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Items: 39

1.

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

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.

Am J Phys Anthropol. 2019 Jan;168 Suppl 67:4-26. doi: 10.1002/ajpa.23737. Epub 2018 Nov 8.

PMID:
30408154
2.

Complex Haplotypes of GSTM1 Gene Deletions Harbor Signatures of a Selective Sweep in East Asian Populations.

Saitou M, Satta Y, Gokcumen O.

G3 (Bethesda). 2018 Aug 30;8(9):2953-2966. doi: 10.1534/g3.118.200462.

3.

An evolutionary transcriptomics approach links CD36 to membrane remodeling in replicative senescence.

Saitou M, Lizardo DY, Taskent RO, Millner A, Gokcumen O, Atilla-Gokcumen GE.

Mol Omics. 2018 Aug 6;14(4):237-246. doi: 10.1039/c8mo00099a.

PMID:
29974107
4.

Complex evolution of the GSTM gene family involves sharing of GSTM1 deletion polymorphism in humans and chimpanzees.

Saitou M, Satta Y, Gokcumen O, Ishida T.

BMC Genomics. 2018 Apr 25;19(1):293. doi: 10.1186/s12864-018-4676-z.

5.

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

Taskent RO, Gokcumen O.

Hum Biol. 2017 Apr;89(2):107-117. Review.

PMID:
29299965
6.

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

Gokcumen O.

Hum Biol. 2017 Jan;89(1):5-6. No abstract available.

PMID:
29285968
7.

Variation and Functional Impact of Neanderthal Ancestry in Western Asia.

Taskent RO, Alioglu ND, Fer E, Melike Donertas H, Somel M, Gokcumen O.

Genome Biol Evol. 2017 Dec 1;9(12):3516-3524. doi: 10.1093/gbe/evx216.

8.

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

Xu D, Pavlidis P, Taskent RO, Alachiotis N, Flanagan C, DeGiorgio M, Blekhman R, Ruhl S, Gokcumen O.

Mol Biol Evol. 2017 Oct 1;34(10):2704-2715. doi: 10.1093/molbev/msx206.

9.

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

Xu D, Jaber Y, Pavlidis P, Gokcumen O.

BMC Bioinformatics. 2017 Sep 26;18(1):426. doi: 10.1186/s12859-017-1844-0.

10.

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

Bekpen C, Künzel S, Xie C, Eaaswarkhanth M, Lin YL, Gokcumen O, Akdis CA, Tautz D.

BMC Genomics. 2017 Mar 6;18(1):222. doi: 10.1186/s12864-017-3595-8.

11.

Regulation of lipids is central to replicative senescence.

Lizardo DY, Lin YL, Gokcumen O, Atilla-Gokcumen GE.

Mol Biosyst. 2017 Feb 28;13(3):498-509. doi: 10.1039/c6mb00842a.

PMID:
28128379
13.

Atopic Dermatitis Susceptibility Variants in Filaggrin Hitchhike Hornerin Selective Sweep.

Eaaswarkhanth M, Xu D, Flanagan C, Rzhetskaya M, Hayes MG, Blekhman R, Jablonski NG, Gokcumen O.

Genome Biol Evol. 2016 Nov 11;8(10):3240-3255.

14.

Recent evolution of the salivary mucin MUC7.

Xu D, Pavlidis P, Thamadilok S, Redwood E, Fox S, Blekhman R, Ruhl S, Gokcumen O.

Sci Rep. 2016 Aug 25;6:31791. doi: 10.1038/srep31791.

15.

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

Tica J, Lee E, Untergasser A, Meiers S, Garfield DA, Gokcumen O, Furlong EE, Park PJ, Stütz AM, Korbel JO.

BMC Genomics. 2016 May 10;17:342. doi: 10.1186/s12864-016-2670-x.

16.

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

Hoover KC, Gokcumen O, Qureshy Z, Bruguera E, Savangsuksa A, Cobb M, Matsunami H.

Chem Senses. 2015 Sep;40(7):481-8. doi: 10.1093/chemse/bjv030. Epub 2015 Jun 13.

17.

Geographic distribution and adaptive significance of genomic structural variants: an anthropological genetics perspective.

Eaaswarkhanth M, Pavlidis P, Gokcumen O.

Hum Biol. 2014 Fall;86(4):260-75. Review.

PMID:
25959693
18.

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

Lin YL, Pavlidis P, Karakoc E, Ajay J, Gokcumen O.

Mol Biol Evol. 2015 Apr;32(4):1008-19. doi: 10.1093/molbev/msu405. Epub 2015 Jan 2.

19.

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

Alkan C, Kavak P, Somel M, Gokcumen O, Ugurlu S, Saygi C, Dal E, Bugra K, Güngör T, Sahinalp SC, Özören N, Bekpen C.

BMC Genomics. 2014 Nov 7;15:963. doi: 10.1186/1471-2164-15-963.

20.

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

Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L; 1000 Genomes Project Consortium, Lee C, Gerstein M.

Genome Res. 2013 Dec;23(12):2042-52. doi: 10.1101/gr.154625.113. Epub 2013 Sep 11.

21.

Primate genome architecture influences structural variation mechanisms and functional consequences.

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.

Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15764-9. doi: 10.1073/pnas.1305904110. Epub 2013 Sep 6.

22.

Vif proteins from diverse primate lentiviral lineages use the same binding site in APOBEC3G.

Letko M, Silvestri G, Hahn BH, Bibollet-Ruche F, Gokcumen O, Simon V, Ooms M.

