Anil Korkut, PhD
Department of Bioinformatics and Computational Biology, Division of Discovery Science
Present Title & Affiliation
Primary Appointment
Associate Professor, Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
Associate Professor, Statistics Department, Rice University, Houston, TX
Regular Member, Quantitative Sciences, MD Anderson Cancer Center/UT Health Graduate School of Biomedical Sciences, Houston, TX
Dual/Joint/Adjunct Appointment
Associate Professor, Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
Associate Professor, Statistics, Rice University, Houston, Texas
Regular Member, Quantitative Sciences, MD Anderson Cancer Center/UT Health Graduate School of Biomedical Sciences, Houston, TX
Research Interests
Our ultimate goal, as our research group, is to predict how cells respond to intrinsic and environmental perturbations such as therapeutic interventions in cancer. At UT MD Anderson Cancer Center (MDACC), we have established a basic and translational research program integrating drug perturbation experiments, predictive modeling of drug responses, and multiplexed tissue imaging for spatially resolved single-cell proteomics. Our research focuses on developing data-driven and machine-learning methods for drug response prediction. We have developed models that provide deep biological insights across broader patient cohorts, mapping oncogenic co-alterations and precision combination therapy targets. Our network modeling strategies have examined how targeted agents rewire cancer cells, identifying combination therapy candidates involving BET, MAPK, PARP, SHP2, BRD4, and MCL1 inhibitors in solid tumors. We have developed multiplexed imaging-based spatial proteomics technologies to characterize tumor ecosystems. More recently, my group has been developing biologically informed deep learning methods to build interpretable and predictive AI models of drug response and precision oncology. Within the TCGA network, we have led multi-omics analyses, including pan-cancer studies of the TGF-beta pathway , breast/gynecological cancers and several other key oncogenic processes that resulted in high impact publications in Cell and Cancer Cell. I have spearheaded the computational analysis of multi-omics and spatial omics data from translational studies, which focus on ML-modeling for response prediction in cancer. Our research have been supported by major external funding, the University of Texas, and internal MDACC funds.
Education & Training
Degree-Granting Education
| 2009 | Columbia University, New York, New York, US, Biochemistry and Molecular Biology, Ph.D |
| 2004 | Columbia University, New York, New York, US, Molecular Biophysics, MPhil |
| 2002 | Columbia University, New York, New York, US, Molecular Biophysics, MA |
| 2001 | Bogazici University, Istanbul, TR, Molecular Biology & Genetics, BA |
| 2001 | Bogazici University, Istanbul, TR, Chemistry, BA |
Postgraduate Training
| 2009-2014 | Research Scholar, Computational Biology, Memorial Sloan Kettering Cancer Center, New York, New York |
Experience & Service
Faculty Academic Appointments
Assistant Professor, Statistics Department, Rice University, Houston, TX, 2021 - 2023
Assistant Professor, Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 2016 - 2023
Research Associate, Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 2014 - 2016
Visiting Researcher, Cell Biology, Harvard Medical School, Cambridge, MA, 1999 - 1999
Administrative Appointments/Responsibilities
Senator, The University of Texas MD Anderson Cancer Center, Houston, Texas, 2023 - 2025
Member, UT Health-MDACC GSBS Fellowship Committee, Houston, TX, 2021 - 2022
Admissions Committee Member, UT Health-MDACC GSBS, Houston, 2019 - 2021
External Member, Faculty and Search Committee, Department of Biostatistics, Houston, TX, 2019 - 2020
External Member, Faculty Search Committee, Department of Diagnostic Radiology, Houston, TX, 2019 - 2019
External Member, Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 2018 - Present
Senator, The University of Texas MD Anderson Cancer Center, Houston, TX, 2018 - 2021
Other Professional Positions
Project Lead, The University of Texas MD Anderson Cancer Center, Houston, Texas, 2023 - 2025
Bioinformatics Lead, UT MDACC, Houston, TX, 2021 - 2022
Member, UT MDACC, Houston, TX, 2019 - Present
Graduate Research Assistant, Columbia University, New York, NY, 2003 - 2009
Extramural Institutional Committee Activities
Member, Multi-omics Core Facility, External Advisory Board, Baylor College of Medicine, 2020 - Present
Member, Admissions Committee Member, UT Health-MDACC GSBS, The University of Texas MD Anderson Cancer Center, GSBS, 2019 - 2021
External Member, Faculty Search Committee, Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, 2019
External Member, Biostatistics Faculty Search Committee, The University of Texas MD Anderson Cancer Center, 2018 - 2021
Honors & Awards
| 2024 | Waun Ki Hong Award for Excellence in Team Science, MD Anderson Cancer Center |
| 2023 - 2024 | Sabin Family Fellowship, Andrew Sabin Family Foundation |
| 2023 | MD Anderson Excellence in Research Award, MD Anderson Cancer Center |
| 2022 - Present | Humboldt Research Fellowship for Experienced Researchers, Humboldt Foundation (Federal Government of Germany) |
| 2017 - 2019 | Award for Innovation in Cancer Informatics, Fund for Innovation in Cancer Informatics (ICI) |
| 2017 - 2019 | University of Texas Rising STARs Award, University of Texas MD Anderson Cancer Center |
| 2017 | Searle Scholarship, MDACC nomination |
| 2011 | Charles Revson Foundation Award (MSKCC Nominee), Memorial Sloan Kettering Cancer Center |
| 2009 | Columbia University PhD Distinction Award, Columbia University |
| 2002 | Howard Hughes Medical Institute Pre-Doctoral Fellowship (Honorable Mention), Howard Hughes University |
| 2001 | The Faculty of Arts and Sciences Valedictorian Award, Bogazici University |
| 2001 | President's Award, Bogazici University |
| 2001 | Highest GPA of Double Major Program graduates, Bogazici University |
| 1997 | Turkish Science and Technology Council Merit Fellowship, Turkish Science and Technology Council |
Professional Memberships
Selected Presentations & Talks
Local Presentations
- 2025. Enabling precision oncology through computational biology with emphasis on spatial proteomics. Invited, US.
