jbloomlab's repositories
SARS2-mut-fitness
Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates
alignparse
Align sequences and then parse features.
SARS2-RBD-escape-calc
SARS-CoV-2 RBD antibody escape calculator
dms_variants
Analyze deep mutational scanning of barcoded variants.
new_2nd_gen_BA2_variant
simple tabulation of mutations in new second-generation BA.2 saltation variant
barcoded_flu_pdmH1N1
Barcoded pdmH1N1 virus hashing experiment
reedmuenchcalculator
A python script for computing TCID50 using the Reed-Muench formula
polyclonal
Model mutational escape from polyclonal antibodies.
CoV_identities
Identities among SARS-CoV-2 variants and SARS-related coronaviruses
Ab-CGGnaive_DMS
deep mutational scanning of the CGGnaive antibody
MeV_SSPE_Dynamics
A spatial analysis of measles virus variant dynamics in the brain.
SARS2-cocktail-vax-for-Weissman
SARS-CoV-2 cocktail vaccine of designed spike mutants
ZIKV_DMS_NS3_EvansLab
Deep mutational scanning of Zika virus strain MR766 nonstructural protein 3 (NS3) with Matt Evans lab
ZIKV_DMS_NS5_EvansLab
deep mutational scanning of ZIKV E protein +/- IFN with Matt Evans lab
flu_seqneut_DRIVE_2021-22_repeat_vax
sequencing-based neutralization assays with H1N1 library against 2021-2022 DRIVE sera
HIV_Broad_Human_Sera_MAP
Deep mutational scanning of HIV Envelope using human sera
SARS-CoV-2_aerosol_bottleneck
Investigating how aerosol size impacts the SARS-CoV-2 transmission bottleneck.
SARS2-cocktail-vax
Cocktail of SARS-CoV-2 spikes with predicted future mutation
SARS2-RBD-escape-mutants
designed escape mutants of the RBD of SARS-CoV-2 that contain potential future antigenic mutations
SARS2-spike-predictor-phenos
SARS-CoV-2 spike phenotypes (from DMS and other sources) potentially useful for predicting evolution
seqneut-pipeline
Pipeline for analyzing sequencing-based neutralization assays
ZIKV_MAP_GooLab
Zika virus mutational antigenic profiling with Leslie Goo lab