Allison F. Carey

FLASH predicts phenotype from sequence using deep learning, achieving high accuracy on unseen variants and identifying new virulence predictors across microbes.

The paper detects Mtb transcripts in human granuloma cells using scRNA-seq, finding sequence variations suggesting potential adaptive mechanisms.

This study identifies Mtb genes essential for survival in vaccinated and previously infected hosts using TnSeq, revealing differences in genetic requirements across immunization strategies.

This study uses scRNA-seq to analyze granulomatous lymph nodes from TB patients, identifying cell types, signaling networks, and Mtb RNA detection in infected cells.

The paper introduces SPLASH and compactors to efficiently discover microbial genetic elements and perform strain typing without reference genomes.