Stephen J. Salipante

This study shows the type VI secretion system (T6SS) in Bacteroides acidifaciens helps maintain its presence in a wild mouse gut microbiome by antagonizing other Bacteroidales, but its effect depends on ecological context.

The paper introduces UHVDB, an updateable human virome database and toolkit, and demonstrates its utility in analyzing oral/airway samples from Cystic Fibrosis patients.

This paper introduces a novel fecal microbiota transplant method using 'poopsicles' to reduce stress in mice, showing lower corticosterone levels and better microbial similarity compared to traditional gavage.

The paper evaluates variant-calling algorithms for identifying indels in haploid bacterial genomes using synthetic reads and finds that high-quality soft-clipped reads improve detection of medium-length indels.

This paper introduces a method called 3D-seq to map DNA-protein interaction sites in vivo using a modified cytosine deaminase, demonstrating its application in Pseudomonas aeruginosa transcription factors.

The paper designs single molecule molecular inversion probes targeting clinically relevant variants using the CIViC database, demonstrating high sensitivity and discovering missed variants in cancer samples.