptional edge detection performance, remarkably, with 95% less computational cost while withstanding 50% bit-flip errors. The results underscore the great potential of our stochastic edge detection approach in developing lightweight, error-tolerant edge vision hardware and systems for autonomous driving, virtual/augmented reality, medical imaging diagnosis, industrial automation, and beyond.\\
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Song Lekai et al.](/content/explore/abc0afd0-b123-4e5a-a079-7ea7757632e3?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8738945/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
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7 \| May \| 2025\\
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First observations of the seiche that shook the world (complete materials)\\
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This capsule contains all necessary materials to replicate the analysis in the manuscript "First observations of the seiche that shook the world". Notebooks are labeled according to either the figure which they produce, or the section they correspond to.\\
\\
Thomas Monahan, Tianning Tang, Stephen Roberts & Thomas Adcock](/content/explore/062c08df-2a2e-4677-bd8d-5cfd851f2583?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/3854946/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
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22 \| May \| 2025\\
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Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell\\
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Apollo is a comprehensive simulation software for epidemics in a population complete with within-host dynamics. It is powered by CATE, our large-scale parallel processing architecture.\\
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Apollo is a stochastic evolutionary simulator for haploid viruses, designed to study the progression of a disease across a population. Apollo’s simulations move forward in time and aim to facilitate the design of highly dynamic and robust simulation models for studying within-host viral evolution and disease spread.\\
\\
Deshan Perera et al.](/content/explore/a2f74216-b0e4-4f23-937d-26e16e223240?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2120968/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Computer Science\\
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14 \| Jul \| 2025\\
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Route-Centric Ant-Inspired Memories Enable Panoramic Route-Following in a Car-like Robot](/content/explore/ac670a70-8f95-402d-b8f6-744eb3bbfd0c?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[**Route-Centric Ant-Inspired Memories Enable Panoramic Route-Following in a Car-like Robot** \\
Code (and dataset) for our submitted paper "Route-Centric Ant-Inspired Memories Enable Panoramic Route-Following in a Car-like Robot" in _Nature Communications_.\\
\\
You can download the paper via: **Upon Publication**](/content/explore/ac670a70-8f95-402d-b8f6-744eb3bbfd0c?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[The explicative video is available at](/content/explore/ac670a70-8f95-402d-b8f6-744eb3bbfd0c?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [\[YouTube\]](https://youtu.be/6YIkDhN4SaY)

## One-Sentence Summary

Our work presents an ant-inspired Mushroom Body model on a compact, low-cost robotic platform, achieving continuous, efficient, and adaptable navigation in real-world environments with minimal computational resources.

## Abstract

Solitary foraging ants excel at route following using minimal neural resources, Robots don't. Recent biological studies proposed lateralized, nest-centric memories to explain ants' direct visual homing but did not address how ants follow curved visual routes away from their nest. We present a biologically inspired neuromorphic model for one-shot panoramic route learning and continuous route following, implemented on a compact car-like robot, Antcar. We demonstrate that route-centric lateralized memories, inspired by the insect mushroom body, enable Antcar to achieve bi-directional route-following, with motivation-driven recognition of route extremities and familiarity-based velocity control. With rigorous Lyapunov-based stability analysis and an empirical memory scalability evaluation, the model was tested over 1.6 km across 113 challenging real-world trials. The system achieves less than 25 cm median lateral error using minimal resources (800-pixel input, 300 MB RAM, 500 mW power, and 18.75 kB memory per 50 m route), offering insights into insect cognition and advancing autonomous robotics under strict resource constraints.

## Project Setup and Environment Preparation

Just run the run.sh file and it will run every code, it will put the results in results folder, you can see the figures generated in the results/figure folder. You will find the generated Jupyter notebooks as well and the mapping folders for different oscillations amplitude of learning.

## Citation

If this work is helpful, please cite as: \*\*\* Upon Publication\*\*\*
The code used in the AntCar robot for real-time learning and route following is available upon request.

## Acknowledgments

G.G. was supported by a doctoral fellowship grant from Aix Marseille University and the French Ministry of Defense (AID - Agence Innovation D'{e}fense, agreement #A01D22020549 ARM/DGA /AID). G.G., J.R.S. and F.R. were also supported by Aix Marseille University and the CNRS (Life Science, Information Science, and Engineering and Science & technology Institutes). The facilities for the experimental tests has been mainly provided by ROBOTEX 2.0 (Grants ROBOTEX ANR-10-EQPX-44-01 and TIRREX ANR-21-ESRE-0015).

## Contact

gabriel.gattaux\_at\_univ-amu.fr

## License

\[License\]

Gabriel Gattaux, Antoine Wystrach, Julien Serres & Franck Ruffier

[Open Capsule](/content/capsule/6511740/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
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30 \| Apr \| 2025\\
\\
Polarization-Sensitive In-Sensor Computing in Chiral Organic Integrated 2D p-n Heterostructures for Mixed-Multimodal Image Processing\\
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Decomposition and image recognition of mixed circularly polarized images (MNIST and Fasion-MNIST patterns)using software-based CNN algorithm\\
\\
Changsoon Choi & Je-Jun Lee](/content/explore/e607b507-ffa7-4705-9e58-52586db8b53e?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/0506609/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
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28 \| Apr \| 2025\\
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SKSR1 identified as key virulence factor in Cryptosporidium by genetic crossing\\
\\
Cryptosporidium is a major cause of severe diarrhea. Although Cryptosporidium isolates exhibit significant differences in infectivity and virulence, the genetic determinants for these traits are not clear. In this study, we used classical genetics to cross two Cryptosporidium parvum isolates of different virulence and used bulk segregant analysis of whole-genome sequences from the progeny to identify quantitative trait loci (QTL) associated with Cryptosporidium infectivity and virulence. Of the 23 genes in three QTL, two had loss-of-function mutations in the low-virulence isolates, including the SKSR1 gene encoding a variant secretory protein. Deletion of the SKSR1 gene or expression of the frame-shifted sequence reduced the pathogenicity of the virulent isolate. SKSR1 is expressed in small granules and secreted into the parasite-host interface during invasion. These results demonstrate that SKSR1 is an important virulence factor in Cryptosporidium, and suggest that the extended SKSR protein family, encoded by clusters of subtelomeric genes, may contribute to pathogenesis.\\
\\
Tianyi Hou](/content/explore/a73754a4-acc0-4817-983c-b0d942b9e294?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/0441727/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
27 \| Apr \| 2025\\
\\
Identifying T cell antigen at the atomic level with graph convolution network (deepAntigen)\\
\\
Precise identification of T cell antigens in silico is crucial for the development of cancer mRNA vaccine. However, current computational methods only utilize sequence-level rather than atomic-level features to identify T cell antigens, resulting in most of the identified antigens failing to elicit immune responses. Herein, we proposed deepAntigen, a graph convolutional network-based framework, to identify T cell antigens at the atomic level for the first time. deepAntigen achieved excellent performance in the prediction of antigen-human leukocyte antigen (HLA) binding and antigen-T cell receptor (TCR) interactions, which can provide comprehensive guidance for identification of T cell antigens.\\
\\
Jinhao Que](/content/explore/b4ff946e-f728-42f7-a21e-15bd605faa92?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6907488/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
\\
22 \| Aug \| 2025\\
\\
Figure code and data of 'Anthropogenic forcing drives equatorward migration of heatwave locations across continents'\\
\\
The main code and data of five figures in the manuscript 'Anthropogenic forcing drives equatorward migration of heatwave locations across continents'\\
\\
Juan, Feng et al.](/content/explore/df39a3a4-83ba-4f6d-a68a-23513fdf4916?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/3962766/tree/v4/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
25 \| Apr \| 2025\\
\\
Chromogranin A (CgA) Deficiency Attenuates Tauopathy by Altering Epinephrine–Alpha Adrenergic Receptor Signaling\\
\\
RNA-Seq script for WT, hTau, and CgA-KO/hTau mouse prefrontal cortex gene expression analysis.\\
\\
Suborno Jati et al.](/content/explore/8b82f1f9-7c65-4318-9226-ea7f31f4b0a9?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8795409/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
\\
11 \| Nov \| 2025\\
\\
LSTMCI: a data-driven dynamic model for inverter-based resources\\
\\
**Data-Driven Dynamic Modeling for Inverter-Based Resources Using Neural Network**  **Overview** \\
\\
This project presents a data-driven approach for developing dynamic models of Inverter-Based Resources (IBRs), specifically focusing on wind farms (WF), PV power stations (PV), and grid-forming battery energy storage systems (BESS). \\
By utilizing a neural network-based modeling technique (LSTMCI), the project aims to capture and simulate the complex dynamic behaviors of IBRs for power system simulation and analysis.\\
\\
**System Requirements**  **Hardware requirements** \\
\\
This work was performed on the following hardware:\\
\\
- a PC with Intel i7-12700 4.9GHz 12-core CPU;\\
- a high performance computing cluster with four Tesla A100 GPU of 32 GB memory.\\
\\
**Software requirements** \\
\\
The package has been tested on the following operating systems:\\
\\
- Windows 11 Pro\\
- Linux: Ubuntu 22.04.5 LTS\\
\\
**Software dependencies** \\
\\
The work was implemented using Python with PyTorch (version 11.7 as listed below).\\
\\
**Installation guide** \\
\\
We recommend installing Python via Anaconda and then installing the required Python packages through conda. Key dependencies include:\\
\\
- NVIDIA® GPU drivers ( **Optional**, required for GPU acceleration)\\
- CUDA® Toolkit ( **Optional**, required for GPU acceleration)\\
- cuDNN ( **Optional**, required for GPU acceleration)\\
- Anaconda\\
- Python 3.9\\
- pytorch-cuda 11.7 (Choose the appropriate version based on your hardware and CUDA setup)\\
- numpy\\
- scipy\\
- matplotlib\\
\\
**Getting Started**  **Model training** \\
\\
This work involves training models separately for wind farms (WF), PV power stations (PV), and grid-forming battery energy storage systems (BESS). Within each model's directory, you will find three folders:\\
\\
1. `dataset`: Used to store training data. Training data is saved in `.mat` format.\\
\\
The training directory includes a Python script (e.g., `WF_LSTMCI.py`) responsible for executing the model training.\\
\\
When the script finishes executing, there will be two folders in the `../results` directory.\\
\\
1. `param_save`: Used to store the trained models.\\
2. `process_save`: Used to store training process logs and the Loss information.\\
\\
**Time-domain simulator** \\
\\
This section describes the time-domain simulation using LSTM-CI. The time-domain simulator consists of three Python files:\\
\\
1. `model_lib.py`: Contains the model structures.\\
2. `sim_utils.py`: Contains general utility functions used by the simulator.\\
3. `Simulator.py`: The time-domain simulator script.\\
\\
This directory also contains two folders:\\
\\
1. `Models`: Used to store the parameter files for the LSTM-CI models.\\
2. `TestSystem`: Used to store test system information.\\
\\
Simulation result plots are placed in `../results` .\\
\\
NA](/content/explore/bef2b650-cdfe-4658-8199-1a6ad16d8d91?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6293530/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
\\
24 \| Apr \| 2025\\
\\
Real-time 3D Temperature Reconstruction in Microwave Cancer Hyperthermia from Scarce Temperature Measurements\_REVISED\_2nd\\
\\
This capsule reports the code and the data useful to reproduce the new results reported in the revised version of the article "Real-time 3D Temperature Reconstruction in Microwave Cancer Hyperthermia from Scarce Temperature Measurements" resubmitted to Nature Communications after the second round of revisions.\\
\\
Rossella Gaffoglio et al.](/content/explore/dfba1eb2-6c31-4876-9d9f-0996d7729ec0?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/5700830/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
\\
24 \| Apr \| 2025\\
\\
Integrating Genetics for Early Prediction of Gestational Diabetes Mellitus: Insights from Non-invasive Prenatal Sequencing of 116,144 Pregnant Women in China\\
\\
A prediction model of gestational diabetes mellitus at early stage.\\
\\
Yuqin Gu, Hao Zheng & Siyang Liu](/content/explore/6b02b84b-c6ca-4242-ad22-bce8820028fb?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6258530/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
\\
23 \| Apr \| 2025\\
\\
Monitored long-range interacting systems: spin-wave theory for quantum trajectories\\
\\
A simple demonstration code to illustrate the simulation of spin-wave quantum trajectories in a monitored collective (infinite-range) spin system. The code reproduces Figure 2 of the associated publication from scratch, where spin-wave results are benchmarked against exact ones.\\
\\
Zejian Li, Anna Delmonte, Xhek Turkeshi & Rosario Fazio](/content/explore/dc0846b7-ce64-47b7-bc0c-521f8994765a?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8698806/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
\\
25 \| Apr \| 2025\\
\\
Intestinal permeability of N-acetylcysteine is driven by gut microbiota-dependent cysteine palmitoylation\\
\\
Trillions of intestinal microbiota are essential to the permeability of orally administered drugs. However, identifying microbial-drug interactions remains challenging due to the highly variable composition of intestinal flora among individuals. Using single-pass intestinal perfusion (SPIP) platform, we established the microbiota-based permeability screening framework involving germ-free (GF) and specific-pathogen-free (SPF) rats to compare in-situ Peff-values and metabolomic profiles of 32 orally administered drugs with disputable classifications of permeability. In contrast with SPF controls, N-Acetylcysteine (NAC) exhibited significantly increased permeability in GF rats, which was inversely related to reduced cysteine-3-ketosphinganine by Bacteroides. To further validate these microbiome features, we integrated clinical descriptors from a prospective cohort of 319 participants to optimize a 15-feature eXtreme Gradient Boosting (XGB) model. This machine learning (ML) model of clinical prediction revealed that cysteine palmitoylation by intestinal microbiota has significantly affected NAC permeability, thus leading to discordant biopharmaceutics classification.\\
\\
Yuhang Zhang et al.](/content/explore/5b84bba6-46a2-4b41-98f8-33f6cd111440?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9444975/tree/v3/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
\\
11 \| Apr \| 2025\\
\\
Glucose-Lowering Medication Use for Diabetes: National Evidence from 62 Low- and Middle-Income Countries\\
\\
See README.\\
\\
Felix Teufel](/content/explore/4db6de5f-50db-42ee-ab59-8c2e9b776552?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8981386/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
10 \| Apr \| 2025\\
\\
Code for the paper: Epidemic-induced local awareness behavior inferred from surveys and genetic sequence data\\
\\
This repository was written by Gergely Odor accompanies the paper "Epidemic-induced local awareness behavior inferred from surveys and genetic sequence data" by Gergely Odor and Marton Karsai. It contains tools to detect superspreading events in Amino Acid Collision Clusters (AACCs) and computes the Event Containment Scores (ECSs).\\
\\
Gergely Odor & Marton Karsai](/content/explore/14b803fc-1838-4069-993a-b17d45dabeda?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/0017019/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
\\
9 \| Apr \| 2025\\
\\
Measurement of microwave photon correlations at millikelvin with a thermal detector\\
\\
Source data and analyzing codes\\
\\
Qiming Chen](/content/explore/6c5ecf51-381b-42b3-a336-d7628707ea55?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/3610149/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
7 \| Apr \| 2025\\
\\
Dynamic single-cell metabolomics reveals cell-cell interaction between tumor cells and macrophages\\
\\
This code can deal with single-cell metabolomics data produced by organic mass spectrometry technology.\\
\\
Yi Zhang](/content/explore/6349d222-b641-45aa-973a-3ce9967d8248?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/1461230/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
\\
1 \| May \| 2025\\
\\
Luminescence-enabled three-dimensional temperature bioimaging\\
\\
researching the emission spectrum changed by temperature and tissue thickness by convolutional neural networks. Predicting temperature and thickness of tissue by different emission spectra.\\
\\
Liyan Ming et al.](/content/explore/318bf851-cc49-4b8e-9d33-2a2ae1e27d0d?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9246465/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
\\
15 \| Aug \| 2025\\
\\
Effects of individual variation and seasonal vaccination on disease risks\\
\\
Code capsule accompanying the manuscript "Effects of individual variation and seasonal vaccination on disease risks" by Hart _et al_.\\
\\
Running this capsule reproduces Figure 2 of the paper (expected run time around 22 minutes).\\
\\
William S Hart](/content/explore/1dc5b1c3-d45e-4f6a-99d7-8d06769df06c?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2437452/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
\\
2 \| Apr \| 2025\\
\\
custom code for: Predicting IVF live birth probabilities using live machine learning, center-specific models\\
\\
Manuscript: Predicting IVF live birth probabilities using machine learning, center-specific models: validation results and potential benefits over national registry-based models\\
\\
The demo data and custom code described here is associated with the above manuscript.\\
\\
Elizabeth Nguyễn](/content/explore/fea4eaf5-9cd7-4fa6-ace4-b0057979d2a3?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6295990/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
1 \| Apr \| 2025\\
\\
The mammalian longevity associated acetylome\\
\\
This project offers a comprehensive pipeline for the analysis of orthologous proteins, creation of a replacement matrix, and conducting statistical tests to identify correlations between amino acid changes and lifespan. The pipeline is specifically tailored for Mus musculus or Homo sapiens PTM (Post-Translational Modification) data.\\
\\
Sarit](/content/explore/b791b276-7a68-4645-aec3-11c0e1a04b39?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2708864/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
\\
1 \| Apr \| 2025\\
\\
Pacific Sub-Decadal Sea Surface Temperature Variations Contributed to Recent Antarctic Sea Ice Decline Trend\\
\\
We include NCL programs and observed and simulated datasets in this capsule. Several NCL programs are needed for Figure 1, Figure S2, and Figure S11. Please see the readme file for instructions in the directories of these three figures.Other figures can be reproduced by running the NCL programs. For example, “ncl Figure1/Figure1.ncl" for Figure 1 and “ncl Figure2.ncl” for Figure 2.\\
\\
Qigang Wu](/content/explore/f73d773a-2577-4788-90ad-ef5cec58793e?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2995636/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
\\
31 \| Mar \| 2025\\
\\
The health impacts and genetic architecture of food liking in cardio-metabolic diseases\\
\\
Establishing links between food liking traits(FLTs) and development of cardiometabolic diseases(CMDs), and investigating biological mechanisms and share genetic architecture underlying these associations, is a critical step toward achieving personalized nutritional interventions for CMDs. Here, we systematically evaluated the temporal and genetical relationships between 176 FLTs and CMDs. By integrating observational- and genetic-results, we identified two detrimental FLTs\[bacon and diet fizzy drinks(DFD)\] and four protective FLTs(broccoli, prawns, pizza, and lentils/beans). These FLTs cause distinct habitual food intake patterns, influencing cardiometabolic proteins and associated biological processes. Notably, we discovered three significant genetic links: DFD with heart-failure(HF), bacon with type-2-diabetes(T2D), and lentils/beans with T2D, identifying 54 pleiotropic single-nucleotide-variants(SNVs) that impact both phenotypes. These SNVs can be mapped to 251 genes, exhibiting tissue-specific expression patterns, and four genes can be used as drug targets that concurrently regulate DFD liking and HF occurrence, suggesting that regulation of these genes may prevent the progression of CMDs.\\
\\
Wenbo Jiang](/content/explore/b0d5edb7-fbb6-486a-b860-88656a7f9a30?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/3188832/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
\\
28 \| Mar \| 2025\\
\\
Learning-based 3D human kinematics estimation using behavioral constraints from activity classification\\
\\
Code for kinematics estimation and IMU data\\
\\
Daekyum Kim](/content/explore/bdc6203f-ea0f-4eb0-a42a-2c9be0cf63ed?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8880404/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
2 \| Apr \| 2026\\
\\
Compute capsule for Clusia genomes shed light on the evolution and diversity of CAM physiotypes\\
\\
**This capsule runs the Clusia panomics database!**\\
\\
Through a combination of chromosome level assembly and annotation, comparative multiomics, and physiological phenotyping, we demonstrate that polyploidization during genus evolution and subsequent diploidization may have shaped the emergence of extant C3+CAM physiotypes in Clusia.\\
\\
Hannes M. Kramml](/content/explore/7422d3ab-7df0-4413-bef8-c6bb3cc29407?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/4663284/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
26 \| Mar \| 2025\\
\\
Heterogeneity-Preserving Discriminative Feature Selection for Disease-Specific Subtype Discovery\\
\\
This repository encompasses a range of subtype detection algorithms, with a primary focus on the PHet (Preserving Heterogeneity) algorithm. The PHet algorithm is designed to conduct recurrent subsampling differential analysis and interquartile range (IQR) calculations between conditions, in order to pinpoint a minimal set of features that preserve heterogeneity while maximizing the quality of subtype clustering. Through the utilization of public datasets from microarray and single-cell RNA-seq studies, PHet has demonstrated its effectiveness in identifying disease subtypes, surpassing the performance of previous outlier-based methods. While this guide offers a tutorial on executing 25 different algorithms, it does not delve into an exhaustive description of every feature within the package. For additional information about arguments and functionalities, it is recommended to execute "python main.py --help".\\
\\
Abdur Rahman M. A. Basher](/content/explore/77f5b73c-7c6d-4492-9356-7f9e9b834f7b?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/5132825/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Computer Science\\
\\
25 \| Mar \| 2025\\
\\
Supplementary code for: Optimization on multifractal loss landscapes explains a diverse range of geometrical and dynamical properties of deep learning\\
\\
"Gradient descent and its variants are foundational in solving optimization problems across many disciplines. In deep learning, these optimizers demonstrate a remarkable ability to dynamically navigate complex loss landscapes, ultimately converging to solutions that generalize well. To elucidate the mechanism underlying this ability, we introduce a novel theoretical framework that models the complexities of loss landscapes as multifractal." This code provides numerical simulation and analysis of gradient descent on a multifractal loss landscape.\\
\\
Andrew Ly & Pulin Gong](/content/explore/9ba5f7dc-1f58-45d9-81de-0a0513be4bb8?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9558945/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
21 \| Mar \| 2025\\
\\
DeepPlant: An Accurate Cross-Species 5mC Detection Tool for Oxford Nanopore Sequencing in Plants\\
\\
Nanopore sequencing enables comprehensive detection of 5-methylcytosine (5mC), particularly in transposable elements and centromeric regions. However, CHH methylation detection in plants is limited by the scarcity of high-methylation positive samples, reducing generalization across species. Dorado, the only tool for plant 5mC detection on the R10.4 platform, lacks extensive species testing. To address this, we reanalyzed bisulfite sequencing (BS-seq) data to screen species with abundant high-methylation CHH sites, generating new datasets that cover diverse 9-mer motifs. We developed DeepPlant, a deep learning model incorporating both Bi-LSTM and Transformer architectures, which significantly improves CHH detection accuracy and performs well for CpG and CHG motifs. Evaluated across species, DeepPlant achieved high whole-genome methylation frequency correlations (0.705 to 0.881) with BS-seq data on CHH motifs, improved by 14.0% to 117.6% compared to Dorado. DeepPlant also demonstrated superior single-molecule accuracy, F1-score, and stability, offering strong generalization for plant epigenetics research.\\
DeepPlant is a specialized training and inference framework for Oxford Nanopore sequencing data. The model leverages Bi-LSTM architecture and is implemented in Python for training. For feature extraction and modification calling, it utilizes C++ integrated with libtorch.\\
\\
Chuanle Xiao](/content/explore/e58e29a7-5d37-44c6-ac6b-c8d26d4dfbcf?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/7657522/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
20 \| Mar \| 2025\\
\\
Enhancing Kinase-Inhibitor Activity and Selectivity Prediction Through Multimodal and Multiscale Contrastive Learning with Attention Consistency\\
\\
MMCLKin is a deep learning framework designed to accurately predict kinase-inhibitor selectivity and activity by extracting and integrating their critical interaction information across diverse modalities and scales.\\
\\
Yanan Tian](/content/explore/a7b4ccdb-fdbd-4625-911d-ead8febd41a2?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/5286759/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
29 \| Oct \| 2025\\
\\
SIDISH Identifies High-Risk Disease-Associated Cells and Biomarkers by Integrating Single-Cell Depth and Bulk Breadth\\
\\
SIDISH: **S** emi-supervised **I** terative **D** eep Learning for **I** dentifying **S** ingle-cell **H** igh-risk Populations\\
\\
Yasmin Jolasun et al.](/content/explore/5ad16e68-7a6c-44a5-85db-097fb3fa54b0?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/4643434/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
18 \| Mar \| 2025\\
\\
Angiogenic and Immune Predictors of Neoadjuvant Axitinib Response in Renal Cell Carcinoma with Venous Tumour Thrombus\\
\\
Code for a leave-one-out cross validation machine learning (ML) model integrating results from the NAXIVA Phase II clinical trial to find the most predictive biomarkers for this cohort of patients.\\
\\
Software dependencies: \\
numpy (v2.0.2)\\
pandas (v2.2.3)\\
scikit-learn (v1.5.2)\\
\\
Two models were produced:\\
\\
- Model 1: Week 1 features\\
- Model 2: Week 1 features + fold-change features between Week 1 and Week 3\\
\\
For each model, run the relevant script (mod1 or mod2), where the relevant data is in a folder '/data', and the results output to '/results'. The results csv contains the results for each leave-one-out iteration, with a list of the features selected in the feature reduction step and the weights assigned to each feature by the logistic regression model.\\
\\
Rebecca Wray, Hania Paverd & Ines Machado](/content/explore/e5f9c7d1-35a9-4912-84a2-7e1c17b8d0e3?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6654756/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Social Sciences\\
\\
17 \| Mar \| 2025\\
\\
The Spatiotemporal Scaling Laws of Urban Population Dynamics\\
\\
The code used for data preprocessing and analysis has been custom developed in Python (3.6) and Matlab (R2022b).\\
\\
anonymous](/content/explore/b61b5fa6-3c11-4645-a12d-77afee3b3c7c?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/5509967/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
16 \| Mar \| 2025\\
\\
Predictive Biophysical Neural Network Modeling of a Compendium of in vivo Transcription Factor DNA Binding Profiles for Escherichia coli\\
\\
Predictive biophysical neural network modeling of TF binding ChIP-Seq data\\
\\
James Galagan, Patrick Lally & Laura Gomez](/content/explore/5c1a57b7-5b8b-4bf0-b897-e961c09b681b?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9709912/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
15 \| Mar \| 2025\\
\\
O-glycosylation of intrinsically disordered regions regulates homeostasis of membrane proteins in streptococci\\
\\
A script to run DR-BERT (disordered regions prediction) and tmbed (secreted and membrane proteins predictions) and aggregate the results.\\
\\
Catherine Chaton & Konstantin Korotkov](/content/explore/9e293159-475a-401c-87bf-3b0f95121e21?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9230049/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Social Sciences\\
\\
14 \| Mar \| 2025\\
\\
Floods and cause-specific mortality in the United States: A triply robust approach\\
\\
Data structure of the "Final\_data\_sample\_fake.rds". This is for the fake, data sample to ensure the example R code can be run. The result from this fake dataset cannot be used for any other purposes.\\
\\
Lingzhi Chu](/content/explore/ead48c67-5112-4199-b2a2-53d5215d4c4e?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/0308824/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
14 \| Mar \| 2025\\
\\
Comprehensive Biosynthetic Analysis of Human Microbiome Reveals Diverse Protective Ribosomal Peptides](/content/explore/1e7bc5a1-896e-4e11-9b55-3260b6681f29?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[RiPPs are a class of diverse and widespread natural products produced by a multitude of producers, including bacteria, fungi, and plants. They often exhibit diverse structures, various biological functions, and manifold roles in physiology and ecology, allowing them to mediate the communications between microbes or between microbes and human hosts. In this study, using precursor-centric and PTM-centric approaches, we systematically examined the RiPP biosynthetic potential of 306,481 genomes of the human microbiota to identify 12,076 yet-to-be-discovered RiPP families, largely expanding the chemical landscape of RiPPs. Big data omics analysis reveals that numerous RiPP families are inversely related to various diseases, suggesting their potential protective effects on health.](/content/explore/1e7bc5a1-896e-4e11-9b55-3260b6681f29?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[This repository of codes can also be found in](/content/explore/1e7bc5a1-896e-4e11-9b55-3260b6681f29?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [https://github.com/ZHANGJianArya/RiPPs\_human-microbiome](https://github.com/ZHANGJianArya/RiPPs_human-microbiome)

