2019 & Preprints
Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host speciesL. 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 microbiomesA. 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 softwareS. Mangul, L. Martin, E. Eskin, and R. Blekhman
Genome Biology, 2019
Rxivist.org: Sorting biology preprints using social media and readership metricsR. Abdill and R. Blekhman
PLOS Biology, 2019
Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seqA. 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
Interactions between the gut microbiome and host gene regulation in cystic fibrosisGargi Dayama, Sambhawa Priya, David E Niccum, Alexander Khoruts, and R. Blekhman
Gut microbiota has a widespread and modifiable effect on host gene regulationA. 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.
BugBase predicts organism level microbiome phenotypesT. Ward, J. Larson, J. Meulemans, B. Hillmann, J. Lynch, D. Sidiropoulos, J. Spear, G. Caporaso, R. Blekhman, R. Knight, R. Fink, and D. Knights.
Challenges and recommendations to improve the installability and archival stability of omics computational toolsS. 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 constraintsA. 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.
Population dynamics of the human gut microbiome: change is the only constantS. Priya and R. Blekhman
Genome Biology, 2019
Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironmentM. 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 cancerC. Yuan, M. B. Burns, S. Subramanian, and R. Blekhman
Integrating tumor genomics into studies of the microbiome in colorectal cancerM. B. Burns and R. Blekhman
Gut Microbes, 2018 (Invited Addendum)
The gut microbiome of nonhuman primates: Lessons in ecology and evolutionJ. 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 gutL. E. Grieneisen and R. Blekhman
mSystems, 2018 (invited commentary)
Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancersV. 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
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
Functional genomics of host–microbiome interactions in humansF. 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 compositionJ. 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 variationD. 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 patternsA. 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 PathogensY. 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.
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 dataR. 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 SweepM. 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 microbiomeA. L. Richards, M. B. Burns, A. Alazizi, L. B. Barreiro, R. Pique-Regi, R. Blekhman, and F. Luca.
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 baboonsJ. 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.
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 regionsF. 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 microbiomeJ. 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.
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
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)
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)
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
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)
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)
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)
Selective constraints in experimentally defined primate regulatory regions.
D. J. Gaffney, R. Blekhman, and J. Majewski.
PLoS Genetics, 2008 Aug 15;4(8)
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)
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)
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)
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
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
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
The evolution of gene regulation in primates.
Ph.D. thesis, The University of Chicago, 2010