Anil Korkut, PhD

Peer-Reviewed Articles

1. Yan G, Luna A, Wang H, Bozorgui B, Li X, Sanchez M, Dereli Z, Kahraman N, Kara G, Chen X, Zheng C, McGrail D, Sahni N, Lu Y, Babur O, Cokol M, Lim B, Ozpolat B, Sander C, Mills GB, Korkut A. BET inhibition induces vulnerability to MCL1 targeting through upregulation of fatty acid synthesis pathway in breast cancer. Cell Rep 40(11):111304, 2022. PMID: 36103824.
2. Li X, Dowling EK, Yan G, Dereli Z, Bozorgui B, Imanirad P, Elnaggar JH, Luna A, Menter DG, Pilié PG, Yap TA, Kopetz S, Sander C, Korkut A. Precision Combination Therapies Based on Recurrent Oncogenic Coalterations. Cancer Discov 12(6):1542-1559, 2022. PMID: 35412613.
3. Carapeto F, Bozorgui B, Shroff RT, Chagani S, Solis Soto L, Foo WC, Wistuba I, Meric-Bernstam F, Shalaby A, Javle M, Korkut A, Kwong LN. The immunogenomic landscape of resected intrahepatic cholangiocarcinoma. Hepatology 75(2):297-308, 2022. e-Pub 2021. PMID: 34510503.
4. Luna A, Siper MC, Korkut A, Durupinar F, Dogrusoz U, Aslan JE, Sander C, Demir E, Babur O. Analyzing causal relationships in proteomic profiles using CausalPath. STAR Protoc 2(4):100955, 2021. e-Pub 2021. PMID: 34877547.
5. Akcakanat A, Zheng X, Cruz Pico CX, Kim TB, Chen K, Korkut A, Sahin A, Holla V, Tarco E, Singh G, Damodaran S, Mills GB, Gonzalez-Angulo AM, Meric-Bernstam F. Genomic, Transcriptomic, and Proteomic Profiling of Metastatic Breast Cancer. Clin Cancer Res 27(11):3243-3252, 2021. e-Pub 2021. PMID: 33782032.
6. Babur Ö, Luna A, Korkut A, Durupinar F, Siper MC, Dogrusoz U, Vaca Jacome AS, Peckner R, Christianson KE, Jaffe JD, Spellman PT, Aslan JE, Sander C, Demir E. Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. Patterns (N Y) 2(6):100257, 2021. e-Pub 2021. PMID: 34179843.
7. Zhao M, Scott S, Evans KW, Yuca E, Saridogan T, Zheng X, Wang H, Korkut A, Cruz Pico CX, Demirhan M, Kirby B, Kopetz S, Diala I, Lalani AS, Piha-Paul S, Meric-Bernstam F. Combining Neratinib with CDK4/6, mTOR, and MEK Inhibitors in Models of HER2-positive Cancer. Clin Cancer Res 27(6):1681-1694, 2021. e-Pub 2021. PMID: 33414137.
8. Yuan B, Shen C, Luna A, Korkut A, Marks DS, Ingraham J, Sander C. CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy. Cell Syst 12(2):128-140.e4, 2021. e-Pub 2020. PMID: 33373583.
9. Zhao W, Li J, Chen MM, Luo Y, Ju Z, Nesser NK, Johnson-Camacho K, Boniface CT, Lawrence Y, Pande NT, Davies MA, Herlyn M, Muranen T, Zervantonakis IK, von Euw E, Schultz A, Kumar SV, Korkut A, Spellman PT, Akbani R, Slamon DJ, Gray JW, Brugge JS, Lu Y, Mills GB, Liang H. Large-Scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines. Cancer Cell 38(6):829-843.e4, 2020. e-Pub 2020. PMID: 33157050.
10. Nyman E, Stein RR, Jing X, Wang W, Marks B, Zervantonakis IK, Korkut A, Gauthier NP, Sander C. Perturbation biology links temporal protein changes to drug responses in a melanoma cell line. PLoS Comput Biol 16(7):e1007909, 2020. e-Pub 2020. PMID: 32667922.
11. Donehower LA, Soussi T, Korkut A, Liu Y, Schultz A, Cardenas M, Li X, Babur O, Hsu TK, Lichtarge O, Weinstein JN, Akbani R, Cancer Genome Atlas Network, Wheeler DA. Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas. Cell Rep 28(5):1370-1384.e5, 2019. PMID: 31365877.
