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flu-ha-h5-2.3.4.4-dms-informed-surveillance

Deep mutational scanning phenotypes of clade 2.3.4.4b influenza H5 HA

flu_mortality

Influenza excess mortality over time

flu_pb1flank-gfp_neut_assay

PB1flank-eGFP neutralization assay details

flu_seqneut_drive_2021-22_repeat_vax

sequencing-based neutralization assays with H1N1 library against 2021-2022 DRIVE sera

flu_single_cell

clean analysis of infections with "pure" influenza virus sequenced on 10X Chromium

flua-20_d2_map_in_vivo

gga_codon_muts_oligo_design

Design oligos for Golden-Gate assembly mutagenesis

ha_antibody_ease_of_escape

comparison of ease of escape of WSN influenza from various narrow and broad anti-HA antibodies

ha_numbering

converts among numbering schemes for influenza hemagglutinin

ha_stalkbnab_map

Mutational antigenic profiling of stalk bnAbs in H1 vs H3

herpesvirus-glycoprotein-analysis

Analysis of natural diversity in herpesvirus glycoproteins

hiv_broad_human_sera_map

Deep mutational scanning of HIV Envelope using human sera

hiv_env_macaque_receptor_dms

deep mutational scanning of HIV BF520 Env in cells with macaque receptors

hom_m1_dms

Nancy Hom M1 deep mutational scanning analyzed by Lauren Gentles

human-cov-antigenic-drift-references

papers / background on human seasonal CoV antigenic drift

ifnsorted_flu_single_cell

single-cell sequencing of flu infected cells enriched for IFN+ ones

influenzatransmissionhuilingcollaboration

collaboration with Hui-Ling Yen to study influenza transmission

jbloomlab.github.io

A website for the Bloom lab

latticeproteins

Implements lattice models of proteins, and allows their evolution

map_118

Mutational anitgenic profiling of 1-18

map_flu_serum_perth2009_h3_ha

mutational antigenic profiling of Perth/2009 H3 HA against serum

map_flu_serum_vietnam_h3_perth2009

mutational antigenic profiling of 2010-2011 Vietnam serum samples against Perth/2009 (H3N2)

map_nhp_fp_abs

Mutational antigenic profiling of a panel FP-targeting antibody lineages isolated from vaccinated NHP.

map_vaccine_fp_abs

mers-pdf2180-rbd_dms

Deep mutational scanning of the MERS and PDF-2180 CoV receptor-binding domains

mev_sspe_dynamics

A spatial analysis of measles virus variant dynamics in the brain.

multiplet_freq

Calculate multiplet frequency in single-cell RNA sequencing when cells are mixed in arbitrary proportions

mutational_antigenic_profiling

Computer code for the analyses presented in "Complete mapping of viral escape from neutralizing antibodies" (PLoS Pathog. 2017 Mar 13;13(3):e1006271. doi: 10.1371/journal.ppat.1006271)

neutcurve

Fit and plot neutralization curves

new_2nd_gen_ba2_variant

simple tabulation of mutations in new second-generation BA.2 saltation variant