Joseph F. Petrosino

Cenote-Taker 3 is a tool for virus discovery and annotation in genomic data, outperforming existing tools in speed and accuracy.

This study analyzes RSV evolutionary dynamics across pre-pandemic, pandemic, and post-pandemic periods in Houston, finding reduced diversity during the pandemic and increased non-synonymous mutations in RSV/B.

This paper presents a probe-based capture enrichment method to obtain full-length genomes of RSV and HuNoV from clinical samples, achieving high completeness and improving variant tracking.

The paper measures tryptophan metabolites in fecal samples from healthy individuals and links them to bacterial abundance and predicted microbial sources.

The paper describes how the Yale Generations Project adapted its recruitment, consent, and DNA sample acquisition processes to remote methods during the COVID-19 pandemic, resulting in continued enrollment and sample collection.

The paper analyzes intra-host RSV genetic variation using short-read sequencing, finding low variation but differences between genomic and transcriptomic data.

The paper presents a high-quality, complete reference genome for Cryptosporidium parvum using Oxford Nanopore and Illumina reads, enabling comprehensive genomic studies.

This study identifies major sources of transcriptomic variation in human intestinal organoids, showing that culture methods like substrate and format have large effects compared to experimental manipulations.

This study develops an oligonucleotide capture sequencing method to generate SARS-CoV-2 genomic and transcriptome sequences from clinical samples, revealing differential transcriptional activity and ORF10 expression.

This study evaluates how fecal collection conditions and 16S rRNA sequencing protocols affect gut microbiome analysis across two centers, finding that center-specific differences outweigh collection method variations.