12. Wang Y, Xu X, Maglic D, Dill MT, Mojumdar K, Ng PK, Jeong KJ, Tsang YH, Moreno D, Bhavana VH, Peng X, Ge Z, Chen H, Li J, Chen Z, Zhang H, Han L, Du D, Creighton CJ, Mills GB, Cancer Genome Atlas Research Network (including Korkut, A), Camargo F, Liang H. Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer. Cell Rep 25(5):1304-1317.e5, 2018. PMID: 30380420.
13. Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C, Cancer Genome Atlas Analysis Network (including Korkut, A), Greenleaf WJ, Chang HY. The chromatin accessibility landscape of primary human cancers. Science 362(6413), 2018. PMID: 30361341.
14. Korkut A, Zaidi S, Kanchi RS, Rao S, Gough NR, Schultz A, Li X, Lorenzi PL, Berger AC, Robertson G, Kwong LN, Datto M, Roszik J, Ling S, Ravikumar V, Manyam G, Rao A, Shelley S, Liu Y, Ju Z, Hansel D, de Velasco G, Pennathur A, Andersen JB, O'Rourke CJ, Ohshiro K, Jogunoori W, Nguyen BN, Li S, Osmanbeyoglu HU, Ajani JA, Mani SA, Houseman A, Wiznerowicz M, Chen J, Gu S, Ma W, Zhang J, Tong P, Cherniack AD, Deng C, Resar L, Cancer Genome Atlas Research Network, Weinstein JN, Mishra L, Akbani R. A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily. Cell Syst 7(4):422-437.e7, 2018. e-Pub 2018. PMID: 30268436.
15. Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C, Cancer Genome Atlas Research Network (Including Korkut, A), Rätsch G. Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. Cancer Cell 34(2):211-224.e6, 2018. e-Pub 2018. PMID: 30078747.
16. Vangapandu HV, Chen H, Wierda WG, Keating MJ, Korkut A, Gandhi V. Proteomics profiling identifies induction of caveolin-1 in chronic lymphocytic leukemia cells by bone marrow stromal cells. Leuk Lymphoma 59(6):1-12, 2018. e-Pub 2017. PMID: 28971726.
17. Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CE, Cancer Genome Atlas Research Network (including Korkut, A), Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L. The Immune Landscape of Cancer. Immunity 48(4):812-830.e14, 2018. e-Pub 2018. PMID: 29628290.
18. Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N, Cancer Genome Atlas Research Network, Weinstein JN, Mills GB, Levine DA, Akbani R. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell 33(4):690-705.e9, 2018. e-Pub 2018. PMID: 29622464.
19. Liu J, Lichtenberg T, Hoadley KA, Poisson LM, Lazar AJ, Cherniack AD, Kovatich AJ, Benz CC, Levine DA, Lee AV, Omberg L, Wolf DM, Shriver CD, Thorsson V, Cancer Genome Atlas Research Network (Including Korkut, A), Hu H. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell 173(2):400-416.e11, 2018. PMID: 29625055.
20. Liu Y, Sethi NS, Hinoue T, Schneider BG, Cherniack AD, Sanchez-Vega F, Seoane JA, Farshidfar F, Bowlby R, Islam M, Kim J, Chatila W, Akbani R, Kanchi RS, Rabkin CS, Willis JE, Wang KK, McCall SJ, Mishra L, Ojesina AI, Bullman S, Pedamallu CS, Lazar AJ, Sakai R, Cancer Genome Atlas Research Network (Including Korkut, A), Thorsson V, Bass AJ, Laird PW. Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. Cancer Cell 33(4):721-735.e8, 2018. e-Pub 2018. PMID: 29622466.
21. Wang Z, Yang B, Zhang M, Guo W, Wu Z, Wang Y, Jia L, Li S, Cancer Genome Atlas Research Network (Including Korkut, A), Xie W, Yang D. lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer. Cancer Cell 33(4):706-720.e9, 2018. e-Pub 2018. PMID: 29622465.
22. Taylor AM, Shih J, Ha G, Gao GF, Zhang X, Berger AC, Schumacher SE, Wang C, Hu H, Liu J, Lazar AJ, Cancer Genome Atlas Research Network (Including Korkut, A), Cherniack AD, Beroukhim R, Meyerson M. Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer Cell 33(4):676-689.e3, 2018. e-Pub 2018. PMID: 29622463.
23. Chen H, Li C, Peng X, Zhou Z, Weinstein JN, Cancer Genome Atlas Research Network (Including Korkut, A), Liang H. A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. Cell 173(2):386-399.e12, 2018. PMID: 29625054.
24. Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, MC3 Working Group, Cancer Genome Atlas Research Network Network (Including Korkut, A) , Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell 173(2):371-385.e18, 2018. PMID: 29625053.
25. Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, Cancer Genome Atlas Research Network (including Korkut, A), Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell 173(2):355-370.e14, 2018. PMID: 29625052.
26. Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kaminska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwinska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ, Cancer Genome Atlas Research Network (Including Korkut, A), Stuart JM, Hoadley KA, Laird PW, Noushmehr H, Wiznerowicz M. Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell 173(2):338-354.e15, 2018. PMID: 29625051.
27. Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M, Cancer Genome Atlas Research Network (Including Korkut, A), Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell 173(2):321-337.e10, 2018. PMID: 29625050.
28. Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA, Getz G, Cancer Genome Atlas Research Network (including Korkut, A). Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell 173(2):305-320.e10, 2018. PMID: 29625049.
29. Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, Shen R, Taylor AM, Cherniack AD, Thorsson V, Akbani R, Bowlby R, Wong CK, Wiznerowicz M, Sanchez-Vega F, Robertson AG, Schneider BG, Lawrence MS, Noushmehr H, Malta TM, Cancer Genome Atlas Network (Including Korkut, A), Stuart JM, Benz CC, Laird PW. Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell 173(2):291-304.e6, 2018. PMID: 29625048.
30. Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwiatkowski DJ, Lui W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WY, Robertson AG, Cancer Genome Atlas Research Network (Including Korkut, A), Spellman PT, Rathmell WK, Linehan WM. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep 23(1):313-326.e5, 2018. PMID: 29617669.
31. Chiu HS, Somvanshi S, Patel E, Chen TW, Singh VP, Zorman B, Patil SL, Pan Y, Chatterjee SS, Cancer Genome Atlas Research Network (Including Korkut, A), Sood AK, Gunaratne PH, Sumazin P. Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. Cell Rep 23(1):297-312.e12, 2018. PMID: 29617668.
32. Seiler M, Peng S, Agrawal AA, Palacino J, Teng T, Zhu P, Smith PG, Cancer Genome Atlas Research Network (Including Korkut, A), Buonamici S, Yu L. Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types. Cell Rep 23(1):282-296.e4, 2018. PMID: 29617667.
33. Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ, Cancer Genome Atlas Research Network (Including Korkut, A), Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L. Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell Rep 23(1):270-281.e3, 2018. PMID: 29617666.
34. Peng X, Chen Z, Farshidfar F, Xu X, Lorenzi PL, Wang Y, Cheng F, Tan L, Mojumdar K, Du D, Ge Z, Li J, Thomas GV, Birsoy K, Liu L, Zhang H, Zhao Z, Marchand C, Weinstein JN, Cancer Genome Atlas Research Network (including Korkut, A), Bathe OF, Liang H. Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. Cell Rep 23(1):255-269.e4, 2018. PMID: 29617665.
35. Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I, Cancer Genome Atlas Research Network (Including Korkut, A), Monnat RJ, Xiao Y, Wang C. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep 23(1):239-254.e6, 2018. PMID: 29617664.
36. Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ, Fusion Analysis Working Group, Cancer Genome Atlas Research Network (Including Korkut, A), Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter M, Shmulevich I, Ding L. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep 23(1):227-238.e3, 2018. PMID: 29617662.
37. Ge Z, Leighton JS, Wang Y, Peng X, Chen Z, Chen H, Sun Y, Yao F, Li J, Zhang H, Liu J, Shriver CD, Hu H, Cancer Genome Atlas Research Network (Including Korkut, A), Piwnica-Worms H, Ma L, Liang H. Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types. Cell Rep 23(1):213-226.e3, 2018. PMID: 29617661.
38. Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Cancer Genome Atlas Research Network (Including Korkut, A), Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep 23(1):194-212.e6, 2018. PMID: 29617660.
39. Saltz J, Gupta R, Hou L, Kurc T, Singh P, Nguyen V, Samaras D, Shroyer KR, Zhao T, Batiste R, Van Arnam J, Cancer Genome Atlas Research Network (including Korkut, A), Shmulevich I, Rao AUK, Lazar AJ, Sharma A, Thorsson V. Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images. Cell Rep 23(1):181-193.e7, 2018. PMID: 29617659.
40. Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N, Cancer Genome Atlas Research Network (Including Korkut, A), Sanchez Y, Greene CS. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Rep 23(1):172-180.e3, 2018. PMID: 29617658.
41. Huang L, Malu S, McKenzie JA, Andrews MC, Talukder AH, Tieu T, Karpinets T, Haymaker C, Forget MA, Williams LJ, Wang Z, Mbofung RM, Wang ZQ, Davis RE, Lo RS, Wargo JA, Davies MA, Bernatchez C, Heffernan T, Amaria RN, Korkut A, Peng W, Roszik J, Lizée G, Woodman SE, Hwu P. The RNA-binding Protein MEX3B Mediates Resistance to Cancer Immunotherapy by Downregulating HLA-A Expression. Clin Cancer Res. e-Pub 2018. PMID: 29496759.
