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Omer Gokcumen, Ph.D. - Publications

Affiliations: 
2008 University of Pennsylvania, Philadelphia, PA, United States 
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63 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 Yilmaz F, Karageorgiou C, Kim K, Pajic P, Beck CR, Torregrossa AM, Lee C, Gokcumen O. Ancient gene duplications primed the amylase locus for adaptive evolution upon the onset of agriculture. Biorxiv : the Preprint Server For Biology. PMID 38077078 DOI: 10.1101/2023.11.27.568916  0.764
2023 Russell M, Aqil A, Saitou M, Gokcumen O, Masuda N. Gene communities in co-expression networks across different tissues. Plos Computational Biology. 19: e1011616. PMID 37976327 DOI: 10.1371/journal.pcbi.1011616  0.736
2023 Veilleux CC, Garrett EC, Pajic P, Saitou M, Ochieng J, Dagsaan LD, Dominy NJ, Perry GH, Gokcumen O, Melin AD. Human subsistence and signatures of selection on chemosensory genes. Communications Biology. 6: 683. PMID 37400713 DOI: 10.1038/s42003-023-05047-y  0.784
2023 Russell M, Saitou M, Gokcumen O, Masuda N. Gene communities in co-expression networks across different tissues. Arxiv. PMID 37292479  0.795
2023 Aqil A, Gill S, Gokcumen O, Malhi RS, Reese EA, Smith JL, Heaton TT, Lindqvist C. A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska. Iscience. 26: 106581. PMID 37138779 DOI: 10.1016/j.isci.2023.106581  0.771
2023 Sun YH, Cui H, Song C, Shen JT, Zhuo X, Wang RH, Yu X, Ndamba R, Mu Q, Gu H, Wang D, Murthy GG, Li P, Liang F, Liu L, ... ... Gokcumen O, et al. Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity. Nature Communications. 14: 812. PMID 36781861 DOI: 10.1038/s41467-023-36354-x  0.305
2023 Aqil A, Speidel L, Pavlidis P, Gokcumen O. Balancing selection on genomic deletion polymorphisms in humans. Elife. 12. PMID 36625544 DOI: 10.7554/eLife.79111  0.795
2022 Campelo Dos Santos AL, Owings A, Sullasi HSL, Gokcumen O, DeGiorgio M, Lindo J. Genomic evidence for ancient human migration routes along South America's Atlantic coast. Proceedings. Biological Sciences. 289: 20221078. PMID 36322514 DOI: 10.1098/rspb.2022.1078  0.314
2022 Pajic P, Shen S, Qu J, May AJ, Knox S, Ruhl S, Gokcumen O. A mechanism of gene evolution generating mucin function. Science Advances. 8: eabm8757. PMID 36026444 DOI: 10.1126/sciadv.abm8757  0.801
2021 Saitou M, Masuda N, Gokcumen O. Similarity-based analysis of allele frequency distribution among multiple populations identifies adaptive genomic structural variants. Molecular Biology and Evolution. PMID 34718708 DOI: 10.1093/molbev/msab313  0.808
2021 Saitou M, Resendez S, Pradhan AJ, Wu F, Lie NC, Hall NJ, Zhu Q, Reinholdt L, Satta Y, Speidel L, Nakagome S, Hanchard NA, Churchill G, Lee C, Atilla-Gokcumen GE, ... ... Gokcumen O, et al. Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor. Science Advances. 7: eabi4476. PMID 34559564 DOI: 10.1126/sciadv.abi4476  0.778
2020 Saitou M, Gaylord EA, Xu E, May AJ, Neznanova L, Nathan S, Grawe A, Chang J, Ryan W, Ruhl S, Knox SM, Gokcumen O. Functional Specialization of Human Salivary Glands and Origins of Proteins Intrinsic to Human Saliva. Cell Reports. 33: 108402. PMID 33207190 DOI: 10.1016/j.celrep.2020.108402  0.799
2020 Xu D, Gokcumen O, Khurana E. Loss-of-function tolerance of enhancers in the human genome. Plos Genetics. 16: e1008663. PMID 32243438 DOI: 10.1371/Journal.Pgen.1008663  0.671
2020 Taskent O, Lin YL, Patramanis I, Pavlidis P, Gokcumen O. Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage. Genetics. PMID 32234956 DOI: 10.1534/Genetics.120.303167  0.824
2020 Eaaswarkhanth M, Dos Santos ALC, Gokcumen O, Al-Mulla F, Thanaraj TA. Genome-wide Selection Scan in an Arabian Peninsula Population Identifies a TNKS haplotype Linked to Metabolic Traits and Hypertension. Genome Biology and Evolution. PMID 32068798 DOI: 10.1093/Gbe/Evaa033  0.525
