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Items: 28

1.

Dynamical Rearrangement of Human Epidermal Growth Factor Receptor 2 upon Antibody Binding: Effects on the Dimerization.

Magalhães PR, Machuqueiro M, Almeida JG, Melo A, D S Cordeiro MN, Verde SC, Gümüş ZH, Moreira IS, D G Correia J, Melo R.

Biomolecules. 2019 Nov 5;9(11). pii: E706. doi: 10.3390/biom9110706.

2.

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma.

Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümüş ZH, Geizler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H; Clinical Proteomic Tumor Analysis Consortium.

Cell. 2019 Oct 31;179(4):964-983.e31. doi: 10.1016/j.cell.2019.10.007.

3.

Oncogenic G12D mutation alters local conformations and dynamics of K-Ras.

Vatansever S, Erman B, Gümüş ZH.

Sci Rep. 2019 Aug 13;9(1):11730. doi: 10.1038/s41598-019-48029-z.

4.

Ancestral reconstruction reveals mechanisms of ERK regulatory evolution.

Sang D, Pinglay S, Wiewiora RP, Selvan ME, Lou HJ, Chodera JD, Turk BE, Gümüş ZH, Holt LJ.

Elife. 2019 Aug 13;8. pii: e38805. doi: 10.7554/eLife.38805.

5.

ImmuneRegulation: a web-based tool for identifying human immune regulatory elements.

Kalayci S, Selvan ME, Ramos I, Cotsapas C, Harris E, Kim EY, Montgomery RR, Poland G, Pulendran B, Tsang JS, Klein RJ, Gümüş ZH.

Nucleic Acids Res. 2019 Jul 2;47(W1):W142-W150. doi: 10.1093/nar/gkz450.

6.

Comprehensive functional genomic resource and integrative model for the human brain.

Wang D, Liu S, Warrell J, Won H, Shi X, Navarro FCP, Clarke D, Gu M, Emani P, Yang YT, Xu M, Gandal MJ, Lou S, Zhang J, Park JJ, Yan C, Rhie SK, Manakongtreecheep K, Zhou H, Nathan A, Peters M, Mattei E, Fitzgerald D, Brunetti T, Moore J, Jiang Y, Girdhar K, Hoffman GE, Kalayci S, Gümüş ZH, Crawford GE; PsychENCODE Consortium, Roussos P, Akbarian S, Jaffe AE, White KP, Weng Z, Sestan N, Geschwind DH, Knowles JA, Gerstein MB.

Science. 2018 Dec 14;362(6420). pii: eaat8464. doi: 10.1126/science.aat8464.

7.

Rare, Pathogenic Germline Variants in Fanconi Anemia Genes Increase Risk for Squamous Lung Cancer.

Esai Selvan M, Klein RJ, Gümüş ZH.

Clin Cancer Res. 2019 Mar 1;25(5):1517-1525. doi: 10.1158/1078-0432.CCR-18-2660. Epub 2018 Nov 13.

PMID:
30425093
8.

Exploring Biological Networks in 3D, Stereoscopic 3D, and Immersive 3D with iCAVE.

Kalayci S, Gümüş ZH.

Curr Protoc Bioinformatics. 2018 Mar;61(1):8.27.1-8.27.26. doi: 10.1002/cpbi.47.

PMID:
30040198
9.

High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation.

Lencz T, Yu J, Palmer C, Carmi S, Ben-Avraham D, Barzilai N, Bressman S, Darvasi A, Cho JH, Clark LN, Gümüş ZH, Joseph V, Klein R, Lipkin S, Offit K, Ostrer H, Ozelius LJ, Peter I, Atzmon G, Pe'er I.

Hum Genet. 2018 Apr;137(4):343-355. doi: 10.1007/s00439-018-1886-z. Epub 2018 Apr 28.

PMID:
29705978
10.

Inhibition of colorectal cancer genomic copy number alterations and chromosomal fragile site tumor suppressor FHIT and WWOX deletions by DNA mismatch repair.

Jahid S, Sun J, Gelincik O, Blecua P, Edelmann W, Kucherlapati R, Zhou K, Jasin M, Gümüş ZH, Lipkin SM.

