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    136 repositories

    • jbloomlab.github.io

      Public
      A website for the Bloom lab
      Vue
      •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • flu_seqneut_H3N2_2023-2024

      Public
      sequencing-based neutralization assay on H3N2 HA variants from 2023-2024
      Jupyter Notebook
      •0•0•0•0•Updated Dec 16, 2024Dec 16, 2024

    • 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•1•1•0•Updated Dec 16, 2024Dec 16, 2024

    • polyclonal

      Public
      Model mutational escape from polyclonal antibodies.
      Jupyter Notebook
      •
      Other
      •0•3•3•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

    • Ab-CGGnaive_DMS

      Public
      deep mutational scanning of the CGGnaive antibody
      Jupyter Notebook
      •0•1•3•1•Updated Nov 22, 2024Nov 22, 2024

    • SARS2-RBD-escape-calc

      Public
      SARS-CoV-2 RBD antibody escape calculator
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •2•11•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
      •5•19•3•1•Updated Nov 8, 2024Nov 8, 2024

    • bench-to-byte

      Public
      A biologist's guide to crafting quality code
      JavaScript
      •0•3•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•0•0•1•Updated Oct 7, 2024Oct 7, 2024

    • seqneut-pipeline

      Public
      Pipeline for analyzing sequencing-based neutralization assays
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•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

    • neutcurve

      Public
      Fit and plot neutralization curves
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•9•0•0•Updated Sep 24, 2024Sep 24, 2024

    • binarymap

      Public
      Binary representations of protein/nucleotide sequences.
      Python
      •
      Other
      •1•0•0•0•Updated Sep 20, 2024Sep 20, 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

    • alignparse

      Public
      Align sequences and then parse features.
      Jupyter Notebook
      •
      Other
      •9•17•0•0•Updated Aug 25, 2024Aug 25, 2024

    • gga_codon_muts_oligo_design

      Public
      Design oligos for Golden-Gate assembly mutagenesis
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 24, 2024Aug 24, 2024

    • ZIKV_DMS_NS3_EvansLab

      Public
      Deep mutational scanning of Zika virus strain MR766 nonstructural protein 3 (NS3) with Matt Evans lab
      Jupyter Notebook
      •0•1•0•0•Updated Jul 26, 2024Jul 26, 2024

    • phydms

      Public
      phylogenetic analyses informed by deep mutational scanning data
      phylogeneticsmolecular-evolutiondeep-mutational-scanningprotein-evolution
      HTML
      •
      GNU General Public License v3.0
      •4•14•2•2•Updated Jun 12, 2024Jun 12, 2024

    • reedmuenchcalculator

      Public
      A python script for computing TCID50 using the Reed-Muench formula
      Python
      •3•4•0•0•Updated Jun 4, 2024Jun 4, 2024

    • SARS2-RBD-escape-mutants

      Public
      designed escape mutants of the RBD of SARS-CoV-2 that contain potential future antigenic mutations
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated May 2, 2024May 2, 2024

    • SARS2-cocktail-vax

      Public
      Cocktail of SARS-CoV-2 spikes with predicted future mutation
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Apr 29, 2024Apr 29, 2024

    • SARS-CoV-2-RBD_MAP_Karolinska

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 21, 2024Apr 21, 2024

    • dms_variants

      Public
      Analyze deep mutational scanning of barcoded variants.
      Jupyter Notebook
      •
      Other
      •9•6•1•0•Updated Apr 10, 2024Apr 10, 2024

    • ZIKV_Y2H_198-209_combinatorial_library

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Mar 11, 2024Mar 11, 2024

    • SARS-CoV-2_aerosol_bottleneck

      Public
      Investigating how aerosol size impacts the SARS-CoV-2 transmission bottleneck.
      Python
      •0•0•0•0•Updated Jan 31, 2024Jan 31, 2024

    • CoV_identities

      Public
      Identities among SARS-CoV-2 variants and SARS-related coronaviruses
      HTML
      •1•2•1•0•Updated Nov 9, 2023Nov 9, 2023

    • SARS-CoV-2-XBB.1.5_Spike_DMS_validations

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 7, 2023Nov 7, 2023

    • dmslogo

      Public
      draw sequence logos tailored to deep mutational scanning (DMS) data
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•12•2•0•Updated Oct 11, 2023Oct 11, 2023

    • MeV_SSPE_Dynamics

      Public
      A spatial analysis of measles virus variant dynamics in the brain.
      HTML
      •0•1•0•0•Updated Oct 5, 2023Oct 5, 2023