Kadir C. Akdemir, Ph.D.
Department of Neurosurgery, Division of Surgery
About Dr. Kadir C. Akdemir
Kadir Akdemir, Ph.D. is an Assistant Professor of the Department of Neurosurgery at MD Anderson. Raised in Turkey, he studied computer science and genetics at Yeditepe University in Istanbul. He obtained a PhD from the University of Texas Health Science Center at Houston for his work on p53 protein’s functions during human embryonic stem cell differentiation. He then completed his post-doctoral training with Dr. Andrew Futreal at MD Anderson’s Genomic Medicine department on cancer genomics and three-dimensional chromatin organization. His work on the integration of the three-dimensional chromatin organization with cancer genomic datasets provided unique insights into the mechanisms and consequences of somatic alterations observed in human tumors (Akdemir et al. Nature Genetics - PMID: 3302066; Akdemir et. al. Nature Genetics - PMID: 32024999). He has an extensive research program focused on genomic alterations observed in human central nervous system tumors.
Dr. Akdemir has been part of the several international genomic efforts such as the International Cancer Genome Consortia’s pan-cancer whole-genome analyses initiative and NIH’s 4Dnucleome comprehensive chromatin profiling initiative. He holds multiple foundation grants. He is collaborating with the world-renowned brain cancer researchers by being a part of the MD Anderson’s SPORE in Brain Cancer Program, GBM Moonshot program and the Break Through Cancer’s GBM program.
His lab has developed a large set of techniques to study mechanisms and patterns of chromatin folding and somatic rearrangements that occur in cancer genomes during neoplastic transformation.
Present Title & Affiliation
Primary Appointment
Assistant Professor, Department of Neurosurgery, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
Research Interests
Central Nervous System Tumors
Rare Tumors
Cancer Genomics
Chromatin Organization
Epigenetics
Education & Training
Degree-Granting Education
| 2013 | UT GSBS/MD Anderson Cancer Center, Houston, Texas, US, Ph.D. in Biomedical Sciences |
| 2008 | Yeditepe University, Istanbul, TR, BS in Computer Engineering |
| 2007 | Yeditepe University, Istanbul, TR, BS in Genetics and Bioengineering |
Postgraduate Training
| 2013-2017 | Research Fellowship, MD Anderson Cancer Center, Houston, Texas |
Experience & Service
Other Professional Positions
Assistant Professor, The University of Texas MD Anderson Cancer Center, Houston, TX, 2020 - 2021
Post-Doctoral Fellow, The University of Texas MD Anderson Cancer Center, Houston, Texas, 2013 - 2018
Graduate Research Assistant, The University of Texas MD Anderson Cancer Center, Houston, Texas, 2008 - 2013
Intern, Harvard Medical School, Cambridge, MA, 2007
Undergraduate Research Assistant, Yeditepe University, Istanbul, Turkey, 2007 - 2008
Extramural Institutional Committee Activities
GSBS PhD Student, Bhargavi Brahmedra Barathi, Examining Committee, The University of Texas MD Anderson Cancer Center, 2025 - Present
GSBS PhD Student, Nisha Naranayan, Advisory Committee, The University of Texas MD Anderson Cancer Center, 2025 - Present
GSBS MD PhD. Student, Yibo Dai, Examining Committee, The University of Texas MD Anderson Cancer Center, 2025 - Present
GSBS MD PhD. Student, Jacob Matia, Examining Committee, The University of Texas MD Anderson Cancer Center, 2025 - Present
GSBS Phd Student, Ahmad Shatta, Advisory Committee, The University of Texas MD Anderson Cancer Center, 2024 - Present
GSBS PhD Student, Ece Kilinc, Advisory Committee, The University of Texas MD Anderson Cancer Center, 2024 - Present
GSBS PhD Student, Thomas Mitchell, Co-mentor, The University of Texas MD Anderson Cancer Center, 2024 - Present
GSBS PhD student, Mariam Mosaad, Candidacy Exam Committee, The University of Texas MD Anderson Cancer Center, 2024 - Present
