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Anil Korkut, Ph.D. - Publications

Institution:
Columbia University, New York, NY
Area:
biological macromolecules
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40 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Musall BC, Rauch DE, Mohamed RMM, Panthi B, Boge M, Candelaria RP, Chen H, Guirguis MS, Hunt KK, Huo L, Hwang KP, Korkut A, Litton JK, Moseley TW, Pashapoor S, et al. Diffusion Tensor Imaging for Characterizing Changes in Triple-Negative Breast Cancer During Neoadjuvant Systemic Therapy. Journal of Magnetic Resonance Imaging : Jmri. PMID 38294179 DOI: 10.1002/jmri.29267  0.312
2023 Panthi B, Mohamed RM, Adrada BE, Boge M, Candelaria RP, Chen H, Hunt KK, Huo L, Hwang KP, Korkut A, Lane DL, Le-Petross HC, Leung JWT, Litton JK, Pashapoor S, et al. Longitudinal dynamic contrast-enhanced MRI radiomic models for early prediction of response to neoadjuvant systemic therapy in triple-negative breast cancer. Frontiers in Oncology. 13: 1264259. PMID 37941561 DOI: 10.3389/fonc.2023.1264259  0.317
2023 Vishnoi M, Dereli Z, Yin Z, Kong EK, Kinali M, Thapa K, Babur O, Yun K, Abdelfattah N, Li X, Bozorgui B, Rostomily RC, Korkut A. A prognostic matrix code defines functional glioblastoma phenotypes and niches. Research Square. PMID 37790408 DOI: 10.21203/rs.3.rs-3285842/v1  0.761
2023 Li X, Korkut A. Recurrent composite markers of cell types and states. Biorxiv : the Preprint Server For Biology. PMID 37503180 DOI: 10.1101/2023.07.17.549344  0.662
2023 Vishnoi M, Dereli Z, Yin Z, Kong EK, Kinali M, Thapa K, Babur O, Yun K, Abdelfattah N, Li X, Bozorgui B, Rostomily RC, Korkut A. A prognostic matrix code defines functional glioblastoma phenotypes and niches. Biorxiv : the Preprint Server For Biology. PMID 37333072 DOI: 10.1101/2023.06.06.543903  0.761
2023 Bozorgui B, Kong EK, Luna A, Korkut A. Mapping the functional interactions at the tumor-immune checkpoint interface. Communications Biology. 6: 462. PMID 37106127 DOI: 10.1038/s42003-023-04777-3  0.731
2022 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, ... ... Korkut A, et al. BET inhibition induces vulnerability to MCL1 targeting through upregulation of fatty acid synthesis pathway in breast cancer. Cell Reports. 40: 111304. PMID 36103824 DOI: 10.1016/j.celrep.2022.111304  0.705
2022 Li X, Dowling EK, Yan G, Dereli Z, Bozorgui B, Imanirad P, Elnaggar JH, Luna A, Menter DG, Pilie PG, Yap TA, Kopetz S, Sander C, Korkut A. Precision combination therapies based on recurrent oncogenic co-alterations. Cancer Discovery. PMID 35412613 DOI: 10.1158/2159-8290.CD-21-0832  0.733
2021 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 Protocols. 2: 100955. PMID 34877547 DOI: 10.1016/j.xpro.2021.100955  0.702
2021 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 (Baltimore, Md.). PMID 34510503 DOI: 10.1002/hep.32150  0.748
2021 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 (New York, N.Y.). 2: 100257. PMID 34179843 DOI: 10.1016/j.patter.2021.100257  0.707
2021 Zhao M, Scott S, Evans KW, Yuca E, Saridogan T, Zheng X, Wang H, Korkut A, Cruz Pico CX, Demirhan ME, Kirby B, Kopetz S, Diala I, Lalani AS, Piha-Paul S, et al. Combining neratinib with CDK4/6, mTOR and MEK inhibitors in models of HER2-positive cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 33414137 DOI: 10.1158/1078-0432.CCR-20-3017  0.596
2020 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 Systems. PMID 33373583 DOI: 10.1016/j.cels.2020.11.013  0.449
2020 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, ... ... Korkut A, et al. Large-Scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines. Cancer Cell. PMID 33157050 DOI: 10.1016/j.ccell.2020.10.008  0.3
2020 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 Computational Biology. 16: e1007909. PMID 32667922 DOI: 10.1371/Journal.Pcbi.1007909  0.579
2020 Shen J, Yuan B, Luna A, Korkut A, Marks D, Ingraham J, Sander C. Abstract 2102: Interpretable machine learning for perturbation biology Cancer Research. 80: 2102-2102. DOI: 10.1158/1538-7445.Am2020-2102  0.526
2019 Donehower LA, Soussi T, Korkut A, Liu Y, Schultz A, Cardenas M, Li X, Babur O, Hsu TK, Lichtarge O, Weinstein JN, Akbani R, Wheeler DA. Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas. Cell Reports. 28: 3010. PMID 31509758 DOI: 10.1016/J.Celrep.2019.08.061  0.777
2019 Donehower LA, Soussi T, Korkut A, Liu Y, Schultz A, Cardenas M, Li X, Babur O, Hsu TK, Lichtarge O, Weinstein JN, Akbani R, Wheeler DA. Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas. Cell Reports. 28: 1370-1384.e5. PMID 31365877 DOI: 10.1016/J.Celrep.2019.07.001  0.793
2019 Luna A, Wang H, Babur O, Sander C, Korkut A. Abstract 3820: Discovery of adaptive resistance pathways and anti-resistance combination therapies from phosphoproteomic data using graphical models Cancer Research. DOI: 10.1158/1538-7445.Sabcs18-3820  0.637