- 2025. Enabling Precision Oncology through Computational Biology. Invited. Enjoy Science. Houston, Texas, US.
- 2024. Towards a biologically informed machine learning framework for precision oncology. Invited. Data Science Forum. Houston, Texas, US.
- 2024. Towards a biologically informed machine learning framework for precision oncology. Invited. Research Town Hall. Houston, Texas, US.
- 2023. Enabling precision oncology through computational biology. Invited. Research Town Hall. Houston, Texas, US.
National Presentations
- 2024. Learning tumor-immune interactions through a single cell spatial proteomic atlas in gastrointestinal cancers. Invited, US.
- 2024. Enabling precision oncology through computational biology. Invited, US.
- 2024. Mechanistic maps of adaptive responses to therapeutic stress to optimize combination therapies. Invited, US.
- 2018. TargetScore: A data-driven network biology algorithm for overcoming adaptive resistance to cancer therapy. Conference. Gordon Research Conference. Smithfield, RI, US.
- 2013. Perturbation biology—Inferring signaling networks in cellular systems. Invited. 2013 Cold Spring Harbor Laboratory meeting on Systems Biology: Networks. Cold Springs Harbor, NY, US.
- 2013. Perturbation cell biology: network models of drug response in cancer cells. Invited. The First Annual Winter q-bio Meeting: Quantitative Biology on the Hawaiian Islands. Waikiki Beach, HI, US.
International Presentations
- 2024. Enabling precision oncology through computational biology. Invited, DE.
- 2024. Enabling precision oncology through computational biology. Invited, PT.
- 2024. Enabling Precision Oncology Through Computational Biology. Invited, DE.
- 2024. Enabling precision oncology through computational biology. Invited, DE.
- 2023. Enabling precision oncology through computational biology. Invited, TR.
- 2016. Perturbation biology: inferring signaling networks in cellular systems. European Conference on Computational Biology. Invited. 2016 European Conference on Computational Biology (ECCB). Hague, NL.
- 2016. Overcoming resistance to targeted cancer therapy with network pharmacology. International Conference on Systems Biology. Invited. International Conference on Systems Biology (ICCSB). Barcelona, ES.
Formal Peers
- 2022. Precision Combination Therapies based on oncogenic co-alterations. Invited, US.
- 2019. Precision Combination Therapies based on oncogenic co-alterations. Invited. Houston, TX, US.
- 2018. Discovery of anticancer drug combinations through quantitative pharmacology. Invited. Boston, MA, US.
- 2018. Therapeutic targeting of adaptation to nti-cancer agents. Invited. Portland, OR, US.
- 2017. Discovery of anticancer drug combinations through quantitative pharmacology. Invited. Helsinki, FI.
- 2017. Overcoming resistance to targeted cancer therapy with network pharmacology. Invited. Houston, TX, US.
- 2016. Network Models of signaling and proteomic diversity in melanoma. Invited. New York, NY, US.
- 2013. Network Models of signaling and proteomic diversity in melanoma. Invited. Cambridge, MA, US.
- 2009. Conformational transitions of macromolecules. Invited. Washington, DC, US.
- 2009. Structural plasticity and conformational transitions of HIV entry protein gp120. Invited. New York, NY, US.
Grant & Contract Support
| Date: | 2026 - 2031 |
| Title: | Targeting Cancer-related Bone Loss for Cognitive Impairment and Neuropathy in Breast Cancer |
| Funding Source: | NIH |
| Role: | Co-I |
| ID: | R01CA303306 |
| Date: | 2026 - 2029 |
| Title: | Role of CDH1 mutations in lobular breast cancer bone metastases |
| Funding Source: | Cancer Prevention and Research Institute of Texas |
| Role: | Co-I |
| ID: | RP270437 |
| Date: | 2026 - 2029 |
| Title: | Lineage plasticity sensitizes FGFR3-mutant bladder cancer to FGFR inhibitors |
| Funding Source: | Cancer Prevention and Research Institute of Texas |
| Role: | Collaborator |
| ID: | RP270421 |
| Date: | 2026 - 2029 |
| Title: | Collaborative Research: Formulating Cellular Adaptations to Environmental Perturbations through ML and LLMs |
| Funding Source: | NSF |
| Role: | PI |
| ID: | XF3XM969642N96 |
| Date: | 2026 - 2031 |
| Title: | OPTIMA: Oncology Precision Trials using Individualized Model Avatars |
| Funding Source: | NIH |
| Role: | MPI |
| ID: | R01OD041802 |
| Date: | 2026 - 2029 |
| Title: | Optimizing systemic therapy for patients with high-risk, early-stage triple-negative breast cancer: A personalized approach |
| Funding Source: | Conquer Cancer Foundation |
| Role: | Collaborator |
| ID: | 00029074 |
| Date: | 2026 - 2028 |
| Title: | Tumor Evolution in Li-Fraumeni Syndrome: A Multi-omics Approach |
| Funding Source: | CURE Childhood Cancer |
| Role: | Co-I |
| ID: | 00029696 |
| Date: | 2026 - 2031 |
| Title: | Lineage plasticity sensitizes FGFR3-mutant bladder cancer to FGFR inhibitors |
| Funding Source: | NIH |
| Role: | Co-I |
| ID: | R01CA311111 |
| Date: | 2026 - 2031 |
| Title: | Functional characterization of the lineage plasticity landscape of cholangiocarcinoma |
| Funding Source: | NCI |
| Role: | Collaborator |
| ID: | R01CA299653 |
| Date: | 2026 - 2030 |
| Title: | Transforming systemic therapy for patients with high-risk, early-stage triple-negative breast cancer: A personalized, data-driven approach |
| Funding Source: | DoD Era of Hope |
| Role: | Co-I |
| ID: | GRANT14451603 |
| Date: | 2026 - 2027 |
