Sara Javornik Cregeen

EsViritu is a viral pathogen profiler that accurately detects and reconstructs virus genomes from metagenomes with high sensitivity and specificity.

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 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 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.