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Ran Blekhman, Ph.D. - Publications

Affiliations: 
2010 Human Genetics University of Chicago, Chicago, IL 
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46 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Abdill RJ, Graham SP, Rubinetti V, Albert FW, Greene CS, Davis S, Blekhman R. Integration of 168,000 samples reveals global patterns of the human gut microbiome. Biorxiv : the Preprint Server For Biology. PMID 37873416 DOI: 10.1101/2023.10.11.560955  0.759
2022 Fink I, Abdill RJ, Blekhman R, Grieneisen L. : Visualizing Microbiome Time Series Data in R. Msystems. e0138021. PMID 35499306 DOI: 10.1128/msystems.01380-21  0.732
2022 Abdill RJ, Adamowicz EM, Blekhman R. Public human microbiome data are dominated by highly developed countries. Plos Biology. 20: e3001536. PMID 35167588 DOI: 10.1371/journal.pbio.3001536  0.747
2020 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, ... ... Blekhman R, et al. Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome. Cell. PMID 32916129 DOI: 10.1016/J.Cell.2020.08.007  0.352
2020 Grieneisen L, Muehlbauer AL, Blekhman R. Microbial control of host gene regulation and the evolution of host-microbiome interactions in primates. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 375: 20190598. PMID 32772669 DOI: 10.1098/Rstb.2019.0598  0.403
2020 Abdill RJ, Adamowicz EM, Blekhman R. International authorship and collaboration across bioRxiv preprints. Elife. 9. PMID 32716295 DOI: 10.7554/Elife.58496  0.735
2020 Dayama G, Priya S, Niccum DE, Khoruts A, Blekhman R. Interactions between the gut microbiome and host gene regulation in cystic fibrosis. Genome Medicine. 12: 12. PMID 31992345 DOI: 10.1186/S13073-020-0710-2  0.317
2019 Priya S, Blekhman R. Population dynamics of the human gut microbiome: change is the only constant. Genome Biology. 20: 150. PMID 31366367 DOI: 10.1186/S13059-019-1775-3  0.334
2019 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, ... ... Blekhman R, et al. Challenges and recommendations to improve the installability and archival stability of omics computational tools. Plos Biology. 17: e3000333. PMID 31220077 DOI: 10.1371/Journal.Pbio.3000333  0.73
2019 Sharma AK, Pafčo B, Vlčková K, Červená 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. 20: 493. PMID 31200636 DOI: 10.1186/S12864-019-5813-Z  0.36
2019 Abdill RJ, Blekhman R. Rxivist.org: Sorting biology preprints using social media and readership metrics. Plos Biology. 17: e3000269. PMID 31112533 DOI: 10.1371/Journal.Pbio.3000269  0.736
2019 Abdill RJ, Blekhman R. Meta-Research: Tracking the popularity and outcomes of all bioRxiv preprints. Elife. 8. PMID 31017570 DOI: 10.7554/Elife.45133  0.74
2019 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. Nature Microbiology. PMID 30692672 DOI: 10.1038/S41564-018-0338-9  0.391
2018 Brooks AW, Priya S, Blekhman R, Bordenstein SR. Gut microbiota diversity across ethnicities in the United States. Plos Biology. 16: e2006842. PMID 30513082 DOI: 10.1371/Journal.Pbio.2006842  0.332
2018 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. American Journal of Primatology. e22867. PMID 29862519 DOI: 10.1002/Ajp.22867  0.388
2018 Gomez A, Torralba M, Nelson KE, Stumpf R, Blekhman R, Petrzelkova K. Host microbe interactions in the primate gut: Implications for human origins The Faseb Journal. 32: 101.1-101.1. DOI: 10.1096/Fasebj.32.1_Supplement.101.1  0.324
2017 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. PMID 29126115 DOI: 10.1093/Gigascience/Gix107  0.318
2017 Luca F, Kupfer SS, Knights D, Khoruts A, Blekhman R. Functional Genomics of Host-Microbiome Interactions in Humans. Trends in Genetics : Tig. PMID 29107345 DOI: 10.1016/J.Tig.2017.10.001  0.357
2017 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. Molecular Biology and Evolution. 34: 2704-2715. PMID 28957509 DOI: 10.1093/Molbev/Msx206  0.335
2016 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, et al. Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens. Cell. 167: 657-669.e21. PMID 27768889 DOI: 10.1016/J.Cell.2016.09.025  0.329
2016 Eaaswarkhanth M, Xu D, Flanagan C, Rzhetskaya M, Hayes MG, Blekhman R, Jablonski N, Gokcumen O. Atopic Dermatitis Susceptibility Variants In Filaggrin Hitchhike Hornerin Selective Sweep. Genome Biology and Evolution. PMID 27678121 DOI: 10.1093/Gbe/Evw242  0.365
