User profiles for S. T. Westreich

Samuel T. Westreich

DNAnexus
Verified email at ucdavis.edu
Cited by 353

[PDF][PDF] PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

…, J Wagner, J McDaniel, SH Stephens, ST Westreich… - Cell genomics, 2022 - cell.com
The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling
in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied …

[HTML][HTML] SAMSA2: a standalone metatranscriptome analysis pipeline

ST Westreich, ML Treiber, DA Mills, I Korf, DG Lemay - BMC bioinformatics, 2018 - Springer
Background Complex microbial communities are an area of growing interest in biology.
Metatranscriptomics allows researchers to quantify microbial gene expression in an …

[HTML][HTML] SAMSA: a comprehensive metatranscriptome analysis pipeline

ST Westreich, I Korf, DA Mills, DG Lemay - BMC bioinformatics, 2016 - Springer
Background Although metatranscriptomics—the study of diverse microbial population activity
based on RNA-seq data—is rapidly growing in popularity, there are limited options for …

[HTML][HTML] Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization

ST Westreich, A Ardeshir, Z Alkan, ME Kable, I Korf… - Microbiome, 2019 - Springer
Background Idiopathic chronic diarrhea (ICD) is a common cause of morbidity and mortality
among juvenile rhesus macaques. Characterized by chronic inflammation of the colon and …

Bacterial and fungal symbionts in pollen provisions of a native solitary bee in urban and rural environments

LR Westreich, ST Westreich, PC Tobin - Microbial Ecology, 2023 - Springer
Among insects, symbionts such as bacteria and fungi can be linked to their physiology and
immature development, and in some cases are part of a defense system against parasites …

[HTML][HTML] BigTop: a three-dimensional virtual reality tool for GWAS visualization

ST Westreich, M Nattestad, C Meyer - BMC bioinformatics, 2020 - Springer
Background Genome-wide association studies (GWAS) are typically visualized using a two-dimensional
Manhattan plot, displaying chromosomal location of SNPs along the x-axis and …

Native solitary bee reproductive success depends on early season precipitation and host plant richness

LR Westreich, ST Westreich, PC Tobin - Oecologia, 2023 - Springer
Spring-emerging bees depend upon the synchronized bloom times of angiosperms that provide
pollen and nectar for offspring. The emergence of such bees and bloom times are linked …

Fecal metatranscriptomics and glycomics suggest that bovine milk oligosaccharides are fully utilized by healthy adults

ST Westreich, J Salcedo, B Durbin-Johnson… - The Journal of nutritional …, 2020 - Elsevier
Human milk oligosaccharides play a vital role in the development of the gut microbiome in
the human infant. Although oligosaccharides derived from bovine milk (BMO) differ in content …

Evaluation of Spodick's sign and other electrocardiographic findings as indicators of STEMI and pericarditis

MD Witting, KM Hu, AA Westreich, S Tewelde… - The Journal of …, 2020 - Elsevier
… elevation, measured from the J point, in lead III greater than in lead II (ST elevation III > II);
ST convex upward or horizontal except in lead V 1 ; RT checkmark (ST elevation with abrupt …

Metatranscriptomics: Monitoring gut microbiome activity in response to diet

ST Westreich, I Korf, DA Mills, DG Lemay - The FASEB Journal, 2016 - Wiley Online Library
The study of the gut microbiome—the collection of microflora within the intestinal tract—is
growing in popularity as associations are found between diet and nutrition, gut microflora …