| Title: | Defining targetable vulnerabilities in residual triple-negative breast cancer after neoadjuvant therapy through integrated multi-omic spatial profiling |
| Funding Source: | Gilead Sciences |
| Role: | Mentor |
| ID: | FP00028820 |
| Date: | 2026 - 2027 |
| Title: | MFSD14A and the Bone Microenvironment in TNBC: In Vivo and Translational Profiling |
| Funding Source: | ELSA U PARDEE FOUNDATION |
| Role: | Co-I |
| ID: | FP00027663 |
| Date: | 2026 - 2028 |
| Title: | Role of CDH1 mutations in lobular breast cancer bone metastases |
| Funding Source: | Susan G. Komen for the Cure |
| Role: | PI |
| ID: | FP00027496 |
| Date: | 2026 - 2029 |
| Title: | Ammonia Survival Pathways in Triple-Negative Breast Cancer: The Emerging Role of MFSD14A in Bone Metastasis |
| Funding Source: | DoD |
| Role: | Co-I |
| ID: | GRANT14450560 |
| Date: | 2025 - 2030 |
| Title: | OPTIMA: Oncology Precision Trials using Individualized Model Avatars |
| Funding Source: | NCI |
| Role: | MPI |
| ID: | UM1CA321705 |
| Date: | 2025 - 2030 |
| Title: | OPTIMA: Oncology Precision Trials using Individualized Model Avatars |
| Funding Source: | NIH |
| Role: | Co-I |
| ID: | UM1TR006048 |
| Date: | 2025 - 2028 |
| Title: | Functional Proteomics RPPA Platform at MD Anderson |
| Funding Source: | Adelson Medical Research Foundation |
| Role: | Co-I |
| ID: | AWD00009720 |
| Date: | 2025 - 2029 |
| Title: | Targeting ganglioside GD2 to overcome chemotherapy-resistance in triple-negative breast cancer |
| Funding Source: | DOD |
| Role: | Co-I |
| ID: | BC240226 |
| Date: | 2025 - 2028 |
| Title: | Functional characterization of the lineage plasticity landscape of cholangiocarcinoma |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Collaborator |
| ID: | RP250260 |
| Date: | 2025 - 2029 |
| Title: | ADC-MATCH: Optimizing treatment selection with antibody-drug conjugates |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-I |
| ID: | RP250096 |
| Date: | 2024 - 2031 |
| Title: | CTSA Health Informatics |
| Funding Source: | NIH |
| Role: | Co-I |
| ID: | UM1TR004906 |
| Date: | 2024 - 2029 |
| Title: | Unraveling Ovarian Cancer’s Complexity: A Clinically Relevant Three-Dimensional Atlas |
| Funding Source: | NIH/NCI |
| Role: | MPI |
| ID: | 1 U01 CA294463-01 |
| Date: | 2024 - 2029 |
| Title: | Role of p38/MAP14 in aggressive thyroid cancers |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 1 R01 CA2855-01A1 |
| Date: | 2024 - 2029 |
| Title: | Advancing Precision Immuno-Oncology In Biliary Tract Cancers |
| Funding Source: | NIH/NCI |
| Role: | Core Co-Director |
| ID: | 1 P50 CA291589-01 |
| Date: | 2024 - 2025 |
| Title: | Mechanistic maps of adaptive responses to therapeutic stress to optimize combination therapies |
| Funding Source: | MDACC Bridge |
| Role: | PI |
| ID: | 30-12609-21 |
| Date: | 2024 - 2027 |
| Title: | Therapeutic vulnerabilities and predictors of response to chemo(immuno)therapy in patients with high-risk, early stage triple-negative breast cancer (TNBC) |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| ID: | RP240293 |
| Date: | 2024 - 2026 |
| Title: | Cancer Center Support (CORE) Grant – Merit Extension |
| Funding Source: | NIH |
| Role: | Co-I |
| ID: | 4P30CA016672-48 |
| Date: | 2023 - 2028 |
| Title: | Optimizing HER2-targeted therapy with the biparatropic HER2 antibody zanidatamab |
| Funding Source: | NIH/NCI |
| Role: | MPI |
| ID: | 1 R01 CA285469-01 |
| Date: | 2023 - 2025 |
| Title: | Novel targeted combination treatment strategies for aggressive thyroid cancers |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 1 R21 CA277280-01A1 |
| Date: | 2023 - 2024 |
| Title: | Therapeutic vulnerabilities and predictors of response to chemo(immuno)therapy in patients with high-risk, early-stage triple-negative breast cancer (TNBC) |
| Funding Source: | MD Anderson |
| Role: | PI |
| ID: | 600815-30-128757-21 |
| Date: | 2023 - 2028 |
| Title: | Role of 038/MAP14 in aggressive thyroid cancers |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 1 R01 CA285518-01 |
| Date: | 2023 - 2026 |
| Title: | Therapeutic vulnerabilities and predictors of response to chemo(immuno)therapy in patients with high-risk, early stage triple-negative breast cancer (TNBC) |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| ID: | RP230134 |
| Date: | 2023 - 2025 |
| Title: | spREFLECT: Spatial heterogeneity and therapeutic vulnerabilities in tumor ecosystems |
| Funding Source: | Andrew Sabin Family Foundation Fellowship |
| Role: | PI |
| ID: | 600815-80-128411-21 |
| Date: | 2023 - 2026 |
| Title: | Novel combination therapies for anaplastic thyroid cancer |
| Funding Source: | Department of Defense (DOD) |
| Role: | Co-I |
| ID: | RA220221 |
| Date: | 2023 - 2026 |
| Title: | REFLECT: Recurrent Features Leveraged for Combination Therapy |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 1 U01 CA274547-01A1 |
| Date: | 2023 - 2025 |
| Title: | Role of the LSD1/BHC80 Complex in Sertoli Cells |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 1 R21 HD111762-01 |
| Date: | 2023 - 2025 |
| Title: | High Dimensional Causal Discovery for Cellular Perturbation Response Prediction with Application to LINCS L1000 |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 1 R21 HG012964-01 |
| Date: | 2023 - 2026 |
| Title: | Novel combination therapies for anaplastic thyroid cancer |
| Funding Source: | DoD |
| Role: | Co-I |
