Terrance Shea

Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species

This study benchmarks plasmid detection and reconstruction tools on short-read assemblies from diverse bacterial species, finding performance varies with database coverage and assembly quality.

Insights into global antimicrobial resistance dynamics through the sequencing of enteric bacteria from U.S. international travelers

This study sequences AMR bacteria from U.S. travelers to identify regional resistance patterns and detect emerging threats.

Comparative genomics of Cryptococcus and Kwoniella reveals pathogenesis evolution and contrasting karyotype dynamics via intercentromeric recombination or chromosome fusion

The paper compares the genomes of pathogenic and non-pathogenic Cryptococcus species with related Kwoniella species, revealing gene gains/losses and chromosome fusion mechanisms linked to pathogenesis.

Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

The paper develops a method to trace horizontal gene transfer and persistence of carbapenem resistance genes across bacterial species using genomic data from clinical isolates.

Chromosomal rearrangements and loss of subtelomeric adhesins linked to clade-specific phenotypes in Candida auris

The paper identifies chromosomal rearrangements and loss of subtelomeric adhesins in Clade II of Candida auris, linking these to reduced virulence and outbreak potential compared to other clades.

Evolutionary persistence of DNA methylation for millions of years after ancient loss of a de novo methyltransferase

The paper shows that DNA methylation persists in Cryptococcus neoformans despite the loss of a de novo methyltransferase, with methylation patterns maintained through replication and natural selection.

Whole genome analysis illustrates global clonal population structure of the ubiquitous dermatophyte pathogen Trichophyton rubrum

The paper analyzes genome sequences of Trichophyton rubrum and Trichophyton interdigitale to show that T. rubrum is clonal with limited genetic variation and no evidence of sexual reproduction.