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Ran Blekhman

TitleAssociate Professor
InstitutionUniversity of Chicago
DepartmentMedicine-Genetic Medicine
AddressChicago IL 60637
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    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. 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. Synchrony and idiosyncrasy in the gut microbiome of wild baboons. Nat Ecol Evol. 2022 07; 6(7):955-964. PMID: 35654895.
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    2. Priya S, Burns MB, Ward T, Mars RAT, Adamowicz B, Lock EF, Kashyap PC, Knights D, Blekhman R. Identification of shared and disease-specific host gene-microbiome associations across human diseases using multi-omic integration. Nat Microbiol. 2022 06; 7(6):780-795. PMID: 35577971.
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    3. Fink I, Abdill RJ, Blekhman R, Grieneisen L. BiomeHorizon: Visualizing Microbiome Time Series Data in R. mSystems. 2022 Jun 28; 7(3):e0138021. PMID: 35499306.
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    4. Abdill RJ, Adamowicz EM, Blekhman R. Public human microbiome data are dominated by highly developed countries. PLoS Biol. 2022 02; 20(2):e3001536. PMID: 35167588.
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    5. 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. Interspecies variation in hominid gut microbiota controls host gene regulation. Cell Rep. 2021 11 23; 37(8):110057. PMID: 34818542.
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    6. 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. The gut microbiome in konzo. Nat Commun. 2021 09 10; 12(1):5371. PMID: 34508085.
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    7. 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. Gut microbiome heritability is nearly universal but environmentally contingent. Science. 2021 07 09; 373(6551):181-186. PMID: 34244407.
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    8. 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. Multi-Omics Analyses Show Disease, Diet, and Transcriptome Interactions With the Virome. Gastroenterology. 2021 10; 161(4):1194-1207.e8. PMID: 34245762.
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    9. 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, Labaj 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. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell. 2021 06 24; 184(13):3376-3393.e17. PMID: 34043940.
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    10. 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. Erratum for Gomez et al., "Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints". mSphere. 2021 Mar 17; 6(2). PMID: 33731474.
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    11. Sharma AK, Petrzelkova K, Pafco B, Jost Robinson CA, Fuh T, Wilson BA, Stumpf RM, Torralba MG, Blekhman R, White B, Nelson KE, Leigh SR, Gomez A. Traditional Human Populations and Nonhuman Primates Show Parallel Gut Microbiome Adaptations to Analogous Ecological Conditions. mSystems. 2020 Dec 22; 5(6). PMID: 33361321.
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    12. 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. Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome. Cell. 2020 Nov 12; 183(4):1137-1140. PMID: 33186523.
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    13. 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. Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome. Cell. 2020 09 17; 182(6):1460-1473.e17. PMID: 32916129.
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    14. Grieneisen L, Muehlbauer AL, Blekhman R. Microbial control of host gene regulation and the evolution of host-microbiome interactions in primates. Philos Trans R Soc Lond B Biol Sci. 2020 09 28; 375(1808):20190598. PMID: 32772669.
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    15. Abdill RJ, Adamowicz EM, Blekhman R. International authorship and collaboration across bioRxiv preprints. Elife. 2020 07 27; 9. PMID: 32716295.
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    16. Dayama G, Priya S, Niccum DE, Khoruts A, Blekhman R. Interactions between the gut microbiome and host gene regulation in cystic fibrosis. Genome Med. 2020 01 28; 12(1):12. PMID: 31992345.
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    17. Richards AL, Muehlbauer AL, Alazizi A, Burns MB, Findley A, Messina F, Gould TJ, Cascardo C, Pique-Regi R, Blekhman R, Luca F. Gut Microbiota Has a Widespread and Modifiable Effect on Host Gene Regulation. mSystems. 2019 Sep 03; 4(5). PMID: 31481602.
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    18. 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. Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints. mSphere. 2019 07 31; 4(4). PMID: 31366708.
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    19. Priya S, Blekhman R. Population dynamics of the human gut microbiome: change is the only constant. Genome Biol. 2019 07 31; 20(1):150. PMID: 31366367.
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    20. 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. Challenges and recommendations to improve the installability and archival stability of omics computational tools. PLoS Biol. 2019 06; 17(6):e3000333. PMID: 31220077.
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    21. Sharma AK, Pafco B, Vlcková K, Cervená B, Kreisinger J, Davison S, Beeri K, Fuh T, Leigh SR, Burns MB, Blekhman R, Petrželková KJ, Gomez A. Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq. BMC Genomics. 2019 Jun 14; 20(1):493. PMID: 31200636.
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    22. Abdill RJ, Blekhman R. Rxivist.org: Sorting biology preprints using social media and readership metrics. PLoS Biol. 2019 05; 17(5):e3000269. PMID: 31112533.
