Jeffrey M. Roach

Deep-learning-based interpolation of longitudinal microbiome data powers biologically informative discovery

This paper introduces BGOB, a deep learning framework for longitudinal microbiome interpolation, improving analysis of microbial community trajectories and revealing disease-related associations.

The impact of transplant location on the gut microbiome and resistome in patients undergoing hematopoietic stem cell transplantation at home versus in the hospital

This study compares the gut microbiome and resistome of patients undergoing home versus hospital hematopoietic stem cell transplantation, finding no significant differences but noting confounding factors in secondary analyses.

Gut Microbial Impact on Colitis and Colitis-Associated Carcinogenesis in a Primary Sclerosing Cholangitis-IBD Model

This study develops a PSC-IBD mouse model and shows that dysbiotic microbiota and bile acid metabolism drive colitis and carcinogenesis.

Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data

The paper evaluates ten differential expression methods for metatranscriptomics data using real and simulated datasets, finding the logistic-beta test has highest sensitivity and reasonable type I error control.

BZINB model-based pathway analysis and module identification facilitates integration of microbiome and metabolome data

The paper introduces a BZINB model-based method for integrating microbiome and metabolome data, showing improved accuracy in identifying correlations compared to traditional methods.