Talima Pearson

MetaTracer assigns taxonomic and gene expression to metatranscriptomic reads using nucleotide alignment, achieving high accuracy in simulated and real datasets.

This study tracks prevalence and co-carriage of respiratory pathogens in nursing home residents, finding distinct colonization patterns and persistence differences.

This paper develops a low-cost amplicon sequencing assay to rapidly characterize Staphylococcus aureus intrahost diversity directly from samples, enabling transmission analysis without whole-genome sequencing.

This paper introduces and validates population sequencing methods to analyze phylogenetic diversity in bacterial populations without haplotype reconstruction, demonstrating applications in tracking transmission and understanding pathogen dynamics.

The paper investigates leptospirosis transmission among brown rats in Boston, finding high genetic structure and limited dispersal, with Leptospira clades linked to specific rat populations and a human case linked to rats.

The paper generates a draft genome of the Sverdlovsk 1979 Bacillus anthracis strain and places it phylogenetically within a clade of vaccine strains, finding no evidence of genetic manipulation.

KlebSeq is a diagnostic tool that detects Klebsiella pneumoniae and identifies antimicrobial resistance and virulence traits using amplicon sequencing for healthcare surveillance.

The paper introduces ISG, an open-source pipeline for identifying and annotating nucleotide variants in bacterial genomes, showing it is faster and more flexible than existing tools.