Repositories list

• jbloomlab.github.io

  Public
  A website for the Bloom lab

  Vue

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• seqneut-pipeline

  Public
  Pipeline for analyzing sequencing-based neutralization assays

  Python

  •

  MIT License

  •22 forks•11 star•00 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• SARS2-spike-pango

  Public
  Spike protein sequences and tree of different SARS-CoV-2 Pango lineages

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 13, 2026Apr 13, 2026

• nextstrain-prot-titers-tree

  Public
  Build interactive `nextstrain` trees on protein sequences designed to display neutralization titer values

  Python

  •

  MIT License

  •00 forks•00 stars•11 issue•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• phydms

  Public
  phylogenetic analyses informed by deep mutational scanning data

  phylogeneticsmolecular-evolutiondeep-mutational-scanning+ 1

  phylogeneticsmolecular-evolutiondeep-mutational-scanningprotein-evolution

  HTML

  •

  GNU General Public License v3.0

  •66 forks•1515 stars•22 issues•22 pull requests•Updated Apr 5, 2026Apr 5, 2026

• flu-seqneut-2025to2026

  Public
  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

  •11 fork•00 stars•11 issue•00 pull requests•Updated Mar 12, 2026Mar 12, 2026

• flu-seqneut-2025

  Public
  HTML

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 9, 2026Mar 9, 2026

• ha-preference-shifts

  Public
  Comparison of amino-acid preferences across influenza HA subtypes

  HTML

  •00 forks•00 stars•11 issue•00 pull requests•Updated Mar 8, 2026Mar 8, 2026

• flu_seqneut_H3N2_2023-2024

  Public
  sequencing-based neutralization assay on H3N2 HA variants from 2023-2024

  Jupyter Notebook

  •00 forks•22 stars•00 issues•00 pull requests•Updated Mar 3, 2026Mar 3, 2026

• flu_seqneut_FirstExposures

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated 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

  •11 fork•1212 stars•22 issues•00 pull requests•Updated Feb 12, 2026Feb 12, 2026

• 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 ant…

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 19, 2026Jan 19, 2026

• cov-229E-spike-phylo

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 9, 2026Jan 9, 2026

• polyclonal

  Public
  Model mutational escape from polyclonal antibodies.

  Jupyter Notebook

  •

  Other

  •00 forks•33 stars•33 issues•00 pull requests•Updated Dec 12, 2025Dec 12, 2025

• CoV_identities

  Public
  Identities among SARS-CoV-2 variants and SARS-related coronaviruses

  HTML

  •11 fork•22 stars•11 issue•00 pull requests•Updated Nov 11, 2025Nov 11, 2025

• neutcurve

  Public
  Fit and plot neutralization curves

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •33 forks•99 stars•00 issues•00 pull requests•Updated Nov 4, 2025Nov 4, 2025

• alignparse

  Public
  Align sequences and then parse features.

  Jupyter Notebook

  •

  Other

  •1010 forks•1717 stars•11 issue•00 pull requests•Updated Oct 24, 2025Oct 24, 2025

• Virus-Antibody-Passaging

  Public
  Pipeline for identifying antibody escape mutations in antibody passaged virus

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 9, 2025Jul 9, 2025

• RSV-evolution-neut

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 3, 2025Jun 3, 2025

• binarymap

  Public
  Binary representations of protein/nucleotide sequences.

  Python

  •

  Other

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 6, 2025Apr 6, 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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 12, 2025Mar 12, 2025

• Ab-CGGnaive_DMS

  Public
  deep mutational scanning of the CGGnaive antibody

  Jupyter Notebook

  •00 forks•11 star•22 issues•11 pull request•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

  •00 forks•22 stars•00 issues•11 pull request•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

  •11 fork•22 stars•11 issue•00 pull requests•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

  •00 forks•11 star•11 issue•00 pull requests•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

  •33 forks•1313 stars•00 issues•00 pull requests•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

  •77 forks•2121 stars•33 issues•11 pull request•Updated Nov 8, 2024Nov 8, 2024

• bench-to-byte

  Public
  A biologist's guide to crafting quality code

  JavaScript

  •11 fork•44 stars•11 issue•00 pull requests•Updated Nov 5, 2024Nov 5, 2024