2020 Gokcumen O, Frachetti M. The Impact of Ancient Genome Studies in Archaeology Annual Review of Anthropology. 49. DOI: 10.1146/Annurev-Anthro-010220-074353  0.367
2019 Gokcumen O. Archaic hominin introgression into modern human genomes. American Journal of Physical Anthropology. PMID 31702050 DOI: 10.1002/Ajpa.23951  0.533
2019 Thamadilok S, Choi KS, Ruhl L, Schulte F, Kazim AL, Hardt M, Gokcumen O, Ruhl S. Human and Non-Human Primate Lineage-Specific Footprints in the Salivary Proteome. Molecular Biology and Evolution. PMID 31614365 DOI: 10.1093/Molbev/Msz223  0.383
2019 Saitou M, Gokcumen O. An Evolutionary Perspective on the Impact of Genomic Copy Number Variation on Human Health. Journal of Molecular Evolution. PMID 31522275 DOI: 10.1007/S00239-019-09911-6  0.831
2019 Saitou M, Gokcumen O. Resolving the Insertion Sites of Polymorphic Duplications Reveals a HERC2 Haplotype under Selection. Genome Biology and Evolution. 11: 1679-1690. PMID 31124564 DOI: 10.1093/Gbe/Evz107  0.844
2019 Pajic P, Pavlidis P, Dean K, Neznanova L, Romano RA, Garneau D, Daugherity E, Globig A, Ruhl S, Gokcumen O. Independent amylase gene copy number bursts correlate with dietary preferences in mammals. Elife. 8. PMID 31084707 DOI: 10.7554/Elife.44628  0.782
2019 Lin YL, Gokcumen O. Fine-scale characterization of genomic structural variation in the human genome reveals adaptive and biomedically relevant hotspots. Genome Biology and Evolution. PMID 30887040 DOI: 10.1093/Gbe/Evz058  0.504
2019 Pajic P, Pavlidis P, Dean K, Neznanova L, Romano R, Garneau D, Daugherity E, Globig A, Ruhl S, Gokcumen O. Author response: Independent amylase gene copy number bursts correlate with dietary preferences in mammals Elife. DOI: 10.7554/Elife.44628.018  0.397
2018 Quillen EE, Norton HL, Parra EJ, Lona-Durazo F, Ang KC, Illiescu FM, Pearson LN, Shriver MD, Lasisi T, Gokcumen O, Starr I, Lin YL, Martin AR, Jablonski NG. Shades of complexity: New perspectives on the evolution and genetic architecture of human skin. American Journal of Physical Anthropology. PMID 30408154 DOI: 10.1002/Ajpa.23737  0.47
2018 Saitou M, Satta Y, Gokcumen O. Complex Haplotypes of Gene Deletions Harbor Signatures of a Selective Sweep in East Asian Populations. G3 (Bethesda, Md.). PMID 30061374 DOI: 10.1534/G3.118.200462  0.525
2018 Saitou M, Lizardo DY, Taskent RO, Millner A, Gokcumen O, Atilla-Gokcumen GE. An evolutionary transcriptomics approach links CD36 to membrane remodeling in replicative senescence. Molecular Omics. PMID 29974107 DOI: 10.1039/c8mo00099a  0.799
2018 Saitou M, Satta Y, Gokcumen O, Ishida T. Complex evolution of the GSTM gene family involves sharing of GSTM1 deletion polymorphism in humans and chimpanzees. Bmc Genomics. 19: 293. PMID 29695243 DOI: 10.1186/S12864-018-4676-Z  0.468
2017 Taskent RO, Gokcumen O. The Multiple Histories of Western Asia: Perspectives from Ancient and Modern Genomes. Human Biology. 89: 107-117. PMID 29299965 DOI: 10.13110/Humanbiology.89.2.01  0.384
2017 Gokcumen O. Evolution, Function, and Deconstructing Histories: A New Generation of Anthropological Genetics. Human Biology. 89: 5-6. PMID 29285968 DOI: 10.13110/Humanbiology.89.1.06  0.343
2017 Taskent RO, Alioglu D, Fer E, Donertas HM, Somel M, Gokcumen O. Variation and functional impact of Neanderthal ancestry in Western Asia. Genome Biology and Evolution. PMID 29040546 DOI: 10.1093/gbe/evx216  0.417
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  0.654
2017 Xu D, Jaber Y, Pavlidis P, Gokcumen O. VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences. Bmc Bioinformatics. 18: 426. PMID 28950836 DOI: 10.1186/S12859-017-1844-0  0.563
2017 Bekpen C, Künzel S, Xie C, Eaaswarkhanth M, Lin YL, Gokcumen O, Akdis CA, Tautz D. Segmental duplications and evolutionary acquisition of UV damage response in the SPATA31 gene family of primates and humans. Bmc Genomics. 18: 222. PMID 28264649 DOI: 10.1186/S12864-017-3595-8  0.458