GSBS PhD Student Annette Machado, Candidacy Exam Committee, The University of Texas MD Anderson Cancer Center, 2024 - Present
GSBS PhD Student, Yibo Dai, Advisory Committee, The University of Texas MD Anderson Cancer Center, 2024 - Present
GSBS PhD Student, Mitheera V, Advisory Committee, The University of Texas MD Anderson Cancer Center, 2024 - Present
GSBS PhD Student, D’Shaunique Walters, Advisory Committee, The University of Texas MD Anderson Cancer Center, 2024 - Present
GSBS PhD Student, Ping Xu, Examining Committee, The University of Texas MD Anderson Cancer Center, 2024 - Present
MS Student, Caitlyn Czdinder, Advisory Committee, The University of Texas MD Anderson Cancer Center, 2024 - Present
MS Student, Seuoyoung Jeon, Advisory Committee, The University of Texas MD Anderson Cancer Center, 2024 - Present
GSBS PhD Student, Lana Al Hasani, Advisory Committee, The University of Texas MD Anderson Cancer Center, 2024 - Present
GSBS PhD Student, Junke (Kris) Wang, Examining Committee, The University of Texas MD Anderson Cancer Center, 2023
GSBS MD PhD. Student, Jacob Matia, Advisory Committee, The University of Texas MD Anderson Cancer Center, 2023 - Present
GSBS PhD Student, Bhargavi Brahmedra Barathi, Advisory Committee, The University of Texas MD Anderson Cancer Center, 2023 - Present
Member, Brain Tumor Center Executive Committee, The University of Texas MD Anderson Cancer Center, 2023 - Present
GSBS Master's Student, Shuangjie You, Advisory Committee, The University of Texas MD Anderson Cancer Center, 2022 - Present
GSBS PhD Student, Tapsi Kumar, Examining Committee, The University of Texas MD Anderson Cancer Center, 2022
School of Public Health Professionals, Gabrielle Carillo, Advisory Committee, The University of Texas MD Anderson Cancer Center, 2021 - 2022
Honors & Awards
| 2021 - 2023 | UT Rising Stars Award, University of Texas MD Anderson Cancer Center |
| 2018 - 2020 | Emerson Collective Cancer Research Funds, Emerson |
| 2016 | Junior Scientist Travel Award, CSHL Nuclear Organization |
| 2012 | MD Anderson Graduate Student Award in Basic Science, The University of Texas MD Anderson Cancer Center |
| 2011 | Graduate School Travel Award, The University of Texas MD Anderson Cancer Center |
| 2010 - 2011 | MD Anderson Center for Cancer Epigenetic Fellowship, The University of Texas MD Anderson Cancer Center |
| 2003 - 2008 | Yeditepe University Deans Scholar, Yeditepe University |
Professional Memberships
Selected Presentations & Talks
Local Presentations
- 2024. Annual Cellular and Molecular Biophysics Conference. Invited. Houston, Texas, US.
- 2023. Biochemistry Lecture. Invited. Galveston, Texas, US.
- 2019. MD Anderson Cancer Medicine Grand Round. Invited. Houston, Texas, US.
National Presentations
- 2023. Breakthrough Cancer Data Science Meeting. Invited. New York City, New York, US.
- 2023. Mid-Winter SPORE Meeting. Invited. San Francisco, California, US.
- 2023. Breakthrough Cancer and 10X Genomics Joint Meeting. Invited. Houston, Texas, US.
- 2022. The Gordon Conference on Centromere Biology. West Dover, Vermont, US.
- 2021. The Connective Tissue Oncology Society Annual Meeting, US.
- 2020. Multi- Center BRAIN SPORE Meeting. Invited, US.
- 2020. Physical Genomics and Transcriptional Engineering. Invited. Telluride, Colorado, US.
- 2019. Reviewer's Choice Award. Poster. Houston, Texas, US.
- 2019. Genentech. Invited. San Francisco, California, US.
- 2019. Oregon Health and Science University. Invited. Portland, Oregon, US.
- 2019. American Association of Cancer Research. Poster. Atlanta, Georgia, US.
- 2018. University of Rochester - Wilmot Cancer Institute. Invited, New York, US.
- 2018. American Society of Human Genetics (ASHG). San Diego, California, US.
- 2016. NY Epigenomics Symposium. New York, New York, US.
- 2016. Epigenomic. San Juan, PR.
