Skip to content

@Bitbol-Lab Bitbol-Lab

Change the repository type filter

All

    Repositories list

    26 repositories

    • StructPop_Heterogeneity

      Public
      This code was used to generate figures in the paper "Environment heterogeneity creates fast amplifiers of natural selection in graph-structured populations", by…
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 3, 2026Apr 3, 2026

    • ProteomeLM

      Public
      ProteomeLM: A proteome-scale language model allowing fast prediction of protein-protein interactions and gene essentiality across taxa
      Jupyter Notebook
      •
      Apache License 2.0
      •4•24•6•0•Updated Feb 16, 2026Feb 16, 2026

    • Cooperation_Merging

      Public
      This repository provides the python code to perform simulations in the growth-merging-dilution model described in the article "Promotion of cooperation in deme-…
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 24, 2026Jan 24, 2026

    • rag-esm

      Public
      RAG-ESM is a retrieval-augmented framework that allows to condition pretrained ESM2 protein language models on homologous sequences
      Python
      •
      MIT License
      •1•27•0•0•Updated Aug 21, 2025Aug 21, 2025

    • ProtMamba-ssm

      Public
      ProtMamba: a homology-aware but alignment-free protein state space model
      Jupyter Notebook
      •
      Apache License 2.0
      •11•85•0•0•Updated Jun 3, 2025Jun 3, 2025

    • OutOfEquilibrium-ProtSeq

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 29, 2025May 29, 2025

    • partial_sampling_spatially_structured_population

      Public
      Repository for my lab immersion on spatially structured populations with partial updates.
      Jupyter Notebook
      •1•1•0•0•Updated Feb 13, 2025Feb 13, 2025

    • Fine-tuning-MSA-Transformer

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated Feb 4, 2025Feb 4, 2025

    • alphafold

      Public
      Open source code for AlphaFold.
      Python
      •
      Apache License 2.0
      •2.6k•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • Phylogeny-MSA-Transformer

      Public
      Supporting repository for "Protein language models trained on multiple sequence alignments learn phylogenetic relationships" (https://www.nature.com/articles/s4…
      Jupyter Notebook
      •
      MIT License
      •1•17•0•0•Updated Jan 17, 2025Jan 17, 2025

    • Phylogeny-ESM2

      Public
      Monte-Carlo generation of synthetic multiple sequence alignments along phylogenetic trees using a protein language model
      Python
      •0•4•0•0•Updated Jan 15, 2025Jan 15, 2025

    • fitness-landscapes

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

    • DrugRes_StructPop

      Public
      Repository for "Spatial structure facilitates evolutionary rescue by cost-free drug resistance" (2024) by C. Fruet, E. L. Müller, C. Loverdo, and A.-F. Bitbol.
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 2, 2024Sep 2, 2024

    • ProtMamba-frozen-nips

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated May 22, 2024May 22, 2024

    • DiffPaSS

      Public
      Differentiable Pairing using Soft Scores
      Jupyter Notebook
      •
      Apache License 2.0
      •1•10•2•0•Updated May 20, 2024May 20, 2024

    • Phylogeny-sector-inference

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 19, 2024Apr 19, 2024

    • Structured_pop

      Public
      This repository provides the python code used to generate Figures in articles "Frequent asymmetric migrations suppress natural selection in spatially structured…
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Feb 6, 2024Feb 6, 2024

    • Iterative_masking

      Public
      Iterative masking algorithm on MSA Transformer to generate synthetic sequences
      Jupyter Notebook
      •
      Apache License 2.0
      •8•29•0•0•Updated Jan 17, 2024Jan 17, 2024

    • Cooperation_structured_pop

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 16, 2024Jan 16, 2024

    • DiffPALM

      Public
      Differentiable Pairing using Alignment-based Language Models
      machine-learningbioinformaticsprotein-sequences
      machine-learningbioinformaticsprotein-sequenceslanguage-modelprotein-protein-interactionmultiple-sequence-alignmentprotein-structure-prediction
      Jupyter Notebook
      •
      Apache License 2.0
      •3•24•2•0•Updated Jan 5, 2024Jan 5, 2024

    • T4P-T6SS-interplay

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Nov 1, 2023Nov 1, 2023

    • DiffTrees

      Public
      Python
      •0•0•0•0•Updated Sep 27, 2023Sep 27, 2023

    • esm

      Public
      Evolutionary Scale Modeling (esm): Pretrained language models for proteins
      Python
      •
      MIT License
      •787•0•0•0•Updated Aug 10, 2023Aug 10, 2023

    • Phylogeny-contact-inference

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 4, 2023Jan 4, 2023

    • Phylogeny-Partners

      Public
      Jupyter Notebook
      •
      Other
      •1•1•0•0•Updated Apr 24, 2022Apr 24, 2022

    • swalign

      Public
      Smith-Waterman local aligner
      Python
      •
      Other
      •21•0•0•0•Updated Nov 29, 2021Nov 29, 2021
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.