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Articles by Ran Blekhman
What is biology research for?
The number of scientific publications has been growing steadily for decades, but starting in late 2022, the volume of manuscripts submitted to academic journals escalated with unprecedented speed. Monthly submissions to arXiv have nearly doubled [1], and the timing of this inflection matches the public rollout of the first widely used generative artificial intelligence (AI) systems.
The AI Discourse in Academia is Toxic. It Doesn’t have to be.
You are allowed to have a nuanced opinion about AI Photo by Vida Huang on Unsplash On Wednesday I shared a paper on Bluesky. Nothing out of the ordinary; sharing and learning about new papers is one of my favorite aspects of social media, so when I saw a paper I thought was interesting published in Nature that day I shared it with a short note. The paper, Miao et al., 2026, describes a framework that converts a scientific paper into an MCP server that an AI agent can query.
Science Under Threat in the United States: How scientists and institutions should respond
Main text The new Trump administration has wasted no time launching a multi-pronged assault on the scientific enterprise in the United States. Mass firings at the National Institutes of Health (NIH) and the National Science Foundation have gutted these agencies of institutional knowledge and expertise.
Cardiometabolic disease risk in gorillas is associated with altered gut microbial metabolism - npj Biofilms and Microbiomes
Abstract Cardiometabolic disease is the leading cause of death in zoo apes; yet its etiology remains unknown. Here, we investigated compositional and functional microbial markers in fecal samples from 57 gorillas across U.S. zoos, 20 of which are diagnosed with cardiovascular disease, in contrast with 17 individuals from European zoos and 19 wild gorillas from Central Africa.
Temporal patterns of gut microbiota in lemurs (Eulemur rubriventer) living in intact and disturbed habitats in a novel sample type
ASV amplicon sequence variant LEfSe linear discriminant analysis effect size PC principal coordinates PCoA principal coordinate analysis 1 INTRODUCTION Gut microbiome composition is temporally dynamic, and large gaps remain in our understanding of the causes and consequences of microbial change over an individual host's lifetime (Björk et al., 2019; Kolodny & Schulenburg, 2020).
Public human microbiome data are dominated by highly developed countries
Loading metrics Open Access Peer-reviewed Meta-Research Article Richard J. Abdill, Elizabeth M. Adamowicz, Ran Blekhman Richard J. Abdill, Elizabeth M. Adamowicz, Ran Blekhman Published: February 15, 2022 https://doi.org/10.1371/journal.pbio.3001536 Figures Abstract The importance of sampling from globally representative populations has been well established in human genomics.
Meta-Research: International authorship and collaboration across bioRxiv preprints
Abstract Preprints are becoming well established in the life sciences, but relatively little is known about the demographics of the researchers who post preprints and those who do not, or about the collaborations between preprint authors.
International authorship and collaboration in bioRxiv preprints
Abstract As preprints become more integrated into the conventional avenues of scientific communication, it is critical to understand who is being included and who is not. However, little is known about which countries are participating in the phenomenon or how they collaborate with each other. Here, we present an analysis of 67,885 preprints posted to bioRxiv from 2013 through 2019 that includes the first comprehensive dataset of country-level affiliations for all preprint authors.
Population dynamics of the human gut microbiome: change is the only constant
Our gastrointestinal tract harbors a complex ecosystem of trillions of microbial cells, called the gut microbiome, which plays a critical role in maintaining our health. Elucidation of the ecological and evolutionary dynamics of the gut microbiome is essential for determining its effect on host health and disease. Longitudinal studies have reported long-term stability of the high-level taxonomic composition of gut microbiota communities [1, 2].
Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species
You have accessResearch articles Abstract Gut microbiota in geographically isolated host populations are often distinct. These differences have been attributed to between-population differences in host behaviours, environments, genetics and geographical distance. However, which factors are most important remains unknown. Here, we fill this gap for baboons by leveraging information on 13 environmental variables from 14 baboon populations spanning a natural hybrid zone.
Tracking the popularity and outcomes of all bioRxiv preprints
Abstract Researchers in the life sciences are posting work to preprint servers at an unprecedented and increasing rate, sharing papers online before (or instead of) publication in peer-reviewed journals. Though the increasing acceptance of preprints is driving policy changes for journals and funders, there is little information about their usage.
Improving the usability and archival stability of bioinformatics software
Genome Biology201920:47 https://doi.org/10.1186/s13059-019-1649-8 © The Author(s). 2019 Published: 27 February 2019 Abstract Implementation of bioinformatics software involves numerous unique challenges; a rigorous standardized approach is needed to examine software tools prior to their publication. The rapid advancement of genomics and sequencing technologies has led to an overwhelming amount and diversity of new analytical algorithms packaged as software tools [1].
Tracking the popularity and outcomes of all bioRxiv preprints
Abstract Researchers in the life sciences are posting their work to preprint servers at an unprecedented and increasing rate, sharing papers online before (or instead of) publication in peer-reviewed journals. Though the popularity and practical benefits of preprints are driving policy changes at journals and funding organizations, there is little bibliometric data available to measure trends in their usage.
Gut microbiota diversity across ethnicities in the United States
Loading metrics Open Access Peer-reviewed Research Article Andrew W. Brooks, Sambhawa Priya, Ran Blekhman, Seth R. Bordenstein Andrew W. Brooks, Sambhawa Priya, Ran Blekhman, Seth R. Bordenstein Published: December 4, 2018 https://doi.org/10.1371/journal.pbio.2006842 >> See the preprint Figures Abstract Composed of hundreds of microbial species, the composition of the human gut microbiota can vary with chronic diseases underlying health disparities that disproportionally affect ethnic minorities.
Gut Microbiota Diversity across Ethnicities in the United States
Gut Microbiota Diversity across Ethnicities in the United States Andrew W Brooks, Sambhawa Priya, Ran Blekhman, Seth R Bordenstein bioRxiv 342915; doi: https://doi.org/10.1101/342915
Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer
ABSTRACTAlthough variation in gut microbiome composition has been linked with colorectal cancer (CRC), the factors that mediate the interactions between CRC tumors and the microbiome are poorly understood. MicroRNAs (miRNAs) are known to regulate CRC progression and are associated with patient survival outcomes. In addition, recent studies suggested that host miRNAs can also regulate bacterial growth and influence the composition of the gut microbiome.
Genomics and Microbiome Research
Available Positions We are looking for researchers to join our group at the University of Chicago! See below for information on positions for postdocs, graduate students, data scientists, undergrads, and high school students. Ideal candidates will have a quantitative background and interest in computational analysis of genomic data.
Host genetic variation impacts microbiome composition across human body sites
First, we scanned and identified the short reads in the metagenomic sequencing data that map to the human genome. By combining these reads across body sites (primarily originating from nares and cheek swabs [33]) for each individual (Additional file 1: Figure S1), we attained a mean depth of coverage of more than 10 reads per base pair per individual (Additional file 1: Figure S2).
Host genetic variation impacts microbiome composition across human body sites
First, we scanned and identified the short reads in the metagenomic sequencing data that map to the human genome. By combining these reads across body sites (primarily originating from nares and cheek swabs [ 33 ]) for each individual (Additional file 1 : Figure S1), we attained a mean depth of coverage of more than 10 reads per base pair per individual (Additional file 1 : Figure S2).
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