Lab Publications


2017 & Preprints

Discrete mutations in colorectal cancer correlate with defined microbial communities in the tumor microenvironment
M. B. Burns, E. Montassier, J. Abrahante, T. K. Starr, D. Knights, and R. Blekhman
BioRxiv
HOMINID: A framework for identifying associations between host genetic variation and microbiome composition
J. Lynch, K. Tang, J. Sands, M. Sands, E. Tang, S. Mukherjee, D. Knights, and R. Blekhman.
BioRxiv
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.
BioRxiv

2016

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

2015

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

2014



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)

Thesis

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