| ID: | GRANT13720891 |
| Date: | 2022 - 2024 |
| Title: | Pathogenic EMT associated m6A complexes in glioblastoma: memberships, functional dependencies and translational relevance |
| Funding Source: | Houston Methodist |
| Role: | PI |
| Date: | 2022 - 2023 |
| Title: | PERFECT: PERsonalized immunotherapy For Early Curative treatment of Triple-negative breast cancer |
| Funding Source: | Boston Gene |
| Role: | Bioinformatician |
| ID: | AWD00006149 |
| Date: | 2022 - 2024 |
| Title: | p53 Reactivation in p53 Y220C Mutated Solid Tumors |
| Funding Source: | MDACC Moon Shot Program |
| Role: | Bioinformatician |
| ID: | 710499-30-125062-21 |
| Date: | 2022 - 2026 |
| Title: | STRATEGIC ALLIANCE: Feasibility and Clinical Utility of Combined Genomics/Transcriptomics with Systems Biology for Personalized Cancer Therapy |
| Funding Source: | Boston Gene |
| Role: | Collaborator |
| ID: | AWD00006149 |
| Date: | 2022 - 2027 |
| Title: | PERFECT: PERsonalized Immunotherapy For Early, Curative Treatment Of People With Triple-Negative Breast Cancer |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-I |
| Date: | 2022 - 2027 |
| Title: | Effect of Low Magnitude Mechanical Signals on Bone and Muscle Loss due to Androgen Deprivation Therapy for Prostate Cancer |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 1 R01 CA 272521 - 01 |
| Date: | 2022 - 2025 |
| Title: | REFLECT: Recurrent Features Leveraged for Combination Therapy |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 1 U01 CA 274547 - 01 |
| Date: | 2022 - 2024 |
| Title: | Effects of Low Magnitude Mechanical Signals and Zoledronic Acid on Fracture Healing |
| Funding Source: | NIH/NIAMS |
| Role: | Co-I |
| ID: | 1 R21 AR 081559 - 01 |
| Date: | 2022 - 2024 |
| Title: | The recurrent features of spatial heterogeneity in tumer ecosystems |
| Funding Source: | ICI Fund |
| Role: | PI |
| Date: | 2022 - 2022 |
| Title: | Rational Combination Therapy in Ovarian Cancer |
| Funding Source: | ovarian cancer research alliance (OCRA) |
| Role: | Principal Investigator-MDACC |
| ID: | FP00014863 |
| Date: | 2021 - 2025 |
| Title: | Impact of TGF-beta signaling on cell fate decisions and immunity in heterogeneous tissues |
| Funding Source: | NIH/NIGMS |
| Role: | PI |
| ID: | R35 GM142563-01 |
| Date: | 2021 - 2026 |
| Title: | MDACC KRAS G12C SPORE |
| Funding Source: | NIH/NCI |
| Role: | Career Enhancement Program (CEP) Candidate |
| Date: | 2021 - 2023 |
| Title: | Improving AYA cancer survivor clinical outcomes through profiling of anthracycline-induced cardiotoxicity in patient-derived iPSC-cardiomyocytes |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | R21HL159421 |
| Date: | 2021 - 2022 |
| Title: | Overcoming drug resistance in anaplastic thyroid cancer |
| Funding Source: | American Association for Cancer Research (AACR) |
| Role: | Biostatistician |
| ID: | 843138 |
| Date: | 2021 - 2022 |
| Title: | Effective treatment strategies using novel combination therapies in aggressive thyroid cancers |
| Funding Source: | The Elsa U. Pardee Foundation |
| Role: | Co-I |
| ID: | 4853 |
| Date: | 2021 - 2026 |
| Title: | PQ6: Effect of Low Magnitude Mechanical Signals on Bone and Muscle Loss due to Androgen Deprivation Therapy for Prostate Cancer |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 1R01CA258102-01 |
| Date: | 2021 - 2026 |
| Title: | Therapeutic targeting of the interplay between cell-death pathways and immuno-oncological processes in solid tumors |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | R01 CA258416-01 |
| Date: | 2021 - 2026 |
| Title: | Deciphering a new mechanism of thymidine phosphorylase in myeloma bone disease |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 1R01CA258612-01 |
| Date: | 2021 - 2026 |
| Title: | Determining the basis of innate cellular resistance to anthracycline toxicity in Hodgkin lymphoma survivors utilizing patient iPSC-derived cardiac myocytes |
| Funding Source: | Duke University |
| Role: | Co-I |
| Date: | 2021 - 2024 |
| Title: | REFLECT: Recurrent Features Leveraged for Combination Therapy |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | U01 CA248220-01A1 |
| Date: | 2021 - 2023 |
| Title: | Epigenetic regulation of testicular cancers |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | R21 CA259784-01 |
| Date: | 2021 - 2022 |
| Title: | REFLECT: Recurrent Features Leveraged for Combination Therapy |
| Funding Source: | Adverse Incident Bridge Funding |
| Role: | PI |
| ID: | 00059594 |
| Date: | 2021 - 2024 |
| Title: | Mechanisms of cardiotoxicity in the setting of complete estrogen deprivation for breast cancer treatment |
| Funding Source: | Department of Defense (DOD) |
| Role: | Biostatistician |
| ID: | BC201607 |
| Date: | 2021 - 2024 |
| Title: | Role of Bone-derived TGF-β on Glucose Metabolism in the Setting of Breast Cancer Bone Metastases |
| Funding Source: | Department of Defense (DOD) |
| Role: | Bioinformatician |
| ID: | W81WH-18-1-0678 |
| Date: | 2021 - 2024 |
| Title: | (PQ#9)Targeting leaky ryanodine receptor (RyR2) to treat and prevent chemotherapy-associated cognitive dysfunction in patients with breast cancer |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 7 R01 CA 206025-06 |
| Date: | 2020 - 2025 |
| Title: | Mechanistic maps of adaptive responses to therapeutic stress to optimize combination therapies |
| Funding Source: | NCI via Sub-award OHSU |
| Role: | PI |