Oncotarget. 2017 May 10;8(42):71574-71586. doi: 10.18632/oncotarget.17776. eCollection 2017 Sep 22.

11.

iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D.

Liluashvili V, Kalayci S, Fluder E, Wilson M, Gabow A, Gümüs ZH.

Gigascience. 2017 Aug 1;6(8):1-13. doi: 10.1093/gigascience/gix054.

12.

SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots.

Moreira IS, Koukos PI, Melo R, Almeida JG, Preto AJ, Schaarschmidt J, Trellet M, Gümüş ZH, Costa J, Bonvin AMJJ.

Sci Rep. 2017 Aug 14;7(1):8007. doi: 10.1038/s41598-017-08321-2.

13.

KDM2B, an H3K36-specific demethylase, regulates apoptotic response of GBM cells to TRAIL.

Kurt IC, Sur I, Kaya E, Cingoz A, Kazancioglu S, Kahya Z, Toparlak OD, Senbabaoglu F, Kaya Z, Ozyerli E, Karahüseyinoglu S, Lack NA, Gümüs ZH, Onder TT, Bagci-Onder T.

Cell Death Dis. 2017 Jun 29;8(6):e2897. doi: 10.1038/cddis.2017.288.

14.

Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pair motions.

Vatansever S, Gümüş ZH, Erman B.

Sci Rep. 2016 Nov 15;6:37012. doi: 10.1038/srep37012.

15.

Gene expression elucidates functional impact of polygenic risk for schizophrenia.

Fromer M, Roussos P, Sieberts SK, Johnson JS, Kavanagh DH, Perumal TM, Ruderfer DM, Oh EC, Topol A, Shah HR, Klei LL, Kramer R, Pinto D, Gümüş ZH, Cicek AE, Dang KK, Browne A, Lu C, Xie L, Readhead B, Stahl EA, Xiao J, Parvizi M, Hamamsy T, Fullard JF, Wang YC, Mahajan MC, Derry JM, Dudley JT, Hemby SE, Logsdon BA, Talbot K, Raj T, Bennett DA, De Jager PL, Zhu J, Zhang B, Sullivan PF, Chess A, Purcell SM, Shinobu LA, Mangravite LM, Toyoshiba H, Gur RE, Hahn CG, Lewis DA, Haroutunian V, Peters MA, Lipska BK, Buxbaum JD, Schadt EE, Hirai K, Roeder K, Brennand KJ, Katsanis N, Domenici E, Devlin B, Sklar P.

Nat Neurosci. 2016 Nov;19(11):1442-1453. doi: 10.1038/nn.4399. Epub 2016 Sep 26.

16.

A Novel Genetic Variant in Long Non-coding RNA Gene NEXN-AS1 is Associated with Risk of Lung Cancer.

Yuan H, Liu H, Liu Z, Owzar K, Han Y, Su L, Wei Y, Hung RJ, McLaughlin J, Brhane Y, Brennan P, Bickeboeller H, Rosenberger A, Houlston RS, Caporaso N, Landi MT, Heinrich J, Risch A, Christiani DC, Gümüş ZH, Klein RJ, Amos CI, Wei Q.

Sci Rep. 2016 Oct 7;6:34234. doi: 10.1038/srep34234.

17.

A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces.

Melo R, Fieldhouse R, Melo A, Correia JD, Cordeiro MN, Gümüş ZH, Costa J, Bonvin AM, Moreira IS.

Int J Mol Sci. 2016 Jul 27;17(8). pii: E1215. doi: 10.3390/ijms17081215.

18.

Comprehensive models of human primary and metastatic colorectal tumors in immunodeficient and immunocompetent mice by chemokine targeting.

Chen HJ, Sun J, Huang Z, Hou H Jr, Arcilla M, Rakhilin N, Joe DJ, Choi J, Gadamsetty P, Milsom J, Nandakumar G, Longman R, Zhou XK, Edwards R, Chen J, Chen KY, Bu P, Wang L, Xu Y, Munroe R, Abratte C, Miller AD, Gümüş ZH, Shuler M, Nishimura N, Edelmann W, Shen X, Lipkin SM.

Nat Biotechnol. 2015 Jun;33(6):656-60. doi: 10.1038/nbt.3239. Epub 2015 May 25.

