Mick Watson

This study shows that 3-NOP reduces methane emissions in ruminants by altering microbial communities and fermentation pathways, but limits productivity gains due to shifts in hydrogen-cycling microbes.

This study isolates and characterizes rumen bacteria using three anaerobic media, showing that different media enrich distinct bacterial genera, highlighting the importance of defined media for studying rumen microbiota.

This study compares the caecal microbiota of XCR1 knockout chickens with and without IBV vaccination, finding that vaccination, not XCR1 absence, significantly alters microbiota composition.

KOunt quantifies KEGG orthologue abundance in metagenomes using a reproducible SnakeMake pipeline.

This study evaluates how reference database choice affects metagenomic read classification accuracy in the rumen microbiome, finding that adding cultured genomes and MAGs improves classification.

The paper uses single-cell RNA sequencing to show that CD16- monocytes are key in the transcriptional response of human monocytes to Toxoplasma infection, revealing transcriptional heterogeneity and cytokine secretion patterns.

The paper presents improved pig reference genomes using long-read sequencing, enhancing continuity and accuracy for pig genetics and genomics research.

The paper shows that errors in long-read assemblies can severely impact protein predictions, leading to truncated or altered proteins.

MAGpy is a Snakemake pipeline that annotates and characterizes metagenome-assembled genomes by comparing them to public databases and performing quality checks and phylogenetic analysis.

The paper predicts polysaccharide utilisation loci (PUL) in 5414 Bacteroidetes genomes using an open-source pipeline.

The paper develops a graph-based visualization method for RNA-Seq data to better understand transcript diversity and assembly issues.

This paper presents a high-resolution gene expression atlas for sheep, identifying transcriptional signatures and functional annotations across tissues and developmental stages.

The paper assembles 220 high-quality microbial genomes from cow rumen metagenomic data, revealing novel species with carbohydrate metabolism enzymes and improving metagenomic classification.

The paper introduces two GUIs for the poRe R package to enable parallel and real-time processing of MinION sequence data with a user-friendly interface.

The paper assembles a single chromosome of Bacteroides fragilis strain BE1 using Illumina and MinION data, achieving a gapless genome with minimal resources.

poRe is an R package for handling nanopore sequencing data, offering data manipulation, organization, summarization, and visualization across Windows and Linux platforms.