Lab Publications

2020 & Preprints

Interactions between the gut microbiome and host gene regulation in cystic fibrosis
Gargi Dayama, Sambhawa Priya, David E Niccum, Alexander Khoruts, and R. Blekhman
Genome Medicine, 2020
International authorship and collaboration in bioRxiv preprints
R. J. Abdill, E. M. Adamowicz, and R. Blekhman
Global genetic cartography of urban metagenomes and anti-microbial resistance
The International MetaSUB Consortium
BugBase predicts organism level microbiome phenotypes
T. Ward, J. Larson, J. Meulemans, B. Hillmann, J. Lynch, D. Sidiropoulos, J. Spear, G. Caporaso, R. Blekhman, R. Knight, R. Fink, and D. Knights.


Tracking the popularity and outcomes of all bioRxiv preprints
R. Abdill and R. Blekhman
eLife, 2019
        What bioRxiv’s first 30,000 preprints reveal about biologists. Nature
        Biologists flock to preprints. Science
        What makes preprints popular? The Node
Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species
L. E. Grieneisen, M. J. E. Charpentier, S. C. Alberts, R. Blekhman, G. Bradburd, J. Tung, and E. A. Archie
Proceedings of the Royal Society B, 2019
        Baboons’ gut makeup is determined mostly by soil, not genetics. Science
Megaphages infect Prevotella and variants are widespread in gut microbiomes
A. E. Devoto, J. M. Santini, M. R. Olm, K. Anantharaman, P. Munk, J. Tung, E. A. Archie, P. J. Turnbaugh, K. D. Seed, R. Blekhman, F. M. Aarestrup, B. C. Thomas, and J. F. Banfield
Nature Microbiology, 2019
Improving the usability and archival stability of bioinformatics software
S. Mangul, L. Martin, E. Eskin, and R. Blekhman
Genome Biology, 2019 Sorting biology preprints using social media and readership metrics
R. Abdill and R. Blekhman
PLOS Biology, 2019
Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq
A. K. Sharma, B. Pafčo, K. Vlčková, B. Červená, J. Kreisinger, S. Davison, K. Beeri, T. Fuh, S. R. Leigh, M. B. Burns, R. Blekhman, K. J. Petrželková, and A. Gomez
BMC Genomics, 2019
Gut microbiota has a widespread and modifiable effect on host gene regulation
A. L. Richards, A. L. Muehlbauer, A. Alazizi, M. B. Burns, A. Findley, F. Messina, T. J. Gould, C. Cascardo, R. Pique-Regi, R. Blekhman, and F. Luca.
mSystems, 2019
Challenges and recommendations to improve the installability and archival stability of omics computational tools
S. Mangul, T. Mosqueiro, R. J. Abdill, D. Duong, K. Mitchell, V. Sarwal, B. Hill, J. Brito, R. Littman, B. Statz, A. Lam, G. Dayama, L. Grieneisen, L. Martin, J. Flint, E. Eskin, and R. Blekhman
PLOS Biology, 2019
Plasticity in the human gut microbiome defies evolutionary constraints
A. Gomez, A. Sharma, E. Mallott, K. Petrzelkova, C. Jost Robinson, C. Yeoman, F. Carbonero, B. Pafco, J. Rothman, A. Ulanov, K. Vlckova, K. R. Amato, S. Schnorr, N. Dominy, D. Modry, A. Todd, M. Torralba, K. Nelson, M. Burns, R. Blekhman, M. Remis, R. Stumpf, B. Wilson, H. Gaskins, P. Garber, B. White, and S. Leigh.
mSphere, 2019
Population dynamics of the human gut microbiome: change is the only constant
S. Priya and R. Blekhman
Genome Biology, 2019


Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment
M. B. Burns, E. Montassier, J. Abrahante, S. Priya, D. E. Niccum, A. Khoruts, T. K. Starr, D. Knights, and R. Blekhman
PLOS Genetics, 2018
Interaction between host microRNAs and the gut microbiota in colorectal cancer
C. Yuan, M. B. Burns, S. Subramanian, and R. Blekhman
mSystems, 2018
Gut microbiota diversity across ethnicities in the United States
A. W. Brooks, S. Priya, R. Blekhman, and S. R. Bordenstein.
PLOS Biology, 2018
        Ethnicity proves reliable indicator of what microbes thrive in the gut Research News @Vanderbilt
Integrating tumor genomics into studies of the microbiome in colorectal cancer
M. B. Burns and R. Blekhman
Gut Microbes, 2018 (Invited Addendum)
The gut microbiome of nonhuman primates: Lessons in ecology and evolution
J. B. Clayton, A. Gomez, K. Amato, D. Knights, D. A. Travis, R. Blekhman, R. Knight, S. Leigh, R. Stumpf, T. Wolf, K. E. Glander, F. Cabana, and T. J. Johnson.
American Journal of Primatology, 2018
Crowdsourcing our national gut
L. E. Grieneisen and R. Blekhman
mSystems, 2018 (invited commentary)
Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers
V. L. Hale, P. Jeraldo, J. Chen, M. Mundy, J. Yao, S. Priya, G. Keeney, K. Lyke, J. Ridlon, B. A. White, A. J. French, S. Thibodeau, C. Diener, O. Resendis-Antonio, J. Gransee, T. Dutta, X.-M. T. Petterson, J. Sung, R. Blekhman, L. Boardman, D. Larson, H. Nelson, and N. Chia
Genome Medicine
Transposon mutagenesis screen in mice identifies TM9SF2 as a novel colorectal cancer oncogene.
C. Clark, M. Maile, P. Blaney, S. Hellweg, A. Strauss, W. Durose, S Priya^, M. B. Burns^, S. Subramanian, R. Blekhman, J. Abrahante, and T. Starr
Scientific Reports


Functional genomics of host–microbiome interactions in humans
F. Luca, S. S. Kupfer, D. Knights, A. Khoruts, and R. Blekhman
Trends in Genetics
HOMINID: A framework for identifying associations between host genetic variation and microbiome composition
J. Lynch, K. Tang, S. Priya, J. Sands, M. Sands, E. Tang, S. Mukherjee, D. Knights, and R. Blekhman.
Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation
D. Xu, P. Pavlidis, R. O. Taskent, N. Alachiotis, C. Flanagan, M. DeGiorgio, R. Blekhman, S. Ruhl, and O. Gokcumen
Molecular Biology and Evolution
        Human spit contains ancestral surprises. Science Magazine
        Archaic Humans within Spitting Distance, Genetically Speaking. GEN
        The secret about human evolution found in spit The Guardian


Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns
A. Gomez, K. Petrzelkova, M. B. Burns, C. J. Yeoman, K. R. Amato, K. Vlckova, D. Modry, A. Todd, C. A. Jost Robinson, M. Remis, M. Torralba, E. Morton, J. D. Umana, F. Carbonero, H. R. Gaskins, K. E. Nelson, B. A. Wilson, R. M. Stumpf, B. A. White, S. R. Leigh, and R. Blekhman.
Cell Reports, 2016
        Giving Up Hunting and Gathering Changed Our Gut Microbiome. Newsweek
        Study Detects Gut Microbiome Differences in African Agriculturist, Hunter-Gatherer Populations. GenomeWeb
        The Microbiomes of Indigenous Peoples Are Different--Does It Matter? Scientific American
Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens
Y. Nédélec, J. Sanz, G. Baharian, Z. A. Szpiech, A. Pacis, A. Dumaine, J.C. Grenier, A. Freiman, A. J. Sams, S. Hebert, A. P. Sabourin, F. Luca, R. Blekhman, R. D. Hernandez, R. Pique-Regi, J. Tung, V. Yotova, and L. B. Barreiro.
Cell, 2016
        Neanderthals mated with European humans and it made their immune systems weaker. Quartz
        Neanderthal DNA affects ethnic differences in immune response. Nature
Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data
R. Blekhman, K. Tang, E. Archie, L. Barreiro, Z. Johnson, M. Wilson, J. Kohn, M. Yuan, L. Gesquiere, L. Grieneisen, and J. Tung.
Scientific Reports, 2016
Atopic Dermatitis Susceptibility Variants In Filaggrin Hitchhike Hornerin Selective Sweep
M. Eaaswarkhanth, D. Xu, C. Flanagan, M. Rzhetskaya, M. G. Hayes, R Blekhman, N. Jablonski, and O. Gokcumen
Genome Biology and Evolution, 2016
Genetic and transcriptional analysis of human host response to healthy gut microbiome
A. L. Richards, M. B. Burns, A. Alazizi, L. B. Barreiro, R. Pique-Regi, R. Blekhman, and F. Luca.
mSystems, 2016
Recent evolution of the salivary mucin MUC7
D. Xu, P. Pavlidis, S. Thamadilok, E. Redwood, S. Fox, R. Blekhman, S. Ruhl, and O. Gokcumen.
Scientific Reports, 2016
        How your spit Evolved. Popular Science


