{"id":17,"date":"2019-06-07T17:16:46","date_gmt":"2019-06-07T17:16:46","guid":{"rendered":"http:\/\/labs.icahn.mssm.edu\/gumuslab\/?page_id=17"},"modified":"2019-06-10T18:47:28","modified_gmt":"2019-06-10T18:47:28","slug":"publications","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/gumuslab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"<ul>\n<li><a href=\"https:\/\/academic.oup.com\/nar\/advance-article\/doi\/10.1093\/nar\/gkz450\/5494773#135956885\">ImmuneRegulation: a web-based tool for identifying human immune regulatory elements<\/a>\u00a0Selim Kalayci, Myvizhi Esai Selvan, Irene Ramos, Chris Cotsapas, Eva Harris, Eun-Young Kim, Ruth R Montgomery, Gregory Poland, Bali Pulendran, John S Tsang, Robert J Klein, Zeynep H G\u00fcm\u00fc\u015f, ImmuneRegulation: a web-based tool for identifying human immune regulatory elements,\u00a0<em>Nucleic Acids Research<\/em>, , gkz450.<\/li>\n<li><a href=\"https:\/\/academic.oup.com\/gigascience\/article-lookup\/doi\/10.1093\/gigascience\/gix054\">iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D.\u00a0<\/a>Liluashvili V, Kalayci S, Fluder E, Wilson M, Gabow A, and G\u00fcm\u00fc\u015f ZH.\u00a0<em>Gigascience\u00a0<\/em>2017; 6(8):1\u201313.<\/li>\n<li><a href=\"http:\/\/www.impactjournals.com\/oncotarget\/index.php?journal=oncotarget&amp;page=article&amp;op=view&amp;path%5B%5D=17776&amp;path%5B%5D=56924\">Inhibition of colorectal cancer genomic copy number alterations and chromosomal fragile site tumor suppressor FHIT and WWOX deletions by DNA mismatch repair.\u00a0<\/a>Jahid S*, Sun J*, Gelincik O, Blecua P, Edelmann W, Kucherlapati R, Zhou K, Jasin M, G\u00fcm\u00fc\u015f ZH* and Lipkin SM*.\u00a0<em>Oncotarget\u00a0<\/em>2017; 8:71574-71586.<\/li>\n<li><a href=\"https:\/\/www.nature.com\/articles\/s41598-017-08321-2\">SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots.\u00a0<\/a>Moreira IS, Koukos PI, Melo R, Almeida JG, Preto AJ, Schaarschmidt J, Trellet M, G\u00fcm\u00fc\u015f ZH, Costa J, Bonvin AMJJ.\u00a0<em>Scientific Reports\u00a0<\/em>2017; 7, Article number: 8007 doi:10.1038\/s41598-017-08321-2.<\/li>\n<li><a href=\"https:\/\/www.nature.com\/cddis\/journal\/v8\/n6\/full\/cddis2017288a.html\">KDM2B, an H3K36-specific demethylase, regulates apoptotic response of GBM cells to TRAIL.\u00a0<\/a>Kurt IC, Sur I, Kaya E, Cingoz A, Kazancioglu S, Kahya Z, Toparlak OD, Senbabaoglu F, Kaya Z, Ozyerli E, Karah\u00fcseyinoglu S, Lack NA, G\u00fcm\u00fc\u015f ZH, Onder TT and Bagci-Onder T.\u00a0<em>Cell Death and Disease\u00a0<\/em>2017; 8, e2897; doi:10.1038\/cddis.2017.288.<\/li>\n<li><a href=\"https:\/\/www.nature.com\/articles\/srep37012\">Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pair motions.<\/a>Vatansever S, G\u00fcm\u00fc\u015f ZH*, Erman B*.\u00a0<em>Scientific Reports\u00a0<\/em>2016; 6, Article number: 37012 doi:10.1038\/srep37012.<\/li>\n<li><a href=\"https:\/\/www.nature.com\/neuro\/journal\/v19\/n11\/full\/nn.4399.html\">Gene expression elucidates functional impact of polygenic risk for schizophrenia.\u00a0<\/a>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, G\u00fcm\u00fc\u015f ZH, Cicek AE, Dang KK, Browne A, Lu C, Xie L, Readhead B, Stahl EA, Xiao J, Parvizi M, Hamamsy T, Fullard JF, Wang YJ, Mahajan MJ, Derry JMJ, 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 E, Hirai K, Roeder K, Brennand KJ, Katsanis N, Domenici E, Devlin B and Sklar P.\u00a0<em>Nature Neuroscience\u00a0<\/em>2016; 19:1442\u20131453.