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    • A website for the Bloom lab
      Vue
      0100Updated Apr 23, 2026Apr 23, 2026
    • Sequencing-based neutralization assays to measure specificity of vaccine response to HAs from H1N1 strains circulating in 2023-2024
      Jupyter Notebook
      MIT License
      0000Updated Apr 17, 2026Apr 17, 2026
    • Pipeline for analyzing sequencing-based neutralization assays
      Python
      MIT License
      2100Updated Apr 14, 2026Apr 14, 2026
    • Spike protein sequences and tree of different SARS-CoV-2 Pango lineages
      Python
      MIT License
      0000Updated Apr 13, 2026Apr 13, 2026
    • Build interactive `nextstrain` trees on protein sequences designed to display neutralization titer values
      Python
      MIT License
      0010Updated Apr 10, 2026Apr 10, 2026
    • phydms

      Public
      phylogenetic analyses informed by deep mutational scanning data
      HTML
      GNU General Public License v3.0
      61522Updated Apr 5, 2026Apr 5, 2026
    • Near real-time data on the human neutralizing antibody landscape to influenza virus as of early 2026 to inform vaccine-strain selection
      HTML
      MIT License
      1010Updated Mar 12, 2026Mar 12, 2026
    • HTML
      MIT License
      0100Updated Mar 9, 2026Mar 9, 2026
    • Comparison of amino-acid preferences across influenza HA subtypes
      HTML
      0010Updated Mar 8, 2026Mar 8, 2026
    • sequencing-based neutralization assay on H3N2 HA variants from 2023-2024
      Jupyter Notebook
      0200Updated Mar 3, 2026Mar 3, 2026
    • Jupyter Notebook
      0000Updated Feb 12, 2026Feb 12, 2026
    • dmslogo

      Public
      draw sequence logos tailored to deep mutational scanning (DMS) data
      Jupyter Notebook
      GNU General Public License v3.0
      11220Updated Feb 12, 2026Feb 12, 2026
    • Quantitative analysis of virus neutralization by IgG versus Fab antibody forms accounting for IgG avidity and the possibility of ligand depletion for potent ant…
      HTML
      MIT License
      0000Updated Jan 19, 2026Jan 19, 2026
    • Python
      0000Updated Jan 9, 2026Jan 9, 2026
    • Model mutational escape from polyclonal antibodies.
      Jupyter Notebook
      Other
      0330Updated Dec 12, 2025Dec 12, 2025
    • Identities among SARS-CoV-2 variants and SARS-related coronaviruses
      HTML
      1210Updated Nov 11, 2025Nov 11, 2025
    • neutcurve

      Public
      Fit and plot neutralization curves
      Jupyter Notebook
      GNU General Public License v3.0
      3900Updated Nov 4, 2025Nov 4, 2025
    • Align sequences and then parse features.
      Jupyter Notebook
      Other
      101710Updated Oct 24, 2025Oct 24, 2025
    • Pipeline for identifying antibody escape mutations in antibody passaged virus
      HTML
      0000Updated Sep 4, 2025Sep 4, 2025
    • sequencing-based neutralization assays using 2023-2024 H3/H1 libraries and sera from the Ellebedy lab
      HTML
      0000Updated Jul 9, 2025Jul 9, 2025
    • Jupyter Notebook
      0000Updated Jun 3, 2025Jun 3, 2025
    • binarymap

      Public
      Binary representations of protein/nucleotide sequences.
      Python
      Other
      1000Updated Apr 6, 2025Apr 6, 2025
    • Growth rates of influenza viruses with HAs in H3 2023-2024 sequencing-based neutralization libraries
      HTML
      MIT License
      0000Updated Mar 12, 2025Mar 12, 2025
    • deep mutational scanning of the CGGnaive antibody
      Jupyter Notebook
      0121Updated Feb 3, 2025Feb 3, 2025
    • Deep mutational scanning of Zika virus strain MR766 nonstructural protein 3 (NS3) with Matt Evans lab
      Jupyter Notebook
      0201Updated Jan 8, 2025Jan 8, 2025
    • Deep mutational scanning phenotypes of clade 2.3.4.4b influenza H5 HA
      Python
      MIT License
      1210Updated Dec 16, 2024Dec 16, 2024
    • deep mutational scanning of ZIKV E protein +/- IFN with Matt Evans lab
      Jupyter Notebook
      0110Updated Dec 12, 2024Dec 12, 2024
    • SARS-CoV-2 RBD antibody escape calculator
      Jupyter Notebook
      GNU General Public License v3.0
      31300Updated Nov 19, 2024Nov 19, 2024
    • Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates
      Jupyter Notebook
      MIT License
      72131Updated Nov 8, 2024Nov 8, 2024
    • A biologist's guide to crafting quality code
      JavaScript
      1410Updated Nov 5, 2024Nov 5, 2024
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