Works by Gokcumen, Omer

Results: 38

Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection.

Published in:

Genome Biology, 2011, v. 12, n. 5, p. 1, doi. 10.1186/gb-2011-12-5-r52

By:

Gokcumen, Omer;
Babb, Paul L.;
Iskow, Rebecca C.;
Qihui Zhu;
Xinghua Shi;
Mills, Ryan E.;
Ionita-Laza, Iuliana;
Vallender, Eric J.;
Clark, Andrew G.;
Johnson, Welkin E.;
Lee, Charles

Publication type:

Article

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

Published in:

Journal of Molecular Evolution, 2020, v. 88, n. 1, p. 104, doi. 10.1007/s00239-019-09911-6

By:

Saitou, Marie;
Gokcumen, Omer

Publication type:

Article

Genome-Wide Selection Scan in an Arabian Peninsula Population Identifies a TNKS Haplotype Linked to Metabolic Traits and Hypertension.

Published in:

Genome Biology & Evolution, 2020, v. 12, n. 3, p. 77, doi. 10.1093/gbe/evaa033

By:

Eaaswarkhanth, Muthukrishnan;
Santos, Andre Luiz Campelo dos;
Gokcumen, Omer;
Al-Mulla, Fahd;
Thanaraj, Thangavel Alphonse

Publication type:

Article

Resolving the Insertion Sites of Polymorphic Duplications Reveals a HERC2 Haplotype under Selection.

Published in:

Genome Biology & Evolution, 2019, v. 11, n. 6, p. 1679, doi. 10.1093/gbe/evz107

By:

Saitou, Marie;
Gokcumen, Omer

Publication type:

Article

Fine-Scale Characterization of Genomic Structural Variation in the Human Genome Reveals Adaptive and Biomedically Relevant Hotspots.

Published in:

Genome Biology & Evolution, 2019, v. 11, n. 4, p. 1136, doi. 10.1093/gbe/evz058

By:

Lin, Yen-Lung;
Gokcumen, Omer

Publication type:

Article

Variation and Functional Impact of Neanderthal Ancestry in Western Asia.

Published in:

Genome Biology & Evolution, 2017, v. 9, n. 12, p. 3516, doi. 10.1093/gbe/evx216

By:

Taskent, Recep Ozgur;
Alioglu, Nursen Duha;
Fer, Evrim;
Donertas, Handan Melike;
Somel, Mehmet;
Gokcumen, Omer

Publication type:

Article

Atopic Dermatitis SusceptibilityVariants inFilaggrin Hitchhike Hornerin Selective Sweep.

Published in:

Genome Biology & Evolution, 2016, v. 8, n. 10, p. 3240, doi. 10.1093/gbe/evw242

By:

Eaaswarkhanth, Muthukrishnan;
Duo Xu;
Flanagan, Colin;
Rzhetskaya, Margarita;
Hayes, M. Geoffrey;
Blekhman, Ran;
Jablonski, Nina G.;
Gokcumen, Omer

Publication type:

Article

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

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2670-x

By:

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

Publication type:

Article

Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa.

Published in:

BMC Genomics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2164-15-963

By:

Alkan, Can;
Kavak, Pınar;
Somel, Mehmet;
Gokcumen, Omer;
Uğurlu, Serkan;
Saygı, Ceren;
Dal, Elif;
Buğra, Kuyaş;
Güngör, Tunga;
Cenk Sahinalp, S.;
Özören, Nesrin;
Bekpen, Cemalettin

Publication type:

Article

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

Published in:

BMC Evolutionary Biology, 2016, v. 16, p. 1, doi. 10.1186/s12862-016-0842-6

By:

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

Publication type:

Article

Impact of constitutional copy number variants on biological pathway evolution.

Published in:

BMC Evolutionary Biology, 2013, v. 13, n. 1, p. 1, doi. 10.1186/1471-2148-13-19

By:

Poptsova, Maria;
Banerjee, Samprit;
Gokcumen, Omer;
Rubin, Mark A.;
Demichelis, Francesca

Publication type:

Article

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

Published in:

Nature, 2010, v. 464, n. 7289, p. 704, doi. 10.1038/nature08516

By:

Conrad, Donald F.;
Pinto, Dalila;
Redon, Richard;
Feuk, Lars;
Gokcumen, Omer;
Yujun Zhang;
Aerts, Jan;
Andrews, T. Daniel;
Barnes, Chris;
Campbell, Peter;
Fitzgerald, Tomas;
Min Hu;
Chun Hwa Ihm;
Kristiansson, Kati;
MacArthur, Daniel G.;
MacDonald, Jeffrey R.;
Onyiah, Ifejinelo;
Wing Chun Pang, Andy;
Robson, Sam;
Stirrups, Kathy