| ID: | U01 CA253472 |
| Date: | 2020 - 2025 |
| Title: | Pleiotropic roles of RBPJ in Sertoli cells |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 1R01HD103629-01 |
| Date: | 2020 - 2025 |
| Title: | Impact of TGF-beta signaling on cell fate decisions and immunity in heterogeneous tissues |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | R35 GM137838 |
| Date: | 2020 - 2023 |
| Title: | Combination of immuno and targeted therapies guided by multi-omics characterization of the TP53 pathway, TGF-beta pathway and stromal signature in breast cancer |
| Funding Source: | Department of Defense (DOD) |
| Role: | Co-PI |
| ID: | BC200871 P2 |
| Date: | 2020 - 2022 |
| Title: | Profiling patient iPSC-cardiomyocytes to link mechanisms of anthracycline-induced cardiotoxicity to clinical endpoints |
| Funding Source: | NIH/NHLBI |
| Role: | Co-I |
| ID: | R21 HL150517 |
| Date: | 2020 - 2025 |
| Title: | Overcoming Resistance to Targeted Therapies in HER2+ Breast Cancer |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Date: | 2020 - 2023 |
| Title: | REFLECT: Recurrent Features Leveraged for Combination Therapy |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | U01 CA248220 |
| Date: | 2020 - 2023 |
| Title: | Novel therapies for patients with trastuzumab and pertuzumab resistant HER2+ breast cancer |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| ID: | RP200358 |
| Date: | 2019 - 2024 |
| Title: | A systems approach to targeting adaptive responses to therapeutic interventions in breast and ovarian cancers using PerturbProt |
| Funding Source: | Oregon Health Science University (via NIH Subaward) |
| Role: | PI |
| Date: | 2019 - 2024 |
| Title: | Impact of TGF-beta signaling on cell fate decisions in heterogeneous tissues |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Date: | 2019 - 2024 |
| Title: | Cancer Center Support (CORE) Grant |
| Funding Source: | NIH/NCI |
| Role: | Core Leader |
| ID: | 5 P30 CA016672-04 |
| Date: | 2019 - 2024 |
| Title: | CTSA Informatics Core |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 5 UL1 TR003167-05 |
| Date: | 2019 - 2024 |
| Title: | Center for Clinical and Translational Sciences |
| Funding Source: | National Center for Advancing Translational Sciences |
| Role: | Co-I |
| ID: | 5 UL1 TR003167-04 |
| Date: | 2019 - 2022 |
| Title: | Overcoming Resistance to Targeted Therapies in HER2+ Breast Cancer |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| ID: | RP190253 |
| Date: | 2018 - 2019 |
| Title: | Discovery of combination therapies in colorectal cancer |
| Funding Source: | MD Anderson CRC Moon Shot |
| Role: | Co-PI |
| Date: | 2018 - 2021 |
| Title: | Quantitative models of cell signaling in single cells and cell populations |
| Funding Source: | Kinship Foundation |
| Role: | PI |
| Date: | 2018 - 2020 |
| Title: | Phopshoproteomics-Guided Discovery of Effective Combination Therapies in Cancer |
| Funding Source: | DOD/Congressionally Directed Medical Research Programs (DOD/CDMRP) |
| Role: | PI |
| Date: | 2018 - 2021 |
| Title: | Overcoming Resistance to Targeted Therapies in HER2+ Breast Cancer |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| ID: | RP180385 |
| Date: | 2018 - 2018 |
| Title: | Task 2: Mechanistic Inference to Explain Proteomic Profiles for Phase 3 |
| Funding Source: | Oregon Health Science University |
| Role: | Principal Investigator-MDACC |
| Date: | 2018 - 2021 |
| Title: | Rational Combination Therapy in Ovarian Cancer |
| Funding Source: | Ovarian Cancer Research via subaward Oregon Health & Science University |
| Role: | Principal Investigator-MDACC |
| ID: | 545152 |
| Date: | 2017 - 2020 |
| Title: | Capitalizing on therapeutic liabilities in RAS mutant cancers with a rational combination therapy with PARP and MEK inhibitors |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Principal Investigator-MDACC |
| ID: | RP170640 |
| Date: | 2017 - 2020 |
| Title: | Overcoming Resistance to Targeted Therapies in HER2+ Breast Cancer |
| Funding Source: | DOD/Congressionally Directed Medical Research Programs (DOD/CDMRP) |
| Role: | PI |
| Date: | 2017 - 2019 |
| Title: | Overcoming tumor-intrinsic resistance to immune checkpoint inhibition |
| Funding Source: | American Association for Cancer Research (AACR) |
| Role: | PI |
| Date: | 2017 - 2020 |
| Title: | Genomics Guided Discovery of Effective Combination Therapies in Cancer |
| Funding Source: | Fund for Innovation in Cancer Informatics |
| Role: | PI |
| ID: | FP00002123 |
| Date: | 2017 - 2019 |
| Title: | Laboratory of Network Pharmacology |
| Funding Source: | University of Texas, STARS |
| Role: | PI |
| Date: | 2016 - 2021 |
| Title: | Startup Up Fund - A Korkut |
| Funding Source: | The University of Texas MD Anderson Cancer Center |
| Role: | Principal Investigator-MDACC |
| ID: | 600815-30-116658-15 |
| Date: | 2016 - 2021 |
| Title: | Integrated analysis of protein expression data from the Reverse Phase Protein Array (RPPA) platform |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 5U24CA210950-05 |
| Date: | 2003 - 2019 |
| Title: | Bioinformatics Shared Resources (PP-SR22) |
| Funding Source: | MD Anderson Cancer Center Support Group |
| Role: | Collaborator |
| ID: | P30CA016672 |
Selected Publications
Peer-Reviewed Articles
- 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. Communications Biology, 2025. e-Pub 2025. PMID: 37333072.