Jian ZHANG & Dengwei ZHANG

[Open Capsule](/content/capsule/4092596/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
15 \| Jul \| 2025\\
\\
Episodic Transport of Protein Aggregates Achieves a Positive Size Selectivity in Aggresome Formation - Stochastic Model Gillespie Simulation\\
\\
This is the code for the simulation of the cargo-transport stochastic model for the manuscript "Episodic Transport of Protein Aggregates Achieves a Positive Size Selectivity in Aggresome Formation".\\
\\
Ying Lu & Rui Fang](/content/explore/2185c319-8333-435f-97b5-6c5850b32fd9?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2585107/tree/v3/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
\\
21 \| Apr \| 2025\\
\\
Movie-watching evokes ripple-like activity within events and at event boundaries\\
\\
This capsule demonstrates de analyses described in the paper “Movie-watching evokes ripple-like activity within events and at event boundaries “ by Marta Silva, Xiongbo Wu, Marc Sabi, Estefanía Conde-Blanco, Pedro Roldan, Antonio Donaire, Mar Carreño, Nikolai Axmacher, Christopher Baldassano and Lluís Fuentemilla.\\
\\
Marta Silva et al.](/content/explore/d3cae998-6e77-4d4e-bf20-1c544cc152ae?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/4543503/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
\\
10 \| Mar \| 2025\\
\\
Code for "Increasing extreme winds challenge offshore wind energy resilience"\\
\\
The most central process of calculating and visualizing the fifty-year return period wind speed is presented here, with 'Extremewind1' as the main function. The rest of the analysis and calculations are in the github code at the end of the article.\\
\\
Yanan Zhao & Zhenzhong Zeng](/content/explore/1a0fb1d9-290e-4428-a68d-6671ff8344b8?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/6982819/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
6 \| Mar \| 2025\\
\\
Nonlinear microbial thermal response and its implications for abrupt soil organic carbon responses to warming\\
\\
This study leveraged three independent soil datasets at broad spatial scales including direct estimates of microbial CUE (n = 618) and heterotrophic respiration (n = 591 and 660) to investigate the microbial thermal response and its implications for SOC responses to warming. The data and code deposited here are used to support the results of figure 1-4 of main text.\\
\\
Kailiang Yu et al.](/content/explore/164839e8-fa5f-4b4b-b9eb-4411413b5326?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2793111/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
6 \| Mar \| 2025\\
\\
Narrow window data-independent acquisition on the Orbitrap Astral Mass Spectrometer enables fast and deep coverage of the plasma glycoproteome\\
\\
Goes through mass spectrometry data and annotates per PSM the ion coverage.\\
\\
Douwe Schulte & Shelley Jager](/content/explore/6a76787d-fe7a-431e-9d73-7d341946f5e2?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/3859388/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
\\
5 \| Mar \| 2025\\
\\
Effective integration of drone technology for mapping and managing palm species in the Peruvian Amazon\\
\\
This model is designed to detect and segment three economically important palm species in the Amazon rainforest: \\
\*Mauritia Flexuosa \\
\*Euterpe Precatoria\\
\*Oenocarpus Bataua\\
It utilizes drone-based mapping imagery to classify pixels into one of four categories (including background)\\
\\
Ximena Tagle et al.](/content/explore/47cde907-bec0-4e64-a95a-58a2a7783c18?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/7739905/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Engineering\\
\\
4 \| Mar \| 2025\\
\\
Autonomous Driving Comfort Prediction: Improve Comfort through Global Path Planning\\
\\
ADCP MODEL\\
Autonomous Driving Comfort Prediction: Improve Comfort through Global Path Planning.\\
\\
Zhengxian Chen & Chaosheng Huang](/content/explore/f29a3b1f-cec8-4be5-86bd-f1bb0824d2b0?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8174284/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Chemistry\\
\\
4 \| Mar \| 2025\\
\\
A reactivity index including orbital overlap directions for predicting π electron properties and reactivity vectors\\
\\
A python based wave function analysis program\\
\\
Xiaofei Shi, Donghui Wei & JInshuai Song](/content/explore/730b5347-3d90-4e44-bca9-901a4afdf98d?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9313818/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
3 \| Mar \| 2025\\
\\
A scalable and accurate framework for large-scale genome-wide gene-environment interaction analysis and its application to time-to-event and ordinal categorical traits\\
\\
A scalable and accurate framework for large-scale genome-wide gene-environment interaction (G×E) analysis.\\
\\
Yuzhuo Ma, Yanlong Zhao, Ji-Feng Zhang & Wenjian Bi](/content/explore/66446f4e-3724-450d-9890-2af67b11861f?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8544858/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
28 \| Feb \| 2025\\
\\
Retracing Human Genetic Histories and Natural Selection Using Precise Local Ancestry Inference\\
\\
In an increasingly diverse world, including admixed individuals in genomic studies is imperative for equity and portability. A crucial first step is precise local ancestry inference (LAI). We have developed Orchestra, a LAI model with unprecedented accuracy, and trained on over 10,000 single-origin individuals from 35 worldwide populations. We employed Orchestra to delve into genetic relationships and demographic histories, with a focus on Latin Americans, a prime example of admixture, and the Ashkenazi Jewish, whose origins have long been debated. Finally, Orchestra enabled us to map signatures of selection, notably identifying trace Scandinavian ancestry in British samples and unveiling an immune-rich region linked to respiratory infections. Our work advances the field of LAI and holds promise for improvements in future applications for admixed populations.\\
\\
Jon Lerga-Jaso et al.](/content/explore/7e11e945-4ba3-4cf2-9519-11f69e1bf009?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9597346/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
\\
27 \| Feb \| 2025\\
\\
The greater role of Southern Ocean warming compared to Arctic warming in shifting future tropical rainfall patterns\\
\\
This data and source code are used to analyze the importance of Southern Ocean warming based on CMIP6 data and CESM2 SST nudging experiments.\\
\\
Hyein Jeong, Hyo-Seok Park, Sarah M. Kang & Eui-Seok Chung](/content/explore/bfeef087-524c-4a7e-876b-1979f750e4c0?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8183946/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
\\
25 \| Feb \| 2025\\
\\
Dynamics and drivers of tidal flat morphology in China\\
\\
The MATLAB code for generating the images in the article and the original data.\\
\\
Shuai Liu](/content/explore/a0a9953f-717e-464d-be0a-fd384150c6fc?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/2635585/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
\\
25 \| Feb \| 2025\\
\\
Pathogenic Germline Variants in Chinese Pancreatic Adenocarcinoma Patients\\
\\
Putting pancreatic cancer screening into perspective for high-risk individuals could significantly reduce cancer morbidity and mortality. Previous studies have profiled somatic mutations in pancreatic adenocarcinoma (PAAD). In contrast, the prevalence of mutations in PAAD predisposition genes has not defined, especially in the Asian population. Here we provide a comprehensive germline mutation map of PAAD in 1,123 Chinese cancer patients in comparison with 853 Asian reference cohort.\\
\\
Xiaoyi Yin & Jing Li](/content/explore/2fc91319-c4be-48eb-b8ce-9f052e5fc8df?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9785138/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Earth Sciences\\
\\
24 \| Feb \| 2025\\
\\
Global data-driven prediction of fire activity - Code & Data\\
\\
All files within this directory are used to generate the model/data/plots used in the submissions.\\
\\
For the generation of the dataframes used for training the various data-driven models we use (Input data not present in this folder are available from ERA5-Land) : \\
\\
**MAKE\_PICKLE\_\*.py** \\
\\
This generates the following pickle files:\\
\\
**TRAIN\_\*\_10PER\_2019\_2021.pk1** \\
\\
Once those pickle files are generated the XGBoost models are then trained using :\\
\\
**TR\_\*.py** \\
\\
This generates the model files, which are then used with the input data to generate ERA5 and forecast data :\\
\\
**MAKE\_GLOBAL\_MAPS\_ERA5.py** \\
\\
The output modelled data are then available as :\\
\\
**POF\_\*\_ERA5.nc** \\
\\
Computation of radar plot scores are made using :\\
\\
**SCORES\_FULL.py** \\
\\
Output of statistical analysis are available as:\\
\\
**correlation\_fwi.pkl**  **obs\_correlation\_fwi.pkl** **\*RELIABILITY.pkl** **\*RADAR.pkl** \\
\\
Region specific observations and forecasts are provided in :\\
\\
**NEN\***  **NWN\*** \\
\\
For plotting the plots are made using the following scripts :\\
\\
**FIG\_\*.ipynb** \\
\\
For access to data note present in this capsule please access the ftp site:\\
\\
ftp server: ftp.ecmwf.int\\
username: ecmwf\_fire\\
password: FhXekWMuy\\
\\
Francesca Di Giuseppe](/content/explore/e83faae4-fe63-40ca-88eb-9f82d6bb035b?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/7714230/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
\\
11 \| Mar \| 2025\\
\\
Sensing flow gradients is necessary for learning autonomous underwater navigation\\
\\
Code and Data for manuscript entitled "Sensing flow gradients is necessary for learning autonomous underwater navigation".\\
\\
In this manuscript, we explored how an artificial swimmer can learn to reach a specific destination in unsteady flows by relying solely on egocentric observations.\\
\\
We showed that egocentric learning requires sensing flow gradients. We then systematically analyzed the robustness of the egocentric and geocentric policies to transfer from low- to high-fidelity flow representations, as well as transfer to different Reynolds numbers. We showed that egocentric policies naturally obey rotational symmetries, and we benchmark the performance of the RL policies everywhere in the flow field, including at locations outside the training domain. Lastly, we interpreted the behavior of the RL policies using tools from dynamical systems, in light of flow physics, and in comparison to classic control arguments.\\
\\
The readme file (/code/RLnavigation\_code\_organzied/README.md) explains the companion code, data and contains detail on how to run the numerical examples in the manuscript.\\
\\
Yusheng Jiao, Haotian Hang, Josh Merel & Eva Kanso](/content/explore/1b835f5c-c9c0-40a4-828e-a9eb46f58baa?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/4194339/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Physics\\
\\
26 \| Feb \| 2025\\
\\
A robust and omnidirectional-sensitive electronic antenna for tactile induced perception\\
\\
Code for manuscript submitted to nature communications titled "A robust and omnidirectional-sensitive electronic antenna for tactile induced perception"\\
\\
REN Hao](/content/explore/82fee670-1e7d-4900-b8ab-4aa8e2bcfd0f?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8009266/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
20 \| Feb \| 2025\\
\\
Dscamb regulates cone mosaic formation in zebrafish via filopodium-mediated homotypic recognition\\
\\
Zebrafish has four types of cone photoreceptors. They are organized into a regular pattern (cone mosaic) in the retina. This simulation mimics the behavior of red cones that use filopodia to recognize and stay away from other red cones, establishing their regular spacing. The two jupyter notebook scripts are for Figure 5g (WT and Mut Red cones simulation in jupyter notebook python.ipynb) and Supplementary Figure 6 (sticky filopodial tips.ipynb), respectively.\\
\\
Dongpeng Hu](/content/explore/40b3becf-95c9-49a1-9141-590dab259758?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/4252423/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Chemistry\\
\\
20 \| Feb \| 2025\\
\\
Probing Nuclear Quantum Effects in Electrocatalysis via a Machine-Learning Enhanced Grand Canonical Constant Potential Approach\\
\\
A grand canonical path integral hybrid Monte Carlo method.\\
A Deep Potential force field in which the total electron number can be adjusted.\\
\\
Bin Jin, Menglin Sun, Xiaolong Yang & Shenzhen Xu](/content/explore/83d43c0a-2fd2-488d-ba33-c527e1cd070f?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/8297012/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Biology\\
\\
17 \| Feb \| 2025\\
\\
Marine ecosystem restoration: achievements and challenges for the next decade\\
\\
Marine ecosystem restoration success stories are needed to incentivize society and private enterprises to build capacity and stimulate investments. Yet, we still must demonstrate that restoration efforts can effectively contribute to achieving the targets set by the UN Decade on Ecosystem Restoration. Here we conduct a meta-analysis on 764 active restoration interventions across a wide range of marine habitats worldwide. We show that marine ecosystem restorations have an average success of ca. 64%, and are: 1) viable for a large variety of marine habitats, including deep-sea ecosystems; 2) highly successful for saltmarshes, tropical coral reefs and habitat-forming species such as animal forests; 3) successful at all spatial scales, so that restoration over large spatial scales can done using multiple interventions at small-spatial scales that better represent the natural variability; 4) scalable through dedicated policies, regulations, and financing instruments. Restoration interventions were surprisingly effective even in areas where direct human impacts persisted, demonstrating that successful restorations do not require preventive removal of all stressors. These results demonstrate the immediate feasibility of a global “blue restoration” plan even for deep-sea ecosystems, enabled by increasing availability of new and cost-effective technologies.\\
\\
Roberto Danovaro et al.](/content/explore/7be7f89f-c1a5-402f-81f9-1171e02362b9?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/5370144/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Bioinformatics\\
\\
1 \| Aug \| 2025\\
\\
TEtrimmer: a novel tool to automate the manual curation of transposable elements\\
\\
Transposable elements (TEs) are repetitive DNA sequences capable of moving within the genome and play important roles in gene regulation and genome evolution. Accurate annotation of TEs is crucial for downstream analyses but challenging due to their sequence diversity and often fragmented occurrence within genomes. At present, the construction of high-quality TE consensus libraries relies heavily on time-consuming manual curation, which is not possible to be widely applied. To address this, we here present TEtrimmer, a novel tool to automate and replace the traditional manual curation of TEs. TEtrimmer introduces new algorithms to automate key steps of manual curation. For instance, it first combines phylogenetic analysis and DBSCAN to cluster TE alignment patterns precisely. Additionally, TEtrimmer innovatively introduces a sliding-window strategy to remove lowly conserved regions of TE-derived multiple sequence alignments. TEtrimmer also provides detailed report plots and features a graphical user interface (GUI) application for the convenient inspection and improvement of each processed TE consensus sequence. Tested on the genomes of six organisms belonging to various kingdoms of eukaryotic life, TEtrimmer consistently improved the identification of intact TEs compared to the established tools EDTA2 and RepeatModeler2. Hence, TEtrimmer offers a user-friendly solution to generate high-quality TE consensus libraries.\\
\\
Jiangzhao Qian et al.](/content/explore/29cf4e02-0536-4731-890b-6efbc5824b1c?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/4802564/tree/v2/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Medical Sciences\\
\\
12 \| Feb \| 2025\\
\\
VascularBC-ST: the code to analyze the Vascular microenvironment of Breast Cancer using Spatial Transcriptome\\
\\
Breast cancers present intricate microenvironments comprising heterotypic cellular interactions. A global map outlining the spatial organization of breast cancer has yet to be established. Herein, we leverage the DNA nanoball-based genome-wide in situ sequencing (Stereo-seq) to visualize the geospatial architecture of 30 primary breast tumors and metastatic lymph nodes. The unprecedented high-resolution mapping accurately localizes distinct cell populations within the ecosystem and unveils the delicate structure of tumor vasculature, thus highlighting endothelial heterogeneity in biological phenotypes, spatial distribution, and intercellular crosstalk. In particular, we identify the immunomodulatory function of venules, where ACKR1+ endothelial cells and CCL21+ vascular smooth muscle cells constitute a chemokine-rich niche to synergistically promote lymphocyte extravasation into tumors. High numbers of venules predict more immune infiltration and better clinical outcome. This study represents currently the most comprehensive survey of the spatial atlas of breast cancer and provides mechanistic insights into the venular regulation of immune infiltration.\\
\\
Nan Sun](/content/explore/92dc37e1-30d8-44a7-8262-a30c1594b9e7?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) [Open Capsule](/content/capsule/9477017/tree/v1/index.html)

published in [Nature Communications](/content/explore?query=Nature%20Communications&refine=journal/index.html)

[Computer Science\\
\\
10 \| Jun \| 2025\\
\\
Learning Interpretable Network Dynamics via Universal Neural Symbolic Regression](/content/explore/dbbd5b69-ffa3-4674-92a4-27f1e73c2dbb?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[|     |\\
| --- |\\
| **Learning Interpretable Network Dynamics via Universal Neural Symbolic Regression** |\\
\\
🎉 This is a PyTorch/GPU implementation of the paper **Learning Interpretable Network Dynamics via Universal Neural Symbolic Regression**, which aims to address multiple interrelated problems related to the discovery of governing equations in complex network dynamics.\\
\\
**Learning Interpretable Network Dynamics via Universal Neural Symbolic Regression**](/content/explore/dbbd5b69-ffa3-4674-92a4-27f1e73c2dbb?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html)

[📝\ [Paper](https://arxiv.org/abs/2411.06833)\]

JiLin University

### 🔑 Key Insight:

The main task of this paper is to develop a computational tool, LLC(Law of Change Learning), that automatically and efficiently identifies symbolic patterns and governing equations that describe the dynamics of complex networks. This involves inferring ordinary differential equations (Odes) from observed data on network dynamics.

### 🛠️ Dataset

📦 Data preparation: This approach involves generating synthetic data to validate the performance of the algorithm.

###### The implementation of synthetic data for the six common scenarios is in.m files in the./code/data file directory.

###### Predator data is in the./code/data/predator file directory

###### The data of real epidemic and pedestrian dynamics scenario is in ./code/real\_data/ and ./code/data/pedestrain file directories.

### 🛠️ Process Description

\\*\\* Note that example.py is only a running demo due to computable resource limitations, with reducing the number of training epoch, data size of the neural network, and using a GP-based PySR instead of a pre-trained symbolic regression model. Therefore, there is no guarantee of accuracy for the results.
If you want to reproduce the results in the paper, please follow these steps and configure and run again in a suitable computing environment.