<\/li>\n<li><a href=\"https:\/\/www.nature.com\/articles\/srep34234\">A Novel Genetic Variant in Long Non-coding RNA Gene NEXN-AS1 is Associated with Risk of Lung Cancer.\u00a0<\/a>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 DA, G\u00fcm\u00fc\u015f ZH, Klein RJ, Amos CI and Wei Q.<em>Scientific Reports\u00a0<\/em>2016; 6, Article number 34234, doi:10.1038\/srep34234.<\/li>\n<li><a href=\"http:\/\/www.mdpi.com\/1422-0067\/17\/8\/1215\">A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces.\u00a0<\/a>Melo R, Fieldhouse R, Melo A, Correia JDG, Cordeiro MNDS, G\u00fcm\u00fc\u015f ZH, Costa J, Bonvin AMJJ and Moreira IS.\u00a0<em>Int. J. Mol. Sci.\u00a0<\/em>2016; 17(8), 1215; doi:10.3390\/ijms17081215.<\/li>\n<li><a href=\"http:\/\/www.nature.com\/nbt\/journal\/v33\/n6\/full\/nbt.3239.html\">Comprehensive models of human primary and metastatic colorectal tumors in immunodeficient and immunocompetent mice by chemokine targeting.\u00a0<\/a>Chen HJ, Sun J, Huang Z, Hou H, Arcilla M, Rakhilin N, Joe D, 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, G\u00fcm\u00fc\u015f ZH, Shuler M, Nishimura N, Edelmann W, Shen X, and Lipkin SM.\u00a0<em>Nature Biotechnology\u00a0<\/em>2015; 33:656-660 doi:10.1038\/nbt.3239<\/li>\n<li><a href=\"http:\/\/www.nature.com\/ncomms\/2015\/150415\/ncomms7879\/full\/ncomms7879.html?WT.ec_id=NCOMMS-20150422\">miR-1269 Promotes Metastasis and Forms a Positive Feedback Loop with TGF-\u03b2.\u00a0<\/a>Bu P, Wang L, Chen KY, Rakhilin N, Sun J, Closa A, Tung KL, King S, Varanko AK, Xu Y, Chen JH, Zessin AS, Shealy J, Cummings B, Hsu D, Lipkin SM, Moreno V, G\u00fcm\u00fc\u015f ZH and Shen X.\u00a0<em>Nature Communications.\u00a0<\/em>2015; 6:6879. doi: 10.1038\/ncomms7879<\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3947637\/\">Integrative Annotation of variants from 1092 Humans: application to cancer genomics.\u00a0<\/a>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, G\u00fcm\u00fc\u015f ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, 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.\u00a0<em>Science.\u00a0<\/em>2013 Oct 3, 342(6154):1235587<\/li>\n<li><a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S1934590913000970\">microRNA mir-34a-regulated bimodal switch targets Notch in colon cancer stem cells.\u00a0<\/a>Bu P, Chen KY, Chen JH, Wang L, Walters J, Sjin YJ, Goerger JP, Sun J, Witherspoon M Rakhilin N, Li J, Yang H, Milsom J, Lee S, Zipfel W, Jin MM, G\u00fcm\u00fc\u015f ZH, Lipkin SM and Shen X.\u00a0<em>Cell Stem Cell\u00a0<\/em>2013; 12(5):602-15.<\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3428084\/\">Chemokine 25-induced signaling suppresses colon cancer invasion and metastasis.\u00a0<\/a>Chen HJ, Edwards R, Tucci S, Bu P, Milsom J, Lee S, Edelmann W, G\u00fcm\u00fc\u015f ZH, Shen X, Lipkin S.\u00a0<em>J. Clin. Invest.\u00a0<\/em>2012 Sep 4;122(9):3184-96.<\/li>\n<li><a href=\"http:\/\/cancerdiscovery.aacrjournals.org\/content\/2\/6\/540.full\">mir-23a regulates the transition from indolent to invasive and metastatic colon cancer.\u00a0<\/a>Jadid S, Sun J, Edwards R, Dizon D, Sikander S, G\u00fcm\u00fc\u015f ZH, Lipkin SM.\u00a0<em>Cancer Discovery,\u00a0<\/em>2012 May 24. [Epub ahead of print]<\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4419739\/\">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.\u00a0<\/a>Freeman K, Staehle MM, G\u00fcm\u00fc\u015f ZH, Vadigepalli R, Gonye Ge, Nichols CN, Ogunnaike BA, Hoek JB, Schwaber JS.\u00a0<em>Alcohol Clin Exp Res\u00a0<\/em>2012 Oct; 36(10:1688-700.