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Items: 31

1.

HOMINID: a framework for identifying associations between host genetic variation and microbiome composition.

Lynch J, Tang K, Priya S, Sands J, Sands M, Tang E, Mukherjee S, Knights D, Blekhman R.

Gigascience. 2017 Dec 1;6(12):1-7. doi: 10.1093/gigascience/gix107.

2.

Functional Genomics of Host-Microbiome Interactions in Humans.

Luca F, Kupfer SS, Knights D, Khoruts A, Blekhman R.

Trends Genet. 2018 Jan;34(1):30-40. doi: 10.1016/j.tig.2017.10.001. Epub 2017 Oct 26. Review.

PMID:
29107345
3.

Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation.

Xu D, Pavlidis P, Taskent RO, Alachiotis N, Flanagan C, DeGiorgio M, Blekhman R, Ruhl S, Gokcumen O.

Mol Biol Evol. 2017 Oct 1;34(10):2704-2715. doi: 10.1093/molbev/msx206.

4.

Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens.

Nédélec Y, Sanz J, Baharian G, Szpiech ZA, Pacis A, Dumaine A, Grenier JC, Freiman A, Sams AJ, Hebert S, Pagé Sabourin A, Luca F, Blekhman R, Hernandez RD, Pique-Regi R, Tung J, Yotova V, Barreiro LB.

Cell. 2016 Oct 20;167(3):657-669.e21. doi: 10.1016/j.cell.2016.09.025.

5.

Genetic and transcriptional analysis of human host response to healthy gut microbiota.

Richards AL, Burns MB, Alazizi A, Barreiro LB, Pique-Regi R, Blekhman R, Luca F.

mSystems. 2016 Jul-Aug;1(4). pii: e00067-16. Epub 2016 Aug 30.

6.

Atopic Dermatitis Susceptibility Variants in Filaggrin Hitchhike Hornerin Selective Sweep.

Eaaswarkhanth M, Xu D, Flanagan C, Rzhetskaya M, Hayes MG, Blekhman R, Jablonski NG, Gokcumen O.

Genome Biol Evol. 2016 Nov 11;8(10):3240-3255.

7.

Recent evolution of the salivary mucin MUC7.

Xu D, Pavlidis P, Thamadilok S, Redwood E, Fox S, Blekhman R, Ruhl S, Gokcumen O.

Sci Rep. 2016 Aug 25;6:31791. doi: 10.1038/srep31791.

8.

Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data.

Blekhman R, Tang K, Archie EA, Barreiro LB, Johnson ZP, Wilson ME, Kohn J, Yuan ML, Gesquiere L, Grieneisen LE, Tung J.

Sci Rep. 2016 Aug 16;6:31519. doi: 10.1038/srep31519.

9.

Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns.

Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR, Vlckova K, Modry D, Todd A, Jost Robinson CA, Remis MJ, Torralba MG, Morton E, Umaña JD, Carbonero F, Gaskins HR, Nelson KE, Wilson BA, Stumpf RM, White BA, Leigh SR, Blekhman R.

Cell Rep. 2016 Mar 8;14(9):2142-2153. doi: 10.1016/j.celrep.2016.02.013. Epub 2016 Feb 25.

10.

Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp.

Gomez A, Rothman JM, Petrzelkova K, Yeoman CJ, Vlckova K, Umaña JD, Carr M, Modry D, Todd A, Torralba M, Nelson KE, Stumpf RM, Wilson BA, Blekhman R, White BA, Leigh SR.

ISME J. 2016 Feb;10(2):532. doi: 10.1038/ismej.2015.252. No abstract available.

11.

Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence.

Morton ER, Lynch J, Froment A, Lafosse S, Heyer E, Przeworski M, Blekhman R, Ségurel L.

PLoS Genet. 2015 Nov 30;11(11):e1005658. doi: 10.1371/journal.pgen.1005658. eCollection 2015 Nov.

12.

Host genetic variation impacts microbiome composition across human body sites.

Blekhman R, Goodrich JK, Huang K, Sun Q, Bukowski R, Bell JT, Spector TD, Keinan A, Ley RE, Gevers D, Clark AG.

Genome Biol. 2015 Sep 15;16:191. doi: 10.1186/s13059-015-0759-1.

13.

Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp.

Gomez A, Rothman JM, Petrzelkova K, Yeoman CJ, Vlckova K, Umaña JD, Carr M, Modry D, Todd A, Torralba M, Nelson KE, Stumpf RM, Wilson BA, Blekhman R, White BA, Leigh SR.

ISME J. 2016 Feb;10(2):514-26. doi: 10.1038/ismej.2015.146. Epub 2015 Aug 28. Erratum in: ISME J. 2016 Feb;10(2):532.

14.

Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment.

Burns MB, Lynch J, Starr TK, Knights D, Blekhman R.

Genome Med. 2015 Jun 24;7(1):55. doi: 10.1186/s13073-015-0177-8. eCollection 2015.

15.

Population genomic analysis of 962 whole genome sequences of humans reveals natural selection in non-coding regions.

