Jesse Bloom
jbloom
I research the evolution of viruses and proteins.
Languages
Top Repositories
Analysis of early Wuhan SARS-CoV-2 sequences from deleted SRA BioProject PRJNA612766
analysis of SARS-CoV-2 sequence submitted to Genbank on Dec-28-2019
Analysis of SARS-CoV-2 read counts versus metagenomic content for Huanan Seafood market sequencing data from Chinese CDC
Python package for mapping epitopes to sequences
case fatality rates of COVI-19, 1918 influenza, seasonal influenza
Map mutational paths through protein sequence space
Repositories
37The Nextstrain website
Match protein sequences to the closest Genbank nucleotide sequences encoding the protein
Analysis of early Wuhan SARS-CoV-2 sequences from deleted SRA BioProject PRJNA612766
Phylogenetic analyses of early SARS-CoV-2 trees
Analysis of SARS-CoV-2 read counts versus metagenomic content for Huanan Seafood market sequencing data from Chinese CDC
tree of sequences from Crits-Christoph et al (2024) paper
Tools for evolutionary forecasting
analysis of SARS-CoV-2 sequence submitted to Genbank on Dec-28-2019
Interactive phylogeny of early SARS-CoV-2 that attempts to reproduce Fig 3a of 2024 study by group of Yong-Zhen Zhang
Plot spike differences among SARS-CoV-2 Pango clades
case fatality rates of COVI-19, 1918 influenza, seasonal influenza
additional analysis of metagenomic samples from the Huanan Seafood Market
Number of mutations relative to Wuhan-Hu-1 in SARS-CoV-2 clades
Molecular clock analysis on Omicron
Lightweight, configurable Sphinx theme
Python package for mapping epitopes to sequences
Map mutational paths through protein sequence space
No description provided.
analyze substitution rate and mutation behavior within variants.
⚠️ DEPRECATED ⚠️ Data is now at data.usaid.gov/Global-Health-Security-in-Development-GHSD-/PREDICT-Emerging-Pandemic-Threats-Project/tqea-hwmr
Analysis of Antarctica sequencing samples contaminated with SARS-CoV-2
No description provided.
Effect of genetic variants in COVID-19
documentation pages
Scripts to investigate the SUKS cluster
This is the development home of the workflow management system Snakemake. For general information, see
Lectures for Genome Sciences 541
:eye: Python library to plot DNA sequence features (e.g. from Genbank files)
demo and homework for Genome Sciences 541
Analysis of mutations in influenza neuraminidase