<\/li>\n<li><a href=\"http:\/\/www.hindawi.com\/journals\/dm\/2012\/926703\/abs\/\">Resistance\/response molecular signature for oral tongue squamous cell carcinoma.\u00a0<\/a>Suresh A, Vannan M, Kumaran D, G\u00fcm\u00fc\u015f ZH, Sivadas P, Murugaian EE, Kekatpure V, Iyer S, Thangaraj K, Kuriakose MA.\u00a0<em>Disease Markers.\u00a0<\/em>2012;32(1):51-64.<\/li>\n<li><a href=\"http:\/\/cancerpreventionresearch.aacrjournals.org\/content\/3\/3\/266.full.html\">Effects of cigarette smoke on the human oral mucosal transcriptome.\u00a0<\/a>Boyle JO*, G\u00fcm\u00fc\u015f ZH*, Kacker A, Choksi VL, Bocker JM, Zhou KK, Yantiss RK, Hughes DB, Du B, Judson BL, Subbaramaiah K, Dannenberg AJ.\u00a0<em>Cancer Prev Res.\u00a0<\/em>2010 Mar; 3(3):266-78. * Co-first author; cover article and featured with a perspectives article<\/li>\n<li><a href=\"http:\/\/ieeexplore.ieee.org\/xpls\/abs_all.jsp?arnumber=5521684\">Quantification and analysis of combination drug synergy in high-throughput transcriptome studies.\u00a0<\/a>G\u00fcm\u00fc\u015f ZH, Siso-Nadal F, Gjyrezi A, McDonagh P, Khalil I, Giannakakou P, Weinstein H.\u00a0<em>IEEE International Conferance on Bioinformatics and Bioengineering,\u00a0<\/em>2010.<\/li>\n<li><a href=\"http:\/\/cancerpreventionresearch.aacrjournals.org\/content\/1\/2\/100.full\">Effects of tobacco smoke on gene expression and cellular pathways in a cellular model of oral leukoplakia.\u00a0<\/a>G\u00fcm\u00fc\u015f ZH, Du B, Kacker A, Boyle JO, Bocker JM, Mukherjee P, Subbaramaiah K, Dannenberg AJ, Weinstein H.\u00a0<em>Cancer Prev Res.\u00a0<\/em>2008 Jul;1(2):100-11. * Cover article and featured with a perspectives article<\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2635340\/\">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.\u00a0<\/a>Chang CW, Poteet E, Schetz JA, G\u00fcm\u00fc\u015f ZH, Weinstein H.\u00a0<em>Neuropharmacology.\u00a0<\/em>2009; 56 Suppl 1:213-25.<\/li>\n<li><a href=\"http:\/\/link.springer.com\/10.1007\/978-0-387-74759-0_392\">Mixed integer nonlinear bilevel programming: deterministic global optimization.\u00a0<\/a>G\u00fcm\u00fc\u015f ZH, Floudas CA.\u00a0<em>Encyclopedia of Optimization,\u00a0<\/em>version II, Kluwer Academic Publishers, 2008.<\/li>\n<li><a href=\"http:\/\/www.springer.com\/us\/book\/9780387747583\">Bilevel programming: Applications in engineering.\u00a0<\/a>G\u00fcm\u00fc\u015f ZH, Sahin KH, Ciric AR.\u00a0<em>Encyclopedia of Optimization,\u00a0<\/em>version II, Kluwer Academic Publishers, 2008.<\/li>\n<li><a href=\"http:\/\/link.springer.com\/article\/10.1007\/s10287-005-0025-1\">Global Optimization of Mixed-Integer Bilevel Programming Problems.\u00a0<\/a>G\u00fcm\u00fc\u015f ZH, Floudas CA.\u00a0<em>Comput. Management Science,\u00a0<\/em>2(3): 181-212, 2005.<\/li>\n<li><a href=\"http:\/\/www.nt.ntnu.no\/users\/skoge\/prost\/proceedings\/focapd_2004\/pdffiles\/papers\/085_45.pdf\">Deterministic Global Optimization of Mixed Integer Bilevel Programming Problems.\u00a0<\/a>G\u00fcm\u00fc\u015f ZH, Floudas CA.\u00a0<em>Foundations of Computer Aided Process Design (FOCAPD) Conference Proceedings,\u00a0<\/em>529-532, 2004.<\/li>\n<li>Global optimization for bilevel programming problems and applications. G\u00fcm\u00fc\u015f ZH.\u00a0<em>PhD Thesis,\u00a0<\/em>Department of Chemical Engineering, Princeton University, 2003.<\/li>\n<li><a href=\"http:\/\/link.springer.com\/article\/10.1023\/A:1011268113791\">Global optimization of nonlinear bilevel programming problems.\u00a0<\/a>G\u00fcm\u00fc\u015f ZH, Floudas CA.