Joseph F. Petrosino

Cenote-Taker 3 for Fast and Accurate Virus Discovery and Annotation of the Virome

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

Evolutionary dynamics of Respiratory Syncytial Virus in pre-pandemic, pandemic, and post-pandemic periods in Houston, Texas, USA

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.

Complete Genomic Characterization of Global Pathogens, Respiratory Syncytial Virus (RSV), and Human Norovirus (HuNoV) Using Probe-based Capture Enrichment.

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.

Recruitment, Consent and DNA Sample Acquisition in a U.S. Precision Health Cohort During the COVID-19 Pandemic

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.

Examining intra-host genetic variation of RSV by short read high-throughput sequencing

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

Fully resolved assembly of Cryptosporidium parvum

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

Drivers of Transcriptional Variance in Human Intestinal Epithelial Organoids

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.

Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals

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.

Influence of fecal collection conditions and 16S rRNA gene sequencing protocols at two centers on human gut microbiota analysis

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.