James C. Kosmopoulos

The paper shows RNA polymerase backtracking promotes type III-A CRISPR DNA targeting by inhibiting GreA anti-backtracking factors, which suppress Cas10-Csm activity.

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.

vClassifier provides species-level taxonomic classification of prokaryotic viruses using phylogeny-informed methods, achieving high congruence with ICTV and NCBI Virus databases.

The paper examines microbial ecophysiology and carbon accrual in peatlands before and after restoration, finding that restored sites show reduced microbial growth rates compared to degraded sites.

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 introduces V-score and VL-score metrics to identify viral signatures in protein families and genomes, finding 38-77% of families are linked to viruses, up to 17x more auxiliary viral genes.

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