First, please download the pretrained models from the official implementation at [100M](https://drive.google.com/drive/folders/1LTKUX-KhoUbW-WOx-ZJ8KitxK7Nov41G), and put the downloaded pretrained model into the folder ./weights/

Then, install the following dependency package (more packages can be found in the official implementation)

Finally, run the relevant files in the Dynamics directory

In the case of LV dynamic, after configuring the environment, simply run the **Rationalnn\_decompose.py** file with **dynamic\_name** set to **LV\_dynamics**

## 📚 Bibtex

If you use this repository, please cite:

bibtex

Copy

```bibtex
@misc{hu2024learninginterpretablenetworkdynamics,
      title={Learning Interpretable Network Dynamics via Universal Neural Symbolic Regression},
      author={Jiao Hu and Jiaxu Cui and Bo Yang},
      year={2024},
      eprint={2411.06833},
      archivePrefix={arXiv},
      primaryClass={cs.AI},
      url={https://arxiv.org/abs/2411.06833},
}

Jiao Hu, Jiaxu Cui & Bo Yang

Open Capsule

published in Nature Communications

Engineering\ \ 8 | Feb | 2025\ \ A Wearable Obstacle Avoidance Device for Visually Impaired Individuals with Cross-Modal Learning\ \ It is challenging for wearable obstacle avoidance devices to simultaneously meet practical demands of high reliability, rapid response, long-lasting duration, and user-friendly design. Here we report a wearable obstacle avoidance device, comprising a set of self-developed glasses (weighing ∼\sim∼ 400 grams, including an ∼\sim∼ 80 grams battery) and a common smartphone. Specifically, the glasses collect the multi-modal data for comprehensive environmental perception, including video and\ depth modalities, and implement a depth-aided video compression module. This module not only adaptively compresses video data to reduce transmission delay to the smartphone, but also operates on a customized FPGA board featuring a multi float-point vector unit streaming processing architecture, thereby facilitating responsive and energy-efficient obstacle detection. Additionally, we design a cross-modal obstacle detection module on the smartphone, which ensures reliable detection and provides user-friendly auditory and tactile alerts by utilizing cross-modal learning based on modal correlations.\ \ Yun Gao et al. Open Capsule

published in Nature Communications

Physics\ \ 6 | Feb | 2025\ \ Path-based packing of icosahedral shells into multi-component aggregates\ \ Code for building different types of icosahedral shells of particles and to assemble them in concentric way.\ \ Diana Nelli Open Capsule

published in Nature Communications

Physics\ \ 5 | Feb | 2025\ \ A Bioinspired In-Materia Analogue Photoelectronic Reservoir Computing for Human Action Processing\ \ Home-made dataset and code for paper “A Bioinspired In-Materia Analogue Photoelectronic Reservoir Computing for Human Action Processing”\ \ Hangyuan Cui Open Capsule

published in Nature Communications

Biology\ \ 5 | Feb | 2025\ \ Supplementary code for: Spatiotemporal computations in the insect celestial compass\ \ Implements the insects' celestial compass, which uses the skylight to estimate the heading direction of the insect. As the sun moves during the day, this compass can adjust for this movement and transform the sun's position into a geocentric compass. Figures 3 and 4 show how the model performs in foraging and migration tasks respectively.\ \ Evripidis Gkanias & Barbara Webb Open Capsule

published in Nature Communications

Biology\ \ 4 | Feb | 2025\ \ Human-mouse proteomics reveals the shared pathways in Alzheimer's disease and delayed protein turnover in the amyloidome\ \ Mouse AD proteomics code\ \ Jay Yarbro Open Capsule

published in Nature Communications

Bioinformatics\ \ 27 | Jan | 2025\ \ CatPred: A comprehensive framework for deep learning in vitro enzyme kinetic parameters kcat, Km and Ki

Quantification of enzymatic activities still heavily relies on experimental assays, which can be expensive and time-consuming. Therefore, methods that enable accurate predictions of enzyme activity can serve as effective digital twins. A few recent studies have shown the possibility of training machine learning (ML) models for predicting the enzyme turnover numbers (kcat) and Michaelis constants (Km) using only features derived from enzyme sequences and substrate chemical topologies by training on in vitro measurements. However, several challenges remain such as lack of standardized training datasets, evaluation of predictive performance on out-of-distribution examples, and model uncertainty quantification. Here, we introduce CatPred, a comprehensive framework for ML prediction of in vitro enzyme kinetics. We explored different learning architectures and feature representations for enzymes including those utilizing pretrained protein language model features and pretrained three-dimensional structural features. We systematically evaluate the performance of trained models for predicting kcat, Km, and inhibition constants (Ki) of enzymatic reactions on held-out test sets with a special emphasis on out-of-distribution test samples (corresponding to enzyme sequences dissimilar from those encountered during training). CatPred assumes a probabilistic regression approach offering query-specific standard deviation and mean value predictions. Results on unseen data confirm that accuracy in enzyme parameter predictions made by CatPred positively correlate with lower predicted variances. Incorporating pre-trained language model features is found to be enabling for achieving robust performance on out-of-distribution samples. Test evaluations on both held-out and out-of-distribution test datasets confirm that CatPred performs at least competitively with existing methods while simultaneously offering robust uncertainty quantification. CatPred offers wider scope and larger data coverage (∼23k, 41k, 12k data-points respectively for kcat, Km and Ki). A Google Colab interface to use the trained models is made available at: https://tiny.cc/catpred. All the codes are also available at https://github.com/maranasgroup/CatPred. This capsule is intended for reproducing the results of the manuscript. Please see README file for more description.

Veda Sheersh Boorla & Costas D. Maranas

Open Capsule

published in Nature Communications

Engineering\ \ 28 | Jan | 2025\ \ A μGal MOEMS gravimeter designed with free-form anti-springs\ \ AELPSO is an optimization algorithm used in this manuscript, which is based on the elite learning method and the concept of collaboration among multiple sub-swarms. The demonstration is based on the Sphere test function, which is a unimodal test function.\ \ Shuang Wu et al. Open Capsule

published in Nature Communications

Engineering\ \ 15 | Sep | 2025\ \ Code for CHAMPS：China Aggregate Metabolism and Provincial Scenario modeling\ \ This code contains only the core parts of the model, including provincial history, demand scenarios, and supply scenarios. The scenarios only show the baseline; for parameter adjustments for other scenarios, refer to the Supporting Information\ \ Zijian Ren et al. Open Capsule

published in Nature Communications

Chemistry\ \ 14 | Feb | 2025\ \ Code for In-Depth Insight into Structure-Reactivity/Regioselectivity Relationship of Lewis Acid Catalyzed Cascade 4πe-Cyclization/Dicycloexpansion Reaction\ \ A model for regioselectivity predicting of 4πe-cyclization/dicycloexpansion reaction developed by Professor Yong-Qiang Tu, which providing a foreseeing thought to design reaction routes or substrates leading to angular tricyclic skeletons.\ \ Ka Lu et al. Open Capsule

published in Nature Communications

Earth Sciences\ \ 25 | Jan | 2025\ \ The unveiling role of South Tropical Atlantic in winter Atlantic Niño inducing La Niña\ \ Codes based on NCL\ \ Guangli Zhang Open Capsule

published in Nature Communications

Earth Sciences\ \ 22 | Jan | 2025\ \ Efficient hybrid numerical modeling of the seismic wavefield in the presence of solid-fluid boundaries\ \ Using full-waveform methods to image small-scale structures buried within the Earth involves computing seismic wave behavior over long distances compared to their wavelengths. This is computationally challenging. "Box Tomography" is a hybrid approach that splits wavefield computation into three parts, only one part is required during imaging. Implementing it in remote areas with fluid-solid boundaries requires creating artificial sources and coupling elastic and acoustic simulations. We propose a unified framework for this, reducing computational costs significantly without losing accuracy. We also present benchmark examples in target regions like the ocean floor and core-mantle boundary.\ \ Chao Lyu, Barbara Romanowicz, Liang Zhao & Yder Masson Open Capsule

published in Nature Communications

Engineering\ \ 17 | Jan | 2025\ \ FEniCS codes to run meso- and macro-scale FE simulations of thermo-electro-mechanical problems\ \ FEniCS codes to run meso- and macro-scale FE simulations of thermo-electro-mechanical problems related to 3D printed conductive thermoplastics.\ \ Javier Crespo-Miguel, Sergio Lucarini & Daniel Garcia-Gonzalez Open Capsule

published in Nature Communications

Medical Sciences\ \ 17 | Jan | 2025\ \ COFFEE (Comprehensive Fetching of Fusion transcripts between ERVs and Exons of human genes) 1.0.0\ \ COFFEE (Comprehensive Fetching of Fusion transcripts between ERVs and Exons of human genes) is a method for identifying transposable elements (TE)-RNAs (e.g. endogenous retrovirus) fused with exons of human genes.\ \ Shunsuke Funaguma et al. Open Capsule

published in Nature Communications

Computer Science\ \ 16 | Jan | 2025\ \ Hybrid Neural Networks for Continual Learning Inspired by Corticohippocampal Circuits\ \ CH-HNN is a neural network model for hybrid neural networks in continual learning, inspired by cortico-hippocampal circuits. This repository contains the code needed to replicate the experiments described in the associated manuscript submitted to Nature Communications.\ \ Qianqian Shi et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 14 | Jan | 2025\ \ Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing\ \ WarpDemuX is an ultra-fast and highly accurate adapter-barcoding and demultiplexing approach.\ \ Wiep van der Toorn Open Capsule

published in Nature Communications

Bioinformatics\ \ 15 | Jan | 2025\ \ Pretrained transformers applied to clinical studies improve predictions of treatment efficacy and associated biomarkers\ \ This capsule contains the code for running the clinical transformer including: Pre training, transfer learning and baseline clinical transformer modeling. \ \ This demo is designed to familiarize with the main components of the clinical transformer, its API and usage. Note that we are using simulated data. \ \ For this demo we simulated a dataset with two populations (long vs short time survivors), the data was split into pre-training, training and testing. We train a clinical transformer with and without transfer learning.\ \ Gustavo Arango Open Capsule

published in Nature Communications

Engineering\ \ 9 | Jan | 2025\ \ Pareto Active Learning Framework for the Accelerated Discovery of Optimal Process Parameters for Additive-manufactured Ti-6Al-4V Alloys with High Strength and Ductility\ \ Optimizing process and heat-treatment parameters of laser powder bed fusion for producing Ti-6Al-4V alloys with high strength and ductility is crucial to meet performance demands in various applications. Nevertheless, inherent trade-offs between strength and ductility render traditional trial-and-error methods inefficient. Herein, we present Pareto active learning framework with targeted experimental validation to efficiently explore vast parameter space of 296 candidates, pinpointing optimal parameters to augment both strength and ductility. All Ti-6Al-4V alloys produced with the pinpointed parameters exhibited higher ductility at similar strength levels and greater strength at similar ductility levels compared to those in previous studies. By improving one property without significantly compromising the other, the framework demonstrated efficacy in overcoming the inherent trade-offs. Ultimately, Ti-6Al-4V alloys with ultimate tensile strength and total elongation of 1188 MPa and 16.4%, respectively, were produced. The proposed framework streamlined discovery of optimal processing parameters and promises accelerated development of high-performance alloys.\ \ Jeong Ah Lee et al. Open Capsule

published in Nature Communications

Social Sciences\ \ 8 | Jan | 2025\ \ Proactive and reactive construction of memory-based preferences\ \ This capsule contains all code and software developed for the following paper:\ \ Nicholas, J., Daw, N. D., & Shohamy, D. (2023). Proactive and reactive construction of memory-based preferences\ \ Jonathan Nicholas, Nathaniel D Daw & Daphna Shohamy Open Capsule

published in Nature Communications

Bioinformatics\ \ 7 | Jan | 2025\ \ Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data\ \ As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host filtration using prior human genome references can introduce false sex biases and inadvertently permit flow-through of host-specific DNA during bioinformatic analyses, which could be exploited for individual identification. To address these issues, we introduce and benchmark three host filtration methods of varying throughput, with concomitant applications across low and high microbial biomass datasets, including skin and fecal samples. We find that these methods are important for obtaining accurate results in low biomass samples (e.g., tissue and blood). Overall, we demonstrate that rigorous host filtration is a key component of privacy-minded analyses of patient microbiomes and provide computationally efficient pipelines for accomplishing this task on large-scale datasets.\ \ Our bioinformatics pipeline designed to provide highly-conservative filtration of human reads from metagenomic next-generation sequencing data. The pipeline is designed to be flexible and can be used with any host reference genome(s), though certain specific human reference genomes are advised. The pipeline is designed to be used with paired-end Illumina sequencing data, but can be easily modified to work with single-end data. The pipeline was originally designed for SLURM job schedulers, but has been containerized to support running on Code Ocean. By default, this pipeline is designed to run Method 1 as described in the manuscript. Due to the runtime and storage constraints of Code Ocean, we have omitted the final index-based filtration step of Method 1. Thus, this reproduction performs fastp-based quality control, followed by minimap-2 based alignment with GRCh38 and CHM13-T2Tv2.0. These two steps alone are sufficient to prevent re-identification of host-derived samples, as depicted in Figure 6. To incorporate the final step providing a computationally-efficient approach to incorporate all currently-available human pangenome references, we advise using Movi to create a comprehensive genome reference on local compute infrastructure.\ \ Caitlin Guccione & Lucas Patel Open Capsule

published in Nature Communications

Physics\ \ 20 | Jan | 2025\ \ Machine learning assisted composition design of high-entropy Pb-free relaxors with giant energy-storage\ \ Herein, with the assistance of machine learning screening, we demonstrated an unprecedented high energy-storage density of 20.7 J cm-3 with a high efficiency of 86% in a high-entropy Pb-free relaxor. A random forest regression model with key descriptors based on limited reported experimental data were developed to predict and screen the elements and chemical compositions of high-entropy systems.\ \ Xingcheng Wang et al. Open Capsule

published in Nature Communications

Biology\ \ 3 | Jan | 2025\ \ Exploring Force-Driven Stochastic Folding Dynamics in Mechano-Responsive Proteins and Implications in Phenotypic Variation\ \ High­ Performance Parallel Magnetic Tweezer program for real­time monitoring of protein folding and unfolding under force.\ \ Pritam Saha et al. Open Capsule

published in Nature Communications

Physics\ \ 2 | Jan | 2025\ \ Supplementary Code for: Enhanced Sampling of Protein Conformational Changes via True Reaction Coordinates from Energy Relaxation\ \ A protein’s function often depends on its multiple conformations. Understanding these conformations and the transitions between them poses a major challenge for both experiment and computation. We present a rigorous physics-based method that enables predictive and near- optimal enhanced sampling of conformational transitions and the resulting conformations. This predictive method is based on our finding that conformational transitions and energy relaxation starting from the same protein structure are controlled by the same reaction coordinates, pointing to a potential generalization of the fluctuation-dissipation theorem, a cornerstone of non- equilibrium statistical mechanics. This insight enables us to compute reaction coordinates—the optimal collective variables for enhanced sampling—from energy relaxation via our recently developed generalized work functional method. We tested our method on two proteins: HIV-1 protease and PDZ2 domain. For HIV-1 protease, we accelerated its flap opening and ligand unbinding—a process with an experimental half-life of 8.9 × 10! s—to 200 ps in simulations, demonstrating near-optimal efficiency. For PDZ2 domain, we discovered a previously unrecognized transient large-scale conformational change at its allosteric sites during ligand unbinding, providing an intuitive mechanism for its allostery—a puzzle in the field for over two decades. This illustrates our method’s predictive capability. Most importantly, our method has a unique advantage: it produces trajectories that preserve the natural dynamics, enabling us to generate unbiased molecular dynamics trajectories of conformational transitions—true computational experiments—at optimal efficiency.\ \ Huiyu Li & Ao Ma Open Capsule

published in Nature Communications

Medical Sciences\ \ 23 | Dec | 2024\ \ Deep learning-enabled liquid-based cytology model for cervical precancer and cancer detection\ \ Official implementation of paper "Deep learning-enabled liquid-based cytology model for cervical precancer and cancer detection". \ \ This codes provide the detection model (with parameters) and the classify model's architecture (only code without parameters).\ \ Peng Xue et al. Open Capsule

published in Nature Communications

Medical Sciences\ \ 21 | Dec | 2024\ \ Parallel circuit in oculomotor nucleus to control eye movements and REM sleep\ \ These data are made available to reviewers for Nature Communications for reviewing purposes only. Reviewers may visualize and run the code in the enclosing Code Ocean Capsule, which reads and analyzes these data.\ \ Chengyong Jiang, Biao Yan & Jiayi Zhang Open Capsule

Biology\ \ 21 | Dec | 2024\ \ Deep learning models to predict the activity of guide RNAs for Cas12a variants\ \ We performed high-throughput analyses to evaluate the activity and compatibility with specific PAMs of 23 Cas12a variants and developed deep learning models for these Cas12a variants to predict gene editing activities at target sequences of interest.\ \ Peng Chen et al. Open Capsule

published in Nature Communications

Biology\ \ 20 | Dec | 2024\ \ Mitochondrial segmentation and function prediction in live-cell images with deep learning\ \ MoDL is a deep learning-based software package for precise mitochondrial segmentation and function prediction in live-cell images, and allows for visualization and outputs detailed data on mitochondrion morphology features and functionality.\ \ OBP Open Capsule

published in Nature Communications

Medical Sciences\ \ 18 | Dec | 2024\ \ Code for "Post-Acute Cardiovascular Outcomes of COVID-19 in Children and Adolescents"\ \ This capsule provides code for manuscript titled "Post-Acute Cardiovascular Outcomes of COVID-19 in Children and Adolescents".\ \ Bingyu Zhang Open Capsule

published in Nature Communications

Earth Sciences\ \ 14 | Dec | 2024\ \ Changes in event soil moisture-temperature coupling can intensify very extreme heat beyond expectations\ \ Code to reproduce results and figures of NCOMMS-24-35329\ \ Douglas Maraun & Martin Jury Open Capsule

published in Nature Communications

Earth Sciences\ \ 14 | Dec | 2024\ \ review: Changes in event soil moisture-temperature coupling can intensify very extreme heat beyond expectations\ \ Code to reproduce results and figures of NCOMMS-24-35329\ \ Douglas Maraun & Martin Jury Open Capsule

published in Nature Communications

Bioinformatics\ \ 29 | Apr | 2025\ \ LipidIN: a comprehensive repository for flash platform-independent annotation and reverse lipidomics (for per review)\ \ Improving annotation accuracy, coverage, speed and depth of lipid profiles remains a significant challenge in traditional lipid annotation. We introduce LipidIN, an advanced framework designed for flash platform-independent annotation. LipidIN features a 168.5-million lipid fragmentation hierarchical library that encompasses all potential chain compositions and carbon-carbon double bond locations. Developed an expeditious querying module speeds to over 100 billion times’ querying in 1 second for all mass spectral libraries. Furthermore, we leverage three relative retention time rules to develop lipid categories intelligence model for reducing false positive annotations and predicting unannotated lipids with a 5.7% estimated false discovery rate covering 8923 lipids cross various species. More importantly, LipidIN integrates a Wide-spectrum Modeling Yield network for regenerating lipid fragment fingerprints to further improve accuracy and coverage with a 20% estimated recall boosting. We further demonstrated the utility of LipidIN in multiple tasks for lipid annotation and biomarker discovery in clinical cohorts.\ \ Hao Xu et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 29 | Apr | 2025\ \ LipidIN: a comprehensive repository for flash platform-independent annotation and reverse lipidomics (WMYn) (for per review)\ \ Improving annotation accuracy, coverage, speed and depth of lipid profiles remains a significant challenge in traditional lipid annotation. We introduce LipidIN, an advanced framework designed for flash platform-independent annotation. LipidIN features a 168.5-million lipid fragmentation hierarchical library that encompasses all potential chain compositions and carbon-carbon double bond locations. Developed an expeditious querying module speeds to over 100 billion times’ querying in 1 second for all mass spectral libraries. Furthermore, we leverage three relative retention time rules to develop lipid categories intelligence model for reducing false positive annotations and predicting unannotated lipids with a 5.7% estimated false discovery rate covering 8923 lipids cross various species. More importantly, LipidIN integrates a Wide-spectrum Modeling Yield network for regenerating lipid fragment fingerprints to further improve accuracy and coverage with a 20% estimated recall boosting. We further demonstrated the utility of LipidIN in multiple tasks for lipid annotation and biomarker discovery in clinical cohorts.\ \ Hao Xu & Tianhang Jiang Open Capsule

published in Nature Communications

Engineering\ \ 16 | Dec | 2024\ \ Principled Neuromorphic Reservoir Computing\ \ This capsule provides the code/data necessary to compute the results reported in the main text and in the Supplementary Material.\ \ Christopher J. Kymn et al. Open Capsule

published in Nature Communications

Biology\ \ 12 | Dec | 2024\ \ Kingdom-specific lipid unsaturation calibrates sequence evolution in membrane arm subunits of eukaryotic respiratory complexes\ \ The Python script filters blast results using parameters such as e-value cut-off, drop multiple entries, etc. The desired organisms list was provided to further filter out blast results. The code can be used to filter any sequence dataset and the criteria can be set as required.\ \ Pooja Gupta et al. Open Capsule

published in Nature Communications

Biology\ \ 5 | Feb | 2025\ \ Striatal arbitration between choice strategies guides few-shot adaptation\ \ This compute capsule contains the full codes and data we used to analyze the rat behavior in the two-step task for "Striatal arbitration between choice strategies guides few-shot adaptation"\ \ Minsu Abel Yang, Min Whan Jung & Sang Wan Lee Open Capsule

published in Nature Communications

Biology\ \ 10 | Dec | 2024\ \ Estimation of ribosome synthesis rate profiles from single-cell microfluidics data

Estimation code and plotting script accompanying the paper "Single-cell data reveal heterogeneity of investment in ribosomes across a bacterial population" (doi: https://doi.org/10.1101/2024.04.26.591328).

Abstract of the paper:

Ribosomes are responsible for the synthesis of proteins, the major component of cellular biomass. Classical experiments have established a linear relationship between the fraction of resources invested in ribosomal proteins and the rate of balanced growth of a microbial population. We extended the study of ribosomal resource allocation from populations to single cells, using a combination of time-lapse fluorescence microscopy and statistical inference. We found a large variability of ribosome concentrations and growth rates in conditions of balanced growth of the model bacterium Escherichia coli. Moreover, the ribosome concentrations and growth rates of individual cells are uncorrelated, contrary to what would be expected from the population-level growth law. A similar large heterogeneity was found during the transition of the bacteria from a poor to a rich growth medium. Whereas some cells immediately adapt ribosomal resource allocation to the new environment, others do so only gradually. Our results thus reveal distinct strategies for investing resources in the molecular machines at the heart of cellular self-replication. This raises the interesting question whether the observed variability is an intrinsic consequence of the stochastic nature of the underlying biochemical processes or whether it improves the fitness of Escherichia coli in its natural environment.