- 2015. Keystone Conference: Epigenomic and DNA Methylation. Keystone, Colorado, US.
- 2013. 4th NIGMS Workshop on Human Stem Cell Research. Bethesda, Maryland, US.
- 2011. CSHL Genome Informatics. Cold Spring Harbor, New York, US.
International Presentations
- 2025. Molecular profiling of brain metastasis. Invited, CL.
- 2025. ecDNA dynamics in glioblastoma. Invited. Society of Neuro-oncology annual meeting, US.
- 2025. Recurrent ERBB2 amplifications in EAC brain metastasis. Invited, GB.
- 2025. ecDNA dynamics in glioblastoma. Conference. Cancer Grand Challenges Conference: ecDNA, Royal Society, London UK, GB.
- 2024. Computational Biology. Invited. Bertinoro, IT.
- 2018. Ontario Institute of Cancer Research (OICR). Invited. Toronto, CA.
Grant & Contract Support
| Date: | 2025 - 2026 |
| Title: | Investigating EGFR-Targeted Therapy Response and In Vivo Modeling of Glioma Tumors with Extrachromosomal DNA Amplifications |
| Funding Source: | Brain SPORE DRP |
| Role: | PI |
| Date: | 2025 - 2026 |
| Title: | Investigating Metastatic Trajectories and Treatment Vulnerabilities in Esophageal Adenocarcinoma Brain Metastasis |
| Funding Source: | Brain Met Research award |
| Role: | PI |
| Date: | 2024 - 2026 |
| Title: | Single-cell chromatin accessibility analysis of chordoma tissues to investigate the TBXT regulation in tumor microenvironment |
| Funding Source: | Chordoma Foundation |
| Role: | PI |
| Date: | 2024 - 2025 |
| Title: | Assessing Tumor Evolution and Immune Landscape in Esophageal Cancer Brain Metastasis |
| Funding Source: | Brain Met Research award |
| Role: | PI |
| Date: | 2024 - 2025 |
| Title: | Investigating and modulation organization of glioma cells with extra-chromosomal oncogene amplifications |
| Funding Source: | Brain SPORE DRP |
| Role: | PI |
| Date: | 2023 - 2025 |
| Title: | Multi-omic profiling of chordoma tissues to explore clinical vulnerabilities upon complex genomic rearrangements |
| Funding Source: | Chordoma Foundation |
| Role: | PI |
| Date: | 2023 - 2025 |
| Title: | Epigenetic modulation of chromatin to enhance cancer immunotherapy response in hypermutated gliomas |
| Funding Source: | Kleberg Innovator/Investigator Award |
| Role: | PI |
| Date: | 2022 - 2027 |
| Title: | Data Science Hub |
| Funding Source: | BreakThrough Cancer |
| Role: | Sub-Principal Investigator |
| Date: | 2022 - 2023 |
| Title: | Leveraging Chromatin Folding Patterns in Chordoma Genomes to Develop Predictive and Prognostic Biomarkers |
| Funding Source: | Institutional Research Grant |
| Role: | PI |
| Date: | 2022 - 2027 |
| Title: | Oncogene and tumor suppressor-induced common fragile sites: a new paradigm for understanding genome instability in cancer |
| Funding Source: | The San Diego Biomedical Research Institute/NIH |
| Role: | Sub-Principal Investigator |
| Date: | 2021 - 2024 |
| Title: | Revolutionizing GBM Therapy |
| Funding Source: | BreakThrough Cancer |
| Role: | Sub-Principal Investigator |
| Date: | 2021 - 2022 |
| Title: | Targeting Resistance Mechanisms in SMARCB1-Deficient Tumors |
| Funding Source: | Department of Defense (DOD) |
| Role: | CO-I |
| ID: | KC200096P1 |
| Date: | 2021 - 2022 |
| Title: | Utilizing integrated genomic and single cell sequencing approaches to target chordoma’s immunotherapeutic vulnerabilities |