Publication type:

Article

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

Published in:

PLoS Genetics, 2020, v. 16, n. 4, p. 1, doi. 10.1371/journal.pgen.1008663

By:

Xu, Duo;
Gokcumen, Omer;
Khurana, Ekta

Publication type:

Article

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

Published in:

Molecular Biology & Evolution, 2022, v. 39, n. 3, p. 1, doi. 10.1093/molbev/msab313

By:

Saitou, Marie;
Masuda, Naoki;
Gokcumen, Omer

Publication type:

Article

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

Published in:

Molecular Biology & Evolution, 2020, v. 37, n. 2, p. 395, doi. 10.1093/molbev/msz223

By:

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

Publication type:

Article

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

Published in:

Molecular Biology & Evolution, 2017, v. 34, n. 10, p. 2704, doi. 10.1093/molbev/msx206

By:

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

Publication type:

Article

The Evolution and Functional Impact of Human Deletion Variants Shared with Archaic Hominin Genomes.

Published in:

Molecular Biology & Evolution, 2015, v. 32, n. 4, p. 1008, doi. 10.1093/molbev/msu405

By:

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

Publication type:

Article

Human subsistence and signatures of selection on chemosensory genes.

Published in:

Communications Biology, 2023, v. 6, n. 1, p. 1, doi. 10.1038/s42003-023-05047-y

By:

Veilleux, Carrie C.;
Garrett, Eva C.;
Pajic, Petar;
Saitou, Marie;
Ochieng, Joseph;
Dagsaan, Lilia D.;
Dominy, Nathaniel J.;
Perry, George H.;
Gokcumen, Omer;
Melin, Amanda D.

Publication type:

Article

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

Published in:

Human Biology, 2017, v. 89, n. 2, p. 1, doi. 10.13110/humanbiology.89.2.01

By:

Taskent, Recep Ozgur;
Gokcumen, Omer

Publication type:

Article

Evolution, Function, and Deconstructing Histories: A New Generation of Anthropological Genetics.

Published in:

Human Biology, 2017, v. 89, n. 1, p. 5, doi. 10.13110/humanbiology.89.1.06

By:

Gokcumen, Omer

Publication type:

Article

Geographic Distribution and Adaptive Significance of Genomic Structural Variants: An Anthropological Genetics Perspective.

Published in:

Human Biology, 2014, v. 86, n. 4, p. 260

By:

Eaaswarkhanth, Muthukrishnan;
Pavlidis, Pavlos;
Gokcumen, Omer

Publication type:

Article

Russian Old Believers: Genetic Consequences of Their Persecution and Exile, as Shown by Mitochondrial DNA Evidence.

Published in:

Human Biology, 2008, v. 80, n. 3, p. 203, doi. 10.3378/1534-6617-80.3.203

By:

RUBINSTEIN, SAMARA;
DULIK, MATTHEW C.;
GOKCUMEN, OMER;
ZHADANOV, SERGEY;
OSIPOVA, LUDMILA;
COCCA, MAGGIE;
MEHTA, NISHI;
GUBINA, MARINA;
POSUKH, OLGA;
SCHURR, THEODORE G.

Publication type:

Article

Evolutionary context of psoriatic immune skin response.

Published in:

Evolution, Medicine & Public Health, 2021, v. 2021, n. 1, p. 474, doi. 10.1093/emph/eoab042

By:

Starr, Izzy;
Seiffert-Sinha, Kristina;
Sinha, Animesh A;
Gokcumen, Omer

Publication type:

Article

Tavuk Kültür, Yumurta Genom.

Published in:

Kebikeç: İnsan Bilimleri İçin Kaynak Araştırmaları Dergisi, 2016, n. 41, p. 295

By:

GÖKÇÜMEN, Ömer

Publication type:

Article

Analysis of somatic retrotransposition in human cancers.

Published in:

2012

By:

Eunjung Lee;
Iskow, Rebecca;
Lixing Yang;
Gokcumen, Omer;
Haseley, Psalm;
Luquette III, Lovelace J.;
Lohr, Jens G.;
Harris, Christopher C.;
Li Ding;
Wilson, Richard K.;
Wheeler, David A.;
Gibbs, Richard A.;
Kucherlapati, Raju;
Lee, Charles;
Kharchenko, Peter V.;
Park, Peter J.

Publication type:

Abstract

Spatiotemporal fluctuations of population structure in the Americas revealed by a meta‐analysis of the first decade of archaeogenomes.