Hidde de Jong, Eugenio Cinquemani & Antrea Pavlou

Open Capsule

published in Nature Communications

Bioinformatics\ \ 8 | Dec | 2024\ \ msiFlow: Automated Workflows for Reproducible and Scalable Multimodal Mass Spectrometry Imaging and Immunofluorescence Microscopy Data Processing and Analysis\ \ msiFlow is a collection of automated workflows for reproducible and scalable multimodal mass spectrometry imaging and immunofluorescence microscopy data processing and analysis\ \ Philippa Spangenberg Open Capsule

published in Nature Communications

Engineering\ \ 5 | Dec | 2024\ [Nat. Commun.] Magnetically reshapable 3D multi-electrode arrays of liquid metals for electrophysiological analysis of brain organoids\ \ Matlab code for analyzing electrophysiological signals of brain organoids\ \ Enji Kim Open Capsule

published in Nature Communications

Bioinformatics\ \ 5 | Dec | 2024\ \ Live Attenuated Influenza Vaccine with Low Proportions of Defective Interfering Particles Elicits Robust Immunogenicity and Cross- Protection\ \ Live Attenuated Influenza Vaccine with Low Proportions of Defective Interfering Particles Elicits Robust Immunogenicity and Cross- Protection\ \ Min Wu & Peihan Wang Open Capsule

published in Nature Communications

Biology\ \ 4 | Dec | 2024\ \ Dynamic Representation of Appetitive and Aversive Stimuli in Nucleus Accumbens Shell D1- and D2-Medium Spiny Neurons\ \ This repository contains the codes developed for the methods used in the section "Calcium Data Analysis" of the manuscript "Dynamic Representation of Appetitive and Aversive Stimuli in Nucleus Accumbens Shell D1- and D2-Medium Spiny Neurons". It also includes example files for usage demonstration purposes. See the README.md file in the "code" folder for more information.\ \ Ana Verónica Domingues et al. Open Capsule

published in Nature Communications

Earth Sciences\ \ 4 | Dec | 2024\ \ Seasonal Changes of Mélange Thickness Coincide With Greenland Calving Dynamics\ \ Code for the Nature Communications manuscript: Seasonal Changes of Mélange Thickness Coincide With Greenland Calving Dynamics\ \ Yue Meng et al. Open Capsule

published in Nature Communications

Physics\ \ 27 | Nov | 2024\ \ Autonomous Design of Ordered Gas Diffusion Layers for High-performing Proton Exchange Membrane Fuel Cells via Bayesian Machine Learning\ \ Capsule for manuscript entitled with Autonomous Design of Ordered Gas Diffusion Layers for High-performing Proton Exchange Membrane Fuel Cells via Bayesian Machine Learning\ \ Jing Sun et al. Open Capsule

published in Nature Communications

Physics\ \ 27 | Nov | 2024\ \ Magnetosensitivity of Tightly Bound Radical Pairs in Biology is Enabled by the Quantum Zeno Effect\ \ Code to simulate the recombination yield of radical pairs subject to quantum Zeno effect\ \ Daniel Kattnig & Matt Denton Open Capsule

published in Nature Communications

Medical Sciences\ \ 27 | Nov | 2024\ \ Generalized cue reactivity in dopamine neurons after opioids Jul 31, 2024 08:58\ \ Cue reactivity is the maladaptive neurobiological and behavioral response upon exposure to drug cues and is a major driver of relapse. A widely accepted assumption in addiction research is that disparate dopamine responses to drug vs. natural rewards and their cues is responsible for the development of addiction. Specifically, the leading hypothesis is that dopamine release by addictive drugs represents a persistently positive reward prediction error that causes runaway enhancement of dopamine responses to drug cues, leading to their pathological overvaluation. However, this hypothesis has not been directly tested. Here, we developed Pavlovian and operant procedures to measure firing responses within the same dopamine neurons to drug versus natural reward cues, which we found to be similarly enhanced compared to cues predicting natural rewards in drug-naïve controls. This enhancement was associated with increased behavioral reactivity to the drug cue, suggesting that dopamine activity may still be relevant to cue reactivity, albeit not as previously hypothesized. These results challenge the prevailing hypothesis of cue reactivity, warranting new models of the impact of opioids on dopaminergic function, and provide critical insights into the neurobiology of cue reactivity.\ \ Khaled Moussawi et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 27 | Nov | 2024\ \ Meta-EA: A gene-specific combination of any available computational tools for predicting missense variant effects\ \ This is an ensemble method for predicting the impact of genetic variants\ \ Panagiotis Katsonis & Olivier Lichtarge Open Capsule

published in Nature Communications

Medical Sciences\ \ 27 | Nov | 2024\ \ Three Dimensional Multiscalar Neurovascular Nephron Connectivity Map of the Human Kidney Across the Lifespan_Code_and_environment

Code for review for the following paper: https://doi.org/10.1101/2024.07.29.605633

Liam McLaughlin

Open Capsule

published in Nature Communications

Biology\ \ 25 | Nov | 2024\ \ Heterochromatic gene silencing controls CD4 T cell susceptibility to regulatory T cell-mediated suppression - scRNAseq analyses\ \ The integrity of the organism depends on close and dynamic interactions between conventional and regulatory (Treg) T cells. The extracellular signals and signaling events that regulate this crosstalk have been extensively characterized. However, how conventional T cells translate Treg-dependent immunosuppressive signals at the chromatin level remains largely unknown. In differentiating CD4+ T helper (Th) cells, we and others previously reported that transcriptional specificity is largely controlled by heterochromatin-dependent gene silencing. We therefore hypothesized that Treg-mediated T cell suppression could also involve the repressive mark H3K9me3 and the histone-binding factor heterochromatin protein 1 (HP1). Using a bone marrow allograft model, in which graft rejection is coordinated by adoptively-transferred naive CD4+ T cells and can be inhibited by Treg, we show that Treg-dependent suppressive signals indeed mobilize HP1a to repress Th-cell effector genes. Unexpectedly, our screen also revealed that T cells deficient for HP1g or the lysine methyltransferase SUV39H1 are better tolerized than their wild-type counterparts. Mechanistically, our transcriptional and epigenetic profiling identified HP1g as a negative regulator of a network of genes functionally associated with T-cell anergy and exhaustion, including those encoding the transcription factor TOX and the inhibitory receptors PD-1, TIM-3 and LAG-3. In response to T cell receptor engagement, the expression of these immune checkpoints is deregulated in HP1g-deficient cells, thus promoting their better inhibition by Treg. Therefore, we demonstrate that H3K9me3-dependent epigenetic pathways critically regulate Th cell susceptibility to Treg-mediated suppression, and we identify HP1a and HP1g as new epigenetic players whose expression may be manipulated to restore protective immune responses or correct immunopathology, respectively.\ \ Julie Noguerol et al. Open Capsule

published in Nature Communications

Engineering\ \ 25 | Nov | 2024\ \ Dislocation Mobility Effects on Material Hardness: Insights from the Anomalous Hardness of the Hard Metals\ \ Semi-Discrete Variational Peierls-Nabarro model used to compare Peierls stress estimates on {110} and {111} crystallographic planes in rocksalt titanium and tantalum carbides.\ \ Brennan R. Watkins & Christopher R. Weinberger Open Capsule

published in Nature Communications

Medical Sciences\ \ 24 | Nov | 2024\ \ Code for "Racial/Ethnic Differences in Long-COVID-Associated Symptoms among Pediatrics Population: Findings from Difference-in-differences Analyses in RECOVER Program"\ \ To illustrate the analysis and perform codes for peer review, we create a synthetic data named demo_data.csv.\ \ Dazheng Zhang & Bingyu Zhang Open Capsule

published in Nature Communications

Physics\ \ 11 | Nov | 2025\ \ Code for "Measuring the magnetic fields in the upper atmospheres of low-mass stars"

This is the original code for measuring the longitudinal magnetic field of the photosphere and chromosphere with LSD, H-alpha, and CA IRT line profiles.

All original spectra, along with the time and star ID, can be downloaded from PolarBase ( http://polarbase.irap.omp.eu). We didn't include our LSD process code here since it is identical to the open-source LSD code LSDpy ( https://github.com/folsomcp/LSDpy).

We include all required spectra data in the "data" for each star: CaIRT: *.lsd: LSD profiles of Ca IRT *.lsdout: information when the LSD is generated *.out: original information of the spectra downloaded from PolarBase *.calsd: output LSD of Ca IRT with the only chromospheric component can be generated by the 'Beff.measurement.py.'

LSD: Similar to Ca IRT, but for all available photospheric lines.

For codes: Beff.measurement.py: Main code for measuring the longitudinal magnetic field from LSD, H-alpha, and Ca IRT. The output results with the name "{star name}_result_beff.txt" are the original data used for the manuscript. fig1.py, fig.py: the code for plotting Fig.1 and Fig. 2.

polarbase_data.py, mdwarf_info.py lsdgenFuns.py: Include support functions.

The output results with the name "{star name}_result_beff.txt" are the original data used for the manuscript. We include the code for plotting Fig.1 and Fig. 2.

You can click "Reproducible Run" and get all results.

Tianqi Cang

Open Capsule

published in Nature Communications

Earth Sciences\ \ 22 | Nov | 2024\ \ Global coastal hardening and severe sandy beach loss projections\ \ Impacts of climate change and human intervention on world's sandy beach\ \ Khin Nawarat Open Capsule

published in Nature Communications

Engineering\ \ 20 | Nov | 2024\ \ Weather-Responsive Adaptive Shading through Biobased and Bioinspired Hygromorphic 4D-Printing\ \ Code for tracking hygromorphic bilayers & analyzing the percentage of shade coverage in adaptive shading elements.\ \ Tiffany Cheng et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 9 | Dec | 2024\ \ Insights from a Methylome-Wide Association Study of Antidepressant Exposure\ \ Code to accompany the manuscript "Insights from a Methylome-Wide Association Study of Antidepressant Exposure". We are unable to provide the data for the code files relating to individual-level data (Prescription_data.Rmd, Self_report.Rmd, OSCA_covariates.R, MOA_MWAS.sh, LASSO_pheno_prep.R, LASSO_GS_MPS.R, MRS_calc.R or MRS_assoc.R). \ \ For code which analyses the results of the MWAS, the MWAS summary statistics are included for the self-report and antidepressant-derived measures (all participants and MDD only). \ The majority of MWAS_downstream.Rmd script can be tested in this regard, and all the code relating to the summary statistics has been put into MWAS_downstream.R for the running of the script. \ \ The meta-analysis of the external cohort summary statistics can be found and run in the MPS_cohorts_res.R and MPS_cohorts_res.Rmd\ \ Data:\ \ GS MWAS results and downstream analyses: \ \ antidep_pheno1_clean_appt_dmr_res.tsv - DMR results for prescription derived MWAS \ selfrep_pheno3_dmr_res.tsv - DMR results for self-report MWAS \ GRM_unadjusted_antidep_pheno1_clean_appt_MOA_ORM_residph_standard_06_10.moa - prescription derived antidepressant exposure MWAS results (All participants)\ GRM_unadjusted_antidep_pheno2_clean_appt_MOA_ORM_residph_standard_06_10.moa - prescription derived antidepressant exposure MWAS results (MDD only)\ GRM_unadjusted_selfrep_pheno3_MOA_ORM_residph_standard_06_10.moa - selfreport antidepressant exposure MWAS results (All participants)\ GRM_unadjusted_selfrep_pheno4_MOA_ORM_residph_standard_06_10.moa - selfreport antidepressant exposure MWAS results (MDD only). \ selfrep_pheno3_GRMunadj_sexstd_ORM_residph_male_23_09.moa - selfreport antidepressant exposure MWAS results (Male only)\ selfrep_pheno3_GRMunadj_sexstd_ORM_residph_female_23_09.moa - selfreport antidepressant exposure MWAS results (Female only)\ \ antidep_FUMA: Prescription derived antidepressant exposure FUMA results (from genes annotated to the top 100 CpGs)\ selfreport_FUMA: Self report antidepressant exposure FUMA results (from genes annotated to the top 100 CpGs)\ antidep_SYNGO: Prescription derived antidepressant exposure SYNGO results ("")\ selfrep_SYNGO: Selfreport antidepressant exposure SYNGO results ("")\ \ External cohort results:\ \ {cohort}_MRS_AD_coefficients.txt: Coefficients from the AD exposure ~ methylation profile score model\ {cohort}_MRS_AD_modmetrics/logL.txt: Model metrics of the AD exposure ~ methylation profile score model.\ \ Paper abstract: \ \ This study tests the association of whole-blood DNA methylation and antidepressant exposure in 16,536 individuals from Generation Scotland (GS). We identified 8 associations (7 novel), and a high concordance of results between self-report and prescription derived measures. There was observed enrichment for genes expressed in the Amygdala and annotated to synaptic vesicle membrane ontology. Two CpGs (cg15071067; DGUOK-AS1 and cg26277237; KANK1) showed correlation between DNA methylation with the time in treatment. There was a significant overlap in the top 1% of CpGs with another independent methylome-wide association study of antidepressant exposure. Finally, a methylation profile score trained on this sample showed a significant association with antidepressant exposure in a meta-analysis of eight independent external datasets. We demonstrate robust associations of DNA methylation and antidepressant exposure, which warrant further investigation to understand more current antidepressant treatments and to inform on the design of more effective and tolerated treatments for depression.\ \ Ella Davyson Open Capsule

published in Nature Communications

Physics\ \ 17 | Nov | 2024\ \ Residual Neural Network enhanced Long Short-Term Memory neural network for train-induced vibration localizing\ \ We construct a Residual Neural Network (ResNet) enhanced Long Short-Term Memory (Lstm) neural network for train-induced vibration localizing (Res-LstmNet). From the diagrams detected by laser interferometer, the Res-LstmNet can label each vibration segment with their occurring position. Therefore, the Res-LstmNet enabled laser interferometer can be used for distributed sensing of high-speed train vibration to provide a real-time health inspection. The input of Res-LstmNet is the STFT picture of vibrations obtained by laser interferometer and the expected output is the location label obtained by DAS. The code uploaded describes how we use the already-trained model to predict location results.\ \ Bo Wang et al. Open Capsule

published in Nature Communications

Biology\ \ 11 | Jun | 2025\ \ Hierarchical Patterns of Soil Biodiversity in the Atacama Desert: Insights Across Biological Scales\ \ Scripts implemented in the biogeographic analysis of nematodes in the Atacama Desert. Models for both genera richness and prediction of reproductive modes were tested using GLS/GLM and random forest. Additional Jaccard similarity index and nucleotide diversity were compared to geographical distance using a Mantel test to check for isolation-by-distance patterns. Testing the models and ecological indexes were performed using R. All of this scripts can be used in reproducible runs to obtain and check the results reported in the manuscript. \ Python scripts to extract the environmental data relevant to each of the sampling spots are provided. However, due to the large size of the input files form the public datasets, they don't run inside the capsules. This can be run on personal computers or HPC systems by only changing the input file paths.\ \ Laura Villegas et al. Open Capsule

published in Nature Communications

Physics\ \ 13 | Nov | 2024\ \ A Classical Chiral Spin Liquid from Chiral Interactions on the Pyrochlore Lattice\ \ Classical Monte Carlo simulation with Gaussian spin flip, over-relaxation, and valley average updates\ \ Daniel Lozano Gomez Open Capsule

published in Nature Communications

Physics\ \ 12 | Nov | 2024\ \ Quantum highway: Observation of minimal and maximal speed limits for few and many-body states\ \ Simulation codes for quantum speed limit bounds calculation in Quantum highway: Observation of minimal and maximal speed limits for few and many-body states.\ \ Zitian Zhu et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 12 | Nov | 2024\ \ Standard operating procedure combined with comprehensive quality control system to enable large-scale urinary proteomics across multiple LC-MS platforms for precision medicine\ \ MSCohort is a tool for extracting comprehensive metrics and assisting users in evaluating and optimizing the performance of DIA proteomics data. The workflow of MSCohort consists of two modules: Intra-experiment analysis and inter-experiment analysis. Intra-experiment analysis enables the systematic evaluation and optimization of individual DIA experiments. Inter-experiment analysis enables the systematic quality evaluation and low-quality experiments detection for large cohort experiments.\ \ ChaoLiu, XiangLiu & XInhangHou Open Capsule

published in Nature Communications

Engineering\ \ 10 | Nov | 2024\ \ Holistic numerical simulation of a quenching process on a 2 real-size multifilamentary superconducting coil\ \ Calculate the distribution of electromagnetic field and temperature field of 4*4 superconducting coil under magnetic field and transport current (the default parameter is only under self-field) and judge whether magnetothermal instability occurs.\ \ Cun Xue Open Capsule

published in Nature Communications

Earth Sciences\ \ 5 | Nov | 2024\ \ Contributions of countries without a carbon neutrality target to limit global warming\ \ This research capsule explores the contributions of countries without a carbon neutrality target (hereafter, the non-CN countries) towards limiting global warming. Our study integrates diverse datasets and modeling approaches to examine the impact of the non-CN countries on global climate mitigation efforts. The primary data files include geospatial mappings and source data for figures. The code files show the processing and analysis of the data.\ \ Jiaxin Zhou & Wei Li Open Capsule

published in Nature Communications

Chemistry\ \ 4 | Nov | 2024\ \ Crystal Structure Generation with Autoregressive Large Language Modeling\ \ CrystaLLM is a Transformer-based Large Language Model of the CIF (Crystallographic Information File) format. The model can be used to generate crystal structures for a given composition and, optionally, space group. The model is based on the GPT-2 architecture. This repository contains code that can be used to reproduce the experiments in the paper 'Crystal Structure Generation with Autoregressive Large Language Modeling'.\ \ Luis Antunes, Keith T. Butler & Ricardo Grau-Crespo Open Capsule

published in Nature Communications

Medical Sciences\ \ 2 | Nov | 2024\ \ INSIHGT: An accessible multi-scale, multi-modal 3D spatial biology platform\ \ These scripts provide the MATLAB code for performing benchmarking analysis of antibody penetration depth and uniformity.\ \ Lai Hei Ming Open Capsule

published in Nature Communications

Medical Sciences\ \ 1 | Nov | 2024\ \ Code Capsule for the Development and Validation of a Real-time Prediction Model for Acute Kidney Injury in Hospitalized Patients\ \ Early prediction of acute kidney injury (AKI) may provide a crucial opportunity for AKI prevention. To date, no prediction model targeting AKI among general hospitalized patients in developing countries has been published. We developed a simple, real-time, interpretable AKI prediction model for general hospitalized patients from a large tertiary hospital in China, and validated it across five independent, geographically distinct, different tiered hospitals. The model containing 20 readily available variables demonstrated consistent, high levels of predictive discrimination in the validation cohort, with AUCs for AKI and critical AKI within 48 hours ranging from 0.74–0.85 and 0.83–0.90 for the transported models and from 0.78-0.89 and 0.86-0.93 for the refitted models, respectively. With optimal probability cutoffs, the refitted model could predict AKI at a median of 102 (42-246) hours in advance in internal validation, and 42-90 hours in advance in external validation. This code capsule can be used to develop simple real-time prediction models to predict AKI within 24/48/72 hours, and validate the model across different sites. You can upload data according to required format, develop and validate the prediction model for different times.\ \ Yuhui Zhang et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 13 | Dec | 2024\ \ SPIDER: Finding spatially variable ligand-receptor interactions with functional support from downstream genes\ \ Example data for "SPIDER: SPtial Interaction-encoDed intErface decipheR" from manuscript "Finding spatially variable ligand-receptor interactions with functional support from downstream genes".\ \ LI Shiying Open Capsule

published in Nature Communications

Earth Sciences\ \ 31 | Oct | 2024\ \ Data and Codes for "Pervasive fire danger continued under a negative emission scenario"\ \ Data and Codes for "Pervasive fire danger continued under a negative emission scenario"\ \ Hyo-Jeong Kim et al. Open Capsule

published in Nature Communications

Engineering\ \ 30 | Oct | 2024\ \ Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning\ \ Training and testing of a LightGBM model to predict a mRNA transcript's steady-state mRNA level & kinetic decay rate.\ \ Daniel Cetnar, Ayaan Hossain & Howard Salis Open Capsule

published in Nature Communications

Earth Sciences\ \ 29 | Oct | 2024\ \ Multi-objective observational constraint of tropical Atlantic and Pacific low-cloud feedbacks mediates conflicting regional climate-sensitivity contributions\ \ Tropical marine low cloud feedback is key to the uncertainty in climate sensitivity, and it depends on the warming pattern of sea surface temperatures (SSTs). Here, we empirically constrain this feedback in two major low cloud regions, the tropical Pacific and Atlantic, using interannual variability. Low cloud sensitivities to local SST and to remote SST, represented by lower-troposphere temperature, are poorly captured in many models of the latest global climate model ensemble, especially in the less-studied tropical Atlantic. The Atlantic favors large positive cloud feedback that appears difficult to reconcile with the Pacific — we apply a Pareto optimization approach to elucidate trade-offs between the conflicting observational constraints. Examining ~200,000 possible combinations of model subensembles, this multi-objective observational constraint narrows the cloud feedback uncertainty among climate models, nearly eliminates the possibility of a negative tropical shortwave cloud feedback in CO2-induced warming, and suggests a 71% increase in the tropical shortwave cloud feedback.\ \ Mengxi Wu, Hui Su & J. David Neelin Open Capsule

published in Nature Communications

Engineering\ \ 14 | May | 2025\ \ Supplementary Codes for "Single-shot two-dimensional nano-size mapping of fluorescent molecules by ultrafast polarization anisotropy imaging"

This folder contains example codes (MATLAB) and a set of example data for the paper titled:\ "Single-shot two-dimensional nano-size mapping of fluorescent molecules by ultrafast polarization anisotropy imaging"\ Author: Peng Wang ( zju07wps@gmail.com) Date: July 18, 2024

This example shows how to obtain molecular size maps from the reconstructed intensity movies of orthogonal polarization states. This corresponds to Figure 2 and Figure 3 in the paper. To try this example, simply run "processCUP2AI.m" in MATLAB (version R2023a or newer)

  1. MATLAB code files 1.1 "processCUP2AI.m" Main data processing codes with the following major operations: a. Load all input data b. Calculate anisotropy movie from intensity movies of two polarization states c. Calculate anisotropy lifetime maps by applying exponential fit at each spatial pixel d. Numerical deconvolution by considering the finite temporal spread of the temporal PSF of the system e. Calculate molecular volume and diameter maps with known temperature and diffusivity f. Plot and save output data

1.2 "lifetimeFit.m" Numerical fitting to determine the anisotropy lifetime from the anisotropy decay curve

1.3 "lifetimeFit_res.m" Residual function used in lifetime fitting, called by "lifetimeFit.m"

  1. Input data files 2.1 "data_1PF_F_125Gfps_1.mat" Data of 1-photon fluorescence from fluorescein at 125-Gfps imaging speed a. cubeL & cubeR: 2D intensity movies of two orthogonal polarization states, reconstructed from CUP2AI raw images b. T: sequence of time stamps (ns) c. x & y: spatial coordinates (mm)

2.2 "cmap_deep2.mat" Colormap used to plot molecular volume map

2.3 "cmap_dense2.mat" Colormap used to plot molecular diameter map

2.4 "lifetimeLUT_data.mat" in "LifetimeLUT" sub-folder Calibrated temporal PSF and numerical deconvolution data for the CUP2AI system

  1. Output data files 3.1 "1_rTau_raw.fig" & "1_rTau_raw.png" Plot of anisotropy lifetime map

3.2 "2_rTau_deconv.fig" & "2_rTau_deconv.png" Plot of anisotropy lifetime map after numerical deconvolution

3.3 "3_molVol.fig" & "3_molVol.png" Plot of molecular volume map

3.4 "4_molDia.fig" & "4_molDia.png" Plot of molecular diameter map

3.5 "dataResult_1PF_F_125Gfps_1.mat" Data after processing a. cubeL & cubeR: 2D intensity movies of two orthogonal polarization states, reconstructed from CUP2AI raw images b. ItH & ItV: spatially averaged intensity evolution for both polarization states c. anisotropy: 3D anisotropy movie d. tauMap: 2D anisotropy lifetime map (ns) e. tauMap_deconv: 2D anisotropy lifetime map after numerical deconvolution (ns) f. tauAvg & tauAvg_deconv: spatially averaged anisotropy lifetime (ns) g. VMap & dMap: 2D molecular volume and diameter maps (Angstrom) h. VAvg & dAvg: spatially averaged molecular volume and diameter (Angstrom) i. Time: sequence of time stamps (ns) j. x & y: spatial coordinates (mm)

Peng Wang

Open Capsule