- Bhinder, B, Friedl, V, Sethuraman, S, Risso, D, Chiotti, K, Mashl, RJ, Ellrott, K, Lee, JA, Wong, C, Gyan, K, Deshpande, A, Imielinski, MB, Bareja, R, Stuart, JM, Peto, M, Hoadley, KA, Lazar, A, Cherniack, AD, Zhu, J, Cao, S, Rubin, MA, Wang, W, Bathe, OF, Robine, N, Ding, L, Laird, PW, Zhou, W, Shen, H, Thorsson, V, Yeh, JJ, Bailey, M, Zhou, DC, Peng, X, Goldman, M, Li, Y, Korkut, A, Sahni, N, Hayes, DN, Mensah, MK, Felau, I, Kemal, A, Caesar-Johnson, SJ, Demchok, JA, Yang, L, Ferguson, ML, Tarnuzzer, R, Wang, Z, Zenklusen, JC, Wang, Z, Chen, K. Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles. Scientific reports 15(1), 2025. e-Pub 2025. PMID: 40615649.
- Zhu, Y, Solis Soto, LM, Pant, S, Vega, EA, Vinuela, E, Bozorgui, B, Vauthey, JN, Aguayo, G, Wang, Z, Lu, W, Chen, X, Mino, B, Kakarala, L, Dai, J, Liu, S, Wani, K, Lazar, A, Carapeto, F, Lee, S, Wistuba, II, Korkut, A, Javle, M, Kwong, L. Population-Specific Immunogenomic Alterations in Gallbladder Cancer and Prognostic Significance. Modern Pathology 38(11), 2025. e-Pub 2025. PMID: 40541865.
- Xu, Z, Zhou, Z, Son, JB, Feng, H, Adrada, BE, Moseley, T, Candelaria, RP, Guirguis, MS, Patel, MM, Whitman, GJ, Leung, J, Le-Petross, H, Mohamed, R, Panthi, B, Lane, DL, Chen, H, Wei, P, Tripathy, D, Litton, J, Valero, V, Huo, L, Hunt, KK, Korkut, A, Thompson, A, Yang, W, Yam, C, Rauch, GM, Ma, J. Deep Learning Models Based on Pretreatment MRI and Clinicopathological Data to Predict Responses to Neoadjuvant Systemic Therapy in Triple-Negative Breast Cancer. Cancers 17(6), 2025. e-Pub 2025. PMID: 40149299.
- Uzunparmak B, Su F, Johnson A, Shaw K, Kong E, Korkut A, Xavier CB, Yuan Y, Fowler N, Paradiso F, Kontselidze L, Butusova A, Bagaev A, Dumbrava E, Rodon J, Hong D, Yap T, Fu S, Naing A, Piha-Paul S, Ferrarotto R, Iorgulescu J, Kulkarni S, Patel K, Meric-Bernstam AF. Comprehensive Genomic and Transcriptomic Analysis to Guide Therapy for Patients with Metastatic Solid Tumors. Cancer Discovery, 2025. e-Pub 2025.
- Meric-Bernstam, F, Johnson, A, Shen, Y, Zheng, X, Su, F, Zheng, X, Zeng, J, Uzunparmak, B, Breuer, E, Holla, V, Kahle, M, Kim, SH, Vu, T, Shaw, K, Dumbrava, E, Su, F, Yap, T, Rodon, J, Routbort, M, Patel, K, Kulkarni, S, Hansel, DE, Iorgulescu, J, Korkut, A, Chen , K. The actionable transcriptome: a framework for incorporating RNA sequencing into precision oncology. Nature Reviews in Clinical Oncology, 2025. e-Pub 2025.
- Li X, Nguyen J, Korkut A. Recurrent composite markers of cell types and states. Genome Research, 2025. e-Pub 2025. PMID: 37503180.
- Dereli Z, Bozorgui B, Sanchez M, Hornstein N, Thibault G, Wang H, Mills GB, Weinstein JN, Overman MJ, Korkut A. A spatially resolved single cell proteomic atlas of Small Bowel Adenocarcinoma. Biorxiv, 2025. e-Pub 2025.
- Franz A, Shen C, Coscia F, Munroe K, Charaoui L, Korkut A, Mann M, Luna A, Sander C. Design of combination therapeutics from protein response to drugs in ovarian cancer cells. Elife, 2025. e-Pub 2025.
- Guirguis MS, Adrada BE, Yam C, Tripathy D, Candelaria R, Yang W, Patel M, Moseley T, Perez F, Whitman GJ, Leung JW, Le-Petross H, Lane DL, Huo L, Litton JK, Valero V, Hunt KK, Arun B, Mohamed R, Sun J, Korkut A, Xu Z, Pashapoor S, White J, Son JB, Thompson A, Wei P, Ma J, Moulder S, Rauch GM. Early tumor volume reduction by breast DCE MRI predicts pathologic complete response to neoadjuvant therapy in triple negative breast cancer. NPJ Breast Cancer, 2025. e-Pub 2025. PMID: 41266347.
- Luna A, Wang H, Wang L, Dereli Z, Yan G, Awashti S, Zhang D, Li X, Babur O, Sahni N, Sander C, Wulf GM, Mills GB, Korkut A. Co-targeting PARP and SHP2 overcomes resistance to apoptosis with synergistic, durable, and complete response in preclinical models of breast cancer. Cancer Research, 2025. e-Pub 2025.
