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1.

Gene communities in co-expression networks across different tissues.

Russell, Madison; Aqil, Alber; Saitou, Marie; Gokcumen, Omer; Masuda, Naoki.

PLoS Comput Biol ; 19(11): e1011616, 2023 Nov.

Article in English | MEDLINE | ID: mdl-37976327

2.

Similarity-Based Analysis of Allele Frequency Distribution among Multiple Populations Identifies Adaptive Genomic Structural Variants.

Saitou, Marie; Masuda, Naoki; Gokcumen, Omer.

Mol Biol Evol ; 39(3)2022 03 02.

Article in English | MEDLINE | ID: mdl-34718708

3.

Loss-of-function tolerance of enhancers in the human genome.

Xu, Duo; Gokcumen, Omer; Khurana, Ekta.

PLoS Genet ; 16(4): e1008663, 2020 04.

Article in English | MEDLINE | ID: mdl-32243438

4.

Genomic evidence for ancient human migration routes along South America's Atlantic coast.

Campelo Dos Santos, Andre Luiz; Owings, Amanda; Sullasi, Henry Socrates Lavalle; Gokcumen, Omer; DeGiorgio, Michael; Lindo, John.

Proc Biol Sci ; 289(1986): 20221078, 2022 11 09.

Article in English | MEDLINE | ID: mdl-36322514

5.

Human and Nonhuman Primate Lineage-Specific Footprints in the Salivary Proteome.

Thamadilok, Supaporn; Choi, Kyoung-Soo; Ruhl, Lorenz; Schulte, Fabian; Kazim, A Latif; Hardt, Markus; Gokcumen, Omer; Ruhl, Stefan.

Mol Biol Evol ; 37(2): 395-405, 2020 02 01.

Article in English | MEDLINE | ID: mdl-31614365

6.

A Single-Organelle Optical Omics Platform for Cell Science and Biomarker Discovery.

Pliss, Artem; Kuzmin, Andrey N; Lita, Adrian; Kumar, Rahul; Celiku, Orieta; Atilla-Gokcumen, G Ekin; Gokcumen, Omer; Chandra, Dhyan; Larion, Mioara; Prasad, Paras N.

Anal Chem ; 93(23): 8281-8290, 2021 06 15.

Article in English | MEDLINE | ID: mdl-34048235

7.

An Evolutionary Perspective on the Impact of Genomic Copy Number Variation on Human Health.

Saitou, Marie; Gokcumen, Omer.

J Mol Evol ; 88(1): 104-119, 2020 01.

Article in English | MEDLINE | ID: mdl-31522275

8.

Archaic hominin introgression into modern human genomes.

Gokcumen, Omer.

Am J Phys Anthropol ; 171 Suppl 70: 60-73, 2020 05.

Article in English | MEDLINE | ID: mdl-31702050

9.

Shades of complexity: New perspectives on the evolution and genetic architecture of human skin.

Quillen, Ellen E; Norton, Heather L; Parra, Esteban J; Lona-Durazo, Frida; Ang, Khai C; Illiescu, Florin Mircea; Pearson, Laurel N; Shriver, Mark D; Lasisi, Tina; Gokcumen, Omer; Starr, Izzy; Lin, Yen-Lung; Martin, Alicia R; Jablonski, Nina G.

Am J Phys Anthropol ; 168 Suppl 67: 4-26, 2019 01.

Article in English | MEDLINE | ID: mdl-30408154

10.

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

Xu, Duo; Pavlidis, Pavlos; Taskent, Recep Ozgur; Alachiotis, Nikolaos; Flanagan, Colin; DeGiorgio, Michael; Blekhman, Ran; Ruhl, Stefan; Gokcumen, Omer.

Mol Biol Evol ; 34(10): 2704-2715, 2017 10 01.

Article in English | MEDLINE | ID: mdl-28957509

11.

VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.

Xu, Duo; Jaber, Yousef; Pavlidis, Pavlos; Gokcumen, Omer.

BMC Bioinformatics ; 18(1): 426, 2017 Sep 26.

Article in English | MEDLINE | ID: mdl-28950836

12.

Segmental duplications and evolutionary acquisition of UV damage response in the SPATA31 gene family of primates and humans.