2016 Pajic P, Lin YL, Xu D, Gokcumen O. The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence. Bmc Evolutionary Biology. 16: 265. PMID 27919236 DOI: 10.1186/S12862-016-0842-6  0.81
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  0.7
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  0.669
2016 Tica J, Lee E, Untergasser A, Meiers S, Garfield DA, Gokcumen O, Furlong EE, Park PJ, Stütz AM, Korbel JO. Next-generation sequencing-based detection of germline L1-mediated transductions. Bmc Genomics. 17: 342. PMID 27161561 DOI: 10.1186/S12864-016-2670-X  0.359
2015 Hoover KC, Gokcumen O, Qureshy Z, Bruguera E, Savangsuksa A, Cobb M, Matsunami H. Global Survey of Variation in a Human Olfactory Receptor Gene Reveals Signatures of Non-Neutral Evolution. Chemical Senses. PMID 26072518 DOI: 10.1093/Chemse/Bjv030  0.523
2015 Lin YL, Pavlidis P, Karakoc E, Ajay J, Gokcumen O. The evolution and functional impact of human deletion variants shared with archaic hominin genomes. Molecular Biology and Evolution. 32: 1008-19. PMID 25556237 DOI: 10.1093/Molbev/Msu405  0.547
2014 Eaaswarkhanth M, Pavlidis P, Gokcumen O. Geographic distribution and adaptive significance of genomic structural variants: an anthropological genetics perspective. Human Biology. 86: 260-75. PMID 25959693 DOI: 10.13110/Humanbiology.86.4.0260  0.507
2014 Alkan C, Kavak P, Somel M, Gokcumen O, Ugurlu S, Saygi C, Dal E, Bugra K, Güngör T, Sahinalp SC, Özören N, Bekpen C. Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa. Bmc Genomics. 15: 963. PMID 25376095 DOI: 10.1186/1471-2164-15-963  0.471
2013 Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L, Lee C, Gerstein M. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome Research. 23: 2042-52. PMID 24026178 DOI: 10.1101/Gr.154625.113  0.743
2013 Gokcumen O, Tischler V, Tica J, Zhu Q, Iskow RC, Lee E, Fritz MH, Langdon A, Stütz AM, Pavlidis P, Benes V, Mills RE, Park PJ, Lee C, Korbel JO. Primate genome architecture influences structural variation mechanisms and functional consequences. Proceedings of the National Academy of Sciences of the United States of America. 110: 15764-9. PMID 24014587 DOI: 10.1073/Pnas.1305904110  0.754
2013 Gokcumen O, Zhu Q, Mulder LC, Iskow RC, Austermann C, Scharer CD, Raj T, Boss JM, Sunyaev S, Price A, Stranger B, Simon V, Lee C. Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence. Plos Genetics. 9: e1003404. PMID 23593015 DOI: 10.1371/Journal.Pgen.1003404  0.766
2013 Poptsova M, Banerjee S, Gokcumen O, Rubin MA, Demichelis F. Impact of constitutional copy number variants on biological pathway evolution. Bmc Evolutionary Biology. 13: 19. PMID 23342974 DOI: 10.1186/1471-2148-13-19  0.471
2012 Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, et al. Regulatory element copy number differences shape primate expression profiles. Proceedings of the National Academy of Sciences of the United States of America. 109: 12656-61. PMID 22797897 DOI: 10.1073/Pnas.1205199109  0.708
2012 Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, et al. Landscape of somatic retrotransposition in human cancers. Science (New York, N.Y.). 337: 967-71. PMID 22745252 DOI: 10.1126/Science.1222077  0.702
2012 Iskow RC, Gokcumen O, Lee C. Exploring the role of copy number variants in human adaptation. Trends in Genetics : Tig. 28: 245-57. PMID 22483647 DOI: 10.1016/J.Tig.2012.03.002  0.766
2012 Dulik MC, Zhadanov SI, Osipova LP, Askapuli A, Gau L, Gokcumen O, Rubinstein S, Schurr TG. Mitochondrial DNA and Y chromosome variation provides evidence for a recent common ancestry between Native Americans and Indigenous Altaians. American Journal of Human Genetics. 90: 229-46. PMID 22281367 DOI: 10.1016/J.Ajhg.2011.12.014  0.793
