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    147 repositories

    • flu-seqneut-2025to2026

      Public
      Near real-time data on the human neutralizing antibody landscape to influenza virus in late 2025 to early 2026 to inform vaccine-strain selection in February 2026
      Python
      •
      MIT License
      •0•0•2•0•Updated Jan 9, 2026Jan 9, 2026

    • flu_seqneut_pdmH1N1_2023-2024_VaccinatedCohorts

      Public
      Sequencing-based neutralization assays to measure specificity of vaccine response to HAs from H1N1 strains circulating in 2023-2024
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 7, 2026Jan 7, 2026

    • ha-preference-shifts

      Public
      Comparison of amino-acid preferences across influenza HA subtypes
      HTML
      •0•0•1•0•Updated Jan 6, 2026Jan 6, 2026

    • cov-229E-spike-phylo

      Public
      Python
      •0•0•0•0•Updated Jan 5, 2026Jan 5, 2026

    • nextstrain-prot-titers-tree

      Public
      Build interactive `nextstrain` trees on protein sequences designed to display neutralization titer values
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 5, 2026Jan 5, 2026

    • jbloomlab.github.io

      Public
      A website for the Bloom lab
      Vue
      •0•1•0•0•Updated Dec 23, 2025Dec 23, 2025

    • polyclonal

      Public
      Model mutational escape from polyclonal antibodies.
      Jupyter Notebook
      •
      Other
      •0•3•3•0•Updated Dec 12, 2025Dec 12, 2025

    • seqneut-pipeline

      Public
      Pipeline for analyzing sequencing-based neutralization assays
      Python
      •
      MIT License
      •1•1•0•0•Updated Dec 5, 2025Dec 5, 2025

    • CoV_identities

      Public
      Identities among SARS-CoV-2 variants and SARS-related coronaviruses
      HTML
      •1•2•1•0•Updated Nov 11, 2025Nov 11, 2025

    • flu-seqneut-2025

      Public
      HTML
      •
      MIT License
      •0•1•0•0•Updated Nov 5, 2025Nov 5, 2025

    • neutcurve

      Public
      Fit and plot neutralization curves
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•9•0•0•Updated Nov 4, 2025Nov 4, 2025

    • rsv

      Public
      Workflow for RSV analyses on Nextstrain.org
      Python
      •6•0•0•0•Updated Oct 27, 2025Oct 27, 2025

    • alignparse

      Public
      Align sequences and then parse features.
      Jupyter Notebook
      •
      Other
      •10•17•1•0•Updated Oct 24, 2025Oct 24, 2025

    • IgG-vs-Fab-neutralization

      Public
      Quantitative analysis of virus neutralization by IgG versus Fab antibody forms accounting for IgG avidity and the possibility of ligand depletion for potent antibodies.
      HTML
      •
      MIT License
      •0•0•0•0•Updated Oct 10, 2025Oct 10, 2025

    • Virus-Antibody-Passaging

      Public
      Pipeline for identifying antibody escape mutations in antibody passaged virus
      HTML
      •0•0•0•0•Updated Sep 4, 2025Sep 4, 2025

    • flu_seqneut_with_Ellebedy_lab

      Public
      sequencing-based neutralization assays using 2023-2024 H3/H1 libraries and sera from the Ellebedy lab
      HTML
      •0•0•0•0•Updated Jul 9, 2025Jul 9, 2025

    • RSV-evolution-neut

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 3, 2025Jun 3, 2025

    • binarymap

      Public
      Binary representations of protein/nucleotide sequences.
      Python
      •
      Other
      •1•0•0•0•Updated Apr 6, 2025Apr 6, 2025

    • flu_seqneut_H3N2_2023-2024

      Public
      sequencing-based neutralization assay on H3N2 HA variants from 2023-2024
      Jupyter Notebook
      •0•2•0•0•Updated Mar 13, 2025Mar 13, 2025

    • flu_H3_2023_seqneut_vs_growth

      Public
      Growth rates of influenza viruses with HAs in H3 2023-2024 sequencing-based neutralization libraries
      HTML
      •
      MIT License
      •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

    • Ab-CGGnaive_DMS

      Public
      deep mutational scanning of the CGGnaive antibody
      Jupyter Notebook
      •0•1•2•1•Updated Feb 3, 2025Feb 3, 2025

    • ZIKV_DMS_NS3_EvansLab

      Public
      Deep mutational scanning of Zika virus strain MR766 nonstructural protein 3 (NS3) with Matt Evans lab
      Jupyter Notebook
      •0•2•0•1•Updated Jan 8, 2025Jan 8, 2025

    • Flu-HA-H5-2.3.4.4-DMS-informed-surveillance

      Public
      Deep mutational scanning phenotypes of clade 2.3.4.4b influenza H5 HA
      Python
      •
      MIT License
      •1•2•1•0•Updated Dec 16, 2024Dec 16, 2024

    • ZIKV_DMS_NS5_EvansLab

      Public
      deep mutational scanning of ZIKV E protein +/- IFN with Matt Evans lab
      Jupyter Notebook
      •0•1•1•0•Updated Dec 12, 2024Dec 12, 2024

    • SARS2-RBD-escape-calc

      Public
      SARS-CoV-2 RBD antibody escape calculator
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•12•0•0•Updated Nov 19, 2024Nov 19, 2024

    • SARS2-mut-fitness

      Public
      Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates
      Jupyter Notebook
      •
      MIT License
      •6•21•3•1•Updated Nov 8, 2024Nov 8, 2024

    • bench-to-byte

      Public
      A biologist's guide to crafting quality code
      JavaScript
      •1•4•1•0•Updated Nov 5, 2024Nov 5, 2024

    • SARS2-spike-predictor-phenos

      Public
      SARS-CoV-2 spike phenotypes (from DMS and other sources) potentially useful for predicting evolution
      Jupyter Notebook
      •
      MIT License
      •0•1•0•1•Updated Oct 7, 2024Oct 7, 2024

    • flu_seqneut_DRIVE_2021-22_repeat_vax

      Public
      sequencing-based neutralization assays with H1N1 library against 2021-2022 DRIVE sera
      Jupyter Notebook
      •0•0•0•0•Updated Sep 24, 2024Sep 24, 2024

    • Herpesvirus-Glycoprotein-Analysis

      Public
      Analysis of natural diversity in herpesvirus glycoproteins
      Python
      •
      MIT License
      •0•0•2•0•Updated Sep 18, 2024Sep 18, 2024