2016 Xu D, Pavlidis P, Thamadilok S, Redwood E, Fox S, Blekhman R, Ruhl S, Gokcumen O. Recent evolution of the salivary mucin MUC7. Scientific Reports. 6: 31791. PMID 27558399 DOI: 10.1038/Srep31791  0.357
2016 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. Scientific Reports. 6: 31519. PMID 27528013 DOI: 10.1038/Srep31519  0.313
2016 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, ... ... Blekhman R, et al. Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns. Cell Reports. PMID 26923597 DOI: 10.1016/J.Celrep.2016.02.013  0.322
2015 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 Genetics. 11: e1005658. PMID 26619199 DOI: 10.1371/Journal.Pgen.1005658  0.339
2015 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 Biology. 16: 191. PMID 26374288 DOI: 10.1186/S13059-015-0759-1  0.368
2015 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, et al. Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp. The Isme Journal. PMID 26315972 DOI: 10.1038/Ismej.2015.146  0.333
2015 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, et al. Population genomic analysis of 962 whole genome sequences of humans reveals natural selection in non-coding regions. Plos One. 10: e0121644. PMID 25807536 DOI: 10.1371/Journal.Pone.0121644  0.319
2014 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. 159: 789-99. PMID 25417156 DOI: 10.1016/J.Cell.2014.09.053  0.308
2014 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. Scientific Reports. 4: 5809. PMID 25069065 DOI: 10.1038/Srep05809  0.589
2012 Blekhman R. A database of orthologous exons in primates for comparative analysis of RNA-seq data Nature Precedings. 7: 1-1. DOI: 10.1038/Npre.2012.7054.1  0.34
2011 Cain CE, Blekhman R, Marioni JC, Gilad Y. Gene expression differences among primates are associated with changes in a histone epigenetic modification. Genetics. 187: 1225-34. PMID 21321133 DOI: 10.1534/Genetics.110.126177  0.688
2010 Barreiro LB, Marioni JC, Blekhman R, Stephens M, Gilad Y. Functional comparison of innate immune signaling pathways in primates. Plos Genetics. 6: e1001249. PMID 21187902 DOI: 10.1371/Journal.Pgen.1001249  0.568
2010 Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y. Sex-specific and lineage-specific alternative splicing in primates. Genome Research. 20: 180-9. PMID 20009012 DOI: 10.1101/Gr.099226.109  0.611
2010 Bainer R, Marioni J, Barriero L, Blekhman R, Onel K, Gilad Y. Abstract LB-332: MDM4 transcription is discordantly regulated by common variants of p53 Cancer Research. 70. DOI: 10.1158/1538-7445.Am10-Lb-332  0.715
2009 Blekhman R, Oshlack A, Gilad Y. Segmental duplications contribute to gene expression differences between humans and chimpanzees. Genetics. 182: 627-30. PMID 19332884 DOI: 10.1534/Genetics.108.099960  0.602
2009 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. Molecular Biology and Evolution. 26: 491-4. PMID 19103638 DOI: 10.1093/Molbev/Msn294  0.568
2009 Blekhman R, Oshlack A, Chabot AE, Smyth GK, Gilad Y. Correction: Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures Plos Genetics. 5. DOI: 10.1371/Annotation/06105Fdb-F0Fa-4Fe2-88D0-Db9F6036509F  0.514
2008 Blekhman R, Oshlack A, Chabot AE, Smyth GK, Gilad Y. Gene regulation in primates evolves under tissue-specific selection pressures. Plos Genetics. 4: e1000271. PMID 19023414 DOI: 10.1371/Journal.Pgen.1000271  0.615
2008 Gaffney DJ, Blekhman R, Majewski J. Selective constraints in experimentally defined primate regulatory regions. Plos Genetics. 4: e1000157. PMID 18704158 DOI: 10.1371/Journal.Pgen.1000157  0.386
2008 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. Current Biology : Cb. 18: 883-9. PMID 18571414 DOI: 10.1016/J.Cub.2008.04.074  0.341
2008 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 Genetics. 4: e1000100. PMID 18566661 DOI: 10.1371/Journal.Pgen.1000100  0.574
2008 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. 3: e1670. PMID 18301748 DOI: 10.1371/Journal.Pone.0001670  0.602
2008 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. 9: 110. PMID 18289391 DOI: 10.1186/1471-2105-9-110  0.308
2007 Chabot A, Shrit RA, Blekhman R, Gilad Y. Using reporter gene assays to identify cis regulatory differences between humans and chimpanzees. Genetics. 176: 2069-76. PMID 17565944 DOI: 10.1534/Genetics.107.073429  0.615
2006 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. Molecular Biology and Evolution. 23: 310-6. PMID 16237210 DOI: 10.1093/Molbev/Msj036  0.357
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