Jesse Bloom's Projects
Lightweight, configurable Sphinx theme
Scripts to investigate the SUKS cluster
case fatality rates of COVI-19, 1918 influenza, seasonal influenza
Effect of genetic variants in COVID-19
redirect to package hosted on jbloomlab
:eye: Python library to plot DNA sequence features (e.g. from Genbank files)
⚠️ DEPRECATED ⚠️ Data is now at data.usaid.gov/Global-Health-Security-in-Development-GHSD-/PREDICT-Emerging-Pandemic-Threats-Project/tqea-hwmr
A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.
Python package for mapping epitopes to sequences
Tools for evolutionary forecasting
High-school level educational module that uses phylogenetics to study flu
Lectures for Genome Sciences 541
course webpage for Genome Sciences 541
demo and homework for Genome Sciences 541
Analysis of SARS-CoV-2 read counts versus metagenomic content for Huanan Seafood market sequencing data from Chinese CDC
additional analysis of metagenomic samples from the Huanan Seafood Market
documentation pages
Map mutations and infer amino-acid preferences from overlapping paired-end amino acid reads
Map mutational paths through protein sequence space
Analysis of mutations in influenza neuraminidase
The Nextstrain website
Molecular clock analysis on Omicron
Analysis of mutations in pandemic H1N1 HA at position 166 (H3 numbering)
phylogenetic analyses with experimentally determined codon models
Analysis of Antarctica sequencing samples contaminated with SARS-CoV-2
Interactive phylogeny of early SARS-CoV-2 that attempts to reproduce Fig 3a of 2024 study by group of Yong-Zhen Zhang
Analysis of early Wuhan SARS-CoV-2 sequences from deleted SRA BioProject PRJNA612766
Plot spike differences among SARS-CoV-2 Pango clades