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2005 1
2006 1
2007 1
2008 7
2009 3
2010 2
2011 2
2014 2
2015 6
2016 8
2017 3
2018 10
2019 11
2020 7
2021 6
2022 5
2023 6
2024 2

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Page 1
Multi-omic approaches for host-microbiome data integration.
Chetty A, Blekhman R. Chetty A, et al. Among authors: blekhman r. Gut Microbes. 2024 Jan-Dec;16(1):2297860. doi: 10.1080/19490976.2023.2297860. Epub 2024 Jan 2. Gut Microbes. 2024. PMID: 38166610 Free PMC article. Review.
Universal gut microbial relationships in the gut microbiome of wild baboons.
Roche KE, Bjork JR, Dasari MR, Grieneisen L, Jansen D, Gould TJ, Gesquiere LR, Barreiro LB, Alberts SC, Blekhman R, Gilbert JA, Tung J, Mukherjee S, Archie EA. Roche KE, et al. Among authors: blekhman r. Elife. 2023 May 9;12:e83152. doi: 10.7554/eLife.83152. Elife. 2023. PMID: 37158607 Free PMC article.
Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome.
Johnson KE, Heisel T, Allert M, Fürst A, Yerabandi N, Knights D, Jacobs KM, Lock EF, Bode L, Fields DA, Rudolph MC, Gale CA, Albert FW, Demerath EW, Blekhman R. Johnson KE, et al. Among authors: blekhman r. bioRxiv [Preprint]. 2023 Jan 25:2023.01.24.525211. doi: 10.1101/2023.01.24.525211. bioRxiv. 2023. PMID: 36747843 Free PMC article. Preprint.
Codiversification of gut microbiota with humans.
Suzuki TA, Fitzstevens JL, Schmidt VT, Enav H, Huus KE, Mbong Ngwese M, Grießhammer A, Pfleiderer A, Adegbite BR, Zinsou JF, Esen M, Velavan TP, Adegnika AA, Song LH, Spector TD, Muehlbauer AL, Marchi N, Kang H, Maier L, Blekhman R, Ségurel L, Ko G, Youngblut ND, Kremsner P, Ley RE. Suzuki TA, et al. Among authors: blekhman r. Science. 2022 Sep 16;377(6612):1328-1332. doi: 10.1126/science.abm7759. Epub 2022 Sep 15. Science. 2022. PMID: 36108023 Free PMC article.
Synchrony and idiosyncrasy in the gut microbiome of wild baboons.
Björk JR, Dasari MR, Roche K, Grieneisen L, Gould TJ, Grenier JC, Yotova V, Gottel N, Jansen D, Gesquiere LR, Gordon JB, Learn NH, Wango TL, Mututua RS, Kinyua Warutere J, Siodi L, Mukherjee S, Barreiro LB, Alberts SC, Gilbert JA, Tung J, Blekhman R, Archie EA. Björk JR, et al. Among authors: blekhman r. Nat Ecol Evol. 2022 Jul;6(7):955-964. doi: 10.1038/s41559-022-01773-4. Epub 2022 Jun 2. Nat Ecol Evol. 2022. PMID: 35654895 Free PMC article.
BiomeHorizon: Visualizing Microbiome Time Series Data in R.
Fink I, Abdill RJ, Blekhman R, Grieneisen L. Fink I, et al. Among authors: blekhman r. mSystems. 2022 Jun 28;7(3):e0138021. doi: 10.1128/msystems.01380-21. Epub 2022 May 5. mSystems. 2022. PMID: 35499306 Free PMC article.
Interspecies variation in hominid gut microbiota controls host gene regulation.
Muehlbauer AL, Richards AL, Alazizi A, Burns MB, Gomez A, Clayton JB, Petrzelkova K, Cascardo C, Resztak J, Wen X, Pique-Regi R, Luca F, Blekhman R. Muehlbauer AL, et al. Among authors: blekhman r. Cell Rep. 2021 Nov 23;37(8):110057. doi: 10.1016/j.celrep.2021.110057. Cell Rep. 2021. PMID: 34818542 Free PMC article.
Multi-Omics Analyses Show Disease, Diet, and Transcriptome Interactions With the Virome.
Mihindukulasuriya KA, Mars RAT, Johnson AJ, Ward T, Priya S, Lekatz HR, Kalari KR, Droit L, Zheng T, Blekhman R, D'Amato M, Farrugia G, Knights D, Handley SA, Kashyap PC. Mihindukulasuriya KA, et al. Among authors: blekhman r. Gastroenterology. 2021 Oct;161(4):1194-1207.e8. doi: 10.1053/j.gastro.2021.06.077. Epub 2021 Jul 7. Gastroenterology. 2021. PMID: 34245762 Free PMC article.