Bekpen, Cemalettin; Künzel, Sven; Xie, Chen; Eaaswarkhanth, Muthukrishnan; Lin, Yen-Lung; Gokcumen, Omer; Akdis, Cezmi A; Tautz, Diethard.

BMC Genomics ; 18(1): 222, 2017 03 06.

Article in English | MEDLINE | ID: mdl-28264649

13.

The Multiple Histories of Western Asia: Perspectives from Ancient and Modern Genomes.

Taskent, Recep Ozgur; Gokcumen, Omer.

Hum Biol ; 89(2): 107-117, 2017 04.

Article in English | MEDLINE | ID: mdl-29299965

14.

The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence.

Pajic, Petar; Lin, Yen-Lung; Xu, Duo; Gokcumen, Omer.

BMC Evol Biol ; 16(1): 265, 2016 12 05.

Article in English | MEDLINE | ID: mdl-27919236

15.

Next-generation sequencing-based detection of germline L1-mediated transductions.

Tica, Jelena; Lee, Eunjung; Untergasser, Andreas; Meiers, Sascha; Garfield, David A; Gokcumen, Omer; Furlong, Eileen E M; Park, Peter J; Stütz, Adrian M; Korbel, Jan O.

BMC Genomics ; 17: 342, 2016 05 10.

Article in English | MEDLINE | ID: mdl-27161561

16.

The evolution and functional impact of human deletion variants shared with archaic hominin genomes.

Lin, Yen-Lung; Pavlidis, Pavlos; Karakoc, Emre; Ajay, Jerry; Gokcumen, Omer.

Mol Biol Evol ; 32(4): 1008-19, 2015 Apr.

Article in English | MEDLINE | ID: mdl-25556237

17.

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division.

Abyzov, Alexej; Iskow, Rebecca; Gokcumen, Omer; Radke, David W; Balasubramanian, Suganthi; Pei, Baikang; Habegger, Lukas; Lee, Charles; Gerstein, Mark.

Genome Res ; 23(12): 2042-52, 2013 Dec.

Article in English | MEDLINE | ID: mdl-24026178

18.

Origins and functional impact of copy number variation in the human genome.

Conrad, Donald F; Pinto, Dalila; Redon, Richard; Feuk, Lars; Gokcumen, Omer; Zhang, Yujun; Aerts, Jan; Andrews, T Daniel; Barnes, Chris; Campbell, Peter; Fitzgerald, Tomas; Hu, Min; Ihm, Chun Hwa; Kristiansson, Kati; Macarthur, Daniel G; Macdonald, Jeffrey R; Onyiah, Ifejinelo; Pang, Andy Wing Chun; Robson, Sam; Stirrups, Kathy; Valsesia, Armand; Walter, Klaudia; Wei, John; Tyler-Smith, Chris; Carter, Nigel P; Lee, Charles; Scherer, Stephen W; Hurles, Matthew E.

Nature ; 464(7289): 704-12, 2010 Apr 01.

Article in English | MEDLINE | ID: mdl-19812545

19.

Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence.

Gokcumen, Omer; Zhu, Qihui; Mulder, Lubbertus C F; Iskow, Rebecca C; Austermann, Christian; Scharer, Christopher D; Raj, Towfique; Boss, Jeremy M; Sunyaev, Shamil; Price, Alkes; Stranger, Barbara; Simon, Viviana; Lee, Charles.

PLoS Genet ; 9(4): e1003404, 2013 Apr.

Article in English | MEDLINE | ID: mdl-23593015

20.

Primate genome architecture influences structural variation mechanisms and functional consequences.

Gokcumen, Omer; Tischler, Verena; Tica, Jelena; Zhu, Qihui; Iskow, Rebecca C; Lee, Eunjung; Fritz, Markus Hsi-Yang; Langdon, Amy; Stütz, Adrian M; Pavlidis, Pavlos; Benes, Vladimir; Mills, Ryan E; Park, Peter J; Lee, Charles; Korbel, Jan O.

Proc Natl Acad Sci U S A ; 110(39): 15764-9, 2013 Sep 24.

Article in English | MEDLINE | ID: mdl-24014587

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