2012 Brown KH, Dobrinski KP, Lee AS, Gokcumen O, Mills RE, Shi X, Chong WW, Chen JY, Yoo P, David S, Peterson SM, Raj T, Choy KW, Stranger BE, Williamson RE, et al. Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis. Proceedings of the National Academy of Sciences of the United States of America. 109: 529-34. PMID 22203992 DOI: 10.1073/Pnas.1112163109  0.727
2012 Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, et al. Analysis of somatic retrotransposition in human cancers Bmc Proceedings. 6. DOI: 10.1186/1753-6561-6-S6-O23  0.33
2012 Dulik MC, Zhadanov SI, Osipova LP, Askapuli A, Gau L, Gokcumen O, Rubinstein S, Schurr TG. Erratum: Mitochondrial DNA and y chromosome variation provides evidence for a recent common ancestry between native Americans and indigenous altaians ((The American Journal of Human Genetics (2012) 90 (229-246)) American Journal of Human Genetics. 90. DOI: 10.1016/J.Ajhg.2012.02.003  0.778
2012 Matney T, Algaze G, Dulik MC, Erdal OD, Erdal YS, Gokcumen O, Lorenz J, Mergen H. Understanding Early Bronze Age social structure through mortuary remains: A pilot aDNA study from Titriş Höyük, southeastern Turkey International Journal of Osteoarchaeology. 22: 338-351. DOI: 10.1002/Oa.1213  0.675
2011 Ju YS, Kim JI, Kim S, Hong D, Park H, Shin JY, Lee S, Lee WC, Kim S, Yu SB, Park SS, Seo SH, Yun JY, Kim HJ, Lee DS, ... ... Gokcumen O, et al. Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals. Nature Genetics. 43: 745-52. PMID 21725310 DOI: 10.1038/Ng.872  0.714
2011 Gokcumen O, Babb PL, Iskow RC, Zhu Q, Shi X, Mills RE, Ionita-Laza I, Vallender EJ, Clark AG, Johnson WE, Lee C. Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection. Genome Biology. 12: R52. PMID 21627829 DOI: 10.1186/Gb-2011-12-5-R52  0.808
2011 Gokcumen Ö, Gultekin T, Alakoc YD, Tug A, Gulec E, Schurr TG. Biological ancestries, kinship connections, and projected identities in four central Anatolian settlements: insights from culturally contextualized genetic anthropology. American Anthropologist. 113: 116-31. PMID 21560269 DOI: 10.1111/J.1548-1433.2010.01310.X  0.625
2010 Alakoc YD, Gokcumen O, Tug A, Gultekin T, Gulec E, Schurr TG. Y-chromosome and autosomal STR diversity in four proximate settlements in Central Anatolia. Forensic Science International. Genetics. 4: e135-7. PMID 20457085 DOI: 10.1016/J.Fsigen.2010.01.016  0.67
2010 Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, Kim S, Lee S, Suh D, Hong D, Kang HP, Yoo YJ, Shin JY, Kim HJ, Yavartanoo M, Chang YW, et al. Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nature Genetics. 42: 400-5. PMID 20364138 DOI: 10.1038/Ng.555  0.716
2010 Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, et al. Origins and functional impact of copy number variation in the human genome. Nature. 464: 704-12. PMID 19812545 DOI: 10.1038/Nature08516  0.732
2009 Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Lee WC, Lee JS, Seo SH, ... ... Gokcumen O, et al. A highly annotated whole-genome sequence of a Korean individual. Nature. 460: 1011-5. PMID 19587683 DOI: 10.1038/Nature08211  0.722
2009 Gökçümen O, Lee C. Copy number variants (CNVs) in primate species using array-based comparative genomic hybridization. Methods (San Diego, Calif.). 49: 18-25. PMID 19545629 DOI: 10.1016/J.Ymeth.2009.06.001  0.744
2008 Rubinstein S, Dulik MC, Gokcumen O, Zhadanov S, Osipova L, Cocca M, Mehta N, Gubina M, Posukh O, Schurr TG. Russian Old Believers: genetic consequences of their persecution and exile, as shown by mitochondrial DNA evidence. Human Biology. 80: 203-37. PMID 19130794 DOI: 10.3378/1534-6617-80.3.203  0.784
2008 Gokcumen O, Dulik MC, Pai AA, Zhadanov SI, Rubinstein S, Osipova LP, Andreenkov OV, Tabikhanova LE, Gubina MA, Labuda D, Schurr TG. Genetic variation in the enigmatic Altaian Kazakhs of South-Central Russia: insights into Turkic population history. American Journal of Physical Anthropology. 136: 278-93. PMID 18322915 DOI: 10.1002/Ajpa.20802  0.786
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