| Funding Source: | Cancer Research Institute - Chordoma Foundation |
| Role: | Co-I |
| Date: | 2021 - 2024 |
| Title: | The Science and Technology Acquisition and Retention (Stars) Program |
| Funding Source: | The University of Texas System Board of Regents |
| Role: | PI |
| Date: | 2020 - 2025 |
| Title: | Investigating the effects of structural variants on 3D genome organization and gene regulation in cancer genomes |
| Funding Source: | NIH/NCI |
| Role: | Sub-Principal Investigator |
| ID: | 1U01CA260700 |
| Date: | 2019 - 2024 |
| Title: | SPORE in Brain Cancer – Biostatistics and Bioinformatics Core |
| Funding Source: | NIH/NCI |
| Role: | Co-Program Leader |
| ID: | 2P50CA127001 |
| Date: | 2019 - 2021 |
| Title: | Brain SPORE CEP Award |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 2P50CA127001 |
| Date: | 2019 - 2022 |
| Title: | Brain SPORE DRP Award |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Date: | 2018 - 2020 |
| Title: | Leveraging Chromatin Folding Patterns in Osteosarcoma Genomes to Develop Predictive and Prognostic Biomarkers |
| Funding Source: | Emerson Collective Cancer Funds |
| Role: | PI |
Selected Publications
Peer-Reviewed Articles
- Singh, P, D’Rozario, R, Chakraborty, B, Meher, S, Raychaudhuri, D, Tannir, AJ, Li, Y, Majumdar, A, Hawkins, J, Xiong, Y, Lorenzi, PL, Sharma, P, Akdemir, KC, Pilie, PG, Jain, A, Lee, B, Goswami, S. Loss of KDM6A-mediated genomic instability and metabolic reprogramming regulates response to therapeutic perturbations in bladder cancer. Nature communications 17(1), 2026. e-Pub 2026. PMID: 41501085.
- Peng, F, Sinjab, A, Dai, Y, Treekitkarnmongkol, W, Yang, S, Gomez Bolanos, L, Zhou, T, Chen, M, Serrano, A, Krishna, A, Karimi, N, Sharma, M, Basi, A, Pei, G, Liao, J, Liu, Y, Feng, J, Rahal, Z, Liu, Y, Jiang, J, Yu, K, Noun, T, Liu, Y, Khan, KB, Cho, KS, Chen, J, Solis Soto, LM, Mazzilli, SA, Dubinett, SM, Cascone, T, Spira, A, Swisher, SG, Jimbo, N, Hayashi, T, Kishikawa, S, Takamochi, K, Itoh, T, Yao, T, Suzuki, K, Kalhor, N, Wistuba, II, Li, M, Moghaddam, SM, Fujimoto, J, Burks, JK, Myers, JN, Akdemir, KC, Wang, L, Kadara, HN. Multimodal spatial-omics reveal co-evolution of alveolar progenitors and proinflammatory niches in progression of lung precursor lesions. Cancer cell 44(2):321-339.e13, 2026. e-Pub 2026. PMID: 41202811.
- De A, Forero SA, Pirani A, Morales JE, De La Fuente-Granada M, Sebastian S, Huse JT, Ballester LY, Weinberg JS, Lang FF, Akdemir KC, McCarty JH. Single cell spatial profiling of the matrisome identifies region-specific adhesion and signaling networks in glioblastoma. Commun Biol 9(1), 2025. e-Pub 2025. PMID: 41366031.
- Ling, AL, Gantchev, J, Prabhu, MC, Basu, S, Ahn, R, Holdhoff, M, Masud, N, Ball, A, Nikas, O, Villa, GR, Regan, MS, Baquer, G, Ayoub, G, Whittaker, CA, Abou-Mrad, Z, Santos, A, Couturier, C, Elharouni, D, Vogelzang, J, Yu, K, Chen, H, He, Z, Jiang, W, Lucas, CG, Sax, HE, Lang Jr, FF, Puduvalli, VK, Tabar, V, Brennan, CW, Boire, A, Holdhoff, M, Bettegowda, C, Cima, M, Solomon, IH, Yuan, Y, Tak, PP, Sharma, P, White, F, Ligon, KL, Agar, NY, Espejo, A, Sun, JJ, Chen, Y, Jindal, S, Huse, J, Goswami, S, Akdemir, KC, Hu, J, Sharma, P, Buchold, G. Serial multiomics uncovers anti-glioblastoma responses not evident by routine clinical analyses. Science translational medicine 17(819), 2025. e-Pub 2025. PMID: 41061048.