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    23. Abdill RJ, Blekhman R. Tracking the popularity and outcomes of all bioRxiv preprints. Elife. 2019 04 24; 8. PMID: 31017570.
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    24. Grieneisen LE, Charpentier MJE, Alberts SC, Blekhman R, Bradburd G, Tung J, Archie EA. Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species. Proc Biol Sci. 2019 04 24; 286(1901):20190431. PMID: 31014219.
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    25. Mangul S, Martin LS, Eskin E, Blekhman R. Improving the usability and archival stability of bioinformatics software. Genome Biol. 2019 02 27; 20(1):47. PMID: 30813962.
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    26. 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. Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nat Microbiol. 2019 04; 4(4):693-700. PMID: 30692672.
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    27. Burns MB, Blekhman R. Integrating tumor genomics into studies of the microbiome in colorectal cancer. Gut Microbes. 2019; 10(4):547-552. PMID: 30556775.
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    28. Brooks AW, Priya S, Blekhman R, Bordenstein SR. Gut microbiota diversity across ethnicities in the United States. PLoS Biol. 2018 12; 16(12):e2006842. PMID: 30513082.
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    29. 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. Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers. Genome Med. 2018 10 31; 10(1):78. PMID: 30376889.
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    30. Clark CR, Maile M, Blaney P, Hellweg SR, Strauss A, Durose W, Priya S, Habicht J, Burns MB, Blekhman R, Abrahante JE, Starr TK. Transposon mutagenesis screen in mice identifies TM9SF2 as a novel colorectal cancer oncogene. Sci Rep. 2018 10 17; 8(1):15327. PMID: 30333512.
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    31. Grieneisen LE, Blekhman R. Erratum for Grieneisen and Blekhman, "Crowdsourcing Our National Gut". mSystems. 2018 Jul-Aug; 3(4). PMID: 30003142.
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    32. Burns MB, Montassier E, Abrahante J, Priya S, Niccum DE, Khoruts A, Starr TK, Knights D, Blekhman R. Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment. PLoS Genet. 2018 06; 14(6):e1007376. PMID: 29924794.
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    33. 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. The gut microbiome of nonhuman primates: Lessons in ecology and evolution. Am J Primatol. 2018 06; 80(6):e22867. PMID: 29862519.
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    34. Grieneisen LE, Blekhman R. Crowdsourcing Our National Gut. mSystems. 2018 May-Jun; 3(3). PMID: 29795799.
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    35. Yuan C, Burns MB, Subramanian S, Blekhman R. Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer. mSystems. 2018 May-Jun; 3(3). PMID: 29795787.
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    36. Lynch J, Tang K, Priya S, Sands J, Sands M, Tang E, Mukherjee S, Knights D, Blekhman R. HOMINID: a framework for identifying associations between host genetic variation and microbiome composition. Gigascience. 2017 12 01; 6(12):1-7. PMID: 29126115.
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    37. Luca F, Kupfer SS, Knights D, Khoruts A, Blekhman R. Functional Genomics of Host-Microbiome Interactions in Humans. Trends Genet. 2018 01; 34(1):30-40. PMID: 29107345.
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    38. Xu D, Pavlidis P, Taskent RO, Alachiotis N, Flanagan C, DeGiorgio M, Blekhman R, Ruhl S, Gokcumen O. Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation. Mol Biol Evol. 2017 10 01; 34(10):2704-2715. PMID: 28957509.
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    39. Eaaswarkhanth M, Xu D, Flanagan C, Rzhetskaya M, Hayes MG, Blekhman R, Jablonski NG, Gokcumen O. Atopic Dermatitis Susceptibility Variants in Filaggrin Hitchhike Hornerin Selective Sweep. Genome Biol Evol. 2016 11 11; 8(10):3240-3255. PMID: 27678121.
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    40. 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. Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens. Cell. 2016 Oct 20; 167(3):657-669.e21. PMID: 27768889.
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    41. Richards AL, Burns MB, Alazizi A, Barreiro LB, Pique-Regi R, Blekhman R, Luca F. Genetic and transcriptional analysis of human host response to healthy gut microbiota. mSystems. 2016 Jul-Aug; 1(4). PMID: 27709125.
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    42. Xu D, Pavlidis P, Thamadilok S, Redwood E, Fox S, Blekhman R, Ruhl S, Gokcumen O. Recent evolution of the salivary mucin MUC7. Sci Rep. 2016 08 25; 6:31791. PMID: 27558399.
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    43. Blekhman R, Tang K, Archie EA, Barreiro LB, Johnson ZP, Wilson ME, Kohn J, Yuan ML, Gesquiere L, Grieneisen LE, Tung J. Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data. Sci Rep. 2016 08 16; 6:31519. PMID: 27528013.
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    44. 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. Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns. Cell Rep. 2016 Mar 08; 14(9):2142-2153. PMID: 26923597.