published in Nature Communications

Bioinformatics\ \ 22 | Oct | 2024\ \ Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers\ \ Scripts to reproduce analysis in the paper "Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers"\ \ Ida Larsson & Felix Held Open Capsule

published in Nature Communications

Biology\ \ 18 | Oct | 2024\ \ Initiation of Lumen Formation from Junctions via Differential Actomyosin Contractility Regulated by Dynamic Recruitment of Rasip1\ \ MATLAB code to quantify the ratio of the average intensity of a signal between the boundary regions to the central (apical) compartments\ \ Jianmin Yin Open Capsule

published in Nature Communications

Engineering\ \ 31 | Oct | 2024\ \ Integrating spoken instructions into flight trajectory prediction to optimize automation in air traffic control\ \ This repository provides source codes of the proposed spoken instruction aware flight trajectory prediction (SIA-FTP) framework.\ \ Dongyue Guo Open Capsule

published in Nature Communications

Physics\ \ 11 | Oct | 2024\ \ Unsupervised Learning of Individual Kohn-Sham States: Interpretable Representations and Consequences for Downstream Predictions of Many-Body Effects\ \ We provide all essential code for this project, covering the variational autoencoder (VAE) for wavefunctions and charge densities, superbands, and the final dense neural network (NN) for GW band structures. For transparency and reproducibility, we have also included our trained models for both the VAE and the final NN. The provided code outputs demonstrate the key results of our work, reproducing the GW band structure of MoS2 (as shown in Figure 2(e)), the latent space manifold (Figure 3(a)), and the generated wavefunction (Figure 3(b)).\ \ Bowen Hou, Jinyuan Wu & Diana Y. Qiu Open Capsule

published in Nature Communications

Engineering\ \ 11 | Oct | 2024\ \ Analysis and plotting code for "Climate change and its influence on water systems increases the cost of electricity system decarbonization" manuscript

This capsule archives the code used to analyze and plot the outputs of the SWITCH electricity capacity expansion model under a number of climate scenarios. The outputs analyzed here are the result of SWITCH model runs that have been coupled with hydropower and load data from the Western U.S. Water Systems Model (WWSM) created within the WEAP software platform, and load data based on changes in heating and cooling demand from a prior paper. The modeling methods are documented in the manuscript:

J.K. Szinai, D.Yates, P.S.Pérez, M.Staadecker, D.Kammen, A.D.Jones, P.Hidalgo-Gonzalez. Climate change and its influence on water systems increases the cost of electricity system decarbonization. Preprint at https://doi.org/10.21203/rs.3.rs-3359999/v1 (2023).

Julia Szinai et al.

Open Capsule

published in Nature Communications

Medical Sciences\ \ 11 | Oct | 2024\ \ Personalised Antimicrobial Susceptibility Testing: Reproducible main analysis code on synthetic data

Antimicrobial susceptibility testing is a key weapon against antimicrobial resistance, but diagnostic microbiology laboratories rely on one-size-fits-all testing approaches that are often imprecise, inefficient, and inequitable. Here, we report a personalised approach based on clinical prediction modelling that adapts laboratory testing for urinary tract infection to maximise the number of appropriate treatment options available for each patient. We trained, tested, and assessed susceptibility prediction models for 12 antibiotics on real-world healthcare data using an individual-level simulation study design. When combined with decision thresholds that prioritised the use of World Health Organisation Access category antibiotics (antibiotics with the least propensity to induce antimicrobial resistance), the personalised approach delivered more susceptible results (results that encourage prescription of that antibiotic) per specimen for Access category antibiotics than a standard susceptibility testing panel, without compromising the provision of susceptible results overall. These results suggests that personalised antimicrobial susceptibility testing could help tackle antimicrobial resistance by safely providing more World Health Organisation Access category antibiotic treatment options to clinicians who are managing urinary tract infection.\ \ This repository houses reproducible code for the academic paper "Personalised antimicrobial susceptibility testing with clinical prediction modelling informs appropriate antibiotic use" on a small simulated dataset for the purpose of peer review. Instructions on the expected output are provided in the CodeOcean README file.

To reproduce the results of the main analysis in full, please visit https://github.com/amh312/PDAST and follow the instructions in the GitHub README file.

Alex Howard et al.

Open Capsule

published in Nature Communications

Biology\ \ 11 | Oct | 2024\ \ The impact of landscape structure on pesticide exposure to honey bees\ \ For peer review\ \ Yoshiko Sakamoto, Shumpei Hisamoto, Makihiko Ikegami & Koichi Goka Open Capsule

published in Nature Communications

Bioinformatics\ \ 9 | Oct | 2024\ \ A Molecular Video-derived Foundation Model Streamlines Scientific Drug Discovery\ \ VideoMol is a molecular video-based foundation model, pretrained on 120 million frames of 2 million unlabeled drug-like and bioactive molecules with 3D conformations. \ In this capsle, you can reproduce the results in the paper by clicking the button "Reproducible Run".\ \ Hongxin Xiang et al. Open Capsule

published in Nature Communications

Physics\ \ 7 | Oct | 2024\ \ Two-dimensional non-Abelian Thouless pump\ \ This capsule contains the codes for reproducing the simulation results of the 2D non-Abelian Thouless pump, as well as data for the coupling coefficient and gap distance between waveguides.\ \ Yi-Ke Sun et al. Open Capsule

published in Nature Communications

Chemistry\ \ 6 | Oct | 2024\ \ 3T Ab Initio Electrochemical Reactor\ \ Fast ab initio electrochemical reaction trajectory generator enabled by multi-scale energy minimization algorithm (Tiered Tensor Transform, or 3T)\ \ Jonathan Pradana Mailoa, Xin Li & Shengyu Zhang Open Capsule

published in Nature Communications

Chemistry\ \ 4 | Oct | 2024\ \ MolE: A foundation model for molecular graphs using disentangled attention\ \ Models that accurately predict properties based on chemical structure are valuable tools in the chemical sciences. However, for many properties, public and private training sets are typically small, making it difficult for models to generalize well outside of the training data. Recently, this lack of generalization has been mitigated by using self-supervised pretraining on large unlabeled datasets, followed by finetuning on smaller, labeled datasets. Inspired by these advances, we report MolE, a Transformer architecture adapted for molecular graphs together with a two-step pretraining strategy. The first step of pretraining is a self-supervised approach focused on learning chemical structures trained on ~842 million molecular graphs, and the second step is a massive multi-task approach to learn biological information. We show that finetuning models that were pretrained in this way perform better than the best published results on 10 of the 22 ADMET tasks included in the Therapeutic Data Commons leaderboard (c. September 2023).\ \ Oscar Méndez-Lucio, Christos A. Nicolau & Berton Earnshaw Open Capsule

published in Nature Communications

Medical Sciences\ \ 3 | Oct | 2024\ \ Dopamine Release Plateau and Outcome Signals in Dorsal Striatum Contrast with Classic Reinforcement Learning Formulations [Qlearning]\ \ Trial-averaged plots of RPE from simple Q-learning model.\ \ Daniel J. Gibson Open Capsule

published in Nature Communications

Medical Sciences\ \ 3 | Oct | 2024\ \ Dopamine Release Plateau and Outcome Signals in Dorsal Striatum Contrast with Classic Reinforcement Learning Formulations [lickPETH]\ \ Construct lick peri-event time histogram aligned on the trial start.\ \ Ming Jun Kim Open Capsule

published in Nature Communications

Medical Sciences\ \ 3 | Oct | 2024\ \ Dopamine Release Plateau and Outcome Signals in Dorsal Striatum Contrast with Classic Reinforcement Learning Formulations [PC1maps]\ \ Make maps of PC1 amplitude in coronal plane.\ \ Daniel J. Gibson Open Capsule

published in Nature Communications

Medical Sciences\ \ 3 | Oct | 2024\ \ Dopamine Release Plateau and Outcome Signals in Dorsal Striatum Contrast with Classic Reinforcement Learning Formulations [get_evtPhmAUC]\ \ Compute area under photometry curves for one session.\ \ Ming Jun Kim Open Capsule

published in Nature Communications

Medical Sciences\ \ 3 | Oct | 2024\ \ Dopamine Release Plateau and Outcome Signals in Dorsal Striatum Contrast with Classic Reinforcement Learning Formulations [cueTrace]\ \ Exract photometry waveform aligned on R or L cue onset.\ \ Ming Jun Kim Open Capsule

published in Nature Communications

Medical Sciences\ \ 3 | Oct | 2024\ \ Dopamine Release Plateau and Outcome Signals in Dorsal Striatum Contrast with Classic Reinforcement Learning Formulations [lickROCs]\ \ Compute area under ROC curve for one session.\ \ Ming Jun Kim Open Capsule

published in Nature Communications

Medical Sciences\ \ 3 | Oct | 2024\ \ Dopamine Release Plateau and Outcome Signals in Dorsal Striatum Contrast with Classic Reinforcement Learning Formulations [splickTrace]\ \ Extract photometry waveform aligned on spontaneous licks.\ \ Ming Jun Kim Open Capsule

published in Nature Communications

Medical Sciences\ \ 3 | Oct | 2024\ \ Dopamine Release Plateau and Outcome Signals in Dorsal Striatum Contrast with Classic Reinforcement Learning Formulations [pkTrace_GFP_ISO]\ \ Photometry peak analysis.\ \ Ming Jun Kim Open Capsule

published in Nature Communications

Mathematics\ \ 3 | Oct | 2024\ \ Generative Learning for Forecasting the Dynamics of Complex Systems\ \ Sampled code for G-LED\ \ Han Gao & Sebastian Kaltenbach Open Capsule

published in Nature Communications

Bioinformatics\ \ 3 | Oct | 2024\ \ The integrated molecular and histological analysis defines subtypes of esophageal squamous cell carcinoma (18-324977-4)\ \ A universal framework for the extracting features from digital H&E images using multiple CNN pretrained models. Extracting features from multiple CNNs models captures a wider range of functionally relevant features.\ \ The core of this tool is built in python3.8 with tensorflow backend and keras functional API, while the downstream analysis is implemented in R programming language.\ \ Chinedu Anthony Anene Open Capsule

published in Nature Communications

Chemistry\ \ 5 | Mar | 2025\ \ Code for In-Depth Insight into Structure-Reactivity/Regioselectivity of Lewis Acid Catalyzed Cascade 4πe-Cyclization/Dicycloexpansion Reaction\ \ A model for regioselectivity predicting of 4πe-cyclization/dicycloexpansion reaction developed by Professor Yong-Qiang Tu, which providing a foreseeing thought to design reaction routes or substrates leading to angular tricyclic skeletons.\ \ Ka Lu et al. Open Capsule

published in Nature Communications

Physics\ \ 27 | Sep | 2024\ \ Long-lived topological time-crystalline order on a quantum processor\ \ python code for simulation and plotting results.\ \ Liang Xiang et al. Open Capsule

published in Nature Communications

Computer Science\ \ 20 | Sep | 2024\ \ Deep-prior ODEs Augment Fluorescence Imaging with Chemical Sensors\ \ This code contains the method Deep spatiotemporal priors for Uncoupling Sensors Kinetics (DUSK). The run file estimates the spatiotemporal distribution of a chemical species of interest (CSI) in a simulated case and on one real data.\ \ Note: if the model is already optimized for the same configuration, the script does not re-run the optimization.\ \ Thanh-an Michel Pham et al. Open Capsule

published in Nature Communications

Physics\ \ 19 | Sep | 2024\ \ Spin-orbit entanglement driven by the Jahn-Teller effect\ \ Spin-orbit entanglement in 4d or 5d shells is invoked to explain some correlated phases in transition metal oxides, like spin-orbit Mott insulators, quantum spin liquids or excitonic magnetism. There is also an interest to realize such quantum phases in 3d compounds, though this is challenging due to their smaller spin-orbit coupling. Here we demonstrate that the Jahn-Teller effect in Mn3+ reduces the energy gap between electronic configurations of different spin multiplicity that, despite a weak spin-orbit coupling, lead to strong spin-orbit entanglement. Our results show a rare example of synergistic effects of Jahn-Teller and spin-orbit interactions and provide a way to entangle spin and orbital degrees of freedom in d-metal oxides, which allow further paths to explore quantum effects in Jahn-Teller systems.\ \ Alejandro S. Miñarro et al. Open Capsule

published in Nature Communications

Engineering\ \ 4 | Dec | 2024\ \ The code for the manuscript entitled: Monitoring Long-term Cardiac Activity with Contactless Radio Frequency Signals\ \ This capsule contains the core code of the method proposed in the manuscript.\ \ Bin-Bin Zhang et al. Open Capsule

published in Nature Communications

Biology\ \ 10 | Sep | 2024\ \ Cell type and regulatory analysis in amphioxus illuminates evolutionary origin of the vertebrate head\ \ !Work in progress!\ This repository contains scripts and input data used for analysis of single cell RNA-Seq data presented in Markos et al 2023. Data consist of four 10X datasets, each representing selected stage of Amphioxus (Branchiostoma floridae) embryonic development. Aim of the analyses is to annotate the data and investigate developmental trajectories (transitions) across the identified celltypes and stages (timepoints) according to the hypotheses presented in the paper.\ \ Anna Markos & Jan Kubovciak Open Capsule

published in Nature Communications

Earth Sciences\ \ 9 | Sep | 2024\ \ Anomalous scaling of branching tidal networks in global coastal wetlands and mudflats\ \ theoretical model and post-processing of image data used in the paper\ \ Fan Xu & Zeng Zhou Open Capsule

published in Nature Communications

Biology\ \ 21 | Apr | 2025\ \ A normative principle governing memory transfer in cerebellar motor learning\ \ This capsule contains data and codes to replicate the results of all the experiments carried out in this study. \ \ Abstract: The cerebellum, consisting of the cerebellar cortex and nuclei, plays a crucial role in motor learning and exhibits a phenomenon known as systems consolidation, where memory traces are transferred from the cortex to the nuclei. However, the underlying principles and mechanisms governing this memory transfer remain unclear. In this study, we propose a normative framework extending the bias-variance tradeoff that predicts task difficulty as a key factor regulating memory transfer. We model the cerebellum as a dual learning system composed of a complex cortical networks and simpler nuclear network, with a cost function that trades off bias, variance, and overhead costs. Computational simulations and in-vivo optogenetic experiments in mice demonstrate that easier tasks promote greater transfer to the simpler system during consolidation, while harder tasks favor retention in the complex system. Moreover, task difficulty correlates with the specificity of the learned response to untrained stimulus conditions. Our findings provide a unifying framework to explain previously disparate experimental observations and predict novel aspects of cerebellar learning and memory consolidation.\ \ Hyojin Bae, Jewoo Seo, Chang-Eop Kim & Sang Jeong Kim Open Capsule

published in Nature Communications

Medical Sciences\ \ 8 | Sep | 2024\ \ Direct evaluation of antiplatelet therapy in coronary artery disease by comprehensive image-based profiling of circulating platelets\ \ Code for image analysis in the paper entitled 'Direct evaluation of antiplatelet therapy in coronary artery disease by comprehensive image-based profiling of circulating platelets'\ \ Kazutoshi Hirose et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 6 | Sep | 2024\ \ An explainable end-to-end deep learning method for direct analysis of mass spectrometry data to reveal disease-specific metabolic profiles\ \ Code and Raw Data for An end-to-end deep learning method for mass spectrometry data analysis to reveal disease-specific metabolic profiles\ \ Yongjie Deng Open Capsule

Associated article published in Nature Communications

Earth Sciences\ \ 18 | Sep | 2024\ \ A machine learning paradigm for necessary observations to reduce uncertainties in aerosol climate forcing\ \ A machine learning algorithm to retrieve higher level of aerosol properties from lidar observations\ \ Jens Redemann & Lan Gao Open Capsule

published in Nature Communications

Physics\ \ 30 | Aug | 2024\ \ Intrinsic Dipole Hall effect in tMoTe2 moir\'{e}: magnetoelectricity and contact-free signature of topological transitions\ \ calculate Intrinsic dipole Hall effect in twisted bilayer MoTe2\ \ Feng-Ren Fan Open Capsule

published in Nature Communications

Bioinformatics\ \ 29 | Aug | 2024\ \ MBSeq: Single cell/nuclei DNA- and RNA-seq of LFS Medulloblastoma samples

This capsule implements an example analysis of scDNAseq data from 10x CNV kit for detecting chromothripsis in single-cell detected genomic sub clones, from the related manuscript.

A relatively simple sample (LFS Relapse Nuclei) is used to demonstrate the approach. Analysis for other samples associated with the manuscript can be replicated using the same environment, by downloading the corresponding code from the associated GitHub repository: https://github.com/PMBio/MB_scSeq/

All relevant input files can be downloaded from Zenodo: 10.5281/zenodo.13348419

Petr Smirnov

Open Capsule

Engineering\ \ 28 | Aug | 2024\ \ Behavioral biometric optical tactile sensor that instantaneously decouples dynamic touch signals in real time\ \ Machine learning code for luminescence profile analysis\ \ Changil Son et al. Open Capsule

published in Nature Communications

Biology\ \ 21 | Aug | 2024\ \ Codes for "Giant viruses are unexpectedly large reservoirs of antibiotic resistance genes"\ \ This capsule contains plotting codes for the manuscript "Giant viruses are unexpectedly large reservoirs of antibiotic resistance genes" that is currently under review in Nature Communications (NCOMMS-24-04578A).\ \ Xinzhu Yi et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 19 | Aug | 2024\ \ An end-to-end framework for the prediction of protein structure and fitness from single sequence\ \ SPIRED-Fitness: an end-to-end framework for the prediction of protein structure and fitness from single sequence\ \ Yinghui Chen, Yunxin Xu, Di Liu & Yaoguang Xing Open Capsule

published in Nature Communications

Earth Sciences\ \ 14 | Aug | 2024\ \ Calibrating cable voltages into the Florida Current volume transport

This set of routines converts the motion-induced voltages measured on a submarine cable between Florida and Grand Bahama Island into the Florida Current volume transport estimates via linear transfer coefficients. The main function is /code/cable_voltage2transport.m. The raw voltages are provided in file /data/voltage_raw.mat. The raw voltages are corrected for the secular change in the Earth's magnetic field (EMF). The yearly time series of the vertical component of the EMF in the Florida Straits is obtained from the NOAA NCEI Magnetic Field Calculator ( https://www.ngdc.noaa.gov/geomag/calculators/magcalc.shtml#igrfwmm) and provide in the file /data/MagneticField_27n795w.dat. The Florida Current volume transports estimated from ship sections at 27N are provided in the file /data/FC_section_transport.dat.

Denis L. Volkov, Ryan H. Smith & Rigoberto F. Garcia

Open Capsule

published in Nature Communications

Bioinformatics\ \ 24 | Feb | 2025\ \ VITAP: A High Precision Tool for DNA and RNA Viral Classification Based On Meta-omic Data\ \ A alignment/graph-based Viral Taxonomic Assignment Pipeline (VITAP) for meta-comic-derived DNA and RNA viral sequences.\ \ Kaiyang Zheng Open Capsule

published in Nature Communications

Engineering\ \ 14 | Aug | 2024\ \ 2-dimensional impact-damping electrostatic actuators with elastomer-enhanced auxetic structure\ \ The Buckled_Electro_Beam folder contains matlab code for simulating the deformation of the buckled electro-beam under electrostatic force and load force. The main script in Buckled_Electro_Beam folder is esforce.m. It calls shooting_v2.m, which iteratively finds the shape of buckled electro-beam, to calculate the electrostatic force and momentum along the beam.\ \ The Form_Finding folder contains matlab code for simulating the deformation of AELA in both longitudinal and lateral directions. The shape of AELA under different loads and voltages can be obtained by runing form_finding.m and loop_form_finding.m in Form_Finding folder.\ \ Xuechuan Wang Open Capsule

published in Nature Communications

Biology\ \ 10 | Jan | 2025\ \ Code for the manuscript entitled "Failure to replicate a superiority effect in crowding" by Ozkirli, Pascucci & Herzog, 2025.\ \ This capsule contains the analysis script as well as the data used in the study.\ \ Ayberk Ozkirli, David Pascucci & Michael H. Herzog Open Capsule

published in Nature Communications

Medical Sciences\ \ 14 | Aug | 2024\ \ Towards clinically relevant dose ratios for Cabamiquine and Pyronaridine combination using immediate ex-vivo/in-silico P. falciparum field isolate data\ \ Final NONMEM model describing the joint effects of cabamiquine and pyronaridine in vitro. R script to visualise simulation results.\ \ Sebastian Wicha Open Capsule

published in Nature Communications

Computer Science\ \ 12 | Aug | 2024\ \ Exhaustive local chemical space exploration using a transformer model\ \ This code allows to reproduce the results of the paper "Exhaustive local chemical space exploration using a transformer model"\ \ Alessandro Tibo Open Capsule

published in Nature Communications

Physics\ \ 8 | Aug | 2024\ \ Photonic probabilistic machine learning using quantum vacuum noise\ \ Code and data for paper "Photonic probabilistic machine learning using quantum vacuum noise"\ \ Seou Choi et al. Open Capsule

published in Nature Communications

Medical Sciences\ \ 8 | Aug | 2024\ \ Clinical-grade whole genome sequencing-based haplarithmisis enables all forms of preimplantation genetic testing\ \ This capsule is the code of data processing and visualization for whole genome sequencing - preimplantation genetic testing (WGS-PGT).\ \ Anouk Janssen et al. Open Capsule

published in Nature Communications

Biology\ \ 7 | Aug | 2024\ \ From resonance to chaos: modulating spatiotemporal patterns through a synthetic optogenetic oscillator\ \ Oscillations are a recurrent phenomenon in biological systems across scales, including circadian clocks, metabolic oscillations and embryonic genetic oscillators. Despite their fundamental significance in biology, deciphering core principles of biological oscillators is very challenging due to the multiscale complexity of genetic networks and the difficulty in perturbing organisms in vivo. In this study, we tackle this challenge by re-designing the well-characterised synthetic oscillator, known as “repressilator”, in Escherichia coli and controlling it using optogenetics, thus introducing the “optoscillator”. When we apply periodic light pulses, the optoscillator behaves as a forced oscillator. Bacterial colonies harboring synthetic oscillators manifest oscillations as spatial ring patterns. Leveraging this feature, we systematically investigate the number, intensity and sharpness of the rings under different regimes of light exposure. By integrating experimental approaches with mathematical modeling, we show that this simple oscillatory circuit can generate complex dynamics that, depending on the external periodic forcing, are transformed into distinct spatial patterns. We report the observation of synchronisation, resonance, undertone and period doubling. Furthermore, we present evidence supporting the existence of a chaotic regime. This work highlights the intricate spatiotemporal patterns accessible by synthetic oscillators and underscores the potential of our approach in understanding the underlying principles governing biological oscillations.\ \ Park, Jung Hun, Holló, Gábor & Schaerli, Yolanda Open Capsule

published in Nature Communications

Biology\ \ 15 | Jul | 2025\ \ Episodic Transport of Protein Aggregates Achieves a Positive Size Selectivity in Aggresome Formation - Trajectory Segmentation

The code is for the segmentation of trajectories of cargoes transported by the dynein motor.\ Segmentation was performed using a MATLAB package “slmengine” (D'Errico, J., SLM - Shape Language Modeling ( https://www.mathworks.com/matlabcentral/fileexchange/24443-slm-shape-language-modeling). MATLAB Central File Exchange. Retrieved May 19, 2024) with a fixed root mean squared error (RMSE) or a fixed number of segments. For low-resolution tracking experiments, we used a fixed RMSE = 0.025 and set the maximal segment number as 10. For high-resolution experiments, we first used a fixed RMSE = 0.01 and set the maximal segment number as 20 to process the entire trajectory, and then extracted the transport segments determined as described below to perform a second round of segmentation using a fixed segment number, calculated as the transport segment length in seconds divided by 0.5. All parameters mentioned above were chosen based on visual examination. For each trajectory, the velocity of each segment was determined as the slope after performing linear regression on the distance over time. Segments with the smallest absolute values of velocity were selected, which were most likely to be the "Pause" state. The number of segments selected as pauses was less than 1/3 of the total segment number. Selected pauses were then used to calculate the mean square displacement (MSD) over time and fitted by a linear function. The diffusion constant was calculated as half of the slope. The mean value of the diffusion constant calculated from all selected segments was used as the diffusion constant D for the trajectory. A hypothesis test for all other segments not selected as pauses was then performed, given the null hypothesis that “the displacement given the segment length t should follow a Gaussian distribution with the mean equal to 0, and the standard deviation equal to the square root of 2Dt.” The segment was designated as "Transport engaged (+)” for low-resolution experiments and “Transport (+)” for high-resolution experiments if the displacement fell to the right tail of the Gaussian distribution; and "Transport engaged (-)” or “Transport (-)” for the left tail. For the low-resolution experiments, the cutoff bounds on both tails were 0.025, achieving a goodness-of-fit = 0.072 (normalized root mean square error (NRMSE), calculated as RMSE divided by the range of the variable). For high-resolution experiments, the cutoff bounds are 0.05 on both tails for the first round of segmentation and 0.005 and 0.1 on the left and right tails respectively for the second round of segmentation, achieving a goodness-of-fit = 0.0217 (NRMSE). These parameters were chosen to allow the segmentation results most consistent with visual examination. Lastly, any adjacent segments with the same designations were connected as a single segment.

