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    33 repositories

    • mlab-groceries

      Public
      Vibe coded web app managing Marks lab groceries (because Amazon sucks)
      HTML
      •0•2•0•0•Updated Jul 8, 2026Jul 8, 2026

    • ML-antibody-discovery

      Public
      Jupyter Notebook
      •
      MIT License
      •1•2•0•0•Updated May 7, 2026May 7, 2026

    • EVcouplings

      Public
      Evolutionary couplings from protein and RNA sequence alignments
      proteinstructure-prediction3d-structure
      proteinstructure-prediction3d-structureprotein-complexes
      Jupyter Notebook
      •
      Other
      •83•309•59•7•Updated Apr 20, 2026Apr 20, 2026

    • popEVE-genecollapsing

      Public
      popEVE's gene collapsing simulation for discovering disease-gene associations from de novo variants
      Python
      •
      MIT License
      •0•0•1•0•Updated Apr 15, 2026Apr 15, 2026

    • priority-viruses

      Public
      Official repository for the paper "Evaluating variant effect prediction across viruses"
      Jupyter Notebook
      •2•21•0•0•Updated Mar 30, 2026Mar 30, 2026

    • LOL-EVE

      Public
      Placehoolder for LOL-EVE model and publication analysis scripts
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Sep 26, 2025Sep 26, 2025

    • popEVE

      Public
      Python
      •
      GNU General Public License v3.0
      •6•52•1•0•Updated Sep 4, 2025Sep 4, 2025

    • PROSE

      Public
      Python
      •
      MIT License
      •0•2•0•0•Updated May 29, 2025May 29, 2025

    • ML_affinity_maturation

      Public
      Repository containing the code performing ML assisted affinity maturation
      Jupyter Notebook
      •
      MIT License
      •0•6•0•0•Updated Apr 7, 2025Apr 7, 2025

    • sequenceMDS

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • EVEscape

      Public
      Official repository for the paper "Learning from pre-pandemic data to forecast viral antibody escape"
      Python
      •
      MIT License
      •13•1•0•1•Updated Mar 5, 2024Mar 5, 2024

    • Vax_design

      Public
      Jupyter Notebook
      •
      MIT License
      •1•6•0•0•Updated Mar 5, 2024Mar 5, 2024

    • SeqDesign

      Public
      Protein design and variant prediction using autoregressive generative models
      Python
      •
      MIT License
      •21•122•2•0•Updated Jan 23, 2024Jan 23, 2024

    • nanobody-polyreactivity

      Public
      Polyreactivity Website
      Python
      •
      MIT License
      •8•23•2•0•Updated Jun 26, 2023Jun 26, 2023

    • BEAR

      Public
      This repository is for the paper "A generative nonparametric Bayesian model for whole genomes"
      tensorflowprobabilistic-programmingbiological-data-analysis
      tensorflowprobabilistic-programmingbiological-data-analysisgenomes
      Python
      •
      MIT License
      •4•16•1•0•Updated Jun 7, 2023Jun 7, 2023

    • ZIP_benchmark

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 1, 2023Jun 1, 2023

    • plmc

      Public
      Inference of couplings in proteins and RNAs from sequence variation
      protein-structureprotein-interactionprotein-sequences
      protein-structureprotein-interactionprotein-sequencesundirected-graphssequence-alignments
      C
      •
      MIT License
      •39•124•8•2•Updated Jan 21, 2023Jan 21, 2023

    • detectDesign

      Public
      toolkit for finding likely cas9 off-target binding and effect on gene expression, designing sgRNAs and pairs of sgRNAs with minimal off-target effect on gene-ex…
      Jupyter Notebook
      •2•7•0•1•Updated Jun 22, 2022Jun 22, 2022

    • DeepSequence

      Public
      A generative latent variable model for biological sequence families.
      Python
      •
      MIT License
      •47•256•5•5•Updated Mar 15, 2022Mar 15, 2022

    • variational-synthesis

      Public
      Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AISTATS, 2022).
      generative-modelprotein-sequencesdna-sequences
      generative-modelprotein-sequencesdna-sequencesexperimental-design
      Python
      •
      MIT License
      •13•38•1•0•Updated Feb 17, 2022Feb 17, 2022

    • GerA-suppData-2021

      Public
      HTML
      •1•0•0•0•Updated Oct 27, 2021Oct 27, 2021

    • MuE

      Public
      A package for making MuE observation models in Edward2.
      machine-learningproteinstensorflow
      machine-learningproteinstensorflowprobabilistic-programmingbiological-sequences
      Python
      •
      MIT License
      •2•13•0•0•Updated Jun 10, 2021Jun 10, 2021

    • EVE

      Public
      Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning"
      Python
      •
      MIT License
      •62•10•0•0•Updated Apr 29, 2021Apr 29, 2021

    • edward2

      Public
      A fork of Edward2, for use with the MuE package.
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 3, 2020Oct 3, 2020

    • EVdeimmunization

      Public
      Dual optimization of de-immunization and protein function
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 27, 2020Apr 27, 2020

    • EVzoom

      Public
      Visually explore covariation in protein families
      evolutionprotein-interactionprotein-sequences
      evolutionprotein-interactionprotein-sequencesundirected-graphsd3jsamino-acids
      JavaScript
      •6•41•0•0•Updated Dec 8, 2019Dec 8, 2019

    • NEMO

      Public
      Learning protein structure with a differentiable simulator
      Python
      •7•27•2•0•Updated Jul 8, 2019Jul 8, 2019

    • 3D_from_DMS_Extended_Data

      Public
      Jupyter Notebook
      •5•10•0•0•Updated Apr 28, 2019Apr 28, 2019

    • variants_pharmacogenes

      Public
      This repository contains the code used to analyse data and produce figures for the manuscript "Genetic variation in human drug-related genes"
      Jupyter Notebook
      •4•10•0•0•Updated Dec 19, 2017Dec 19, 2017

    • EVmutation

      Public
      Mutation effects predicted from sequence co-variation
      HTML
      •14•76•0•0•Updated Sep 3, 2017Sep 3, 2017
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