Yu F, Lu J, Liu X, Gazave E, Chang D, Raj S, Hunter-Zinck H, Blekhman R, Arbiza L, Van Hout C, Morrison A, Johnson AD, Bis J, Cupples LA, Psaty BM, Muzny D, Yu J, Gibbs RA, Keinan A, Clark AG, Boerwinkle E.

PLoS One. 2015 Mar 25;10(3):e0121644. doi: 10.1371/journal.pone.0121644. eCollection 2015.

16.

Social networks predict gut microbiome composition in wild baboons.

Tung J, Barreiro LB, Burns MB, Grenier JC, Lynch J, Grieneisen LE, Altmann J, Alberts SC, Blekhman R, Archie EA.

Elife. 2015 Mar 16;4. doi: 10.7554/eLife.05224.

17.

Human genetics shape the gut microbiome.

Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, Van Treuren W, Knight R, Bell JT, Spector TD, Clark AG, Ley RE.

Cell. 2014 Nov 6;159(4):789-99. doi: 10.1016/j.cell.2014.09.053.

18.

Comparative metabolomics in primates reveals the effects of diet and gene regulatory variation on metabolic divergence.

Blekhman R, Perry GH, Shahbaz S, Fiehn O, Clark AG, Gilad Y.

Sci Rep. 2014 Jul 28;4:5809. doi: 10.1038/srep05809.

19.

Gene expression differences among primates are associated with changes in a histone epigenetic modification.

Cain CE, Blekhman R, Marioni JC, Gilad Y.

Genetics. 2011 Apr;187(4):1225-34. doi: 10.1534/genetics.110.126177. Epub 2011 Feb 14.

20.

Functional comparison of innate immune signaling pathways in primates.

Barreiro LB, Marioni JC, Blekhman R, Stephens M, Gilad Y.

PLoS Genet. 2010 Dec 16;6(12):e1001249. doi: 10.1371/journal.pgen.1001249.

21.

Sex-specific and lineage-specific alternative splicing in primates.

Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y.

Genome Res. 2010 Feb;20(2):180-9. doi: 10.1101/gr.099226.109. Epub 2009 Dec 15.

22.

Segmental duplications contribute to gene expression differences between humans and chimpanzees.

Blekhman R, Oshlack A, Gilad Y.

Genetics. 2009 Jun;182(2):627-30. doi: 10.1534/genetics.108.099960. Epub 2009 Mar 30.

23.

A signature of evolutionary constraint on a subset of ectopically expressed olfactory receptor genes.

De la Cruz O, Blekhman R, Zhang X, Nicolae D, Firestein S, Gilad Y.

Mol Biol Evol. 2009 Mar;26(3):491-4. doi: 10.1093/molbev/msn294. Epub 2008 Dec 22.

24.

Gene regulation in primates evolves under tissue-specific selection pressures.

Blekhman R, Oshlack A, Chabot AE, Smyth GK, Gilad Y.

PLoS Genet. 2008 Nov;4(11):e1000271. doi: 10.1371/journal.pgen.1000271. Epub 2008 Nov 21. Erratum in: PLoS Genet. 2009 Mar;5(3). doi: 10.1371/annotation/06105fdb-f0fa-4fe2-88d0-db9f6036509f.

25.

Selective constraints in experimentally defined primate regulatory regions.

Gaffney DJ, Blekhman R, Majewski J.

PLoS Genet. 2008 Aug 15;4(8):e1000157. doi: 10.1371/journal.pgen.1000157.

26.

Natural selection on genes that underlie human disease susceptibility.

Blekhman R, Man O, Herrmann L, Boyko AR, Indap A, Kosiol C, Bustamante CD, Teshima KM, Przeworski M.

Curr Biol. 2008 Jun 24;18(12):883-9. doi: 10.1016/j.cub.2008.04.074.

27.

An evolutionarily conserved sexual signature in the primate brain.

Reinius B, Saetre P, Leonard JA, Blekhman R, Merino-Martinez R, Gilad Y, Jazin E.

PLoS Genet. 2008 Jun 20;4(6):e1000100. doi: 10.1371/journal.pgen.1000100.

28.

A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway.

de Candia P, Blekhman R, Chabot AE, Oshlack A, Gilad Y.

PLoS One. 2008 Feb 27;3(2):e1670. doi: 10.1371/journal.pone.0001670.

29.

SPIKE--a database, visualization and analysis tool of cellular signaling pathways.

Elkon R, Vesterman R, Amit N, Ulitsky I, Zohar I, Weisz M, Mass G, Orlev N, Sternberg G, Blekhman R, Assa J, Shiloh Y, Shamir R.

BMC Bioinformatics. 2008 Feb 20;9:110. doi: 10.1186/1471-2105-9-110.

30.

Using reporter gene assays to identify cis regulatory differences between humans and chimpanzees.

Chabot A, Shrit RA, Blekhman R, Gilad Y.

Genetics. 2007 Aug;176(4):2069-76. Epub 2007 Jun 11.

31.

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