Ying Lu & Rui Fang

Open Capsule

published in Nature Communications

Physics\ \ 5 | Aug | 2024\ \ Lightning-induced relativistic electron precipitation from the inner radiation belt\ \ Complete driver script to find bouncing packet microbursts in the inner radiation belt (L<3). Typically, the user will be prompted to specify the dates they would like to see. This script will then print out and plot all of the microbursts found in the specified time period. In this example, since user inputs are not allowed, it is configured to run for just 1 day on which there are 2 microbursts. To reproduce the code as it was used in research, you can run it from January 1, 1997 to December 31st, 2005. For obvious reasons, this code will not do that unless you tell it to.\ \ Max Feinland Open Capsule

published in Nature Communications

Computer Science\ \ 31 | Jul | 2024\ \ An Explainable Neural Network for Visual Recognition using Exemplar-based and Logic-induced Reasoning\ \ Code for reproducing the results of our paper "An Explainable Neural Network for Visual Recognition using Exemplar-based and Logic-induced Reasoning"\ \ Liulei Li Open Capsule

[Medical Sciences\ \ 31 | Jul | 2024\ \ Modelling the effectiveness of an isolation strategy for managing mpox outbreaks with variable infectiousness profiles\ \ This code simulates and evaluates the effectiveness of various isolation rules for mpox patients: symptom-based, fixed-duration, and testing-based rules. Specifically, it calculates numerical values of the following metrics for ending isolation:\ \

  1. Risk of prematurely ending isolation (%)\
  2. Infectious period after ending isolation (days)\
  3. Unnecessarily prolonged isolation period (days)\ \ Yong Dam Jeong](/content/explore/2b8ffd9a-2f46-4947-8f6a-d961cbc922bf?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) Open Capsule

published in Nature Communications

Bioinformatics\ \ 30 | Jul | 2024\ \ Impact of Population Screening for Lynch Syndrome: Insights from the All of Us Data\ \ The README provides a detailed workflow for analyzing genomic data and electronic health records (EHR) from the "All of Us" Research Program, specifically aimed at assessing the impact of Lynch Syndrome (LS) on cancer risk.\ \ Jiheum Park et al. Open Capsule

published in Nature Communications

Earth Sciences\ \ 29 | Jul | 2024\ \ Space-based observations of tropospheric ethane map emissions from fossil fuel extraction\ \ This capsule contains the processed data and code needed to produce the figures in the associated paper.\ \ Jared F. Brewer et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 2 | Oct | 2024\ \ Post-Translational Modification Prediction via Prompt-Based Fine-Tuning of a GPT-2 Model\ \ PTMGPT2 is a suite of models capable of generating tokens that signify modified amino acid residues, crucial for identifying PTM sites. At the core of this platform is PROTGPT2, an autoregressive transformer model, origi- nally trained on 50 million non-annotated sequences spanning the complete spectrum of the protein space. We have adapted PROTGPT2, utilizing it as a pre-trained model, and further fine-tuned it for the specific task of generating classification labels for a given protein sequence. Uniquely, PTMGPT2 employs a zero-shot text classification approach using a generative language model, negating the need for task-specific classification heads.\ \ Palistha Shrestha, Jeevan Kandel, Kil to chong & Hilal Tayara Open Capsule

published in Nature Communications

Earth Sciences\ \ 23 | Jul | 2024\ \ Decreased cloud cover partially offsets the cooling effects of surface albedo change due to deforestation (Luo et al.)\ \ Code for "Decreased cloud cover partially offsets the cooling effects of surface albedo change due to deforestation (Luo et al.)"\ \ Hao Luo Open Capsule

published in Nature Communications

Bioinformatics\ \ 22 | Jul | 2024\ \ Tissue characterization at an enhanced resolution across spatial omics platforms with a unified deep generative model\ \ Recent advances in spatial omics have expanded the spectrum of profiled molecular categories beyond transcriptomics. However, many of these technologies are constrained by limited spatial resolution, hindering our ability to deeply characterize intricate tissue architectures. Existing computational methods mainly focus on the resolution enhancement of transcriptomics data, lacking the extendibility to emerging spatial omics technologies. Here we introduce soScope, a unified generative framework designed to enhance data quality and spatial resolution for molecular profiles obtained from diverse spatial technologies. soScope aggregates multimodal tissue information from omics, spatial relations and images, and jointly infers omics profiles at enhanced resolutions with omics-specific modeling through distribution priors. With comprehensive evaluations on diverse spatial omics platforms, including Visium, spatial-CUT&Tag, and slide-DNA/RNA-seq, soScope improves performances in identifying biologically meaningful intestine and tumor architectures, revealing embryonic heart structure that cannot be resolved at the original resolution and correcting sample and technical biases arising from sequencing and sample processing. Furthermore, soScope is extended to spatial multiomics technology spatial-CITE-seq, leveraging cross-omics reference for simultaneous multiomics enhancement. soScope provides a versatile tool to improve the utilization of continually expanding spatial omics technologies and resources.\ \ Bohan Li et al. Open Capsule

published in Nature Communications

Earth Sciences\ \ 20 | Jul | 2024\ \ Past global warming constraints future Amazon climate-driven carbon source

The data have been preprocessed using bash scripts (mainly, CDO) and then plotted using python in jupyter-notebook. I provide the preprocessed input data. The provided code makes all figures from the manuscript. \ I located the archive with preprocessed netcdf data with sample bash script and this jupyter-notebook in Zenodo:\ Melnikova, I. (2024). Amazon emergent constraint. Nature Communications. https://doi.org/10.5281/zenodo.12195416

Irina Melnikova et al.

Open Capsule

published in Nature Communications

Bioinformatics\ \ 16 | Jul | 2024\ \ HAPI analysis reveals novel enhancer-hijacking mechanisms driving oncogene overexpression caused by complex structural alterations\ \ The purpose of this analysis is to take 3D genomic data, specifically enhancer-promoter interactions, and first identify genes whose promoters are highly interactive with enhancers (HAPI genes). Then, the regulatory network of HAPI genes are identified followed by the calculation of the percent enhancer contribution for normal, inter-chromosomal, and long-range intra enhancers to define enhancer hijacking.\ \ Katelyn L Mortenson et al. Open Capsule

Bioinformatics\ \ 16 | Jul | 2024\ \ High-throughput analysis of dendritic and axonal arbors reveals transcriptomic correlates of neuroanatomy\ \ This code contains code, data, and examples to illustrate the use of pipeline for automated reconstruction and analysis of neuronal morphology from light microscopy images. It includes a trained segmentation model, a notebook showing how to run segmentation and postprocessing such as axon/dendrite relabeling and merging segments, training and testing cell type classifiers, sparse feature selection and statistical tests. \ \n\nAbstract:\nNeuronal anatomy is central to the organization and function of brain cell types. However, anatomical variability within apparently homogeneous populations of cells can obscure such insights. Here, we report large-scale automation of neuronal morphology reconstruction and analysis on a dataset of 813 inhibitory neurons characterized using the Patch-seq method, which enables measurement of multiple properties from individual neurons, including local morphology and transcriptional signature. We demonstrate that these automated reconstructions can be used in the same manner as manual reconstructions to understand the relationship between some, but not all, cellular properties used to define cell types. We uncover gene expression correlates of laminar innervation on multiple transcriptomically defined neuronal subclasses and types. In particular, our results reveal correlates of the variability in Layer 1 (L1) axonal innervation in a transcriptomically defined subpopulation of Martinotti cells in the adult mouse neocortex.\ \ Olga Gliko et al. Open Capsule

published in Nature Communications

Biology\ \ 1 | Aug | 2025\ \ Anthropogenic climate change may lead to reduction in global diazotroph diversity\ \ The data and code associated with the paper "Anthropogenic climate change may lead to reduction in global diazotroph diversity".\ \ Peng Li et al. Open Capsule

published in Nature Communications

Physics\ \ 14 | Jul | 2024\ \ Learning noise-induced transitions by multi-scaling reservoir computing\ \ Noise-induced transitions are ubiquitous in nature and occur in diverse systems with multi-stable states. We develop a concise protocol of the training, by tuning a single hyperparameter for the time scale of the reservoir dynamics, and the trained model generates accurate statistics of the noise-induced transitions.\ \ Zequn, Zhaofan, Zengru & Ying Open Capsule

published in Nature Communications

Earth Sciences\ \ 13 | Jul | 2024\ \ Scalable interpolation of satellite altimetry data with probabilistic machine learning\ \ Python code for performing efficient interpolation of non-stationary altimetry data, using local Gaussian process models. This code contains an example of interpolating gridded radar freeboard data from the CryoSat-2, Sentinel-3A, and Sentinel-3D radar altimeters.\ \ William Gregory et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 10 | Jul | 2024\ \ Whole Brain Alignment of Spatial Transcriptomics between Humans and Mice with BrainAlign\ \ Source code for BrainAlign. The code illustration is in the 'README.md' file.\ \ Biao Zhang, Shuqin Zhang & Shihua Zhang Open Capsule

published in Nature Communications

Earth Sciences\ \ 2 | Sep | 2024\ \ Sketching the spatial disparities in heatwave trends by changing atmospheric teleconnections in the Northern Hemisphere\ \ The code for the article "Sketching the spatial disparities in heatwave trends by changing atmospheric teleconnections in the Northern Hemisphere", Including Python and NCL (NCAR Command Language) codes.\ \ Fenying Cai et al. Open Capsule

published in Nature Communications

Earth Sciences\ \ 8 | Jul | 2024\ \ Deep learning for detecting and characterizing oil and gas well pads in satellite imagery\ \ Replication of results for "Deep learning for detecting and characterizing oil and gas well pads in satellite imagery"\ \ Neel Ramachandran et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 2 | Jul | 2024\ \ Tissue characterization at an enhanced resolution across spatial omics platforms with a unified deep generative model\ \ Recent advances in spatial omics have expanded the spectrum of profiled molecular categories beyond transcriptomics. However, many of these technologies are constrained by limited spatial resolution, hindering our ability to deeply characterize intricate tissue architectures. Existing computational methods mainly focus on the resolution enhancement of transcriptomics data, lacking the extendibility across different omics. Here we introduce soScope, a unified generative framework designed to enhance data quality and spatial resolution for molecular profiles obtained from diverse spatial technologies. soScope aggregates multimodal tissue information from omics, spatial relations and images, and jointly infers omics profiles at enhanced resolutions with omics-specific modeling through distribution priors.\ \ Bohan Li et al. Open Capsule

published in Nature Communications

Medical Sciences\ \ 3 | Jul | 2024\ \ Focal seizures induce spatiotemporally organized spiking activity in the human cortex

Herein lies the code for reproducing the analyses in Diamond, et al. \ Focal seizures induce spatiotemporally organized spiking activity in the human cortex. \ Copyright (C) 2024 Joshua Diamond\ \ This program is free software: you can redistribute it and/or modify\ it under the terms of the GNU General Public License as published by\ the Free Software Foundation, either version 3 of the License, or\ (at your option) any later version.\ \ This program is distributed in the hope that it will be useful,\ but WITHOUT ANY WARRANTY; without even the implied warranty of\ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\ GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

Joshua Diamond

Open Capsule

published in Nature Communications

Physics\ \ 26 | Jun | 2024\ \ A Joint Diffusion/Collision Model for Crystal Growth in Pure Liquid Metals\ \ This Capsule is used to predict the solid and liquid atoms in the liquid/solid system from a snapshot of MD simulations at equilibrium or during solidification, with machine learning. The neural network (NN) classifiers were employed in the machine learning. Before running this Capsule, the JOBLIB files (clf.joblib and scaler.joblib) need to be copied from FOLDER result of the training Capsule to FOLDER data/output/training of this Capsule.\ \ Hua Men Open Capsule

published in Nature Communications

Engineering\ \ 24 | Jun | 2024\ \ Estimation of Joint Torque in Dynamic Activities Using Wearable A-Mode Ultrasound\ \ This is the Muscle Boundary Tracking Algorithm (MBTA) for manuscript submission titled "Estimation of Joint Torque in Dynamic Activities Using Wearable A-Mode Ultrasound".\ \ Yichu Jin Open Capsule

published in Nature Communications

[Bioinformatics\ \ 11 | Feb | 2025\ \ DNA Calorimetric Force Spectroscopy at Single Base Pair Resolution\ \ We report all the codes developed for the research project related to the paper entitled "DNA Calorimetric Force Spectroscopy at Single Base Pair Resolution" by P. Rissone, M. Rico-Pasto, S. B. Smith, and F. Ritort, arXiv preprint arXiv:2404.18785 (2024). Please refer to this paper (or more recent versions) if you use this code for your research work.\ \ / /\ /\ CONTENT ***************************/*\ /**************************/\ \

  • 'NNBPentropies': derive the temperature-dependent NNBP entropies\
  • 'NBPfree_energies': derive the temperature-dependent NNBP free energies\
  • 'row_data': exampling data. Some experimental trajectories at 7, 25, and 42 Celsius degrees. NOTE: The included data are not the actual MiniTweezers output. For simplicity, data have already been pre-analyzed to include the output needed for this analysis.\ \ Detailed information about the code usage can be found in the corresponding folder. An example of a complete analysis (inputs, outputs, and model(s) parameters) is included in each folder to guide through usage and test the programs.\ \ Paolo Rissone, Marc Rico-Pasto, Steven B. Smith & Felix Ritort](/content/explore/81fc3d0a-fbe1-494b-8ed0-bb7a408ac1dd?query=Nature%20Communications&page=6&filter=all&refine=journal/index.html) Open Capsule

published in Nature Communications

Biology\ \ 21 | Jun | 2024\ \ Genome and single-cell transcriptome reveal genetic signatures of swimming pattern and diapause strategy in jellyfish\ \ Supplementary Software 1. Scripts for extracting protein sequences of one-to-one orthologues from each orthogroup.\ Supplementary Software 2. Scripts for individual protein alignments.\ Supplementary Software 3. Scripts for gene loss analyses.\ Supplementary Software 4. Scripts for integrate the datasets corresponding to the medusa.\ \ Zhijun Dong et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 10 | Jun | 2024\ \ Characterize direct protein interactions with latent bioreactive, enrichable and mass spectrometry cleavable unnatural amino acids in live cells\ \ Proximity-based chemical cross-linkable unnatural amino acids (Uaas) have been widely used in the development of covalent drugs and identifications of protein interactors, such as proteins, DNA, RNA and carbohydrates. Site-specific mapping of Uaas induced cross-linking with mass spectrometry (MS) is helpful in characterizing binding sites and non-specific targets of covalent drugs and enhancing the specificity of protein partners identification. However, it is challenging to perform high-throughput identification of cross-linking products due to the complexities of protein samples and the data analysis processes. Therefore, enrichable Uaas will effectively reduce the complexities of protein samples and simplify data analysis. Although several enrichable Uaas have been reported, few cross-linked peptides were identified from mammalian cell samples with these Uaas. Here we developed an enrichable and multiple amino acids reactive Uaa, eFSY, and demonstrated that eFSY is MS cleavable when eFSY-Lys and eFSY-His are the cross-linking products. An identification software, AixUaa was developed to decipher eFSY mass cleavable data. We systematically identified direct interactomes of Thioredoxin 1 (Trx1) and Selenoprotein M (SELM) with eFSY and AixUaa.\ \ LiuDandan Open Capsule

published in Nature Communications

Physics\ \ 5 | Jun | 2024\ \ Electrically Driven Spin Resonance of 4f Electrons in a Single Atom on a Surface\ \ Codes developed for the analysis of electron spin resonance (ESR) results measured in a scanning tunneling miscroscope (STM).\ \ Stefano Reale et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 3 | Jun | 2024\ \ Bayesian Deep-Learning Structured Illumination Microscopy Enables Reliable Super-Resolution Imaging with Uncertainty Quantification\ \ Demo for our manuscript entitled " Bayesian Deep-Learning Structured Illumination Microscopy Enables Reliable Super-Resolution Imaging with Uncertainty Quantification".\ \ Liu Tao, Liu Jiahao & Li Dong Open Capsule

published in Nature Communications

Chemistry\ \ 23 | May | 2024\ \ A code for calculating vibronic coupling and spin-orbit coupling

See also https://github.com/KatsuyukiShizu/d77

Katsuyuki Shizu

Open Capsule

published in Nature Communications

Earth Sciences\ \ 22 | May | 2024\ \ Organic fertilization co-selects genetically linked antibiotic and metal(loid) resistance genes in global soil microbiome

This capsule contains the R code for classifying samples according to the Random Forest model and demo files in the manuscript "Organic fertilization co-selects genetically linked antibiotic and metal(loid) resistance genes in global soil microbiome". If you have any other inquiries or needs related to the article, please do not hesitate to contact us ( syzhang@des.ecnu.edu.cn or liuziteng1006@163.com).

Zi-Teng Liu et al.

Open Capsule

published in Nature Communications

Bioinformatics\ \ 21 | May | 2024\ \ Sopa: a technology-invariant pipeline for analyses of image-based spatial-omics

Sopa is a technology-invariant, memory-efficient pipeline with a unified visualizer for all image-based spatial omics. Built upon the universal SpatialData framework, Sopa optimizes tasks like segmentation, transcript/channel aggregation, annotation, and geometric/spatial analysis. Its output includes user-friendly web reports and visualizer files, as well as comprehensive data files for in-depth analysis. See the source code here: https://github.com/gustaveroussy/sopa

With this Code Ocean capsule, we reproduce the Sopa runs on our synthetic dataset. In particular, we run the Snakemake pipeline twice: once using Cellpose and once using Baysor. The results include the explorer files (open the '.xenium' files on the Xenium Explorer), the HTML web reports, and the '.zarr' directories for further analysis.

Quentin Blampey

Open Capsule

published in Nature Communications

Chemistry\ \ 15 | May | 2024\ \ ChatMOF: An Artificial Intelligence System for Predicting and Generating Metal-Organic Frameworks using Large Language Models\ \ ChatMOF is an autonomous Artificial Intelligence (AI) system that is built to predict and generate of metal-organic frameworks (MOFs). By leveraging a large-scale language model (GPT-4 and GPT-3.5-turbo), ChatMOF extracts key details from textual inputs and delivers appropriate responses, thus eliminating the necessity for rigid structured queries. The system is comprised of three core components (i.e. an agent, a toolkit, and an evaluator) and it forms a robust pipeline that manages a variety of tasks, including data retrieval, property prediction, and structure generation. The study further explores the merits and constraints of using large language models (LLMs) AI system in material sciences using and showcases its transformative potential for future advancements.\ \ Yeonghun Kang Open Capsule

published in Nature Communications

Mathematics\ \ 15 | May | 2024\ \ Reply to: False Conflict and False Confirmation: Crucial Components of AI Accuracy in Medical Decision Making

Investigation of different Error types when human and AI interact and do joint diagnosis in skin cancer prevention.\ This code is based on the public available results from https://figshare.com/s/c7feb070d066a4ccce19 Prior to run this code, you need to download the data and insert the storing path in the script.

Christoph Wies

Open Capsule

published in Nature Communications

Bioinformatics\ \ 14 | May | 2024\ \ Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat\ \ Error correction is the canonical first step in long-read sequencing data analysis. Nanopore R10 reads have error rates below 2%. we introduce DeChat, a novel approach specifically designed for Nanopore R10 reads.DeChat enables repeat- and haplotype-aware error correction, leveraging the strengths of both de Bruijn graphs and variant-aware multiple sequence alignment to create a synergistic approach. This approach avoids read overcorrection, ensuring that variants in repeats and haplotypes are preserved while sequencing errors are accurately corrected.\ \ Yichen Li et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 7 | Aug | 2024\ \ Machine learning predictor PSPire screens for phase-separating proteins lacking intrinsically disordered regions\ \ PSPire is a machine learning model based on integrated residue-level and structure-level features to predict phase-separating proteins. It is written in Python3 and is available as a command line tool.\ \ Shuang Hou Open Capsule

published in Nature Communications

Physics\ \ 10 | May | 2024\ \ Enhanced quantum state transfer: Circumventing quantum chaotic behavior\ \ Experimental results and simulation codes for the paper "Enhanced quantum state transfer: Circumventing quantum chaotic behavior".\ \ Liang Xiang et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 20 | Apr | 2024\ \ CatPred: A comprehensive framework for deep learning in vitro enzyme kinetic parameters kcat, Km and Ki

Veda Sheersh Boorla & Costas D. Maranas

Open Capsule

published in Nature Communications

Physics\ \ 19 | Apr | 2024\ \ Revealing the spatial nature of sublattice symmetry\ \ The code is for the calculation of the energy spectrum and Berry phase of the several models.\ \ Rong Xiao Open Capsule

published in Nature Communications

Social Sciences\ \ 30 | May | 2024\ \ Unravelling the spatial directionality of urban mobility\ \ As it is central to sustainable urban development, urban mobility has primarily been scrutinised for its scaling and hierarchical properties. However, traditional analyses frequently overlook mobility directionality, a critical factor in city centre congestion and suburban development. Here, we apply vector computation to unravel the directional characteristics of urban mobility, introducing a two-dimensional anisotropy-centripetality metric. Utilising travel data from 90 million mobile users across 60 Chinese cities, we effectively quantify mobility patterns through this metric, distinguishing between strong monocentric, weak monocentric, and polycentric patterns. Our findings highlight a stark contrast: residents in monocentric cities face increasing commuting distances as cities expand, in contrast to the consistent commuting patterns observed in polycentric cities. Notably, mobility anisotropy intensifies in the outskirts of monocentric cities, whereas it remains uniform in polycentric settings. Additionally, centripetality wanes as one moves from the urban core, with a steeper decline observed in polycentric cities. Finally, we reveal that employment attraction strength and commuting distance scaling are key to explaining these divergent urban mobility patterns. These insights are pivotal for shaping effective policies aimed at alleviating congestion and guiding suburban housing development.\ \ Pengjun Zhao et al. Open Capsule

Medical Sciences\ \ 18 | Apr | 2024\ \ Deep learning-based intraoperative differentiation of primary CNS lymphoma and glioma: a discovery, multicenter validation, and proof-of concept study\ \ Code for the paper above.\ \ Xinke Zhang et al. Open Capsule

published in Nature Communications