Published in:

American Journal of Biological Anthropology, 2023, v. 180, n. 4, p. 703, doi. 10.1002/ajpa.24673

By:

Campelo dos Santos, Andre Luiz;
Lavalle Sullasi, Henry Socrates;
Gokcumen, Omer;
Lindo, John;
DeGiorgio, Michael

Publication type:

Article

Balancing selection on genomic deletion polymorphisms in humans.

Published in:

eLife, 2023, p. 1, doi. 10.7554/eLife.79111

By:

Aqil, Alber;
Speidel, Leo;
Pavlidis, Pavlos;
Gokcumen, Omer

Publication type:

Article

Global Survey of Variation in a Human Olfactory Receptor Gene Reveals Signatures of Non-Neutral Evolution.

Published in:

Chemical Senses, 2015, v. 40, n. 7, p. 481, doi. 10.1093/chemse/bjv030

By:

Hoover, Kara C.;
Gokcumen, Omer;
Qureshy, Zoya;
Bruguera, Elise;
Savangsuksa, Aulaphan;
Cobb, Matthew;
Matsunami, Hiroaki

Publication type:

Article

Recent evolution of the salivary mucin MUC7.

Published in:

Scientific Reports, 2016, p. 31791, doi. 10.1038/srep31791

By:

Xu, Duo;
Pavlidis, Pavlos;
Thamadilok, Supaporn;
Redwood, Emilie;
Fox, Sara;
Blekhman, Ran;
Ruhl, Stefan;
Gokcumen, Omer

Publication type:

Article

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

Published in:

BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-3595-8

By:

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

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2017, v. 18/, p. 1, doi. 10.1186/s12859-017-1844-0

By:

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

Publication type:

Article

Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human--Neandertal Divergence.

Published in:

PLoS Genetics, 2013, v. 9, n. 4, p. 1, doi. 10.1371/journal.pgen.1003404

By:

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

Publication type:

Article

Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage.

Published in:

Genetics, 2020, v. 215, n. 2, p. 497, doi. 10.1534/genetics.120.303167

By:

Ozgur, Ozgur;
Yen Lung Lin;
Patramanis, Ioannis;
Pavlidis, Pavlos;
Gokcumen, Omer

Publication type:

Article

Filamentation Regulatory Pathways Control Adhesion-Dependent Surface Responses in Yeast.

Published in:

Genetics, 2019, v. 212, n. 3, p. 667, doi. 10.1534/genetics.119.302004

By:

Chow, Jacky;
Starr, Izzy;
Jamalzadeh, Sheida;
Muniz, Omar;
Kumar, Anuj;
Gokcumen, Omer;
Ferkey, Denise M.;
Cullen, Paul J.

Publication type:

Article

Tuning the tropism and infectivity of SARS-CoV-2 virus-like particles for mRNA delivery.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 5, p. 1, doi. 10.1093/nar/gkaf133

By:

Yang, Qi;
Davidson, Bruce A;
Pajic, Petar;
Chen, Xuyang;
Gokcumen, Omer;
Gao, Min;
Neelamegham, Sriram

Publication type:

Article

Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals.

Published in:

Nature Genetics, 2011, v. 43, n. 8, p. 745, doi. 10.1038/ng.872

By:

Young Seok Ju;
Jong-Il Kim;
Sheehyun Kim;
Dongwan Hong;
Park, Hansoo;
Jong-Yeon Shin;
Seungbok Lee;
Won-Chul Lee;
Sujung Kim;
Saet-Byeol Yu;
Sung-Soo Park;
Seung-Hyun Seo;
Ji-Young Yun;
Hyun-Jin Kim;
Dong-Sung Lee;
Yavartanoo, Maryam;
Kang, Hyunseok Peter;
Gokcumen, Omer;
Govindaraju, Diddahally R.;
Jung Hee Jung

Publication type:

Article

Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing.

Published in:

Nature Genetics, 2010, v. 42, n. 5, p. 400, doi. 10.1038/ng.555

By:

Hansoo Park;
Jong-Il Kim;
Young Seok Ju;
Omer Gokcumen;
Ryan E Mills;
Sheehyun Kim;
Seungbok Lee;
Dongwhan Suh;
Dongwan Hong;
Hyunseok Peter Kang;
Yun Joo Yoo;
Jong-Yeon Shin;
Hyun-Jin Kim;
Maryam Yavartanoo;
Young Wha Chang;
Jung-Sook Ha;
Wilson Chong;
Ga-Ram Hwang;
Katayoon Darvishi;
HyeRan Kim

Publication type:

Article

Gene communities in co-expression networks across different tissues.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 11, p. 1, doi. 10.1371/journal.pcbi.1011616

By:

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

Publication type:

Article