Jennifer Chang

Nextstrain automates real-time phylogenetic analysis of open data for endemic and emerging pathogens

Standardized Snakemake pipelines on GitHub Actions fetch open sequence data, curate it, and publish daily or weekly updated phylogenies for 21 viruses and Mycobacterium tuberculosis.

Sources and sinks of influenza A virus genomic diversity in swine from 2009 to 2022 in the United States

This study quantifies the sources and sinks of influenza A virus genomic diversity in U.S. swine from 2009 to 2022, showing regional hotspots and the role of swine transport in diversity spread.

Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella, a global pest of cotton

The paper presents the first chromosome-level genome assembly of the pink bollworm, providing a complete reference for studying Bt resistance and molecular genetics.

polishCLR: a Nextflow workflow for polishing PacBio CLR genome assemblies

polishCLR is a Nextflow workflow for polishing PacBio CLR genome assemblies using best practices, improving accuracy through multiple polishing rounds and evaluation tools.

A chromosome-scale genome assembly of a Bacillus thuringiensis Cry1Ac insecticidal protein resistant strain of Helicoverpa zea

The paper presents a chromosome-scale genome assembly of a Bt-resistant Helicoverpa zea strain to aid in understanding resistance mechanisms and crop protection strategies.