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    45. 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. Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp. ISME J. 2016 Feb; 10(2):532. PMID: 26784513.
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    46. Morton ER, Lynch J, Froment A, Lafosse S, Heyer E, Przeworski M, Blekhman R, Ségurel L. Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence. PLoS Genet. 2015 Nov; 11(11):e1005658. PMID: 26619199.
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    47. Blekhman R, Goodrich JK, Huang K, Sun Q, Bukowski R, Bell JT, Spector TD, Keinan A, Ley RE, Gevers D, Clark AG. Host genetic variation impacts microbiome composition across human body sites. Genome Biol. 2015 Sep 15; 16:191. PMID: 26374288.
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    48. 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. Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp. ISME J. 2016 Feb; 10(2):514-26. PMID: 26315972.
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    49. Burns MB, Lynch J, Starr TK, Knights D, Blekhman R. Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment. Genome Med. 2015; 7(1):55. PMID: 26170900.
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    50. 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. Population genomic analysis of 962 whole genome sequences of humans reveals natural selection in non-coding regions. PLoS One. 2015; 10(3):e0121644. PMID: 25807536.
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    51. Tung J, Barreiro LB, Burns MB, Grenier JC, Lynch J, Grieneisen LE, Altmann J, Alberts SC, Blekhman R, Archie EA. Social networks predict gut microbiome composition in wild baboons. Elife. 2015 Mar 16; 4. PMID: 25774601.
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    52. 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. Human genetics shape the gut microbiome. Cell. 2014 Nov 06; 159(4):789-99. PMID: 25417156.
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    53. Blekhman R, Perry GH, Shahbaz S, Fiehn O, Clark AG, Gilad Y. Comparative metabolomics in primates reveals the effects of diet and gene regulatory variation on metabolic divergence. Sci Rep. 2014 Jul 28; 4:5809. PMID: 25069065.
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    54. Cain CE, Blekhman R, Marioni JC, Gilad Y. Gene expression differences among primates are associated with changes in a histone epigenetic modification. Genetics. 2011 Apr; 187(4):1225-34. PMID: 21321133.
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    55. Barreiro LB, Marioni JC, Blekhman R, Stephens M, Gilad Y. Functional comparison of innate immune signaling pathways in primates. PLoS Genet. 2010 Dec 16; 6(12):e1001249. PMID: 21187902.
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    56. Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y. Sex-specific and lineage-specific alternative splicing in primates. Genome Res. 2010 Feb; 20(2):180-9. PMID: 20009012.
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    57. Blekhman R, Oshlack A, Gilad Y. Segmental duplications contribute to gene expression differences between humans and chimpanzees. Genetics. 2009 Jun; 182(2):627-30. PMID: 19332884.
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    58. De la Cruz O, Blekhman R, Zhang X, Nicolae D, Firestein S, Gilad Y. A signature of evolutionary constraint on a subset of ectopically expressed olfactory receptor genes. Mol Biol Evol. 2009 Mar; 26(3):491-4. PMID: 19103638.
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    59. Blekhman R, Oshlack A, Chabot AE, Smyth GK, Gilad Y. Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet. 2008 Nov; 4(11):e1000271. PMID: 19023414.
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    60. Gaffney DJ, Blekhman R, Majewski J. Selective constraints in experimentally defined primate regulatory regions. PLoS Genet. 2008 Aug 15; 4(8):e1000157. PMID: 18704158.
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    61. Blekhman R, Man O, Herrmann L, Boyko AR, Indap A, Kosiol C, Bustamante CD, Teshima KM, Przeworski M. Natural selection on genes that underlie human disease susceptibility. Curr Biol. 2008 Jun 24; 18(12):883-9. PMID: 18571414.
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    62. Reinius B, Saetre P, Leonard JA, Blekhman R, Merino-Martinez R, Gilad Y, Jazin E. An evolutionarily conserved sexual signature in the primate brain. PLoS Genet. 2008 Jun 20; 4(6):e1000100. PMID: 18566661.
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    63. de Candia P, Blekhman R, Chabot AE, Oshlack A, Gilad Y. A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway. PLoS One. 2008 Feb 27; 3(2):e1670. PMID: 18301748.
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    64. 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. SPIKE--a database, visualization and analysis tool of cellular signaling pathways. BMC Bioinformatics. 2008 Feb 20; 9:110. PMID: 18289391.
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    65. Chabot A, Shrit RA, Blekhman R, Gilad Y. Using reporter gene assays to identify cis regulatory differences between humans and chimpanzees. Genetics. 2007 Aug; 176(4):2069-76. PMID: 17565944.
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    66. Dagan T, Blekhman R, Graur D. The "domino theory" of gene death: gradual and mass gene extinction events in three lineages of obligate symbiotic bacterial pathogens. Mol Biol Evol. 2006 Feb; 23(2):310-6. PMID: 16237210.
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