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    115 repositories

    • mutational-embedding-vectors

      Public
      Python
      •0•0•0•0•Updated Feb 12, 2026Feb 12, 2026

    • kikawa-seqneut-2025-2026-VCM

      Public
      Nextstrain analysis of Kikawa et al. neutralization assay experiments for 2025-2026 Northern Hemisphere VCM
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 11, 2026Feb 11, 2026

    • blotter

      Public
      bedford lab research
      HTML
      •94•68•2•1•Updated Feb 11, 2026Feb 11, 2026

    • bacterial-args

      Public
      Recombination-aware bacterial phylgoeography using ARGs
      Jupyter Notebook
      •0•0•0•0•Updated Feb 11, 2026Feb 11, 2026

    • evofr

      Public
      Tools for evolutionary forecasting
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •1•14•16•1•Updated Feb 9, 2026Feb 9, 2026

    • trajectories

      Public
      Evolutionary trajectories
      Python
      •
      Other
      •0•1•0•0•Updated Feb 9, 2026Feb 9, 2026

    • ncov-usa-mig

      Public
      Analysis of SARS-CoV-2 Surveillance Sequences Across the United States
      epidemiologyvirologyinfectious-diseases
      HTML
      •0•1•0•0•Updated Jan 28, 2026Jan 28, 2026

    • phylogeo-signal

      Public
      Code and data for: "Characterizing the informativeness of pathogen genome sequence datasets about transmission between population groups"
      R
      •
      MIT License
      •0•0•0•0•Updated Jan 16, 2026Jan 16, 2026

    • esm-selection

      Public
      Python
      •0•0•0•0•Updated Jan 8, 2026Jan 8, 2026

    • cytb

      Public
      Nextstrain build for mammalian cytochrome b
      Python
      •
      Other
      •0•0•0•0•Updated Jan 8, 2026Jan 8, 2026

    • sequence-vaes

      Public
      Variational Autoencoders for biological sequences
      Jupyter Notebook
      •0•0•0•0•Updated Dec 16, 2025Dec 16, 2025

    • embedded-pathways

      Public
      Using ESM to chart evolution through embedding space
      Mathematica
      •
      Other
      •1•0•0•0•Updated Dec 10, 2025Dec 10, 2025

    • flu-forecasting-delays

      Public archive
      Timely vaccine strain selection and genomic surveillance improve evolutionary forecast accuracy of seasonal influenza A/H3N2
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 3, 2025Dec 3, 2025

    • mpox-la

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 29, 2025Nov 29, 2025

    • relative-fitness-mechanisms

      Public
      Frequency dynamics predict viral fitness, antigenic relationships and epidemic growth
      Jupyter Notebook
      •0•3•0•0•Updated Oct 14, 2025Oct 14, 2025

    • cholera

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Oct 7, 2025Oct 7, 2025

    • egg-adaptation

      Public
      Adaptation of influenza virus to chicken eggs
      Jupyter Notebook
      •0•0•0•0•Updated Sep 10, 2025Sep 10, 2025

    • kikawa-seqneut-2025-VCM

      Public
      Nextstrain analysis of Kikawa et al. neutralization assay experiments for 2025 Southern Hemisphere VCM
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 4, 2025Sep 4, 2025

    • ai-phylogeo

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 21, 2025Aug 21, 2025

    • fitness-flux

      Public
      Fitness dynamics of SARS-CoV-2 and seasonal influenza H3N2
      Mathematica
      •1•1•0•1•Updated Aug 14, 2025Aug 14, 2025

    • adaptive-evolution

      Public
      An atlas of continuous adaptive evolution in endemic human viruses
      Jupyter Notebook
      •0•4•0•0•Updated Aug 1, 2025Aug 1, 2025

    • vscode-guide

      Public template
      A guide on practical uses for the popular text editor by members of the Bedford Lab
      0•0•0•0•Updated Jul 23, 2025Jul 23, 2025

    • rt-from-frequency-dynamics

      Public
      Inferring variant-specific effective reproduction numbers from combined case and sequencing data
      Mathematica
      •5•46•3•1•Updated Jun 27, 2025Jun 27, 2025

    • measurements-panel

      Public
      Manuscript and data describing joint visualization of influenza serology and phylogeny
      TeX
      •
      MIT License
      •0•0•0•0•Updated May 14, 2025May 14, 2025

    • popcast

      Public
      Long-term forecasts for pathogen populations
      Python
      •
      MIT License
      •0•1•1•0•Updated May 7, 2025May 7, 2025

    • phylo-kernel-public

      Public
      Code and data for: "Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences".
      R
      •
      MIT License
      •2•1•1•1•Updated Feb 7, 2025Feb 7, 2025

    • ncov-escape

      Public
      Predicting changes in lineage fitness from phenotypic predictors
      Jupyter Notebook
      •
      MIT License
      •409•0•0•0•Updated Dec 24, 2024Dec 24, 2024

    • pathogen-embed

      Public
      Create reduced dimension embeddings for pathogen sequences
      Python
      •
      MIT License
      •0•1•6•0•Updated Dec 2, 2024Dec 2, 2024

    • cartography

      Public
      Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2
      HTML
      •
      MIT License
      •1•5•1•0•Updated Nov 20, 2024Nov 20, 2024

    • loes-2024-neutralization-nextstrain

      Public
      Phylogenetic analysis and visualization of H1N1pdm neutralization data from Loes et al. 2024
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024