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📢 Latest Research from Gerstein Lab

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🚀 Welcome to the Gerstein Lab GitHub!

Explore Our Research

Table of Contents
  1. About The Lab
  2. Contributing
  3. Contact
  4. Acknowledgments

About The Lab

The Gerstein Lab bridges quantitative disciplines like computer science and statistics with molecular biology to tackle practical challenges and analyze large-scale biological data. Our work frequently involves collaboration within multi-disciplinary teams and participation in consortia such as PsychENCODE, ENCODE, GSP/CMG, and 1000 Genomes. Below, we outline key areas of our research, all contributing to our overarching mission of interpreting personal genomes and advancing the field of biomedical data science. See lab permissions and copyright statement here.

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Repo Categories

This section presents an organized overview of all our repositories.

Genome Annotation

  • alleleDB Stargazers
  • AlleleSeq2 Stargazers
  • annotation-k-mer-extractor Stargazers
  • ASTRO Stargazers
  • aloft Stargazers
  • Bay2Ctrls Stargazers
  • ChromosomePaintingTool Stargazers
  • cortexData Stargazers
  • exceRpt Stargazers
  • FunSeq2 Stargazers
  • FusionSeq Stargazers
  • GRAM Stargazers
  • HiC-spector Stargazers
  • Intensification Stargazers
  • IQSeq Stargazers
  • LARVA Stargazers
  • LESSeq Stargazers
  • MatchedFilter Stargazers
  • MUSIC Stargazers
  • MOAT Stargazers
  • MOBI Stargazers
  • MotifTools Stargazers
  • MrTADFinder Stargazers
  • pcawgAdditiveVariance Stargazers
  • PeakSeq Stargazers
  • PsychENCODE_SingleCell_Integrative Stargazers
  • Regulatory_Targets Stargazers
  • retrodup Stargazers
  • rpgQTL Stargazers
  • RSEQtools Stargazers
  • scan-atac-sim Stargazers
  • starrpeaker Stargazers
  • texp Stargazers
  • Thunder Stargazers
  • transferQTL Stargazers
  • uORFs Stargazers
  • vat Stargazers

Disease Genomics

  • ABCD Stargazers
  • dAsthma Stargazers
  • decoasthma Stargazers
  • PsychENCODE-DSPN Stargazers
  • PsychENCODE_SingleCell_Integrative Stargazers
  • RADAR Stargazers
  • siglasso Stargazers
  • UMG Stargazers

Personal Genomics & Genomic Privacy

  • FANCY Stargazers
  • HEPRS Stargazers
  • iDASH-blockchain Stargazers
  • idash19 Stargazers
  • idash19bc Stargazers
  • idash19he Stargazers
  • idash20FL Stargazers
  • idash22bc Stargazers
  • idash23bc Stargazers
  • PLIGHT Stargazers
  • privaseq4 Stargazers
  • SAMChain Stargazers

Data Science & Biological Networks

  • LatentDAG Stargazers
  • Loregic Stargazers
  • network-viewer Stargazers
  • NGR Stargazers
  • OrthoClust Stargazers

Molecular Motion & Structures

  • BC-Design Stargazers
  • Frustration Stargazers
  • MolLM Stargazers
  • ProteinGraph_construction Stargazers
  • peptide Private
  • PPT Stargazers
  • ProteinGraph_construction Stargazers
  • vossvolvox Stargazers
  • STRESS Stargazers
  • STRESSserver Stargazers

Interpretable Machine Learning Tools

  • BioCoder Stargazers
  • chronODE Stargazers
  • chemagent Stargazers
  • DECODE Stargazers
  • DeepVelo Stargazers
  • esprnn Stargazers
  • Factual_ClinicalSumm Stargazers
  • fmgene Stargazers
  • forest-fire-clustering Stargazers
  • GenAI4Drug Stargazers
  • MedAgents Stargazers
  • MedAgents-2 Private
  • MEDIQA-Chat-2023 Stargazers
  • MIMIR Stargazers
  • ML-Bench Stargazers
  • MedAgents Stargazers
  • MolLM Stargazers
  • Musevo Stargazers
  • Struc-Bench Stargazers
  • ThermoNet Stargazers
  • RetrievalDecider Private
  • shiny-dim-reduction Stargazers
  • step-back-profiling Stargazers
  • SVFX Stargazers
  • swebench Private

Yale Class - Biomedical Data Science: Mining & Modeling

class_website_image
  • cbb752b25
  • cbb752b23
  • cbb752b22
  • cbb752b21
  • cbb752b20
  • cbb752b19

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Contributing

Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.

If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". Don't forget to give the project a star! Thanks again!

  1. Fork the Project
  2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
  3. Commit your Changes (git commit -m 'Add some AmazingFeature')
  4. Push to the Branch (git push origin feature/AmazingFeature)
  5. Open a Pull Request

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Contact

PI Email: mark@GersteinLab.org

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Acknowledgments

We sincerely thank our collaborators, alumni, and Yale University for their invaluable contributions and support. Special thanks to our funding sources whose generosity has been vital to our research in computational biology and biomedical data science. Your collective efforts inspire and sustain the Gerstein Lab’s mission—thank you!

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Popular repositories Loading

  1. ML-Bench ML-Bench Public

    The Official Repo of ML-Bench: Evaluating Large Language Models and Agents for Machine Learning Tasks on Repository-Level Code (https://arxiv.org/abs/2311.09835)

    Python 286 7

  2. MedAgents MedAgents Public

    Python 228 34

  3. ThermoNet ThermoNet Public

    ThermoNet is a computational method for quantitative prediction of the impact of single-point mutations on protein thermodynamic stability. The core algorithm of ThermoNet is an ensemble of deep 3D…

    Python 110 21

  4. GenAI4Drug GenAI4Drug Public

    66 5

  5. Struc-Bench Struc-Bench Public

    Python 47 5

  6. BioCoder BioCoder Public

    Jupyter Notebook 40 11

Repositories

Showing 10 of 124 repositories
  • chronODE Public
    gersteinlab/chronODE’s past year of commit activity
    Python 3 0 0 0 Updated Feb 13, 2025
  • cbb752b25 Public
    gersteinlab/cbb752b25’s past year of commit activity
    CSS 0 0 0 0 Updated Feb 13, 2025
  • .github Public

    This is the repo for the public organization profile.

    gersteinlab/.github’s past year of commit activity
    0 MIT 0 0 0 Updated Feb 11, 2025
  • ASTRO Public
    gersteinlab/ASTRO’s past year of commit activity
    Python 2 0 0 0 Updated Feb 8, 2025
  • chemagent Public
    gersteinlab/chemagent’s past year of commit activity
    Python 22 4 2 0 Updated Feb 3, 2025
  • cbb752b23 Public
    gersteinlab/cbb752b23’s past year of commit activity
    CSS 0 0 0 0 Updated Jan 13, 2025
  • HEPRS Public
    gersteinlab/HEPRS’s past year of commit activity
    Go 0 MIT 0 0 0 Updated Jan 3, 2025
  • Bay2Ctrls Public
    gersteinlab/Bay2Ctrls’s past year of commit activity
    R 0 0 0 0 Updated Dec 27, 2024
  • MOBI Public
    gersteinlab/MOBI’s past year of commit activity
    Shell 0 MIT 0 0 0 Updated Dec 27, 2024
  • ABCD Public
    gersteinlab/ABCD’s past year of commit activity
    R 1 0 0 0 Updated Dec 16, 2024

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