Michael J. Roach

This study investigates whether FIT samples can reveal a microbial signature of sessile serrated lesions, finding no significant differences in community structure but suggesting potential functional differences.

This study identifies novel host dependency factors for dengue virus NS1 using proximity proteomics and functional validation, highlighting TM9SF3 as a potential antiviral target.

OpusTaxa provides an open-source workflow for streamlined shotgun metagenomic analysis, enabling taxonomic profiling, assembly, and functional analysis with minimal user configuration.

This paper introduces a method for targeted sequencing of expressed mutations in single cells using RNA-templated gap filling with BstFL polymerase, enabling simultaneous transcriptomic and mutation profiling.

This study shows lithium affects behavior and physiology through the gut-brain axis by activating gut enterochromaffin cells, challenging the belief that lithium acts directly on the brain.

This study shows that monocrotaline-treated rats exhibit exaggerated lung responses to lipopolysaccharide, characterized by pro-inflammatory gene expression and increased thrombotic factors.

Phynteny combines ESM2 protein embeddings, a BiLSTM, and circular-attention transformer layers to exploit phage gene order, assigning one of nine PHROG functional categories to unannotated genes.

The paper identifies neurogenesis-related gene expression as a clone-specific hallmark of brain metastasis in breast cancer using a new optical barcoding tool.

The paper analyzes 15,000 bacterial genomes to investigate the presence of antimicrobial resistance (AMR) genes in prophages across human body sites and regions, finding diverse AMR genes associated with prophages.

Sphae is a bioinformatics pipeline that rapidly assesses phage therapeutic potential by analyzing genomic markers for safety and efficacy in under ten minutes.

The paper quantifies the compound processing potential of gut and soil metagenomes to link microbiome function to human health and ecosystem quality.

Hybracter improves bacterial genome assembly accuracy and speed, outperforming existing tools in hybrid and long-read-only modes, especially for small plasmids.

Head-to-head on serial prostate adenocarcinoma sections: Xenium gave higher sensitivity, wider dynamic range and closer agreement with snRNA-seq; CosMx segmented cells better out of the box.

Phables improves phage genome recovery from fragmented viral metagenome assemblies, recovering more high-quality genomes and resolving variants with high nucleotide identity.

This study isolates and characterizes three novel Crassvirales phages infecting Bacteroides cellulosilyticus WH2, revealing they do not co-evolve with their hosts and share a conserved tail spike protein involved in host interaction.

The paper analyzes prophage DNA in human microbiome bacterial genomes, showing site- and health-related variations in prophage content and its impact on bacterial growth and microbiome structure.

The paper quantifies the benefits and costs of prophages in bacterial genomes, showing uniform prophage density and estimating their energetic contribution.

Hecatomb is a bioinformatics platform for viral metagenomics that enables read and contig analysis, integrating reference databases and providing tools for virome discovery.

The paper presents a gold-standard dataset of manually curated bacterial genomes and a framework to evaluate prophage prediction algorithms, showing their performance metrics across seven tools.

The paper presents new genome assemblies for five Brettanomyces species, revealing structural variations, gene expansions, and horizontal gene transfer events related to their adaptation and domestication.

Purge Haplotigs reduces synteny issues in diploid genome assemblies by reassigning duplicate contigs, improving assembly quality with minimal impact on completeness.

The paper identifies genetic markers distinguishing Chardonnay clones and reveals inbreeding between its parent species, Gouais blanc and Pinot noir.