19.

miR-1269 promotes metastasis and forms a positive feedback loop with TGF-β.

Bu P, Wang L, Chen KY, Rakhilin N, Sun J, Closa A, Tung KL, King S, Kristine Varanko A, Xu Y, Huan Chen J, Zessin AS, Shealy J, Cummings B, Hsu D, Lipkin SM, Moreno V, Gümüş ZH, Shen X.

Nat Commun. 2015 Apr 15;6:6879. doi: 10.1038/ncomms7879.

20.

Integrative annotation of variants from 1092 humans: application to cancer genomics.

Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M.

Science. 2013 Oct 4;342(6154):1235587. doi: 10.1126/science.1235587.

21.

A microRNA miR-34a-regulated bimodal switch targets Notch in colon cancer stem cells.

Bu P, Chen KY, Chen JH, Wang L, Walters J, Shin YJ, Goerger JP, Sun J, Witherspoon M, Rakhilin N, Li J, Yang H, Milsom J, Lee S, Zipfel W, Jin MM, Gümüş ZH, Lipkin SM, Shen X.

Cell Stem Cell. 2013 May 2;12(5):602-15. doi: 10.1016/j.stem.2013.03.002.

22.

Chemokine 25-induced signaling suppresses colon cancer invasion and metastasis.

Chen HJ, Edwards R, Tucci S, Bu P, Milsom J, Lee S, Edelmann W, Gümüs ZH, Shen X, Lipkin S.

J Clin Invest. 2012 Sep;122(9):3184-96. doi: 10.1172/JCI62110. Epub 2012 Aug 6.

23.

miR-23a promotes the transition from indolent to invasive colorectal cancer.

Jahid S, Sun J, Edwards RA, Dizon D, Panarelli NC, Milsom JW, Sikandar SS, Gümüs ZH, Lipkin SM.

Cancer Discov. 2012 Jun;2(6):540-53. doi: 10.1158/2159-8290.CD-11-0267. Epub 2012 Mar 30.

24.

Rapid temporal changes in the expression of a set of neuromodulatory genes during alcohol withdrawal in the dorsal vagal complex: molecular evidence of homeostatic disturbance.

Freeman K, Staehle MM, Gümüş ZH, Vadigepalli R, Gonye GE, Nichols CN, Ogunnaike BA, Hoek JB, Schwaber JS.

Alcohol Clin Exp Res. 2012 Oct;36(10):1688-700. doi: 10.1111/j.1530-0277.2012.01791.x. Epub 2012 Apr 6.

25.

Resistance/response molecular signature for oral tongue squamous cell carcinoma.

Suresh A, Vannan M, Kumaran D, Gümüs ZH, Sivadas P, Murugaian EE, Kekatpure V, Iyer S, Thangaraj K, Kuriakose MA.

Dis Markers. 2012;32(1):51-64. doi: 10.3233/DMA-2012-0860.

26.

Effects of cigarette smoke on the human oral mucosal transcriptome.

Boyle JO, Gümüs ZH, Kacker A, Choksi VL, Bocker JM, Zhou XK, Yantiss RK, Hughes DB, Du B, Judson BL, Subbaramaiah K, Dannenberg AJ.

Cancer Prev Res (Phila). 2010 Mar;3(3):266-78. doi: 10.1158/1940-6207.CAPR-09-0192. Epub 2010 Feb 23.

27.

Effects of tobacco smoke on gene expression and cellular pathways in a cellular model of oral leukoplakia.

Gümüş ZH, Du B, Kacker A, Boyle JO, Bocker JM, Mukherjee P, Subbaramaiah K, Dannenberg AJ, Weinstein H.

Cancer Prev Res (Phila). 2008 Jul;1(2):100-11. doi: 10.1158/1940-6207.CAPR-08-0007. Epub 2008 Mar 31.

28.

Towards a quantitative representation of the cell signaling mechanisms of hallucinogens: measurement and mathematical modeling of 5-HT1A and 5-HT2A receptor-mediated ERK1/2 activation.

Chang CW, Poteet E, Schetz JA, Gümüş ZH, Weinstein H.

Neuropharmacology. 2009;56 Suppl 1:213-25. doi: 10.1016/j.neuropharm.2008.07.049. Epub 2008 Aug 13.

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