Biology\ \ 15 | Apr | 2024\ \ Species interactions and metabolic couplings between soil aerobic methanotrophs and denitrifiers in flooded croplands\ \ Correlations between MOA and DR, and between gene abundances associated with methane oxidation (pmoA) and denitrification (nirK and nirS)\ \ Kang-Hua Chen Open Capsule

published in Nature Communications

Earth Sciences\ \ 12 | Apr | 2024\ \ Genetic-linkage proof reveals organic fertilization co-selects for antibiotic and metal resistance genes in the global agricultural soil microbiome

This capsule contains Python code for machine learning and a demo file in the manuscript "Genetic-linkage proof reveals organic fertilization co-selects for antibiotic and metal resistance genes in the global agricultural soil microbiome". If you have any other inquiries or needs related to the article, please do not hesitate to contact us ( syzhang@des.ecnu.edu.cn or liuziteng1006@163.com).

Zi-Teng Liu et al.

Open Capsule

published in Nature Communications

Bioinformatics\ \ 10 | Apr | 2024\ \ De Novo Atomic Protein Structure Modeling for Cryo-EM Density Maps Using 3D Transformer and Hidden Markov Model\ \ Cryo2Struct is a fully automated, ab initio modeling method that generates 3D (three dimensional) atomic structures from cryo-EM density maps without requiring predicted or homologous protein structures as input. Cryo2Struct takes a 3D cryo-EM density map and the corresponding amino acid sequence of a protein as input, automatically producing a multi-chain 3D atomic protein structure as output.\ \ Nabin Giri & Jianlin Cheng Open Capsule

published in Nature Communications

Earth Sciences\ \ 10 | Apr | 2024\ \ Automatic Detection of Methane Emissions in Multispectral Satellite Imagery Using a Vision Transformer\ \ Here we show that deep learning can be leveraged to overcome the trade-off in terms of spectral resolution that comes with multi-spectral satellite data, resulting in a methane detection tool with global coverage and high temporal and spatial resolution. We compare our detections with airborne methane measurement campaigns. Our results suggest that our method is able to detect methane point sources in Sentinel-2 multi-spectral satellite data down to plumes of 0.01 km2, corresponding to 200 to 300 kg CH4/h sources (with variations depending on wind conditions). The assessment of our model on synthetic data as well as on real methane plumes results in an order of magnitude improvement over the state-of-the-art, providing a significant step towards the automated, high resolution detection of methane emissions at a global scale, every few days.\ \ Bertrand Rouet-Leduc Open Capsule

published in Nature Communications

Computer Science\ \ 9 | Apr | 2024\ \ Enhancing Fairness in AI-Enabled Medical Systems: The Attribute Neutral Framework\ \ The Attribute Neutralizer presents an innovative framework that we have devised to enhance the fairness of medical AI systems. This approach facilitates the transformation of original X-ray images into attribute-neutral X-ray images. In comparison to unaltered X-ray images, training medical AI systems on attribute-neutral X-ray images can yield enhanced fairness.\ In practice, the Attribute Neutralizer achieves attribute neutrality in X-ray images by modifying the image's attributes. The parameter α within the Attribute Neutralizer governs the extent of attribute alteration in an X-ray image, ranging from 0 to 1. When α equals 0, the Attribute Neutralizer refrains from altering the attribute. In contrast, an α value of 1 results in the attribute being edited to its opposite counterpart in the original image, such as changing from female to male or from young to old. Attribute-neutral X-ray images are created at α=0.5.\ \ Lianting Hu et al. Open Capsule

published in Nature Communications

Physics\ \ 3 | May | 2024\ \ code for High spin axion insulator\ \ This is the code for High spin axion insulator\ \ Shuai Li et al. Open Capsule

published in Nature Communications

Biology\ \ 10 | Jul | 2024\ \ Prefrontal neuronal dynamics in the absence of task execution\ \ Code for the manuscript "Prefrontal neuronal dynamics in the absence of task execution" submitted to Nature Communication\ \ Wenhao Dang & Shusen Pu Open Capsule

published in Nature Communications

Earth Sciences\ \ 8 | Aug | 2024\ \ Fracture toughness of mixed-mode anticracks in highly porous materials\ \ Supplementary data and data processing for the manuscript "Fracture toughness of mixed-mode anticracks in highly porous materials" (Adam et al.) submitted to Nature Communications with manuscript ID NCOMMS-24-10218\ \ Valentin Adam et al. Open Capsule

published in Nature Communications

Physics\ \ 29 | Mar | 2024\ \ code for high spin axion insulator\ \ code for the results in the work entitled "high spin axion insulator"\ \ Shuai Li et al. Open Capsule

published in Nature Communications

Computer Science\ \ 27 | Mar | 2024\ \ Network Properties Determine Neural Network Performance\ \ We propose a method to predict the performance of neural network by computing the graph property of the corresponding graph.\ \ Chunheng Jiang et al. Open Capsule

published in Nature Communications

Biology\ \ 17 | Mar | 2024\ \ Help must be compensated: synergistic pectin deconstruction premises mutualistic interactions between honeybee gut bacteria\ \ Consumer-resource-model-of-mutualistic-interaction\ \ Wenlong Zuo Open Capsule

published in Nature Communications

Biology\ \ 7 | Aug | 2024\ \ Hyper-diverse antigenic variation and resilience to transmission-reducing intervention in falciparum malaria\ \ Agent-based model code and analysis scripts for NCOMMS-24-09785\ \ Qi Zhan Open Capsule

published in Nature Communications

Computer Science\ \ 4 | Mar | 2024\ \ MILTS (Teach-Student collaborated Multiple Instance Learning)\ \ This is the implementation of paper "Teacher-student collaborated multiple instance learning for pan-cancer PDL1 expression prediction from histopathology slides". MILTS utilizes an iterative, self-refining process to assign labels automatically supporting tile feature extractor training, and combines the statistical summary of tile-level predictions with tokens fused by the transformer to obtain the slide-level embedding for the molecular alternation prediction.\ \ Darui Jin et al. Open Capsule

Biology\ \ 1 | Mar | 2024\ \ Phylogenomic Profiles of Whole-Genome Duplications in Poaceae and Landscape of Differential Duplicate Retention and Losses among Major Poaceae Lineages

Here we provide a test version on the cloud workstation of our custom scripts released on GitHub ( https://github.com/TaikuiZhang/GrassPhylogenomics) for estimation of retention/loss patterns of the rho-derived duplicates. See additional information in the GitHub.

Taikui Zhang

Open Capsule

published in Nature Communications

Biology\ \ 17 | Jun | 2024\ \ Modelling variability and heterogeneity of EMT scenarios highlights nuclear positioning and protrusions as main drivers of extrusion

Julia implementation for a computational model for epithelial-to-mesenchymal transition-like events in a pseudostratified epithelium.

See also https://semtor.github.io/

Steffen Plunder et al.

Open Capsule

published in Nature Communications

Physics\ \ 1 | Mar | 2024\ \ Multilevel design and construction in nanomembrane rolling for three-dimensional angle-sensitive photodetection\ \ Python script for transformation from coordinates in sacrificial layer etching FEM model to elastic mechanical FEM model.\ \ Ziyu Zhang Open Capsule

published in Nature Communications

Chemistry\ \ 23 | Feb | 2024\ \ Supplementary code for ：“ Direct observation of photoinduced sequential spin transition in a halogen-bonded hybrid system by complementary ultrafast optical and electron probes”\ \ Additional information and codes to explain how we build the parameter grid space to search the parameters and structures with the highest Pearson correlation coefficient,\ \ Yifeng Jiang Open Capsule

published in Nature Communications

Physics\ \ 22 | Feb | 2024\ \ Identifying regions of importance in wall-bounded turbulence through explainable deep learning\ \ Despite its great scientific and technological importance, wall-bounded turbulence is an unresolved problem in classical physics that requires new perspectives to be tackled. One of the key strategies has been to study interactions among the energy-containing coherent structures in the flow. Such interactions are explored in this study for the first time using an explainable deep-learning method. The instantaneous velocity field obtained from a turbulent channel flow simulation is used to predict the velocity field in time through a U-net architecture. Based on the predicted flow, we assess the importance of each structure for this prediction using the game-theoretic algorithm of SHapley Additive exPlanations (SHAP). This work provides results in agreement with previous observations in the literature and extends them by revealing that the most important structures in the flow are not necessarily the ones with the highest contribution to the Reynolds shear stress. We also apply the method to an experimental database, where we can identify completely new structures based on their importance score. This framework has the potential to shed light on numerous fundamental phenomena of wall-bounded turbulence, including novel strategies for flow control.\ \ A. Cremades et al. Open Capsule

published in Nature Communications

Physics\ \ 29 | Apr | 2024\ \ Enhanced quantum state transfer: Circumventing quantum chaotic behavior (Monte Carlo Annealing)\ \ The Monte Carlo annealing method used to optimize the 2-D quantum state transfer.\ \ Liang Xiang, Zitian Zhu, Qiujiang Guo & Rubem Mondaini Open Capsule

published in Nature Communications

Earth Sciences\ \ 21 | Feb | 2025\ \ Origin and Evolution of the North Atlantic Oscillation\ \ data and code used in the manuscript. The code is named to correspond with the figures.\ \ Zhihong Song et al. Open Capsule

published in Nature Communications

Medical Sciences\ \ 16 | Feb | 2024\ \ Code accompanying the paper "A machine learning model to predict COVID-19 in-hospital mortality"\ \ Tools for predicting COVID-19 outcomes enable personalized healthcare, potentially easing the disease burden. This collaborative study by 15 institutions across Europe and Canada aimed to develop a machine learning model for forecasting in-hospital mortality post-SARS-CoV-2 infection. Blood samples and clinical data from 1286 COVID-19 patients across four cohorts were analyzed, with 2906 long non-coding RNAs profiled using targeted sequencing. From a discovery cohort of 804 patients, age and the long non-coding RNA LEF1-AS1 were identified as predictive features, yielding an AUC of 0.83 and a balanced accuracy of 0.78 with a feedforward neural network classifier. Validation in an independent cohort of 482 patients showed consistent performance. Cox regression analysis indicated that higher levels of LEF1-AS1 correlated with reduced mortality risk (age-adjusted hazard ratio 0.54, 95% CI 0.40-0.74). Quantitative PCR validated LEF1-AS1's adaptability to hospital settings. Here, we demonstrate a promising predictive model for enhancing COVID-19 patient management.\ \ Yvan Devaux et al. Open Capsule

published in Nature Communications

Computer Science\ \ 3 | Apr | 2024\ \ t-SMILES: A Fragment-based Molecular Representation Framework for De Novo Ligand Design\ \ Effective representation of molecules is a crucial factor affecting the performance of artificial intelligence models. This study introduces a flexible, fragment-based, multiscale molecular representation framework called t-SMILES (tree-based SMILES) with three code algorithms: TSSA, TSDY and TSID. It describes molecules using SMILES-type strings obtained by performing a breadth-first search on a full binary tree formed from a fragmented molecular graph. Systematic evaluations using JTVAE, BRICS, MMPA, and Scaffold show the feasibility of constructing a multi-code molecular description system, where various descriptions complement each other, enhancing the overall performance. In addition, it can avoid overfitting and achieve higher novelty scores while maintaining reasonable similarity on labeled low-resource datasets, regardless of whether the model is original, data-augmented, or pre-trained then fine-tuned. Furthermore, it significantly outperforms classical SMILES, DeepSMILES, SELFIES and baseline models in goal-directed tasks. And it surpasses state-of-the-art fragment, graph and SMILES based approaches on ChEMBL, Zinc, and QM9.\ \ Juanni Wu Open Capsule

published in Nature Communications

Physics\ \ 13 | Feb | 2024\ \ Single-pixel p-graded-n junction spectrometers\ \ Ultra-compact spectrometers are becoming increasingly popular for their promising applications in biomedical analysis, environmental monitoring, and food safety. In this work, we report a novel single-pixel-photodetector spectrometer with a spectral range from 480 nm to 820 nm, based on the AlGaAs/GaAs p-graded-n junction with a voltage-tunable optical response. To reconstruct the optical spectrum, we propose a tailored method called Neural Spectral Fields (NSF) that leverages the unique wavelength and bias-dependent responsivity matrix. Our spectrometer achieves a high spectral wavelength accuracy of up to 0.30 nm and a spectral resolution of up to 10 nm. Additionally, we demonstrate the high spectral imaging performance of the device. The compatibility of our demonstration with the standard III-V process greatly accelerates the commercialization of miniaturized spectrometers.\ \ Jingyi Wang et al. Open Capsule

published in Nature Communications

Engineering\ \ 9 | Feb | 2024\ \ Integrated LCA and LCCA of building renovation solutions and robust optimization\ \ The current code describes the analysis of Life cycle cost (LCC) and Life cycle assessment (LCA) for building renovation process as well as robust optimization considering the future uncertainties. The analyses include the following stages - A1-A3 (production), B4 (replacement), B6 (operational energy use) and C1-C4 (end of life). In case of LCC, the repair is also taken into account. The data is taken from the .txt file where the input parameters are listed as well as the excel file (Components_catalog_data.xlsx) where the possible renovation measures for the envelope are listed.\ \ Alina Galimshina et al. Open Capsule

published in Nature Communications

Medical Sciences\ \ 8 | Feb | 2024\ \ Metabolomic machine learning predictor for diagnosis and prognosis of gastric cancer\ \ This project consist of Random forest model for GC diagnosis and the Survival outcomes prediction of GC patients using Random survival forest (RSF) method.\ \ Yangzi Chen et al. Open Capsule

published in Nature Communications

Earth Sciences\ \ 7 | Feb | 2024\ \ Sinking the unsinkable: Ballast effects of calcite on low-density plastic debris in open oceans\ \ The vertical settling of plastic debris in oceans is poorly understood. Most discharged plastic debris are lighter than seawater, but so far they are largely absent from sea surfaces. The present model considers an overlooked calcite precipitation process accompanied with biofouling, as well as new motion equations for irregular plastic debris. The model successfully reproduces the vertical distribution patterns of plastic debris observed in multiple oceanic sites. It further reveals that plastic debris can distribute at all depths after years of drifting with two accumulation zones at 60400 m of the water column and seafloor. The combination of initial density, size, and shape exhibits strong non-linear effects on the settling trajectories of plastic debris. The present model highlights the importance of calcite-mediated sinking of plastic debris in open oceans.\ \ Xiang-Fei Sun et al. Open Capsule

Biology\ \ 5 | Feb | 2024\ \ Code for 'Design of peptide inhibitors targeting β-catenin using generative deep learning and molecular dynamics simulations'\ \ The capsule contains the data and the code used for the paper 'Design of peptide inhibitors targeting β-catenin using generative deep learning and molecular dynamics simulations'.\ \ Sijie Chen et al. Open Capsule

Mathematics\ \ 12 | Mar | 2024\ \ Higher-order Granger reservoir computing: Simultaneously achieving structures inference and accurate prediction of complex dynamics\ \ Higher-order Granger reservoir computing: Simultaneously achieving structures inference and accurate prediction of complex dynamics\ \ Qunxi Zhu Open Capsule

published in Nature Communications

Biology\ \ 25 | Nov | 2024\ \ Heterochromatic gene silencing controls CD4 T cell susceptibility to regulatory T cell-mediated suppression - bulk analyses\ \ The integrity of the organism depends on close and dynamic interactions between conventional and regulatory (Treg) T cells. The extracellular signals and signaling events that regulate this crosstalk have been extensively characterized. However, how conventional T cells translate Treg-dependent immunosuppressive signals at the chromatin level remains largely unknown. In differentiating CD4+ T helper (Th) cells, we and others previously reported that transcriptional specificity is largely controlled by heterochromatin-dependent gene silencing. We therefore hypothesized that Treg-mediated T cell suppression could also involve the repressive mark H3K9me3 and the histone-binding factor heterochromatin protein 1 (HP1). Using a bone marrow allograft model, in which graft rejection is coordinated by adoptively-transferred naive CD4+ T cells and can be inhibited by Treg, we show that Treg-dependent suppressive signals indeed mobilize HP1a to repress Th-cell effector genes. Unexpectedly, our screen also revealed that T cells deficient for HP1g or the lysine methyltransferase SUV39H1 are better tolerized than their wild-type counterparts. Mechanistically, our transcriptional and epigenetic profiling identified HP1g as a negative regulator of a network of genes functionally associated with T-cell anergy and exhaustion, including those encoding the transcription factor TOX and the inhibitory receptors PD-1, TIM-3 and LAG-3. In response to T cell receptor engagement, the expression of these immune checkpoints is deregulated in HP1g-deficient cells, thus promoting their better inhibition by Treg. Therefore, we demonstrate that H3K9me3-dependent epigenetic pathways critically regulate Th cell susceptibility to Treg-mediated suppression, and we identify HP1a and HP1g as new epigenetic players whose expression may be manipulated to restore protective immune responses or correct immunopathology, respectively.\ \ Julie Noguerol et al. Open Capsule

published in Nature Communications

Earth Sciences\ \ 30 | Jan | 2024\ \ Late Paleozoic Oxygenation of Marine Environments Supported by Dolomite U-Pb Dating - script #1: Tera Wasserburg U-Pb dating\ \ This code determines the U-Pb ages and initial 207Pb/206Pb ratio using the Tera-Wasserburg Concordia scheme, and plots the data in Tera-Wasserburg Concordia plots (Ludwig, 1998).\ \ Michal Ben-Israel Open Capsule

published in Nature Communications

Physics\ \ 22 | Feb | 2024\ \ Complete quantum-inspired framework for computational fluid dynamics\ \ Supplementary code for the paper arXiv:2308.12972\ \ Raghavendra Dheeraj Peddinti, Egor Tiunov & Stefano Pisoni Open Capsule

Earth Sciences\ \ 29 | Jan | 2024\ \ Late Paleozoic Oxygenation of Marine Environments Supported by Dolomite U-Pb Dating - script #2: Calculation of initial 238U/206Pb\ \ Matlab script that calculate the ratio of 238U/206Pb in dolomite precursor carbonate minerals from measured U-Pb dates, 207Pb/206Pb initial values, and the depositional age of the strata.\ \ Uri Ryb Open Capsule

published in Nature Communications

Bioinformatics\ \ 22 | Apr | 2024\ \ HyLight: Strain aware assembly of low coverage metagenomes\ \ HyLight is a strain aware de novo assembly method based on the overlap-layout-consensus (OLC) paradigm that leverages the strengths of NGS and 3rd generation sequencing to rapidly and accurately assemble highly complex metagenomic sequencing data.\ \ Xiongbin Kang et al. Open Capsule

published in Nature Communications

Bioinformatics\ \ 16 | Jan | 2024\ \ Protein language model powers accurate and fast sequence search for remote homology\ \ Reproduce the main results in the paper\ \ Wei Liu Open Capsule

published in Nature Communications

Biology\ \ 4 | Dec | 2024\ \ Hidden route of protein damage through oxygen-confined photooxidation\ \ The codes were used for analyses in the following work.\ \ Title of paper: Hidden route of protein damage through oxygen-confined photooxidation\ \ Seoyoon Kim Open Capsule

Bioinformatics\ \ 3 | Jan | 2024\ \ PanPop : example using TGS dataset

An example of PART algorithm of PanPop software from Github ( https://github.com/starskyzheng/panpop). This example dataset was generated by PanPop pipeline using 84 TGS Arabidopsis thaliana dataset after fill-depth-information.

Zeyu Zheng

Open Capsule

published in Nature Communications

Bioinformatics\ \ 3 | Jan | 2024\ \ MAIVeSS: Streamlined selection of antigenically matched, high-yield viruses for seasonal influenza vaccine production\ \ Vaccines are the main pharmaceutical intervention used against the global public health threat posed by influenza viruses. Timely selection of optimal seed viruses with matched antigenicity between vaccine antigen and circulating viruses and with high yield underscore vaccine efficacy and supply, respectively. Current methods for selecting influenza seed vaccines are labor intensive and time-consuming. Here, we report the Machine-learning Assisted Influenza VaccinE Strain Selection framework, MAIVeSS, that enables streamlined selection of naturally circulating, antigenically matched, and high-yield influenza vaccine strains directly from clinical samples by using molecular signatures of antigenicity and yield to support optimal candidate vaccine virus selection. We applied our framework on publicly available sequences to select A(H1N1)pdm09 vaccine candidates and experimentally confirmed that these candidates have optimal antigenicity and growth in cells and eggs. Our framework can potentially reduce the optimal vaccine candidate selection time from months to days and thus facilitate timely supply of seasonal vaccines.\ \ Cheng Gao et al. Open Capsule

Physics\ \ 29 | Dec | 2023\ \ Chirality Hierarchical Transfer in Homochiral Polymer Crystallization Under High-pressure CO2\ \ Ordered phase transitions are commonly correlated to the phenomenon of symmetry breaking, while disordered phase transitions are characterized by symmetry restoration. Nevertheless, this study demonstrates that the correlation between these factors is not always applicable in chiral polymers subjected to high-pressure CO2. In the absence of racemization, homochiral Poly(lactide acid) exhibits the formation of two dendritic crystals with opposite spiral chirality, resembling vortex shapes, as well as achiral crystals that resemble snowflakes. The transition from homochirality to achirality signifies the chiral symmetry restoration during the ordering process. The primary elements responsible for the hierarchical transfer of chirality from molecule to macroscopic crystal of chiral polymer are surface crowding and frustrated structures. The entropy impact of CO2 can be utilized to programmatically regulate the morphological chirality and crystal structure of two-dimensional crystal assemblies composed of chiral polymer.\ \ Lei Zhang Open Capsule

published in Nature Communications

Physics\ \ 25 | Dec | 2023\ \ Self-supervised dynamic learning for long-term high-fidelity image transmission through unstabilized diffusive media\ \ Dynamic learning multi-memory neural network for image recovery through unstablized MMF\ \ Ziwei Li Open Capsule

published in Nature Communications

Physics\ \ 14 | Jan | 2024\ \ Supplementary code for "Chiral Active Particles are Sensitive Reporters to Environmental Geometry"\ \ This code examines the dynamics of CAPs moving in 2D lattices of disk obstacles through active Brownian dynamics simulations. It can reproduce simulation results presented in the article "Chiral Active Particles are Sensitive Reporters to Environmental Geometry."\ \ Chung Wing CHAN & Rui ZHANG Open Capsule

published in Nature Communications

Computer Science\ \ 15 | Nov | 2023\ \ Revealing Hidden Patterns in Deep Neural Network Feature Space Continuum via Manifold Learning\ \ Deep neural networks (DNNs) extract thousands to millions of task-specific features during model training for inference and decision-making. While visualizing these features is critical to comprehend the learning process and improving the performance of the DNNs, existing visualization techniques work only for classification tasks. For regressions, the feature points lie on a high dimensional (HD) continuum having an inherently complex shape, making a meaningful visualization of the features intractable. Given that the majority of deep learning applications are regression-oriented, a conceptual framework and computation method to reliably visualize the regression features are of great significance. Here, we introduce a manifold discovery and analysis (MDA) method for the task. To run the capsule, please click the "Reproducible Run" on the right panel. It normally takes around 30 minutes to finish all the five analysis tasks (superresolution, segmentation, survival prediction, gene expression prediction, and classification). After the computation is done, please click on the demo_MDA.html in the results folder. All the figures can be found in the html file.\ \ Md Tauhidul Islam et al. Open Capsule

Bioinformatics\ \ 25 | Oct | 2023\ \ Redeconve: deconvolution of spatial transcriptomics at single-cell resolution\ \ Redeconve is an R package designed for deconvoluting spatial transcriptomics on single-cell level. This capsule contains the main functions in our package, and the codes to analyze 6 datasets and draw all the pictures in our manuscript.\ \ Zixiang Zhou, Yunshan Zhong & Zemin Zhang Open Capsule

