Cody Martin

CheckAMG identifies auxiliary viral genes by combining annotation-based prediction with a genome-language model, improving accuracy and uncovering novel genes with no sequence similarity to references.

The paper introduces PST, a protein-based genome language model that outperforms existing methods in relating viral genomes through shared protein content and demonstrates structural and functional awareness.

This study identifies the lysis proteins of phage N4 and shows they differ from T4 in their regulation of lysis inhibition, suggesting distinct mechanisms for controlling phage yield.

This study identifies viruses from hydrothermal vents and shows that while many are endemic, some share proteins related to core functions, suggesting geology influences viral ecology and host coevolution.

The paper introduces fai and zol for large-scale comparative analysis of gene clusters and MGEs, enabling comprehensive orthology inference and evolutionary studies across thousands of genomes.

The paper introduces Prophage-DB, a database of over 350,000 prophages and 35,000 auxiliary metabolic genes, providing insights into prophage diversity, distribution, and ecological roles.

The paper analyzes a 20-year viral time-series in a freshwater lake to uncover seasonal dynamics, environmental drivers, and evolutionary patterns of viral diversity and ecology.

The paper introduces PHAGEPACK, a CRISPR-based assay to systematically identify host genes affecting phage infectivity, revealing new pathways in both permissive and non-permissive E. coli.

This study investigates the evolutionary history of sulfur oxidation by analyzing SAR324 and related bacterial phyla, finding that they are linked to the origins of the reverse dsr pathway.

The paper investigates the molecular basis of polar lysis in phage λ using time lapse fluorescence microscopy, finding that the holin forms two-dimensional rafts at cell poles before lysis.

ViWrap provides a modular pipeline for analyzing viruses in metagenomes, enabling identification, classification, and host prediction through integration of multiple tools.

This study identifies a phage-encoded cationic antimicrobial peptide, Gp28, that disrupts bacterial outer membranes during lysis, functioning similarly to human antimicrobial peptides like LL-37.