2019 Ohshiro K, Zaidi S, Korkut A, Chen J, Rao S, Gu S, Jogunoori W, Mishra B, Akbani R, Mishra L. Abstract 3382: A pan-cancer analysis reveals high frequency genetic alterations in mediators of signaling by the TGF-β superfamily Cancer Research. 79: 3382-3382. DOI: 10.1158/1538-7445.Sabcs18-3382  0.416
2018 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, et al. A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily. Cell Systems. PMID 30268436 DOI: 10.1016/J.Cels.2018.08.010  0.667
2018 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, et al. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell. PMID 29622464 DOI: 10.1016/J.Ccell.2018.03.014  0.713
2018 Huang L, Malu S, McKenzie JA, Andrews MC, Talukder AH, Tieu T, Karpinets TV, Haymaker C, Forget MA, Williams LJ, Wang Z, Mbofung R, Wang ZQ, Davis RE, Lo RS, ... ... Korkut A, et al. The RNA-binding protein MEX3B mediates resistance to cancer immunotherapy by downregulating HLA-A expression. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 29496759 DOI: 10.1158/1078-0432.Ccr-17-2483  0.412
2018 Korkut A, Zaidi S, Kanchi R, Berger AC, Robertson G, Kwong LN, Datto M, Roszik J, Ling S, Schultz A, Ravikumar V, Manyam G, Rao A, Shelley S, Liu Y, et al. Abstract 3413: A pan-cancer atlas of genomic, epigenomic and transcriptomic alterations in the TGF-β pathway Cancer Research. 78: 3413-3413. DOI: 10.1158/1538-7445.Am2018-3413  0.427
2018 Berger A, Korkut A, Kanchi RS, Mills GB, Levine DA, Akbani R. Abstract 3303: A comprehensive TCGA Pan-Cancer molecular study of gynecologic and breast cancers Cancer Research. 78: 3303-3303. DOI: 10.1158/1538-7445.Am2018-3303  0.453
2018 Luna A, Babur Ö, Yan G, Demir E, Sander C, Korkut A. Abstract 2838: Discovery of adaptive resistance pathways and anti-resistance combination therapies in cancer from phosphoproteomic data Cancer Research. 78: 2838-2838. DOI: 10.1158/1538-7445.Am2018-2838  0.791
2018 Zaidi S, Korkut A, Jogunoori W, Chen J, Gu S, Rao S, Ohshiro K, Akbani R, Deng C, Mishra B, Mishra L. Abstract 2226: TGF-β and CEACAMs regulated biomarkers detect early colorectal cancer Cancer Research. 78: 2226-2226. DOI: 10.1158/1538-7445.Am2018-2226  0.386
2018 Zaidi S, Chen J, Korkut A, Gu S, Rao S, Ohshiro K, Jogunoori W, Akbani R, Li S, Deng C, Mishra B, Mishra L. Mo1971 - Crosstalk Between Ceacam and Tgf-β Signaling Pathways and their Role in Colorectal Cancer Gastroenterology. 154: S-868. DOI: 10.1016/S0016-5085(18)32934-2  0.31
2017 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. Leukemia & Lymphoma. 1-12. PMID 28971726 DOI: 10.1080/10428194.2017.1376747  0.304
2015 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 Systems. 1: 197-209. PMID 27135912 DOI: 10.1016/J.Cels.2015.08.014  0.767
2015 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. PMID 26284497 DOI: 10.7554/Elife.04640  0.778
2015 Korkut A, Wang W, Demir E, Aksoy BA, Jing X, Molinelli EJ, Babur Ö, Bemis DL, Sumer SO, Solit DB, Pratilas CA, Sander C. Author response: Perturbation biology nominates upstream–downstream drug combinations in RAF inhibitor resistant melanoma cells Elife. DOI: 10.7554/Elife.04640.031  0.718
2015 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 Systems. 1: 197-209. DOI: 10.1016/S0959-8049(16)61060-2  0.65
2014 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: e97213. PMID 25501559 DOI: 10.1371/Journal.Pone.0097213  0.469
2013 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, et al. Perturbation biology: inferring signaling networks in cellular systems. Plos Computational Biology. 9: e1003290. PMID 24367245 DOI: 10.1371/Journal.Pcbi.1003290  0.554
2013 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. Science Signaling. 6: ra85. PMID 24065146 DOI: 10.1126/Scisignal.2004014  0.573
2013 Korkut A, Wang W, Molinelli E, Miller M, Kaushik P, Aksoy A, Sander C. Abstract 5227: Quantitative network models of signaling and drug response in melanoma. Cancer Research. 73: 5227-5227. DOI: 10.1158/1538-7445.Am2013-5227  0.557
2012 Korkut A, Hendrickson WA. Structural Plasticity and Conformational Transitions of HIV Envelope Glycoprotein gp120 Plos One. 7. PMID 23300605 DOI: 10.1371/Journal.Pone.0052170  0.467
2009 Korkut A, Hendrickson WA. A force field for virtual atom molecular mechanics of proteins Proceedings of the National Academy of Sciences of the United States of America. 106: 15667-15672. PMID 19717427 DOI: 10.1073/Pnas.0907674106  0.468
2009 Korkut A, Hendrickson WA. Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase. Proceedings of the National Academy of Sciences of the United States of America. 106: 15673-8. PMID 19706894 DOI: 10.1073/Pnas.0907684106  0.48
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