- Chen, JH, Addanki, S, Roy, D, Bassett Jr, R, Kalashnikova, E, Spickard, E, Kuerer, HM, Meas, S, Sarli, VN, Korkut, A, White, JB, Rauch, GM, Tripathy, D, Arun, BK, Barcenas, CH, Yam, C, Sethi, H, Rodriguez, AA, Liu, MC, Moulder, S, Lucci, A. Monitoring response to neoadjuvant chemotherapy in triple negative breast cancer using circulating tumor DNA. BMC cancer 24(1), 2024. e-Pub 2024. PMID: 39148033.
- 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, Patel MM, Reed BJ, Scoggins ME, Son JB, Tripathy D, Valero V, Wei P, White JB, Whitman GJ, Xu Z, Yang WT, Yam C, Adrada BE, Ma J. Diffusion Tensor Imaging for Characterizing Changes in Triple-Negative Breast Cancer During Neoadjuvant Systemic Therapy. J Magn Reson Imaging 60(4):1367-1376, 2024. e-Pub 2024. PMID: 38294179.
- Yam, C, Patel, MM, Hill, H, Sun, R, Bassett Jr, R, Kong, EK, Damodaran, S, Koenig, KB, Abouharb, S, Saleem, S, Bisen, AK, Murthy, RK, Ramirez, DL, Rauch, GM, Adrada, BE, Candelaria, RP, Wang, X, Mittendorf, EA, Thompson, A, White, JB, Ravenberg, EE, Clayborn, A, Ding, Q, Booser, DJ, Oke, OC, Brewster, A, Hortobagyi, GN, Ibrahim, NK, Litton, J, Valero, V, Arun, BK, Tripathy, D, Chang, J, Chen, K, Korkut, A, Moulder, S, Huo, L, Lim, B, Ueno, NT. Targeting the Epidermal Growth Factor Receptor Pathway in Chemotherapy-Resistant Triple-Negative Breast Cancer. Cancer Research Communications 4(10):2823-2834, 2024. e-Pub 2024. PMID: 39356138.
- Moffat, GT, Hu, ZI, Meric-Bernstam, F, Kong, EK, Pavlick, D, Ross, JS, Murugesan, K, Kwong, L, De Armas, AD, Korkut, A, Javle, M, Knox, J. KRAS Allelic Variants in Biliary Tract Cancers. JAMA Network Open 7(5), 2024. e-Pub 2024. PMID: 38709532.
- DiPeri TP, Evans KW, Wang B, Zhao M, Akcakanat A, Raso MG, Rizvi YQ, Zheng X, Korkut A, Varadarajan K, Uzunparmak B, Dumbrava EE, Pant S, Ajani JA, Pohlmann PR, Jensen VB, Javle M, Rodon J, Meric-Bernstam F. Co-Clinical Trial of Novel Bispecific Anti-HER2 Antibody Zanidatamab in Patient-Derived Xenografts. Cancer Discov 14(5):828-845, 2024. e-Pub 2024. PMID: 38358339.
- Makawita, S, Lee, S, Kong, EK, Kwong, L, Abouelfetouh, Z, Danner De Armas, A, Xiao, L, Murugesan, K, Danziger, N, Pavlick, D, Korkut, A, Ross, JS, Javle, M. Comprehensive Immunogenomic Profiling of IDH1- / 2 -Altered Cholangiocarcinoma. JCO Precision Oncology 8, 2024. e-Pub 2024. PMID: 38547421.
- Dibra D, Xiong S, Moyer SM, El-Naggar AK, Qi Y, Su X, Kong EK, Korkut A, Lozano G. Mutant p53 protects triple-negative breast adenocarcinomas from ferroptosis in vivo. Sci Adv 10(7):eadk1835, 2024. e-Pub 2024. PMID: 38354236.
- Bozorgui, B, Kong, EK, Luna, A, Korkut, A. Mapping the functional interactions at the tumor-immune checkpoint interface. Communications Biology 6(1), 2023. e-Pub 2023. PMID: 37106127.
- Xu, Z, Rauch, DE, Mohamed, RM, Pashapoor, S, Zhou, Z, Panthi, B, Son, JB, Hwang, K, Musall, BC, Adrada, BE, Candelaria, RP, Leung, J, Le-Petross, H, Lane, DL, Perez, F, White, JB, Clayborn, A, Reed, BJ, Chen, H, Sun, J, Wei, P, Thompson, A, Korkut, A, Huo, L, Hunt, KK, Litton, J, Valero, V, Tripathy, D, Yang, W, Yam, C, Ma, J. Deep Learning for Fully Automatic Tumor Segmentation on Serially Acquired Dynamic Contrast-Enhanced MRI Images of Triple-Negative Breast Cancer. Cancers 15(19), 2023. e-Pub 2023. PMID: 37835523.
- Panthi B, Adrada BE, Candelaria RP, Guirguis MS, Yam C, Boge M, Chen H, Hunt KK, Huo L, Hwang KP, Korkut A, Lane DL, Le-Petross HC, Leung JWT, Litton JK, Mohamed RM, Musall BC, Pashapoor S, Patel MM, Perez F, Son JB, Thompson A, Valero V, Wei P, White J, Xu Z, Pinsky L, Tripathy D, Yang W, Ma J, Rauch GM. Assessment of Response to Neoadjuvant Systemic Treatment in Triple-Negative Breast Cancer Using Functional Tumor Volumes from Longitudinal Dynamic Contrast-Enhanced MRI. Cancers (Basel) 15(4):1025, 2023. e-Pub 2023. PMID: 36831368.
- 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, Perez F, Son JB, Sun J, Thompson A, Tripathy D, Valero V, Wei P, White J, Xu Z, Yang W, Zhou Z, Yam C, Rauch GM, Ma J. Longitudinal dynamic contrast-enhanced MRI radiomic models for early prediction of response to neoadjuvant systemic therapy in triple-negative breast cancer. Front Oncol 13:1264259, 2023. e-Pub 2023. PMID: 37941561.
