Research/Bioinformatics
Finding defense systems in genomes
Most projects in the lab start on the computer. We search bacterial and phage genomes for new immune systems, place them on phylogenetic trees and compare the genes around them to predict what they do.
Skip the TreeMapper demo
Simulated example, not a real analysis: 64 reverse-transcriptase loci on either strand, flipped so each RT points forward and aligned on the RT gene, with plaque-assay results and the reduction in efficiency of plating.
01Find
Bioinformatics & phylogenetics
A typical workflow
- Search genome databases for candidate defense genes
- Group related proteins and build phylogenetic trees
- Compare gene neighborhoods to predict function, then pick candidates to test
- Structure-guided HMM searches
- Phylogenetic trees
- Genome-neighborhood analysis
- TreeMapper
Selected papers
- A census of anti-CRISPR proteins reveals AcrIE9 and AcrIE13 as inhibitors of the Escherichia coli K12 type IE CRISPR-Cas systemPNAS · 2026
- Discovery of Diverse CRISPR Leader Motifs, Putative Functions, and Applications for Enhanced CRISPR Detection and Subtype AnnotationThe CRISPR Journal · 2025
- The Rise and Fall of SARS-CoV-2 Variants and Ongoing Diversification of OmicronViruses · 2022
- SARS-CoV-2 genomic surveillance identifies naturally occurring truncation of ORF7a that limits immune suppressionCell Reports · 2021
- Temporal Detection and Phylogenetic Assessment of SARS-CoV-2 in Municipal WastewaterCell Reports Medicine · 2020
- A Unified Resource for Tracking Anti-CRISPR NamesThe CRISPR Journal · 2018