The gut microbiome in konzo.
Bramble MS, Vashist N, Ko A, Priya S, Musasa C, Mathieu A, Spencer A, Lupamba Kasendue M, Mamona Dilufwasayo P, Karume K, Nsibu J, Manya H, Uy MNA, Colwell B, Boivin M, Mayambu JPB, Okitundu D, Droit A, Mumba Ngoyi D, Blekhman R, Tshala-Katumbay D, Vilain E. Bramble MS, et al. Among authors: blekhman r. Nat Commun. 2021 Sep 10;12(1):5371. doi: 10.1038/s41467-021-25694-1. Nat Commun. 2021. PMID: 34508085 Free PMC article.
Gut microbiome heritability is nearly universal but environmentally contingent.
Grieneisen L, Dasari M, Gould TJ, Björk JR, Grenier JC, Yotova V, Jansen D, Gottel N, Gordon JB, Learn NH, Gesquiere LR, Wango TL, Mututua RS, Warutere JK, Siodi L, Gilbert JA, Barreiro LB, Alberts SC, Tung J, Archie EA, Blekhman R. Grieneisen L, et al. Among authors: blekhman r. Science. 2021 Jul 9;373(6551):181-186. doi: 10.1126/science.aba5483. Science. 2021. PMID: 34244407 Free PMC article.
A global metagenomic map of urban microbiomes and antimicrobial resistance.
Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KR, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, Mutai B, Neches RY, Ng A, Nikolayeva O, Nikolayeva T, Png E, Ryon KA, Sanchez JL, Shaaban H, Sierra MA, Thomas D, Young B, Abudayyeh OO, Alicea J, Bhattacharyya M, Blekhman R, Castro-Nallar E, Cañas AM, Chatziefthimiou AD, Crawford RW, De Filippis F, Deng Y, Desnues C, Dias-Neto E, Dybwad M, Elhaik E, Ercolini D, Frolova A, Gankin D, Gootenberg JS, Graf AB, Green DC, Hajirasouliha I, Hastings JJA, Hernandez M, Iraola G, Jang S, Kahles A, Kelly FJ, Knights K, Kyrpides NC, Łabaj PP, Lee PKH, Leung MHY, Ljungdahl PO, Mason-Buck G, McGrath K, Meydan C, Mongodin EF, Moraes MO, Nagarajan N, Nieto-Caballero M, Noushmehr H, Oliveira M, Ossowski S, Osuolale OO, Özcan O, Paez-Espino D, Rascovan N, Richard H, Rätsch G, Schriml LM, Semmler T, Sezerman OU, Shi L, Shi T, Siam R, Song LH, Suzuki H, Court DS, Tighe SW, Tong X, Udekwu KI, Ugalde JA, Valentine B, Vassilev DI, Vayndorf EM, Velavan TP, Wu J, Zambrano MM, Zhu J, Zhu S, Mason CE; International MetaSUB Consortium. Danko D, et al. Among authors: blekhman r. Cell. 2021 Jun 24;184(13):3376-3393.e17. doi: 10.1016/j.cell.2021.05.002. Epub 2021 May 26. Cell. 2021. PMID: 34043940 Free PMC article.
Erratum for Gomez et al., "Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints".
Gomez A, Sharma AK, Mallott EK, Petrzelkova KJ, Jost Robinson CA, Yeoman CJ, Carbonero F, Pafco B, Rothman JM, Ulanov A, Vlckova K, Amato KR, Schnorr SL, Dominy NJ, Modry D, Todd A, Torralba M, Nelson KE, Burns MB, Blekhman R, Remis M, Stumpf RM, Wilson BA, Gaskins HR, Garber PA, White BA, Leigh SR. Gomez A, et al. Among authors: blekhman r. mSphere. 2021 Mar 17;6(2):e00168-21. doi: 10.1128/mSphere.00168-21. mSphere. 2021. PMID: 33731474 Free PMC article. No abstract available.
Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome.
Mars RAT, Yang Y, Ward T, Houtti M, Priya S, Lekatz HR, Tang X, Sun Z, Kalari KR, Korem T, Bhattarai Y, Zheng T, Bar N, Frost G, Johnson AJ, van Treuren W, Han S, Ordog T, Grover M, Sonnenburg J, D'Amato M, Camilleri M, Elinav E, Segal E, Blekhman R, Farrugia G, Swann JR, Knights D, Kashyap PC. Mars RAT, et al. Among authors: blekhman r. Cell. 2020 Nov 12;183(4):1137-1140. doi: 10.1016/j.cell.2020.10.040. Cell. 2020. PMID: 33186523 Free article. No abstract available.
Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome.
Mars RAT, Yang Y, Ward T, Houtti M, Priya S, Lekatz HR, Tang X, Sun Z, Kalari KR, Korem T, Bhattarai Y, Zheng T, Bar N, Frost G, Johnson AJ, van Treuren W, Han S, Ordog T, Grover M, Sonnenburg J, D'Amato M, Camilleri M, Elinav E, Segal E, Blekhman R, Farrugia G, Swann JR, Knights D, Kashyap PC. Mars RAT, et al. Among authors: blekhman r. Cell. 2020 Sep 17;182(6):1460-1473.e17. doi: 10.1016/j.cell.2020.08.007. Epub 2020 Sep 10. Cell. 2020. PMID: 32916129 Free PMC article.
Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment.
Chng KR, Li C, Bertrand D, Ng AHQ, Kwah JS, Low HM, Tong C, Natrajan M, Zhang MH, Xu L, Ko KKK, Ho EXP, Av-Shalom TV, Teo JWP, Khor CC; MetaSUB Consortium; Chen SL, Mason CE, Ng OT, Marimuthu K, Ang B, Nagarajan N. Chng KR, et al. Nat Med. 2020 Jun;26(6):941-951. doi: 10.1038/s41591-020-0894-4. Epub 2020 Jun 8. Nat Med. 2020. PMID: 32514171 Free PMC article.
Gut Microbiota Has a Widespread and Modifiable Effect on Host Gene Regulation.
Richards AL, Muehlbauer AL, Alazizi A, Burns MB, Findley A, Messina F, Gould TJ, Cascardo C, Pique-Regi R, Blekhman R, Luca F. Richards AL, et al. Among authors: blekhman r. mSystems. 2019 Sep 3;4(5):e00323-18. doi: 10.1128/mSystems.00323-18. mSystems. 2019. PMID: 31481602 Free PMC article.
Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints.
Gomez A, Sharma AK, Mallott EK, Petrzelkova KJ, Jost Robinson CA, Yeoman CJ, Carbonero F, Pafco B, Rothman JM, Ulanov A, Vlckova K, Amato KR, Schnorr SL, Dominy NJ, Modry D, Todd A, Torralba M, Nelson KE, Burns MB, Blekhman R, Remis M, Stumpf RM, Wilson BA, Gaskins HR, Garber PA, White BA, Leigh SR. Gomez A, et al. Among authors: blekhman r. mSphere. 2019 Jul 31;4(4):e00271-19. doi: 10.1128/mSphere.00271-19. mSphere. 2019. PMID: 31366708 Free PMC article.
Challenges and recommendations to improve the installability and archival stability of omics computational tools.
Mangul S, Mosqueiro T, Abdill RJ, Duong D, Mitchell K, Sarwal V, Hill B, Brito J, Littman RJ, Statz B, Lam AK, Dayama G, Grieneisen L, Martin LS, Flint J, Eskin E, Blekhman R. Mangul S, et al. Among authors: blekhman r. PLoS Biol. 2019 Jun 20;17(6):e3000333. doi: 10.1371/journal.pbio.3000333. eCollection 2019 Jun. PLoS Biol. 2019. PMID: 31220077 Free PMC article.
Megaphages infect Prevotella and variants are widespread in gut microbiomes.
Devoto AE, Santini JM, Olm MR, Anantharaman K, Munk P, Tung J, Archie EA, Turnbaugh PJ, Seed KD, Blekhman R, Aarestrup FM, Thomas BC, Banfield JF. Devoto AE, et al. Among authors: blekhman r. Nat Microbiol. 2019 Apr;4(4):693-700. doi: 10.1038/s41564-018-0338-9. Epub 2019 Jan 28. Nat Microbiol. 2019. PMID: 30692672 Free PMC article.
Gut microbiota diversity across ethnicities in the United States.
Brooks AW, Priya S, Blekhman R, Bordenstein SR. Brooks AW, et al. Among authors: blekhman r. PLoS Biol. 2018 Dec 4;16(12):e2006842. doi: 10.1371/journal.pbio.2006842. eCollection 2018 Dec. PLoS Biol. 2018. PMID: 30513082 Free PMC article.
Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers.
