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    39 repositories

    • lpca-spras

      Public
      Logistic PCA integration into SPRAS bioinformatics pipeline
      Python
      •1•0•0•0•Updated Aug 28, 2026Aug 28, 2026

    • yeast-ppi-af3-su26

      Public
      Explore AlphaFold3 predicted yeast protein-protein interactions
      Jupyter Notebook
      •1•0•0•0•Updated Aug 28, 2026Aug 28, 2026

    • active-learning-drug-discovery

      Public
      Iterative chemical screening pipeline for drug discovery
      drug-discoveryactive-learningvirtual-screening
      drug-discoveryactive-learningvirtual-screening
      Jupyter Notebook
      •
      MIT License
      •0•6•13•1•Updated Jul 22, 2026Jul 22, 2026

    • SINGE

      Public
      Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data
      regulatory-networksingle-cell-rna-seqgranger-causality
      regulatory-networksingle-cell-rna-seqgranger-causality
      MATLAB
      •
      MIT License
      •6•11•13•3•Updated Jul 6, 2026Jul 6, 2026

    • ALDD-PstP-Results

      Public
      Active Learning in Drug Discovery PstP Results
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 3, 2026Jul 3, 2026

    • adaptyvbio-nipah

      Public
      Adaptyv Nipah Binder Competition
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Mar 20, 2026Mar 20, 2026

    • metl

      Public
      Mutational Effect Transfer Learning (METL) framework for pretraining and finetuning biophysics-informed protein language models
      Python
      •
      MIT License
      •10•64•3•1•Updated Feb 3, 2026Feb 3, 2026

    • tps

      Public
      Temporal Pathway Synthesizer
      Jupyter Notebook
      •
      Other
      •8•0•0•1•Updated Oct 10, 2025Oct 10, 2025

    • metl-sim

      Public
      High-throughput framework for running molecular simulations for METL
      Python
      •
      MIT License
      •6•22•4•0•Updated Sep 18, 2025Sep 18, 2025

    • metl-pub

      Public
      Supplementary datasets and scripts for the METL manuscript
      Jupyter Notebook
      •
      MIT License
      •1•9•0•0•Updated Sep 18, 2025Sep 18, 2025

    • metl-pretrained

      Public
      Pretrained METL models with minimal dependencies
      Python
      •
      MIT License
      •4•16•1•1•Updated Sep 18, 2025Sep 18, 2025

    • benchmarking-structure-based-models

      Public
      This is a repository of code needed to replicate benchmarks of structure based models in ProteinGym
      Python
      •
      MIT License
      •0•3•0•0•Updated Sep 14, 2025Sep 14, 2025

    • ChemLML

      Public
      Chemical Language Model Linker
      Python
      •
      MIT License
      •1•9•2•0•Updated Aug 22, 2025Aug 22, 2025

    • pathway-localization

      Public
      Scripts, data, and supplementary information for "Graph algorithms for predicting subcellular localization at the pathway level"
      Python
      •
      Creative Commons Attribution 4.0 International
      •1•1•1•0•Updated Aug 8, 2025Aug 8, 2025

    • Assay2Mol

      Public
      Python
      •
      MIT License
      •0•2•0•0•Updated Jul 31, 2025Jul 31, 2025

    • nn4dms

      Public
      Neural networks for deep mutational scanning data
      Jupyter Notebook
      •
      MIT License
      •17•75•0•0•Updated May 30, 2025May 30, 2025

    • ml4bio

      Public
      A graphical interface for sklearn classification to introduce machine learning to biologists
      educationmachine-learning
      educationmachine-learning
      Python
      •
      MIT License
      •3•14•21•1•Updated Mar 19, 2025Mar 19, 2025

    • hiv1-aurkb

      Public
      Scripts for analyzing HIV-1 producer cell proteomic and phosphoproteomic data
      Python
      •
      MIT License
      •1•1•0•0•Updated Oct 31, 2024Oct 31, 2024

    • min-cost-flow

      Public
      Pathway reconstruction with a minimum cost flow algorithm
      Python
      •
      MIT License
      •1•1•1•1•Updated Sep 18, 2024Sep 18, 2024

    • low-n-mlde-review

      Public
      Low N machine learning-assisted directed evolution perspective written with Manubot
      HTML
      •
      Creative Commons Attribution 4.0 International
      •0•0•33•0•Updated Aug 30, 2024Aug 30, 2024

    • osmotic-stress

      Public
      A study of yeast osmotic stress response signaling
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 28, 2024Jun 28, 2024

    • pria-ams-enamine

      Public
      Virtual screening on PriA-SSB with the AMS and Enamine REAL libraries
      machine-learningbiochemistryvirtual-screening
      machine-learningbiochemistryvirtual-screening
      Jupyter Notebook
      •
      MIT License
      •1•7•0•0•Updated Sep 22, 2023Sep 22, 2023

    • rare-disease-network-analysis

      Public
      Network analysis of genetic variants
      Jupyter Notebook
      •
      MIT License
      •0•1•2•0•Updated Aug 31, 2023Aug 31, 2023

    • bds-srop-demo-manuscript

      Public
      Demo manubot manuscript for BDS SROP students
      HTML
      •
      Creative Commons Attribution 4.0 International
      •5•0•0•0•Updated Jul 25, 2023Jul 25, 2023

    • network-notebook-examples

      Public
      Test pandas and networkx in Jupyter notebooks
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jun 7, 2023Jun 7, 2023

    • influenza-pb2

      Public
      Analysis of influenza PB2 protein interactions
      Python
      •
      MIT License
      •1•0•2•0•Updated Dec 24, 2022Dec 24, 2022

    • ssps

      Public
      Sparse Signaling Pathway Sampling: MCMC for signaling pathway inference
      probabilistic-programminggensignaling-pathway
      probabilistic-programminggensignaling-pathwaydynamic-bayesian-network
      Julia
      •
      MIT License
      •0•14•0•0•Updated Oct 24, 2022Oct 24, 2022

    • pathway-parameter-advising

      Public
      Parameter advising for biological pathway creation algorithms
      hyperparameter-tuninggraphletprotein-protein-interaction-network
      hyperparameter-tuninggraphletprotein-protein-interaction-network
      Python
      •
      MIT License
      •0•3•3•0•Updated Sep 7, 2022Sep 7, 2022

    • NetworkMeasures

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 7, 2022Sep 7, 2022

    • SINGE-supplemental

      Public
      Supplemental scripts and analyses for the SINGE manuscript
      regulatory-networksingle-cell-rna-seqgranger-causality
      regulatory-networksingle-cell-rna-seqgranger-causality
      MATLAB
      •
      MIT License
      •1•1•0•0•Updated May 7, 2022May 7, 2022
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