42. Schaub FX, Dhankani V, Berger AC, Trivedi M, Richardson AB, Shaw R, Zhao W, Zhang X, Ventura A, Liu Y, Ayer DE, Hurlin PJ, Cherniack AD, Eisenman RN, Bernard B, Grandori C, Cancer Genome Atlas Network (Including Korkut, A). Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. Cell Syst 6(3):282-300.e2, 2018. PMID: 29596783.
43. Ellrott K, Bailey MH, Saksena G, Covington KR, Kandoth C, Stewart C, Hess J, Ma S, Chiotti KE, McLellan M, Sofia HJ, Hutter C, Getz G, Wheeler D, Ding L, MC3 Working Group, Cancer Genome Atlas Research Network (Including Korkut, A). Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst 6(3):271-281.e7, 2018. PMID: 29596782.
44. Cancer Genome Atlas Research Network.(Including Korkut, A). Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell 32(2):185-203.e13, 2017. PMID: 28810144.
45. Yang Q, Modi P, Korkut A, Fernandes SM, Hanna J, Brown JR, Gandhi V. Changes in Bcl-2 Family Protein Profile During Idelalisib Therapy Mimic Those During Duvelisib Therapy in Chronic Lymphocytic Leukemia Lymphocytes. JCO Precis Oncol 1, 2017. e-Pub 2017. PMID: 32913964.
46. Miller ML, Reznik E, Gauthier NP, Aksoy BA, Korkut A, Gao J, Ciriello G, Schultz N, Sander C. Pan-Cancer Analysis of Mutation Hotspots in Protein Domains. Cell Syst 1(3):197-209, 2015. e-Pub 2015. PMID: 27135912.
47. Cancer Genome Atlas Network (Including Korkut, A). Genomic Classification of Cutaneous Melanoma. Cell 161(7):1681-96, 2015. PMID: 26091043.
48. Korkut A, Wang W, Demir E, Aksoy BA, Jing X, Molinelli EJ, Babur Ö, Bemis DL, Onur Sumer S, Solit DB, Pratilas CA, Sander C. Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells. Elife 4, 2015. e-Pub 2015. PMID: 26284497.
49. Kaushik P, Molinelli EJ, Miller ML, Wang W, Korkut A, Liu W, Ju Z, Lu Y, Mills G, Sander C. Spatial normalization of reverse phase protein array data. PLoS One 9(12):e97213, 2014. e-Pub 2014. PMID: 25501559.
50. Miller ML, Molinelli EJ, Nair JS, Sheikh T, Samy R, Jing X, He Q, Korkut A, Crago AM, Singer S, Schwartz GK, Sander C. Drug synergy screen and network modeling in dedifferentiated liposarcoma identifies CDK4 and IGF1R as synergistic drug targets. Sci Signal 6(294):ra85, 2013. e-Pub 2013. PMID: 24065146.
51. Molinelli EJ, Korkut A, Wang W, Miller ML, Gauthier NP, Jing X, Kaushik P, He Q, Mills G, Solit DB, Pratilas CA, Weigt M, Braunstein A, Pagnani A, Zecchina R, Sander C. Perturbation biology: inferring signaling networks in cellular systems. PLoS Comput Biol 9(12):e1003290, 2013. e-Pub 2013. PMID: 24367245.
52. Korkut A, Hendrickson WA. Structural plasticity and conformational transitions of HIV envelope glycoprotein gp120. PLoS One 7(12):e52170, 2012. e-Pub 2012. PMID: 23300605.
53. Korkut A, Hendrickson WA. Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase. Proc Natl Acad Sci USA 106(37):15673-8, 2009. e-Pub 2009. PMID: 19706894.
54. Korkut A, Hendrickson WA. A force field for virtual atom molecular mechanics of proteins. Proc Natl Acad Sci USA 106(37):15667-72, 2009. e-Pub 2009. PMID: 19717427.
55. Korkut A, Varnali T. Quantitative structure-activity relationship (QSAR) of competitive N-Methyl-D-Aspartate (NMDA) Antagonists. Journal of Molecular Physics 101(22):3285-3291, 2003.

Book Chapters

1. Korkut A, Hendrickson WA. Biomolecular Forms and Functions: A Celebration of 50 years of the Ramachandran Map. In: Stereochemistry of polypeptide conformation in coarse grained analysis. IISc Pre: Singapore, 136-147, 2013.