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    Repositories list

    118 repositories

    • ncov-usa-mig

      Public
      SARS-CoV-2 geographic and demographic structure in the USA
      epidemiologyvirologyinfectious-diseases
      epidemiologyvirologyinfectious-diseases
      HTML
      •0•1•0•0•Updated Aug 28, 2026Aug 28, 2026

    • blotter

      Public
      bedford lab research
      HTML
      •93•68•2•0•Updated Aug 25, 2026Aug 25, 2026

    • mutational-embedding-vectors

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 21, 2026Aug 21, 2026

    • pathogen-embed

      Public
      Create reduced dimension embeddings for pathogen sequences
      Python
      •
      MIT License
      •0•1•3•0•Updated Aug 14, 2026Aug 14, 2026

    • ncov-saltational

      Public
      Characterizing SARS-CoV-2 saltational evolution
      R
      •
      Other
      •0•0•0•0•Updated Aug 7, 2026Aug 7, 2026

    • adaptive-evolution

      Public
      An atlas of continuous adaptive evolution in endemic human viruses
      Jupyter Notebook
      •0•5•0•0•Updated Aug 2, 2026Aug 2, 2026

    • bacterial-args

      Public
      Recombination-aware bacterial phylgoeography using ARGs
      Jupyter Notebook
      •0•0•0•1•Updated Jul 22, 2026Jul 22, 2026

    • fitness-flux

      Public
      Fitness flux in SARS-CoV-2 and influenza H3N2
      Wolfram Language
      •2•1•0•0•Updated Jul 16, 2026Jul 16, 2026

    • rt-from-frequency-dynamics

      Public
      Inferring variant-specific reproduction numbers from case counts and sequencing data
      Wolfram Language
      •
      MIT License
      •5•45•3•1•Updated Jul 6, 2026Jul 6, 2026

    • blotter-deploy

      Public
      Script to build and deploy Bedford lab website
      Ruby
      •0•0•0•2•Updated Jun 30, 2026Jun 30, 2026

    • trajectories

      Public
      Evolutionary trajectories
      Python
      •
      Other
      •1•1•0•0•Updated Jun 24, 2026Jun 24, 2026

    • evofr

      Public
      Tools for evolutionary forecasting
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •1•14•16•0•Updated Jun 19, 2026Jun 19, 2026

    • trellis

      Public
      Evolutionary simulations of lattice proteins
      Python
      •
      Other
      •0•1•0•0•Updated Jun 3, 2026Jun 3, 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 May 27, 2026May 27, 2026

    • snakemake-benchmark-stats

      Public
      Statistics for your Snakemake run from benchmark files.
      JavaScript
      •0•0•0•0•Updated Apr 28, 2026Apr 28, 2026

    • mpox-la

      Public
      Mpox phylodynamics in Los Angeles County, USA, 2023-2024
      Jupyter Notebook
      •0•0•0•0•Updated Mar 8, 2026Mar 8, 2026

    • phylogeo-signal

      Public
      Characterizing the informativeness of pathogen genome sequences
      R
      •
      MIT License
      •0•0•0•0•Updated Jan 16, 2026Jan 16, 2026

    • esm-selection

      Public
      Correlating seasonal influenza fitness with ESM predictions
      Python
      •0•0•0•0•Updated Jan 8, 2026Jan 8, 2026

    • cytb

      Public
      Nextstrain build for mammalian cytochrome b
      Python
      •
      Other
      •1•0•0•1•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•1•0•0•Updated Dec 3, 2025Dec 3, 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

    • 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

    • 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
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