Ran Blekhman

The paper investigates how lifestyle-associated microbiome shifts and host genetics influence gene expression in intestinal organoids, identifying microbiome-dependent allele-specific expression effects.

This study identifies how maternal diet and genetics influence the human milk metabolome, showing diet explains the most variation and uncovering genetic associations with specific metabolites.

The paper analyzes the gut microbiome of South Asian communities to show that urbanization impacts microbiomes differently across communities, with geography and culture playing a stronger role than lifestyle.

This study compares oral microbiomes of Ugandan hunter-gatherers and farmers with global populations, finding that geography and industrialization shape microbial diversity and composition.

The paper links social microbiome transmission to microbial specialization and host lifespan in wild baboons using metagenomic data.

The paper identifies gene-microbe interactions that modulate host gene expression in the human intestine and links them to IBD risk.

The paper investigates host-microbiome metabolic interactions in colorectal cancer using computational and experimental methods, revealing how tumor metabolic changes support pathogenic microbes.

The paper compares host transcriptional responses to urban and rural gut microbiomes, finding urban microbiomes affect innate immune pathways and high-diversity microbiomes trigger stronger host responses.

The paper identifies genetic loci influencing milk gene expression and links these to infant gut microbiome composition in breastfeeding mothers.

The paper develops a microbiome-based age predictor for wild baboons using 13,563 gut microbial profiles and finds that microbiome age reflects current social and environmental conditions but not developmental milestones or lifespan.

The paper investigates the association between human cytomegalovirus in breast milk and milk composition, infant gut microbiome, and infant growth.

The paper investigates how interspecies variation in hominid gut microbiota affects host gene regulation in colonic epithelial cells, finding species-specific gene responses linked to inflammatory diseases.

This study identifies shared and disease-specific host-microbiome interactions in colorectal cancer, inflammatory bowel disease, and irritable bowel syndrome using machine learning.

The paper examines gut microbiome and host gene expression changes in CF patients, identifying CRC-related gene-microbe associations.

The paper shows gut microbiota influences host gene regulation, identifying specific taxa and genes, and demonstrates microbiome manipulation can alter gene expression profiles.

The paper assesses the installability and archival stability of computational biology tools, finding many are inaccessible or hard to install, and recommends policy changes to improve these aspects.

The paper identifies 12 microbial genera and families that reproducibly vary by ethnicity in two U.S. 16S gut microbiota datasets involving 1,673 individuals.

The paper investigates the relationship between miRNA expression in CRC tissues and microbiome composition, identifying miRNAs correlated with bacterial taxa and suggesting potential therapeutic targets.

HOMINID identifies host SNPs correlated with microbiome taxa abundances using Lasso regression, showing improved accuracy over existing methods and identifying 13 SNPs across body sites.

BugBase assigns pathway coverage and traits (Gram stain, oxygen tolerance, pathogenicity) to individual taxa in 16S or shotgun microbiome data, detecting some functional differences bag-of-genes profiles miss.

This study identifies gene expression changes and host SNPs influenced by the gut microbiome in human cells, linking them to microbiome-related diseases.

The paper compares fecal sample storage methods in rhesus macaques and finds that individual identity signatures are consistent across methods, suggesting stored samples are suitable for microbiome analysis.

This study examines the gut microbiota of rural African populations, finding strong correlations between microbiome composition, subsistence mode, and colonization by the parasite Entamoeba.

The paper identifies virulence genes as a signature of the microbiome in the colorectal tumor microenvironment, highlighting novel bacterial taxa and their potential role in cancer development.

The paper examines the gut microbiome and metabolome of BaAka hunter-gatherers, finding adaptations to their diet and immune system tolerance of pathogens.