- 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 Reports 40(11):111304, 2022. e-Pub 2022. PMID: 36103824.
- 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. e-Pub 2022. PMID: 35412613.
- 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 2022. PMID: 34510503.
- 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.
- Ö B, 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.
- 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.
- 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.
- 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 2021. PMID: 33373583.
- 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.
- 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.
- Donehower LA, Soussi T, Korkut A, Liu Y, Schultz A, Cardenas M, Li X, Babur O, Hsu TK, Lichtarge O, Weinstein JN, Akbani R, Atlas Network CG, Wheeler DA. Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas. Cell Rep 28(5):1370-1384.e5, 2019. e-Pub 2019. PMID: 31365877.
- 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, Analysis Network CGA, Greenleaf WJ, Chang HY. The chromatin accessibility landscape of primary human cancers. Science 362(6413), 2018. e-Pub 2018. PMID: 30361341.
- 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, Research Network CGA, 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.
- 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, Research Network CGA, Camargo F, Liang H. Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer. Cell Rep 25(5):1304-1317.e5, 2018. e-Pub 2018. PMID: 30380420.
- Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C, Research Network CGA, 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.
- 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 2018. PMID: 28971726.
- 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, Research Network CGA, Bathe OF, Liang H. Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. Cell Rep 23(1):255-269.e4, 2018. e-Pub 2018. PMID: 29617665.
- 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, Research Network CGA, 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.
- 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, Research Network CGA, 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.
- 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, Research Network CGA, Hu H. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell 173(2):400-416.e11, 2018. e-Pub 2018. PMID: 29625055.
- 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, Research Network CGA, 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.
- Wang Z, Yang B, Zhang M, Guo W, Wu Z, Wang Y, Jia L, Li S, Research Network CGA, 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.
- Taylor AM, Shih J, Ha G, Gao GF, Zhang X, Berger AC, Schumacher SE, Wang C, Hu H, Liu J, Lazar AJ, Research Network CGA, 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.
- Chen H, Li C, Peng X, Zhou Z, Weinstein JN, Research Network CGA, Liang H. A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. Cell 173(2):386-399.e12, 2018. e-Pub 2018. PMID: 29625054.
- 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, Group MC, Network Network CGAR, 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. e-Pub 2018. PMID: 29625053.
- 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, Research Network CGA, 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. e-Pub 2018. PMID: 29625052.
- 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, Research Network CGA, 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. e-Pub 2018. PMID: 29625051.
- 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, Research Network CGA, 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. e-Pub 2018. PMID: 29625050.
- 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, Research Network CGA. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell 173(2):305-320.e10, 2018. e-Pub 2018. PMID: 29625049.
- 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, Atlas Network CG, 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. e-Pub 2018. PMID: 29625048.
- 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, Research Network CGA, 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. e-Pub 2018. PMID: 29617669.
- Chiu HS, Somvanshi S, Patel E, Chen TW, Singh VP, Zorman B, Patil SL, Pan Y, Chatterjee SS, Research Network CGA, 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. e-Pub 2018. PMID: 29617668.
- Seiler M, Peng S, Agrawal AA, Palacino J, Teng T, Zhu P, Smith PG, Research Network CGA, 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. e-Pub 2018. PMID: 29617667.
- 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, Research Network CGA, 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. e-Pub 2018. PMID: 29617666.
- 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, Research Network CGA, 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. e-Pub 2018. PMID: 29617664.
- Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ, Working Group FA, Research Network CGA, 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. e-Pub 2018. PMID: 29617662.
- 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, Research Network CGA, 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. e-Pub 2018. PMID: 29617661.
- 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, Research Network CGA, 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. e-Pub 2018. PMID: 29617660.
- Saltz J, Gupta R, Hou L, Kurc T, Singh P, Nguyen V, Samaras D, Shroyer KR, Zhao T, Batiste R, Van Arnam J, Research Network CGA, 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. e-Pub 2018. PMID: 29617659.
- Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N, Research Network CGA, 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. e-Pub 2018. PMID: 29617658.
- 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, Group MC, Research Network CGA. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst 6(3):271-281.e7, 2018. e-Pub 2018. PMID: 29596782.
- 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, Atlas Network CG. Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. Cell Syst 6(3):282-300.e2, 2018. e-Pub 2018. PMID: 29596783.
- 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, 2018. e-Pub 2018. PMID: 29496759.
- Research Network CGA. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell 32(2):185-203.e13, 2017. e-Pub 2017. PMID: 28810144.
- 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.
- 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.
- Atlas Network CG. Genomic Classification of Cutaneous Melanoma. Cell 161(7):1681-96, 2015. e-Pub 2015. PMID: 26091043.
- Korkut A, Wang W, Demir E, Aksoy BA, Jing X, Molinelli EJ, Ö B, 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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. e-Pub 2003.
Professional Educational Materials
- Korkut, A, Li, X. REFLECT combination therapy database: https://bioinformatics.mdanderson.org/reflect/, 2022.
- Korkut, A, Luna, A, Wang, H. TargetScore web application (adaptive responses to therapy web interface) https://cannin.shinyapps.io/targetscore/, 2021.
- Korkut, A. Korkut laboratory software repository (https://github.com/korkutlab), 2017.
- Korkut A, Wang W, Sander C, Bemis D, Miller M, Root A, Kaushik P, Molinelli E, Jing X, Aksoy BA, Gauthier N, Babur O, Demir E, Sumer SO. Perturbation Biology (http://projects.sanderlab.org/pertbio/). Sander Labs, 2016.
- Korkut A, Hendrickson WA. Virtual Atom Molecular Mechanics (vamm.org). Proc Natl Acad Sci USA, 2009.
Other Articles
- Korkut A Structural plasticity and conformational transitions of biological macromolecules: HIV gp120, 2009.
Book Chapters
- 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, 136-147, 2013.
Patient Reviews
CV information above last modified August 04, 2026