Samuel S. Minot

This study identifies molecular and architectural changes in normal-adjacent field tissue in HNSCC that disrupt epithelial differentiation and may promote cancer development.

This study shows the type VI secretion system (T6SS) in Bacteroides acidifaciens helps maintain its presence in a wild mouse gut microbiome by antagonizing other Bacteroidales, but its effect depends on ecological context.

The paper models microbial community assembly dynamics in Barrett's esophagus and esophageal adenocarcinoma, finding neutral dynamics in normal tissue and BE but not EAC, with H. pylori showing non-neutral behavior in BE non-cancer outcomes.

TCR2HLA infers HLA genotypes from TCR repertoires, enabling identification of immunologically relevant metaclonotypes and discovery of HLA-associated TCRs.

MADDD-seq detects DNA damage and mutations simultaneously in yeast using a modified double barcoding sequencing approach, revealing repair kinetics and mutagenesis over 24 hours.

This paper harmonizes microbiome studies by placing amplicon sequence variants (ASV) on a common phylogenetic tree, improving community relationship accuracy compared to closed-OTU methods.

The paper introduces a tool for gene-level metagenomic analysis to identify genomic islands linked to immunotherapy response in microbiome data.

The paper benchmarks metagenomic tools for coding sequence detection, finding that assembly-based methods have high PPV but low sensitivity at low coverage, while mapping-based methods are more sensitive but struggle with PPV.

The paper introduces a computational method to cluster microbial genes by co-abundance, identifying reproducible gene groups linked to colorectal cancer and inflammatory bowel disease.

This study benchmarks eleven metagenomic classifiers using 846 species and evaluates strategies to reduce false positives in taxonomic classification.