Hale VL, Jeraldo P, Chen J, Mundy M, Yao J, Priya S, Keeney G, Lyke K, Ridlon J, White BA, French AJ, Thibodeau SN, Diener C, Resendis-Antonio O, Gransee J, Dutta T, Petterson XM, Sung J, Blekhman R, Boardman L, Larson D, Nelson H, Chia N. Hale VL, et al. Among authors: blekhman r. Genome Med. 2018 Oct 31;10(1):78. doi: 10.1186/s13073-018-0586-6. Genome Med. 2018. PMID: 30376889 Free PMC article.
The gut microbiome of nonhuman primates: Lessons in ecology and evolution.
Clayton JB, Gomez A, Amato K, Knights D, Travis DA, Blekhman R, Knight R, Leigh S, Stumpf R, Wolf T, Glander KE, Cabana F, Johnson TJ. Clayton JB, et al. Among authors: blekhman r. Am J Primatol. 2018 Jun;80(6):e22867. doi: 10.1002/ajp.22867. Epub 2018 Jun 4. Am J Primatol. 2018. PMID: 29862519 Review.
Crowdsourcing Our National Gut.
Grieneisen LE, Blekhman R. Grieneisen LE, et al. Among authors: blekhman r. mSystems. 2018 May 15;3(3):e00060-18. doi: 10.1128/mSystems.00060-18. eCollection 2018 May-Jun. mSystems. 2018. PMID: 29795799 Free PMC article.
Functional Genomics of Host-Microbiome Interactions in Humans.
Luca F, Kupfer SS, Knights D, Khoruts A, Blekhman R. Luca F, et al. Among authors: blekhman r. Trends Genet. 2018 Jan;34(1):30-40. doi: 10.1016/j.tig.2017.10.001. Epub 2017 Oct 26. Trends Genet. 2018. PMID: 29107345 Free PMC article. Review.
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. Nédélec Y, et al. Among authors: blekhman r. Cell. 2016 Oct 20;167(3):657-669.e21. doi: 10.1016/j.cell.2016.09.025. Cell. 2016. PMID: 27768889 Free article.
Recent evolution of the salivary mucin MUC7.
Xu D, Pavlidis P, Thamadilok S, Redwood E, Fox S, Blekhman R, Ruhl S, Gokcumen O. Xu D, et al. Among authors: blekhman r. Sci Rep. 2016 Aug 25;6:31791. doi: 10.1038/srep31791. Sci Rep. 2016. PMID: 27558399 Free PMC article.
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. Gomez A, et al. Among authors: blekhman r. Cell Rep. 2016 Mar 8;14(9):2142-2153. doi: 10.1016/j.celrep.2016.02.013. Epub 2016 Feb 25. Cell Rep. 2016. PMID: 26923597 Free article.
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. Gomez A, et al. Among authors: blekhman r. ISME J. 2016 Feb;10(2):532. doi: 10.1038/ismej.2015.252. ISME J. 2016. PMID: 26784513 Free PMC article. No abstract available.
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. Gomez A, et al. Among authors: blekhman r. ISME J. 2016 Feb;10(2):514-26. doi: 10.1038/ismej.2015.146. Epub 2015 Aug 28. ISME J. 2016. PMID: 26315972 Free PMC article.
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. Yu F, et al. Among authors: blekhman r. PLoS One. 2015 Mar 25;10(3):e0121644. doi: 10.1371/journal.pone.0121644. eCollection 2015. PLoS One. 2015. PMID: 25807536 Free PMC article.
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. Tung J, et al. Among authors: blekhman r. Elife. 2015 Mar 16;4:e05224. doi: 10.7554/eLife.05224. Elife. 2015. PMID: 25774601 Free PMC article.
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. Goodrich JK, et al. Among authors: blekhman r. Cell. 2014 Nov 6;159(4):789-99. doi: 10.1016/j.cell.2014.09.053. Cell. 2014. PMID: 25417156 Free PMC article.
The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group. Danecek P, et al. Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7. Bioinformatics. 2011. PMID: 21653522 Free PMC article.
An evolutionarily conserved sexual signature in the primate brain.
Reinius B, Saetre P, Leonard JA, Blekhman R, Merino-Martinez R, Gilad Y, Jazin E. Reinius B, et al. Among authors: blekhman r. PLoS Genet. 2008 Jun 20;4(6):e1000100. doi: 10.1371/journal.pgen.1000100. PLoS Genet. 2008. PMID: 18566661 Free PMC article.
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. Elkon R, et al. Among authors: blekhman r. BMC Bioinformatics. 2008 Feb 20;9:110. doi: 10.1186/1471-2105-9-110. BMC Bioinformatics. 2008. PMID: 18289391 Free PMC article.