- Wang Y, Meraz IM, Qudratullah M, Kotagiri S, Han Y, Xi Y, Wang J, Akdemir KC, Roth JA, Lissanu Y. Mutation of SMARCA4 Induces Cancer Cell-Intrinsic Defects in the Enhancer Landscape and Resistance to Immunotherapy. Cancer Res 85(11):1997-2013, 2025. e-Pub 2025. PMID: 40080526.
- Zhao B, Cho CY, Ye L, Keal T, Mitchell T, Martin-Barrio I, Faraj CA, Unal M, Alsing J, Lawson NM, Kim ER, Chavez F, Rangel KM, Singh SK, McCarthy JH, Ashley DM, Yung WKA, Puduvalli V, Nir G, Weinberg JS, Wang L, Ligon KL, Genovese G, Loo PV, Futreal PA, Huse JT, Dixon JR, Lang FF, Akdemir KC. Oncogenic drivers shape the tumor microenvironment in human gliomas. bioRxiv, 2025. e-Pub 2025. PMID: 40475555.
- Beernaert B, Jady-Clark RL, Shah P, Ramon-Gil E, Lawson NM, Brodtman ZD, Tagore S, Stihler F, Carter AS, Clarke S, Liu T, Zhu W, Erdal E, Easton A, Campo L, Browne M, Ash S, Waddell N, Crosby T, Lord SR, Mann DA, Melero I, de Andrea CE, Tijhuis AE, Foijer F, Hammond EM, Akdemir KC, Leslie J, Izar B, Parkes EE. Chromosomal instability shapes the tumor microenvironment of esophageal adenocarcinoma via a cGAS-chemokine-myeloid axis. bioRxiv, 2025. e-Pub 2025. PMID: 40654626.
- Faraj, CA, McCutcheon, IE, Gubbiotti, M, Perni, S, Gule-Monroe, MK, Akdemir, KC, Clark, VE, Bander, ED, Loghin, ME, Prabhu, SS, Lang Jr, FF, Weinberg, J. Extra-central nervous system metastasis from high-grade glioma. Journal of neuro-oncology 173(1):193-204, 2025. e-Pub 2025. PMID: 40055259.
- Akdemir KC. Extra-central nervous system metastasis from high-grade glioma: a single-institution experience. J Neurooncol, 2025. e-Pub 2025. PMID: 40055259.
- Lawson NM, Ye L, Cho CY, Zhao B, Mitchell T, Martin-Barrio I, Beernaert B, Gupta A, Banu M, Lissanu Y, Shaffer S, Tawbi H, Li J, Gule-Monroe MK, Alvarez-Breckenridge CA, Huse JT, Murphy MB, Yin F, Lang FF, Parkes EE, Weinberg JS, Akdemir KC. Recurrent ERBB2 alterations are associated with esophageal adenocarcinoma brain metastases. medRxiv, 2025. e-Pub 2025. PMID: 40061311.
- Bayraktar R, Tang Y, Dragomir MP, Ivan C, Peng X, Fabris L, Zhang J, Carugo A, Aneli S, Liu J, Chen MM, Srinivasan S, Sahnoune I, Bayraktar E, Akdemir KC, Chen M, Narayanan P, Huang W, Ott LF, Eterovic AK, Villarreal OE, Mohammad MM, Peoples MD, Walsh DM, Hernandez JA, Morgan MB, Shaw KR, Davis JS, Menter D, Tam CS, Yeh P, Dawson SJ, Rassenti LZ, Kipps TJ, Kunej T, Estrov Z, Joosse SA, Pagani L, Alix-Panabieres C, Pantel K, Ferajoli A, Futreal A, Wistuba II, Radovich M, Kopetz S, Keating MJ, Draetta GF, Mattick JS, Liang H, Calin GA. The mutational landscape and functional effects of noncoding ultraconserved elements in human cancers. Sci Adv 11(8):eado2830, 2025. e-Pub 2025. PMID: 39970212.
