K. S. Pollard

Contiguous and complete assemblies of Blastocystis gut microbiome-associated protists reveal evolutionary diversification to host ecology

This study presents contiguous and complete assemblies of Blastocystis strains, revealing genetic and metabolic diversity linked to host ecology and horizontal gene transfer.

Three-dimensional genome re-wiring in loci with Human Accelerated Regions

The paper identifies human-specific 3D genome re-wiring in conserved loci, linking accelerated evolution to regulatory rewiring in neural progenitor cells.

Machine-learning dissection of Human Accelerated Regions in primate neurodevelopment

The paper uses machine learning to analyze human-chimpanzee variants in HARs, finding 43% affect chromatin state and 14% affect neurodevelopmental enhancer activity, with species-specific activity predicted by transcription factor footprints.

Microcosm cultures of a complex synthetic community reveal ecology and genetics of gut microbial organization

The paper uses synthetic microbial communities in mucin microcosms to study gut microbial spatial organization and identifies genes associated with mucosal versus lumen enrichment.

A conserved enzyme found in diverse human gut bacteria interferes with anticancer drug efficacy

The paper shows that a conserved enzyme in gut bacteria inactivates anticancer drugs, reducing their efficacy in mice and highlighting microbial contributions to drug metabolism.

Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence

This study uses deep learning to infer 3D genome organization from ancient DNA, revealing how chromatin folding influenced phenotypic and sequence divergence between Neanderthals, Denisovans, and modern humans.

Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community

The paper uses single-cell genome sequencing of mouse stool to improve taxonomic and functional resolution of the mouse gut microbiome by identifying novel species and enhancing metagenomic analysis.

A Human Accelerated Region is a Leydig cell GLI2 Enhancer that Affects Male-Typical Behavior

The paper identifies a human accelerated region (HAR) that functions as a Leydig cell enhancer for Gli2, affecting male-typical behavior in mice.

A diet-dependent enzyme from the human gut microbiome promotes Th17 cell accumulation and colitis

Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

This study uses linked-read sequencing to track genetic and ecological changes in a human gut microbiome during antibiotic treatment and recovery.

A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome

The paper presents a comprehensive genomic resource of over 280,000 human gut microbiome genomes and their protein sequences, highlighting gaps in functional annotations and genomic diversity.

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

This study examines evolutionary dynamics of gut bacteria within and across hosts, finding rapid genetic changes within hosts and challenges to standard population genetic models.

American Gut: an Open Platform for Citizen-Science Microbiome Research

The paper uses citizen-science data to analyze human stool microbiomes, revealing new insights into microbial diversity, metabolome composition, and associations with diet and health.

The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation

This paper shows that the Epstein-Barr virus episome shifts between repressive and active nuclear compartments during latency and reactivation, using interchromosomal interactions to regulate transcription.

Development of Inflammatory Bowel Disease is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice

This study uses longitudinal metagenomic analysis in a mouse model of IBD to identify microbial functional changes linked to disease progression and immune activation.