Host genetic variation impacts microbiome composition across human body sites.
R. Blekhman, J. K. Goodrich, K. Huang, Q. Sun, R. Bukowski, J. T. Bell, T. D. Spector, A. Keinan, R. E. Ley, D. Gevers, and A. G. Clark.
Genome Biology, 2015
        Genetics, Immunity, and the Microbiome. Karen Zusi, The Scientist
        Who is the master of your microbial domain? Jason Tetro, Popular Science
        Host genetic architecture and the landscape of microbiome composition: humans weigh in. Andrew Benson, Genome Biology Research Highlight
Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence.
E. R. Morton, J. Lynch, A. Froment, S. Lafosse , E. Heyer , M. Przeworski, R. Blekhman, and L. Segurel.
PLOS Genetics, 2015
        Surprises Emerge As More Hunter-Gatherer Microbiomes Come In. Ed Yong, National Geographic
Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment.
M. B. Burns, J. Lynch, T. K. Starr, D. Knights, and R. Blekhman.
Genome Medicine, 2015
        New colon cancer culprit found in gut microbiome. Science Daily
        Microbiome Study of Colorectal Cancer Uncovers Signature of Virulence Genes Genome Web
        U research furthers options for colorectal treatment and prevention. Minnesota Daily
        Linking the microbiome and colorectal cancer: an author Q+A. BioMed Central, On Medicine

Social networks predict gut microbiome composition in wild baboons
J. Tung, L. B. Barreiro, M. B. Burns, J.-C. Grenier, J. Lynch, L. E. Grieneisen, J. Altmann, S. C. Alberts, R. Blekhman, and E. A. Archie.
eLife, 2015
        Paper (eLife online viewer)
        Baboon friends swap gut germs, EurikAlert
        Socially structured gut microbiomes in wild baboons, Noah Snyder-Mackler, The Molecular Ecologist
        Metagenomics: Social behavior and the microbiome, Jack Gilbert, eLife Insight
Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp.
A. Gomez, J. M. Rothman, K. Petrzelkova, C. J. Yeoman, K. Vlckova, J. D. Umana, M. Carr, D. Modry, A. Todd, M. Torralba, K. E. Nelson, R. M. Stumpf, B. A. Wilson, R. Blekhman, B. A. White, and S. R. Leigh.
The ISME Journal, 2015

Population genomics analysis of 962 whole genomes of humans reveals natural selection in non-coding regions
F. Yu, J. Lu, X. Liu, E. Gazave, D. Chang, S. Raj, H. Hunter-Zinck, R. Blekhman, L. Arbiza, C. Van Hout, A. Morrison, A. D. Johnson, J. Bis, L. A. Cupples, B. M. Psaty, D. Muzny, J. Yu, R. A. Gibbs, A. Keinan, A. G. Clark, E. Boerwinkle.
PLOS One, 2015


Human genetics shape the gut microbiome
J. K. Goodrich, J. L. Waters, A. C. Poole, J. L. Sutter, O. Koren, R. Blekhman, M. Beaumont, W. Van Treuren, R. Knight, J. T. Bell, T. Spector, A. G. Clark, and R. E. Ley.
Cell, 2014
        Genetics may foster bugs that keep you thin. Science magazine
        The Most Heritable Gut Bacterium is… Wait, What is That? National Geographic / Not Exactly Rocket Science
        Gut Microbiome Heritability. The Scientist
        Body weight heavily influenced by gut microbes: Genes shape body weight by affecting gut microbes. Science Daily

Comparative metabolomics in primates reveals the effects of diet and gene regulatory variation on metabolic divergence
R. Blekhman, G. H. Perry, S. Shahbaz, A. G. Clark, O. Fiehn, and Y. Gilad.
Scientific Reports, 2014
  Paper (pdf)

2013 and earlier

  • Gene expression differences among primates are associated with changes in a histone epigenetic modification.
    C. E. Cain, R. Blekhman, J. C. Marioni, and Y. Gilad.
    Genetics, 2011 Apr;184(4)
      Paper (pdf)
      Appeared in Genetics issue highlights

