jbloom
I research the evolution of viruses and proteins.
Fred Hutchinson Cancer Research Center; Howard Hughes Medical InstituteSeattle, WA
Pinned Repositories
CoV_vs_flu_CFR
case fatality rates of COVI-19, 1918 influenza, seasonal influenza
epitopefinder
Python package for mapping epitopes to sequences
Huanan_market_samples
Analysis of SARS-CoV-2 read counts versus metagenomic content for Huanan Seafood market sequencing data from Chinese CDC
SARS-CoV-2_PRJNA612766
Analysis of early Wuhan SARS-CoV-2 sequences from deleted SRA BioProject PRJNA612766
SARS2_28Dec2019_Genbank_submission
analysis of SARS-CoV-2 sequence submitted to Genbank on Dec-28-2019
dms_variants
Analyze deep mutational scanning of barcoded variants.
neutcurve
Fit and plot neutralization curves
polyclonal
Model mutational escape from polyclonal antibodies.
SARS2-mut-fitness
Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates
SARS2-RBD-escape-calc
SARS-CoV-2 RBD antibody escape calculator
jbloom's Repositories
jbloom/SARS-CoV-2_PRJNA612766
Analysis of early Wuhan SARS-CoV-2 sequences from deleted SRA BioProject PRJNA612766
jbloom/SARS2_28Dec2019_Genbank_submission
analysis of SARS-CoV-2 sequence submitted to Genbank on Dec-28-2019
jbloom/epitopefinder
Python package for mapping epitopes to sequences
jbloom/Huanan_market_samples
Analysis of SARS-CoV-2 read counts versus metagenomic content for Huanan Seafood market sequencing data from Chinese CDC
jbloom/CoV_vs_flu_CFR
case fatality rates of COVI-19, 1918 influenza, seasonal influenza
jbloom/mutpath
Map mutational paths through protein sequence space
jbloom/PRJNA692319_public
Analysis of Antarctica sequencing samples contaminated with SARS-CoV-2
jbloom/SARS2-clade-spike-diffs
Plot spike differences among SARS-CoV-2 Pango clades
jbloom/eidith-1
⚠️ DEPRECATED ⚠️ Data is now at data.usaid.gov/Global-Health-Security-in-Development-GHSD-/PREDICT-Emerging-Pandemic-Threats-Project/tqea-hwmr
jbloom/Huanan_market_samples_addtl_analysis
additional analysis of metagenomic samples from the Huanan Seafood Market
jbloom/Omicron_clock
Molecular clock analysis on Omicron
jbloom/SARS-CoV-2_Shen_et_al
jbloom/SARS2-clock
Number of mutations relative to Wuhan-Hu-1 in SARS-CoV-2 clades
jbloom/alabaster
Lightweight, configurable Sphinx theme
jbloom/cluster_scripts
Scripts to investigate the SUKS cluster
jbloom/COVID-19
Effect of genetic variants in COVID-19
jbloom/dms_tools
redirect to package hosted on jbloomlab
jbloom/DnaFeaturesViewer
:eye: Python library to plot DNA sequence features (e.g. from Genbank files)
jbloom/epistasis
A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.
jbloom/evofr
Tools for evolutionary forecasting
jbloom/GenomeSciences541
Lectures for Genome Sciences 541
jbloom/GS541-course-page
course webpage for Genome Sciences 541
jbloom/GS541_epistasis_homework
demo and homework for Genome Sciences 541
jbloom/huanan-environmental
jbloom/mapmuts
Map mutations and infer amino-acid preferences from overlapping paired-end amino acid reads
jbloom/nextstrain.org
The Nextstrain website
jbloom/phyloExpCM
phylogenetic analyses with experimentally determined codon models
jbloom/rebuild_Lv_SARS2_tree
Interactive phylogeny of early SARS-CoV-2 that attempts to reproduce Fig 3a of 2024 study by group of Yong-Zhen Zhang
jbloom/SC2_variant_rates
analyze substitution rate and mutation behavior within variants.
jbloom/snakemake
This is the development home of the workflow management system Snakemake. For general information, see