J Virol. 2013 Nov;87(21):11861-71. doi: 10.1128/JVI.01944-13. Epub 2013 Aug 28.

23.

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

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.

PLoS Genet. 2013 Apr;9(4):e1003404. doi: 10.1371/journal.pgen.1003404. Epub 2013 Apr 11.

24.

Impact of constitutional copy number variants on biological pathway evolution.

Poptsova M, Banerjee S, Gokcumen O, Rubin MA, Demichelis F.

BMC Evol Biol. 2013 Jan 23;13:19. doi: 10.1186/1471-2148-13-19.

25.

Regulatory element copy number differences shape primate expression profiles.

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, Lee C.

Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12656-61. doi: 10.1073/pnas.1205199109. Epub 2012 Jul 13.

26.

Landscape of somatic retrotransposition in human cancers.

Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ 3rd, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, Park PJ; Cancer Genome Atlas Research Network.

Science. 2012 Aug 24;337(6097):967-71. doi: 10.1126/science.1222077. Epub 2012 Jun 28.

27.

Exploring the role of copy number variants in human adaptation.

Iskow RC, Gokcumen O, Lee C.

Trends Genet. 2012 Jun;28(6):245-57. doi: 10.1016/j.tig.2012.03.002. Epub 2012 Apr 5. Review.

28.

Mitochondrial DNA and Y chromosome variation provides evidence for a recent common ancestry between Native Americans and Indigenous Altaians.

Dulik MC, Zhadanov SI, Osipova LP, Askapuli A, Gau L, Gokcumen O, Rubinstein S, Schurr TG.

Am J Hum Genet. 2012 Feb 10;90(2):229-46. doi: 10.1016/j.ajhg.2011.12.014. Epub 2012 Jan 25. Erratum in: Am J Hum Genet. 2012 Mar 9;90(3):573.

29.

Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis.

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, Zon LI, Freeman JL, Lee C.

Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):529-34. doi: 10.1073/pnas.1112163109. Epub 2011 Dec 27.

30.

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

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, Yavartanoo M, Kang HP, Gokcumen O, Govindaraju DR, Jung JH, Chong H, Yang KS, Kim H, Lee C, Seo JS.

Nat Genet. 2011 Jul 3;43(8):745-52. doi: 10.1038/ng.872.

PMID:
21725310
31.

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

Gokcumen O, Babb PL, Iskow RC, Zhu Q, Shi X, Mills RE, Ionita-Laza I, Vallender EJ, Clark AG, Johnson WE, Lee C.

Genome Biol. 2011;12(5):R52. doi: 10.1186/gb-2011-12-5-r52. Epub 2011 May 31.

32.
33.

Y-chromosome and autosomal STR diversity in four proximate settlements in Central Anatolia.

Alakoc YD, Gokcumen O, Tug A, Gultekin T, Gulec E, Schurr TG.

Forensic Sci Int Genet. 2010 Oct;4(5):e135-7. doi: 10.1016/j.fsigen.2010.01.016. Epub 2010 Feb 23.

PMID:
20457085
34.

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

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, Ha JS, Chong W, Hwang GR, Darvishi K, Kim H, Yang SJ, Yang KS, Kim H, Hurles ME, Scherer SW, Carter NP, Tyler-Smith C, Lee C, Seo JS.

Nat Genet. 2010 May;42(5):400-5. doi: 10.1038/ng.555. Epub 2010 Apr 4.

35.

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

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, Macdonald JR, Onyiah I, Pang AW, Robson S, Stirrups K, Valsesia A, Walter K, Wei J; Wellcome Trust Case Control Consortium, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME.

Nature. 2010 Apr 1;464(7289):704-12. doi: 10.1038/nature08516. Epub 2009 Oct 7.

36.

A highly annotated whole-genome sequence of a Korean individual.

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, Yun JY, Woo HN, Lee H, Suh D, Lee S, Kim HJ, Yavartanoo M, Kwak M, Zheng Y, Lee MK, Park H, Kim JY, Gokcumen O, Mills RE, Zaranek AW, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Kim H, Yang KS, Park WY, Kim H, Church GM, Lee C, Kingsmore SF, Seo JS.

Nature. 2009 Aug 20;460(7258):1011-5. doi: 10.1038/nature08211. Epub 2009 Jul 8.

37.

Copy number variants (CNVs) in primate species using array-based comparative genomic hybridization.

Gökçümen O, Lee C.

Methods. 2009 Sep;49(1):18-25. doi: 10.1016/j.ymeth.2009.06.001. Epub 2009 Jun 21. Review.

38.

Russian Old Believers: genetic consequences of their persecution and exile, as shown by mitochondrial DNA evidence.

Rubinstein S, Dulik MC, Gokcumen O, Zhadanov S, Osipova L, Cocca M, Mehta N, Gubina M, Posukh O, Schurr TG.

Hum Biol. 2008 Jun;80(3):203-37. Erratum in: Hum Biol. 2008 Dec;80(6):675-7.

PMID:
19130794
39.

Genetic variation in the enigmatic Altaian Kazakhs of South-Central Russia: insights into Turkic population history.

Gokcumen O, Dulik MC, Pai AA, Zhadanov SI, Rubinstein S, Osipova LP, Andreenkov OV, Tabikhanova LE, Gubina MA, Labuda D, Schurr TG.

Am J Phys Anthropol. 2008 Jul;136(3):278-93. doi: 10.1002/ajpa.20802.

PMID:
18322915

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