Repositories list

• ncov-saltational

  Public
  Characterizing SARS-CoV-2 saltational evolution

  R

  •

  Other

  •00 forks in blab/ncov-saltational•00 stars in blab/ncov-saltational•00 issues in blab/ncov-saltational•00 pull requests in blab/ncov-saltational•Updated Nov 3, 2026Nov 3, 2026

• ncov-usa-mig

  Public
  SARS-CoV-2 geographic and demographic structure in the USA

  epidemiologyvirologyinfectious-diseases

  epidemiologyvirologyinfectious-diseases

  HTML

  •00 forks in blab/ncov-usa-mig•11 star in blab/ncov-usa-mig•00 issues in blab/ncov-usa-mig•00 pull requests in blab/ncov-usa-mig•Updated Nov 2, 2026Nov 2, 2026

• blotter-deploy

  Public
  Script to build and deploy Bedford lab website

  Ruby

  •00 forks in blab/blotter-deploy•00 stars in blab/blotter-deploy•00 issues in blab/blotter-deploy•11 pull request in blab/blotter-deploy•Updated Oct 23, 2026Oct 23, 2026

• blotter

  Public
  bedford lab research

  HTML

  •9393 forks in blab/blotter•6868 stars in blab/blotter•22 issues in blab/blotter•00 pull requests in blab/blotter•Updated Oct 23, 2026Oct 23, 2026

• fitness-flux

  Public
  Fitness flux in SARS-CoV-2 and influenza H3N2

  Wolfram Language

  •22 forks in blab/fitness-flux•11 star in blab/fitness-flux•00 issues in blab/fitness-flux•00 pull requests in blab/fitness-flux•Updated Oct 16, 2026Oct 16, 2026

• mutational-embedding-vectors

  Public
  Jupyter Notebook

  •00 forks in blab/mutational-embedding-vectors•00 stars in blab/mutational-embedding-vectors•00 issues in blab/mutational-embedding-vectors•00 pull requests in blab/mutational-embedding-vectors•Updated Sep 26, 2026Sep 26, 2026

• pathogen-embed

  Public
  Create reduced dimension embeddings for pathogen sequences

  Python

  •

  MIT License

  •00 forks in blab/pathogen-embed•11 star in blab/pathogen-embed•33 issues in blab/pathogen-embed•00 pull requests in blab/pathogen-embed•Updated Aug 14, 2026Aug 14, 2026

• adaptive-evolution

  Public
  An atlas of continuous adaptive evolution in endemic human viruses

  Jupyter Notebook

  •00 forks in blab/adaptive-evolution•55 stars in blab/adaptive-evolution•00 issues in blab/adaptive-evolution•00 pull requests in blab/adaptive-evolution•Updated Aug 2, 2026Aug 2, 2026

• bacterial-args

  Public
  Recombination-aware bacterial phylgoeography using ARGs

  Jupyter Notebook

  •00 forks in blab/bacterial-args•00 stars in blab/bacterial-args•00 issues in blab/bacterial-args•11 pull request in blab/bacterial-args•Updated Jul 22, 2026Jul 22, 2026

• rt-from-frequency-dynamics

  Public
  Inferring variant-specific reproduction numbers from case counts and sequencing data

  Wolfram Language

  •

  MIT License

  •55 forks in blab/rt-from-frequency-dynamics•4545 stars in blab/rt-from-frequency-dynamics•33 issues in blab/rt-from-frequency-dynamics•11 pull request in blab/rt-from-frequency-dynamics•Updated Jul 6, 2026Jul 6, 2026

• trajectories

  Public
  Evolutionary trajectories

  Python

  •

  Other

  •11 fork in blab/trajectories•11 star in blab/trajectories•00 issues in blab/trajectories•00 pull requests in blab/trajectories•Updated Jun 24, 2026Jun 24, 2026

• evofr

  Public
  Tools for evolutionary forecasting

  Jupyter Notebook

  •

  GNU Affero General Public License v3.0

  •11 fork in blab/evofr•1414 stars in blab/evofr•1616 issues in blab/evofr•00 pull requests in blab/evofr•Updated Jun 19, 2026Jun 19, 2026

• trellis

  Public
  Evolutionary simulations of lattice proteins

  Python

  •

  Other

  •00 forks in blab/trellis•11 star in blab/trellis•00 issues in blab/trellis•00 pull requests in blab/trellis•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

  •00 forks in blab/kikawa-seqneut-2025-2026-VCM•00 stars in blab/kikawa-seqneut-2025-2026-VCM•00 issues in blab/kikawa-seqneut-2025-2026-VCM•00 pull requests in blab/kikawa-seqneut-2025-2026-VCM•Updated May 27, 2026May 27, 2026

• snakemake-benchmark-stats

  Public
  Statistics for your Snakemake run from benchmark files.