  • Functional comparison of innate immune signaling pathways in primates.
    L. B. Barreiro, J. C. Marioni, R. Blekhman, M. Stephens, and Y. Gilad.
    PLoS Genetics, 2010 Dec;6(12)
      Paper (pdf)
      Media coverage: "The Disease Advantage of Chimpanzees", Science Life blog
      Media coverage: "Why Humans Are More Sensitive to Certain Viruses", Science Daily

  • Sex-specific and lineage-specific alternative splicing in primates.
    R. Blekhman, J. C. Marioni, P. Zumbo, M. Stephens, and Y. Gilad.
    Genome Research, 2010 Feb; 20(2): 180-9
      Paper (pdf)
      Data (zip)
      Recommended by Faculty of 1000
      Media coverage: "What Makes a Man a Man?", Science Life blog

  • Segmental duplications contribute to gene expression differences between humans and chimpanzees.
    R. Blekhman, A. Oshlack, and Y. Gilad.
    Genetics, 2009, 182 (627-630)
      Paper (pdf)
      Appeared in Genetics issue highlights (pdf)

  • A signature of evolutionary constraint on ectopically expressed olfactory receptor genes.
    O. De la Cruz, R. Blekhman, X. Zhang, D. Nicolae, S. Firestein, and Y. Gilad.
    Molecular Biology and Evolution, 2009 Mar;26(3)
      Paper (pdf)

  • Gene regulation in primates evolves under tissue-specific selection pressures.
    R. Blekhman, A. Oshlack, A. E. Chabot, G. Smyth, and Y. Gilad.
    PLoS Genetics, 2008 Nov;4(11)
      Paper (pdf)
      Data (zip)

  • Selective constraints in experimentally defined primate regulatory regions.
    D. J. Gaffney, R. Blekhman, and J. Majewski.
    PLoS Genetics, 2008 Aug 15;4(8)
      Paper (pdf)

  • Natural selection on genes that underlie human disease susceptibility.
    R. Blekhman, O. Man, L. Herrmann, A. R. Boyko, A. Indap, C. Kosiol, C. D. Bustamante, K. M. Teshima, and M. Przeworski.
    Current Biology, 2008 Jun 24;18(12)
      Paper (pdf)
      Data (tab-delimited text)
      Blog coverage: Yann Klimentidis
      Blog coverage: Gene Expression

  • An evolutionarily conserved sexual signature in the primate brain.
    B. Reinius, P. Saetre, J. A. Leonard, R. Blekhman, R. Merino-Martinez, Y. Gilad, and E. Jazin.
    PLoS Genetics, 2008 Jun 20;4(6)
      Paper (pdf)
      Highlighted in Nature (pdf)
      Highlighted in Nature Reviews Neuroscience (pdf)
      Media coverage: Times Online
      Media coverage: Science Daily

  • A direct transcriptional target of human FOXO1 mediates response to oxidative stress.
    P. De Candia, R. Blekhman, A. E. Chabot, A. Oshlack, and Y. Gilad.
    PLoS One, 2008, Feb 27;3(2)
      Paper (pdf)

  • SPIKE: a database, visualization and analysis tool of cellular signaling pathways.
    R. Elkon, R. Vesterman, N. Amit, I. Ulitsky, I. Zohar, M. Weisz, G. Mass, N. Orlev, G. Sternberg, R. Blekhman, J. Assa, Y. Shiloh and R. Shamir.
    BMC Bioinformatics, 2008 Feb 20;9:110
      Paper (pdf)
      SPIKE website

  • Using reporter gene assays to identify cis regulatory differences between humans and chimpanzees.
    A. Chabot, R. A. Shrit, R. Blekhman, and Y. Gilad.
    Genetics, 2007, 176(4):2069-76
      Paper (pdf)
      Appeared in Genetics issue highlights

  • The "domino theory" of gene death: gradual and mass gene extinction events in three lineages of obligate symbiotic bacterial pathogens.
    T. Dagan, R. Blekhman, and D. Graur.
    Molecular Biology and Evolution, 2006, 23(2):310-316
      Paper (pdf)


  • The evolution of gene regulation in primates.
    R. Blekhman
    Ph.D. thesis, The University of Chicago, 2010