\u00a0<em>J of Global Optimization.\u00a0<\/em>2:1-31, 2001.<\/li>\n<li><a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/ie001014g\">Global optimization in design under uncertainty: feasibility test and flexibility index problems.\u00a0<\/a>Floudas CA, G\u00fcm\u00fc\u015f ZH and Ierapetritou, M.\u00a0<em>Industrial and Engineering Chemistry Research.\u00a0<\/em>2001; 40(20), 4267-82.<\/li>\n<li><a href=\"https:\/\/www.google.com\/books?hl=en&amp;lr=&amp;id=oWTchfhFErYC&amp;oi=fnd&amp;pg=PA393&amp;dq=Nonlinear+bilevel+programming:+a+deterministic+global+optimization+framework&amp;ots=z7QX-Endeg&amp;sig=dhk8jJ3dqLDc_2a807KMAer6rSc\">Nonlinear bilevel programming: a deterministic global optimization framework.\u00a0<\/a>G\u00fcm\u00fc\u015f ZH, Floudas CA.\u00a0<em>Computer Aided Process Engineering,\u00a0<\/em>2001.<\/li>\n<li><a href=\"http:\/\/link.springer.com\/10.1007\/0-306-48332-7_296\">MINLP: Reactive distillation column synthesis.\u00a0<\/a>Ciric A, G\u00fcm\u00fc\u015f ZH.\u00a0<em>Encyclopedia of Optimization III,\u00a0<\/em>373-379; 2001.<\/li>\n<li><a href=\"http:\/\/link.springer.com\/content\/pdf\/10.1007\/0-306-48332-7_34.pdf\">Bilevel programming: applications in engineering.\u00a0<\/a>Sahin K, G\u00fcm\u00fc\u015f ZH and Ciric AR.\u00a0<em>Encyclopedia of Optimization I,\u00a0<\/em>160-163; 2001.<\/li>\n<li><a href=\"https:\/\/www.google.com\/books?hl=en&amp;lr=&amp;id=N6gACAAAQBAJ&amp;oi=fnd&amp;pg=PA3&amp;dq=Handbook+of+test+problems+in+local+and+global+optimization&amp;ots=Htg9A8VZ-Y&amp;sig=DOJDZGrlV1s4Wbo5HB5KfZYnlqE\">Handbook of test problems in local and global optimization.\u00a0<\/a>Floudas CA, Pardalos PM, Adjiman CS, Esposito WR, G\u00fcm\u00fc\u015f ZH, Harding ST, Klepeis JL, Meyer CA, Schweiger CA. Kluwer Academic Publishers, the Netherlands; 1999.<\/li>\n<li><a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0098135497876302\">Reactive distillation column design with vapor\/liquid\/liquid equilibria.\u00a0<\/a>G\u00fcm\u00fc\u015f ZH, Ciric AR.\u00a0<em>Comp. &amp; Chem. Eng.\u00a0<\/em>21:S983-988, 1997.<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>ImmuneRegulation: a web-based tool for identifying human immune regulatory elements\u00a0Selim Kalayci, Myvizhi Esai Selvan, Irene Ramos, Chris Cotsapas, Eva Harris, Eun-Young Kim, Ruth R Montgomery, Gregory Poland, Bali Pulendran, John S Tsang, Robert J Klein, Zeynep H G\u00fcm\u00fc\u015f, ImmuneRegulation: a web-based tool for identifying human immune regulatory elements,\u00a0Nucleic Acids Research, , gkz450. iCAVE: an open [&hellip;]<\/p>\n","protected":false},"author":321,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-17","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/labs.icahn.mssm.edu\/gumuslab\/wp-json\/wp\/v2\/pages\/17","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/labs.icahn.mssm.edu\/gumuslab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.icahn.mssm.edu\/gumuslab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/gumuslab\/wp-json\/wp\/v2\/users\/321"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/gumuslab\/wp-json\/wp\/v2\/comments?post=17"}],"version-history":[{"count":3,"href":"https:\/\/labs.icahn.mssm.edu\/gumuslab\/wp-json\/wp\/v2\/pages\/17\/revisions"}],"predecessor-version":[{"id":43,"href":"https:\/\/labs.icahn.mssm.edu\/gumuslab\/wp-json\/wp\/v2\/pages\/17\/revisions\/43"}],"wp:attachment":[{"href":"https:\/\/labs.icahn.mssm.edu\/gumuslab\/wp-json\/wp\/v2\/media?parent=17"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}