Bioinformatics\ \ 14 | Jul | 2023\ \ Genomap based unsupervised dimensionality reduction, visualization, clustering, cellular trajectory analysis, and multi-omic integration\ \ In our recent Nature Communications paper, we propose an entropy-based cartography strategy to contrive the high dimensional gene expression data into a configured image format, referred to as genomap, with explicit integration of the genomic interactions. This unique cartography casts the gene-gene interactions into the spatial configuration of genomaps and enables us to extract the deep genomic interaction features and discover underlying discriminative patterns of the data. We show that, for a wide variety of applications (cell clustering and recognition, gene signature extraction, single cell data integration, cellular trajectory analysis, dimensionality reduction, and visualization), the proposed approach drastically improves the accuracies of data analyses as compared to the state-of-the-art techniques.\ \ Md Tauhidul Islam Open Capsule

Associated article published in Nature Communications

Medical Sciences\ \ 20 | Jun | 2023\ \ Oncology Biomarker Discovery (OncoBird)\ \ Identify candidates for predictive biomarkers in oncology trials by leveraging mutually exclusive somatic mutations in tumour subtypes for subgroup analysis.\ \ Ohnmacht AJ et al. Open Capsule

Bioinformatics\ \ 19 | Jul | 2023\ \ Obesity-associated changes in molecular biology of primary breast cancer\ \ Obesity is associated with an increased risk of developing breast cancer (BC) and worse prognosis in BC patients, yet its impact on BC biology remains understudied in humans. This study investigates how the biology of untreated primary BC differs according to patients’ body mass index (BMI) using data from >2,000 patients. We identify several genomic alterations that are differentially prevalent in overweight or obese patients compared to lean patients. We report evidence supporting an ageing accelerating effect of obesity at the genetic level. We show that BMI-associated differences in bulk transcriptomic profile are subtle, while single cell profiling allows detection of more pronounced changes in different cell compartments. These analyses further reveal an elevated and unresolved inflammation of the BC tumor microenvironment associated with obesity, with distinct characteristics contingent on the estrogen receptor status. Collectively, our analyses imply that obesity is associated with an inflammaging-like phenotype. We conclude that patient adiposity may play a significant role in the heterogeneity of BC and should be considered for BC treatment tailoring.\ \ Ha-Linh Nguyen et al. Open Capsule

Biology\ \ 25 | Nov | 2024\ \ HLApollo: A superior transformer model for pan-allelic peptide-MHC-I presentation prediction, with diverse negative coverage, deconvolution and protein language features\ \ Antigen presentation on MHC class I (MHC-I) is key to the adaptive immune response to cancerous cells. Computational prediction of peptide presentation by MHC-I has enabled individualized cancer immunotherapies. Here, we introduce HLApollo, a transformer-based approach with end-to-end modeling of MHC-I sequence, deconvolution, and flanking sequences. To achieve this, we develop a novel training strategy, negative set switching, which greatly reduces overfitting to falsely presumed negatives that are necessarily found in presentation datasets. HLApollo shows a meaningful improvement compared to recent MHC-I models on peptide presentation (20.19% average precision (AP)) and immunogenicity (4.1% AP). As expected, adding gene expression boosts the performance of HLApollo. More interestingly, we show that introduction of features from a protein language model, ESM 1b, remarkably recoups much of the benefits of gene expression in absence of true expression measurements. Finally, we demonstrate excellent pan-allelic generalization, and introduce a framework for estimating the expected accuracy of HLApollo for untrained alleles. This guides the use of HLApollo in a clinical setting, where rare alleles may be observed in some subjects, particularly for underrepresented minorities.\ \ William John Thrift et al. Open Capsule

published in Nature Communications

Medical Sciences\ \ 4 | May | 2023\ \ Neuropathologist-level integrated classification of adult-type diffuse gliomas using deep learning from whole-slide pathological images\ \ A neuropathologist-level integrated diagnosis model for automatically predicting 2021 WHO types and grades of adult-type diffuse gliomas from annotation-free standard whole-slide images.\ \ Zhi-Cheng Li, Yuanshen Zhao & Zhenyu Zhang Open Capsule

Medical Sciences\ \ 12 | Apr | 2023\ \ Epigenetic reprogramming shapes the cellular landscape of schwannoma\ \ Analysis code used for the manuscript titled: Epigenetic reprogramming shapes the cellular landscape of schwannoma\ \ John Liu Open Capsule

Biology\ \ 13 | Sep | 2023\ \ Predicting discrete-time bifurcations with deep learning\ \ Many natural and man-made systems are prone to critical transitions—abrupt and potentially devastating changes in dynamics. Deep learning classifiers can provide an early warning signal (EWS) for critical transitions by learning generic features of bifurcations (dynamical instabilities) from large simulated training data sets. So far, classifiers have only been trained to predict continuous-time bifurcations, ignoring the rich dynamics associated with discrete-time bifurcations such as the period-doubling bifurcation. Here, we train a deep learning classifier to provide an EWS for the five local discrete-time bifurcations of codimension-1. We test the classifier on simulation data from discrete-time models used in physiology, economics and ecology, as well as experimental data of spontaneously beating chick-heart aggregates that undergo a period-doubling bifurcation. The classifier outperforms commonly used EWS under a wide range of noise intensities and rates of approach to the bifurcation. It also predicts the correct bifurcation in most cases, with particularly high accuracy for the period-doubling, Neimark-Sacker and fold bifurcations. Deep learning as a tool for bifurcation prediction is still in its nascence and has the potential to transform the way we monitor systems for critical transitions.\ \ Thomas M. Bury et al. Open Capsule

Biology\ \ 27 | Feb | 2023\ \ Inefficient prioritization of task-relevant attributes during instrumental information demand\ \ In natural settings, people evaluate complex multi-attribute situations and decide which attribute to request information about. Little is known about how people make this selection. How do participants identify individual observations that best predict the value of a multi-attribute situation? Here we show that, in a simple task of information demand, participants inefficiently query attributes that have high individual value but are relatively uninformative about a total payoff. This inefficiency is robust in two instrumental conditions in which gathering less informative observations leads to significantly lower rewards. Across individuals, variations in the sensitivity to informativeness is associated with personality metrics, and shows negative associations with extraversion and thrill seeking and positive associations with stress tolerance and need for cognition. Thus, people select informative queries using sub-optimal strategies that are associated with personality traits and influence consequential choices in multiple settings.\ \ Isabella Rischall, Laura E. Hunter, Greg Jensen & Jacqueline Gottlieb Open Capsule

Bioinformatics\ \ 17 | Jan | 2023\ \ Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data\ \ To run the capsule, please click the "Reproducible Run" on the right panel. It normally takes around 30 minutes to finish all the five analysis tasks (cell recognition, gene signature extraction, multi-omic integration, cellular trajectory analysis, dimensionality reduction and visualization). After the computation is done, please click on the genoMapDemo.html in the results folder. All the figures and results of classification accuracy calculation can be found in the html file.\ \ Md Tauhidul Islam & Lei Xing Open Capsule

Physics\ \ 10 | Nov | 2022\ \ BaGoL (Bayesian Grouping of Localizations)\ \ Single-molecule localization microscopy super-resolution methods such as DNA-PAINT and (d)STORM can generate multiple observed localizations over the time course of data acquisition from each dye or binding site that are not a priori assigned to those specific dyes or binding sites. We describe a Bayesian method of grouping and combining localizations from multiple blinking/binding events that can improve localization precision and can provide better than one nanometer precision under achievable experimental conditions. The known statistical distribution of the number of binding/blinking events per dye/docking strand along with the precision of each localization event are used to generate a posterior probability distribution of the number and location of emitters. We demonstrate the method on a range of synthetic data, DNA origami constructs and biological structures using DNA-PAINT and dSTORM.\ \ Mohamadreza Fazel et al. Open Capsule

Bioinformatics\ \ 9 | Jan | 2023\ \ Leveraging data-driven self-consistency for high-fidelity gene expression recovery\ \ To run the capsule, please click the "Reproducible Run" on the right panel. It normally takes around 25 minutes to finish all the calculation. After the computation is done, please click on the demo_serm.html in the results folder. All the tSNE figures and results of Pearson coefficient calculation can be found in the html file.\ \ Md Tauhidul Islam et al. Open Capsule

Associated article published in Nature Communications

Bioinformatics\ \ 13 | Sep | 2022\ \ CAPITAL: alignment of single-cell trajectory trees\ \ CAPITAL, implemented in Python, is a computational tool for aligning pseudotime trajectories with tree alignment whereby trajectories including branches can be automatically compared. CAPITAL is designed to run in an interactive development environment such as JupyterLab.\ \ Reiichi Sugihara, Yuki Kato, Tomoya Mori & Yukio Kawahara Open Capsule

Engineering\ \ 15 | Aug | 2022\ \ The cross-sectional area change ratio of the microchannel during stretching\ \ We propose a method to convert the 2d point data to the area and apply it to obtain the cross-sectional area change ratio of the microchannel during stretching. The datasets are based on uniaxial tensile tests which are simulated using commercial software ABAQUS Explicit 2020. Three different shapes of silicone pipes, including triangle, square and circular, are modeled. The cavity cross-sectional areas of those pipes are 1mm^2 and the lengths of them are 8mm. The bottom part is fully fixed, and the top part is added 8mm/s velocity loading. Quadratic cubic elements with reduced integration(C3D20RH) are used everywhere in the model. A hyperelastic Yeoh material model is used to describe the mechanical responses of silicone, and the data set used to calibrate this model is imported from the stress-strain results of uniaxial tensile test.\ \ Yuxuan Liao & Dongliang Fan Open Capsule

Bioinformatics\ \ 20 | Jul | 2022\ \ Emap2sec+:Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning\ \ Emap2sec+ is a computational tool using deep learning that can accurately identify structures, alpha helices, beta sheets, other(coils/turns) and DNA/RNA, in cryo-Electron Microscopy (EM) maps of medium to low resolution.\ \ Xiao Wang Open Capsule

Associated article published in Nature Communications

Engineering\ \ 25 | Jan | 2023\ \ Vickrey Exoskeleton Auction Data\ \ Understanding the success of augmentative exoskeletons is critical to their impact on society. Many exoskeletons are developed to address impairments that stem from neuromotor pathology, which provides guidance for understanding their abilities; however, for augmentative exoskeletons that assist able-bodied users, a clear metric of success remains an open question. In this study, we leverage an approach from economics---the Vickrey second-price auction---to quantify the economic value added by lower-limb exoskeletons during uphill walking. In our protocol, participants describe how much compensation is needed to continue walking uphill for consecutive bouts of two minutes. To incentivize truthful descriptions of participant's ``price to walk,'' their compensation amounts were provided in the form of bids in Vickrey auctions before each walking bout. Our overarching hypothesis was that if exoskeletons provided helpful assistance during a difficult task (e.g. walking uphill), this value can be observed and quantified through a lowering of their price to walk. We compared these data across different conditions to determine the marginal value of the exoskeleton weight, assistance, and weight + assistance. Our approach found that the total value of the exoskeleton and its assistance was modest ($3.40/hr, SD:$3.35/hr); while most participants found the assistance itself valuable ($19.76/hr, SD: $19.43/hr), this value was nearly offset by the cost of wearing the exoskeleton weight (-$18.59/hr, SD: $18.28/hr). Interestingly, we noticed a large variance in the economic value across participants, which motivates the ability to separate those individuals that receive substantial value from exoskeleton-assisted locomotion. Our results suggest economic value may be a powerful tool to design and control exoskeletons to maximize user benefit.\ \ Roberto Leo Medrano, Gray Cortright Thomas, Drew Margolin & Elliott J. Rouse Open Capsule

Bioinformatics\ \ 5 | Jan | 2022\ \ Genome binning of viral entities from bulk metagenomics data.\ \ Joachim Johansen, Damian R. Plichta, Jakob Nybo Nissen, Marie Louise Jespersen, Shiraz A. Shah, Ling Deng, Jakob Stokholm, Hans Bisgaard, Dennis Sandris Nielsen, Søren Sørensen, Simon Rasmussen\ \ Joachim Johansen et al. Open Capsule

Bioinformatics\ \ 18 | Oct | 2021\ \ ClusterMap: multi-scale clustering analysis of spatial gene expression

We introduce an unsupervised and annotation-free framework, termed ClusterMap, which incorporates the physical location and gene identity of RNAs, formulates the task as a point pattern analysis problem, and identifies biologically meaningful structures by density peak clustering (DPC). doi: https://doi.org/10.1101/2021.02.18.431337

Yichun He et al.

Open Capsule

Associated article published in Nature Communications

Bioinformatics\ \ 30 | Aug | 2021\ \ High-throughput mediation analysis (Hitman) of human proteome and metabolome identifies mediators of post-surgical diabetes control\ \ To improve the power of mediation in high-throughput studies, we introduce High-throughput mediation analysis (Hitman), which accounts for direction of mediation and applies empirical Bayesian linear modeling. We applied Hitman to the SLIMM-T2D trial, in which participants with type 2 diabetes were randomized to Roux-en-Y gastric bypass (RYGB) or nonsurgical diabetes weight management, and fasting plasma proteome and metabolome were assayed up to 3 years. RYGB had greater improvement in HbA1c, which was mediated by growth hormone receptor (GHR). GHR’s mediation was more significant than clinical mediators, including BMI. GHR decreased at 3 months postoperatively, with increased insulin-like growth factor binding proteins IGFBP1/BP2, and subsequent increases in plasma GH at 1 year. Experimental validation indicated (1) hepatic GHR expression decreased in post-bariatric rats, and (2) GHR knockdown in primary hepatocytes decreased gluconeogenic gene expression and glucose production. Thus, RYGB may induce resistance to diabetogenic effects of GH signaling.\ \ Jonathan M Dreyfuss Open Capsule

Medical Sciences\ \ 18 | Aug | 2021\ \ MesoNet: automated scaling and segmentation of mouse mesoscale cortical maps using machine learning (MBFM code).\ \ We have developed an automated machine learning-based registration and segmentation approach for quantitative analysis of mouse mesoscale cortical images. A deep learning model identifies nine cortical landmarks using only a single raw fluorescent image. Another fully convolutional network was adapted to delimit brain boundaries. This anatomical alignment approach was extended by adding three functional alignment approaches that use sensory maps or spatial-temporal activity motifs. We present this methodology as MesoNet, a robust and user-friendly analysis pipeline using pre-trained models to segment brain regions as defined in the Allen Mouse Brain Atlas. This Python-based toolbox can also be combined with existing methods to facilitate high-throughput data analysis.\ \ Dongsheng Xiao, Brandon J. Forys, Matthieu P. Vanni & Timothy H. Murphy Open Capsule

Medical Sciences\ \ 18 | Aug | 2021\ \ MesoNet: automated scaling and segmentation of mouse mesoscale cortical maps using machine learning.\ \ We have developed an automated machine learning-based registration and segmentation approach for quantitative analysis of mouse mesoscale cortical images. A deep learning model identifies nine cortical landmarks using only a single raw fluorescent image. Another fully convolutional network was adapted to delimit brain boundaries. This anatomical alignment approach was extended by adding three functional alignment approaches that use sensory maps or spatial-temporal activity motifs. We present this methodology as MesoNet, a robust and user-friendly analysis pipeline using pre-trained models to segment brain regions as defined in the Allen Mouse Brain Atlas. This Python-based toolbox can also be combined with existing methods to facilitate high-throughput data analysis.\ \ Dongsheng Xiao, Brandon J. Forys, Matthieu P. Vanni & Timothy H. Murphy Open Capsule

Bioinformatics\ \ 7 | Jul | 2021\ \ ORCESTRA: Orchestrating and sharing large multimodal data for transparent and reproducible research\ \ Reproducibility is essential to open science, as there is limited relevance for findings that can not be reproduced by independent research groups, regardless of its validity. It is therefore crucial for scientists to describe their experiments in sufficient detail so they can be reproduced, scrutinized, challenged, and built upon. However, the intrinsic complexity and continuous growth of biomedical data makes it increasingly difficult to process, analyze, and share with the community in a FAIR (findable, accessible, interoperable, and reusable) manner. To overcome these issues, we created a cloud-based platform called ORCESTRA (orcestra.ca), which provides a flexible framework for the reproducible processing of multimodal biomedical data. \ \ Capsule executes "case studies" for each biomedical data type using data objects generated by ORCESTRA (orcestra.ca)\ \ Anthony Mammoliti et al. Open Capsule

Computer Science\ \ 19 | Jul | 2021\ \ A Generalizable and Accessible Approach to Machine Learning with Global Satellite Imagery\ \ This capsule provides the code, data, and computing environment required to produce the figures appearing in the main text and Supplementary Materials of:\ \ E. Rolf, J. Proctor, T. Carleton, I. Bolliger, V. Shankar, M. Ishihara, B. Recht, and S. Hsiang. "A Generalizable and Accessible Approach to Machine Learning with Global Satellite Imagery," Nature Communications, 2021.\ \ This repository also serves as an example of the generalizability of the MOSAIKS approach, which enables users with access to limited computing resources and without expertise in machine learning or remote sensing to generate observations of new variables in new locations. While this repository reproduces the results from the paper titled above, it also allows users to generate observations of new variables in new research and policy contexts with minimal changes to the existing code base.\ \ Esther Rolf et al. Open Capsule

Computer Science\ \ 30 | Aug | 2021\ \ Market-oriented Job Skill Valuation with Cooperative Composition Neural Network\ \ The code for the peer review, including training/test models, baselines and drawing charts. We have prepared this version according to the software checklist.\ \ Ying Sun et al. Open Capsule

Bioinformatics\ \ 13 | Dec | 2020\ \ Biological and Therapeutic Implications of a Unique Subtype of NPM1 Mutated AML\ \ In acute myeloid leukemia (AML), molecular heterogeneity across patients constitutes a major challenge for prognosis and therapy. AML with NPM1 mutation is a distinct genetic entity in the revised World Health Organization classification. However, differing patterns of co-mutation and response to therapy within this group necessitate further stratification. Here we report two distinct subtypes within NPM1 mutated AML patients, which we label as primitive and committed based on the respective presence or absence of a stem cell signature. Using gene expression (RNA-seq), epigenomic (ATAC-seq) and immunophenotyping (CyToF) analysis, we were able to associate each subtype with specific molecular characteristics, disease differentiation state and patient survival. Using ex vivo drug sensitivity profiling, we show a differential drug response of the subtypes to specific kinase inhibitors, irrespective of the FLT3-ITD status. Differential drug responses of the primitive and committed subtype arewere validated in an independent AML cohort. Our results highlight heterogeneity among NPM1 mutated AML patient samples based on stemness and suggest that the addition of kinase inhibitors to the treatment of cases with the primitive signature, lacking FLT3-ITD, could have therapeutic benefit.\ \ Arvind Singh Mer, Benjamin Haibe-Kains & benjamin.haibe.kains@utoronto.ca Open Capsule

Bioinformatics\ \ 25 | Sep | 2020\ \ AIMOS\ \ Online demonstration for AIMOS - AI-based mouse organ segmentation\ \ Oliver Schoppe Open Capsule

Biology\ \ 3 | Sep | 2020\ \ QMAP-Seq: quantitative and multiplexed chemical-genetic phenotyping in mammalian cells\ \ QMAP-Seq is a quantitative and multiplexed chemical-genetic profiling platform that enables pooled measurement of drug response across multiple cell lines, genetic perturbations, compounds, doses, and replicates from a single next-generation sequencing run. This pipeline allows users to computationally process QMAP-Seq data from fastq files into relative cell number values, heat maps of relative cell number, dose-response curves, and area under the curve (AUC) values.\ \ Sonia Brockway et al. Open Capsule

Associated article published in Nature Communications

Biology\ \ 31 | Jul | 2020\ \ Unconscious reinforcement learning of hidden brain states supported by confidence\ \ This capsule contains the main code and data allowing anyone to reproduce the analyses and figures of the manuscript "Unconscious reinforcement learning of hidden brain states supported by confidence"\ \ Aurelio Cortese, Hakwan Lau & Mitsuo Kawato Open Capsule

Biology\ \ 13 | Jan | 2020\ \ Optimization via Synthesis of Intermediate Recombination States OSIRiS\ \ OSIRiS: Optimization via Synthesis of Intermediate Recombination States.\ Python script to obtain the recombination intermediate DNA sequences of any DNA sequence based on a list of serine integrases of interest. Considering that each state corresponds to a physically different DNA molecule which sequence can be fully predicted, OSIRiS enables the different recombination intermediates to be generated in silico, synthesized, and characterized. OSIRiS therefore decouples scaffold optimization from integrase mediated switching, simplify and shorten the characterization process, and allows for rapid iteration cycles.\ \ Ana Zúñiga et al. Open Capsule

Associated article published in Nature Communications

Bioinformatics\ \ 24 | Sep | 2018\ \ 6mer seed toxicity in tumor suppressive microRNAs: eCDF plots for toxic/nontoxic seed matches in essential and non-essential genes\ \ This capsule takes a set of seeds and sets of genic sequences, and checks whether different parts of genes and different sets of genes have different seed profiles for toxic and non-toxic seeds.\ \ Elizabeth T Bartom & Quan Q Gao Open Capsule

Associated article published in Nature Communications

Bioinformatics\ \ 24 | Sep | 2018\ \ 6mer seed toxicity in tumor suppressive microRNAs: toxic seed and nucleotide distributions, figure 3d, 3e, supplementary figure 5b​\ \ This capsule accompanies the paper "6mer seed toxicity in tumor suppressive microRNAs" and shows the landscape of toxic seeds, non-toxic seeds, and all four single nucleotides across different gene boundaries. Multiple genes are aggregated to show the general patterns in these meta-plots.\ \ Elizabeth T. Bartom Open Capsule

Bioinformatics\ \ 24 | Sep | 2018\ \ 6mer seed toxicity in tumor suppressive microRNAs: transcriptional response when mir34-a or its seed is overexpressed\ \ This capsule examines the impact of miRNA seed presence (specifically for mir34a seeds) on gene expression data.\ \ Elizabeth T Bartom Open Capsule

Medical Sciences\ \ 3 | May | 2018\ \ Gene isoforms as expression-based biomarkers predictive of drug response in vitro [PMID: 29066719]\ \ Next-generation sequencing technologies have recently been used in pharmacogenomic studies to characterize large panels of cancer cell lines at the genomic and transcriptomic levels. Among these technologies, RNA-sequencing enable profiling of alternatively spliced transcripts. Given the high frequency of mRNA splicing in cancers, linking this feature to drug response will open new avenues of research in biomarker discovery. To identify robust transcriptomic biomarkers for drug response across studies, we develop a meta-analytical framework combining the pharmacological data from two large-scale drug screening datasets. We use an independent pan-cancer pharmacogenomic dataset to test the robustness of our candidate biomarkers across multiple cancer types. We further analyze two independent breast cancer datasets and find that specific isoforms of IGF2BP2, NECTIN4, ITGB6, and KLHDC9 are significantly associated with AZD6244, lapatinib, erlotinib, and paclitaxel, respectively. Our results support isoform expressions as a rich resource for biomarkers predictive of drug response.\ \ Zhaleh Safikhani & Petr Smirnov Open Capsule

Associated article published in Nature Communications