  JavaScript

  •00 forks in blab/snakemake-benchmark-stats•00 stars in blab/snakemake-benchmark-stats•00 issues in blab/snakemake-benchmark-stats•00 pull requests in blab/snakemake-benchmark-stats•Updated Apr 28, 2026Apr 28, 2026

• mpox-la

  Public
  Mpox phylodynamics in Los Angeles County, USA, 2023-2024

  Jupyter Notebook

  •00 forks in blab/mpox-la•00 stars in blab/mpox-la•00 issues in blab/mpox-la•00 pull requests in blab/mpox-la•Updated Mar 8, 2026Mar 8, 2026

• phylogeo-signal

  Public
  Characterizing the informativeness of pathogen genome sequences

  R

  •

  MIT License

  •00 forks in blab/phylogeo-signal•00 stars in blab/phylogeo-signal•00 issues in blab/phylogeo-signal•00 pull requests in blab/phylogeo-signal•Updated Jan 16, 2026Jan 16, 2026

• esm-selection

  Public
  Correlating seasonal influenza fitness with ESM predictions

  Python

  •00 forks in blab/esm-selection•00 stars in blab/esm-selection•00 issues in blab/esm-selection•00 pull requests in blab/esm-selection•Updated Jan 8, 2026Jan 8, 2026

• cytb

  Public
  Nextstrain build for mammalian cytochrome b

  Python

  •

  Other

  •11 fork in blab/cytb•00 stars in blab/cytb•00 issues in blab/cytb•11 pull request in blab/cytb•Updated Jan 8, 2026Jan 8, 2026

• sequence-vaes

  Public
  Variational Autoencoders for biological sequences

  Jupyter Notebook

  •00 forks in blab/sequence-vaes•00 stars in blab/sequence-vaes•00 issues in blab/sequence-vaes•00 pull requests in blab/sequence-vaes•Updated Dec 16, 2025Dec 16, 2025

• embedded-pathways

  Public
  Using ESM to chart evolution through embedding space

  Mathematica

  •

  Other

  •11 fork in blab/embedded-pathways•00 stars in blab/embedded-pathways•00 issues in blab/embedded-pathways•00 pull requests in blab/embedded-pathways•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

  •00 forks in blab/flu-forecasting-delays•11 star in blab/flu-forecasting-delays•00 issues in blab/flu-forecasting-delays•00 pull requests in blab/flu-forecasting-delays•Updated Dec 3, 2025Dec 3, 2025

• relative-fitness-mechanisms

  Public
  Frequency dynamics predict viral fitness, antigenic relationships and epidemic growth

  Jupyter Notebook

  •00 forks in blab/relative-fitness-mechanisms•33 stars in blab/relative-fitness-mechanisms•00 issues in blab/relative-fitness-mechanisms•00 pull requests in blab/relative-fitness-mechanisms•Updated Oct 14, 2025Oct 14, 2025

• cholera

  Public
  Jupyter Notebook

  •00 forks in blab/cholera•11 star in blab/cholera•00 issues in blab/cholera•00 pull requests in blab/cholera•Updated Oct 7, 2025Oct 7, 2025

• egg-adaptation

  Public
  Adaptation of influenza virus to chicken eggs

  Jupyter Notebook

  •00 forks in blab/egg-adaptation•00 stars in blab/egg-adaptation•00 issues in blab/egg-adaptation•00 pull requests in blab/egg-adaptation•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

  •00 forks in blab/kikawa-seqneut-2025-VCM•00 stars in blab/kikawa-seqneut-2025-VCM•00 issues in blab/kikawa-seqneut-2025-VCM•00 pull requests in blab/kikawa-seqneut-2025-VCM•Updated Sep 4, 2025Sep 4, 2025

• ai-phylogeo

  Public
  Jupyter Notebook

  •00 forks in blab/ai-phylogeo•00 stars in blab/ai-phylogeo•00 issues in blab/ai-phylogeo•00 pull requests in blab/ai-phylogeo•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

  00 forks in blab/vscode-guide•00 stars in blab/vscode-guide•00 issues in blab/vscode-guide•00 pull requests in blab/vscode-guide•Updated Jul 23, 2025Jul 23, 2025

• measurements-panel

  Public
  Manuscript and data describing joint visualization of influenza serology and phylogeny

  TeX

  •

  MIT License

  •00 forks in blab/measurements-panel•00 stars in blab/measurements-panel•00 issues in blab/measurements-panel•00 pull requests in blab/measurements-panel•Updated May 14, 2025May 14, 2025

• popcast

  Public
  Long-term forecasts for pathogen populations

  Python

  •

  MIT License

  •00 forks in blab/popcast•11 star in blab/popcast•11 issue in blab/popcast•00 pull requests in blab/popcast•Updated May 7, 2025May 7, 2025