R. Blekhman

Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother's milk

This study links the infant gut microbiome and resistome to bacterial strains in mother's milk using metagenomic samples from mother-infant pairs.

Integration of 168,000 samples reveals global patterns of the human gut microbiome

The paper integrates 168,484 human gut microbiome samples to reveal global patterns, showing widespread presence of Firmicutes and regional differences in microbial genera.

Microbes with higher metabolic independence are enriched in human gut microbiomes under stress

The paper identifies high metabolic independence as a marker of gut microbiome changes in IBD, using a software framework to analyze metagenomic data from healthy and IBD patients.

Universal gut microbial relationships in the gut microbiome of wild baboons

The paper analyzes gut microbial relationships in wild baboons and finds that microbial correlations are largely universal across hosts, with positive correlations dominated by shared patterns.

Synchrony and idiosyncrasy in the gut microbiome of wild baboons

This study examines gut microbiome dynamics in wild baboons, finding that microbial dynamics are largely idiosyncratic despite shared environments, with host-specific factors explaining most variation.

Codiversification of gut microbiota with humans

The paper identifies gut microbes that codiversified with human populations, showing vertical transmission and potential population-specific health benefits.

Public human microbiome data dominated by highly developed countries

The paper analyzes global distribution of human microbiome samples and finds they are heavily skewed toward developed countries, with underrepresentation from central and southern Asia.

BiomeHorizon: visualizing microbiome time series data in R

BiomeHorizon is an R package that visualizes longitudinal microbiome time series data using horizon plots, providing proportional and absolute abundance changes across taxa and subjects.

Global Genetic Cartography of Urban Metagenomes andAnti-Microbial Resistance

The paper creates a global metagenomic atlas of urban microbial ecosystems, identifying novel species and geographic variation in antimicrobial resistance genes.

International authorship and collaboration across bioRxiv preprints

This study analyzes bioRxiv preprints to examine international authorship and collaboration patterns across countries.

Tracking the popularity and outcomes of all bioRxiv preprints

Crawled metadata for all 37,648 bioRxiv preprints through November 2018 reveal accelerating submissions and downloads, 67.0 percent publication of 2013-2016 preprints, and a public Rxivist database.

Gut Microbiota Diversity across Ethnicities in the United States

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.

Megaphage infect Prevotella and variants are widespread in gut microbiomes

The paper identifies large phage (Lak phage) in gut microbiomes that infect Prevotella and are widespread, especially in developing-world individuals.

Distinct Microbes, Metabolites, and Ecologies Define the Microbiome in Deficient and Proficient Mismatch Repair Colorectal Cancers

The paper identifies distinct microbial, metabolic, and ecological differences between deficient and proficient mismatch repair colorectal cancers using microbiome and metabolomic analyses.

Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment

This study identifies correlations between colorectal cancer mutations and microbial communities in the tumor microenvironment, suggesting potential functional interactions and implications for diagnostics and therapies.