- Denu RA, Yang RK, Lazar AJ, Patel SS, Lewis VO, Roszik J, Livingston JA, Wang WL, Shaw KR, Ratan R, Zarzour MA, Bird J, Raza S, Akdemir KC, Rodon Ahnert J, Subbiah V, Patel S, Conley AP. Clinico-Genomic Profiling of Conventional and Dedifferentiated Chondrosarcomas Reveals TP53 Mutation to Be Associated with Worse Outcomes. Clin Cancer Res 29(23):4844-4852, 2023. e-Pub 2023. PMID: 37747813.
- Li, J, Lan, ZD, Liao, WT, Horner, J, Xu, X, Liu, J, Yoshihama, Y, Jiang, S, Shim, HS, Slotnik, M, LaBella, KA, Wu, C, Dunner, K, Hsu, WH, Lee, R, Khanduri, I, Terranova, C, Akdemir, KC, Chakravarti, D, Shang, X, Spring, DJ, Wang, YA, DePinho, RA. Histone demethylase KDM5D upregulation drives sex differences in colon cancer. Nature 619(7970):632-639, 2023. e-Pub 2023. PMID: 37344599.
- Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA, Working Group PSV, Consortium P. Author Correction: Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nat Genet 55(6):1079, 2023. e-Pub 2023. PMID: 36944735.
- Hernández-Verdin I, Akdemir KC, Ramazzotti D, Caravagna G, Labreche K, Mokhtari K, Hoang-Xuan K, Peyre M, Bielle F, Touat M, Idbaih A, Duval A, Sanson M, Alentorn A. Pan-cancer landscape of AID-related mutations, composite mutations, and their potential role in the ICI response. NPJ Precis Oncol 6(1):89, 2022. e-Pub 2022. PMID: 36456685.
- Xu Z, Lee DS, Chandran S, Le VT, Bump R, Yasis J, Dallarda S, Marcotte S, Clock B, Haghani N, Cho CY, Akdemir KC, Tyndale S, Futreal PA, McVicker G, Wahl GM, Dixon JR. Structural variants drive context-dependent oncogene activation in cancer. Nature 612(7940):564-572, 2022. e-Pub 2022. PMID: 36477537.
- Bishop AJ, Amini B, Lin H, Raza SM, Patel S, Grosshans DR, Ghia A, Farooqi A, Guadagnolo BA, Mitra D, Akdemir KC, Lazar AJ, Wang WL, Alvarez-Breckenridge C, Bird J, Rhines LD, Somaiah N, Conley AP. Immune Checkpoint Inhibitors Have Clinical Activity in Patients With Recurrent Chordoma. J Immunother 45(8):374-378, 2022. e-Pub 2022. PMID: 35943386.
- Inoue A, Robinson FS, Minelli R, Tomihara H, Rizi BS, Rose JL, Kodama T, Srinivasan S, Harris AL, Zuniga AM, Mullinax RA, Ma X, Seth S, Daniele JR, Peoples MD, Loponte S, Akdemir KC, Khor TO, Feng N, Roszik J, Sobieski MM, Brunell D, Stephan C, Giuliani V, Deem AK, Shingu T, Deribe YL, Menter DG, Heffernan TP, Viale A, Bristow CA, Kopetz S, Draetta GF, Genovese G, Carugo A. Sequential administration of XPO1 and ATR inhibitors enhances therapeutic response in TP53-mutated colorectal cancer. Gastroenterology 161(1):196-210, 2021. e-Pub 2021. PMID: 33745946.
- Yang J, Horton JR, Akdemir KC, Li J, Huang Y, Kumar J, Blumenthal RM, Zhang X, Cheng X. Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations. Nucleic Acids Res 49(9):5084-5094, 2021. e-Pub 2021. PMID: 33877329.
- Akdemir KC, Le VT, Kim JM, Killcoyne S, King DA, Lin YP, Tian Y, Inoue A, Amin SB, Robinson FS, Nimmakayalu M, Herrera RE, Lynn EJ, Chan K, Seth S, Klimczak LJ, Gerstung M, Gordenin DA, O'Brien J, Li L, Deribe YL, Verhaak RG, Campbell PJ, Fitzgerald R, Morrison AJ, Dixon JR, Andrew Futreal P. Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure. Nat Genet 52(11):1178-1188, 2020. e-Pub 2020. PMID: 33020667.
- Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S, Group MW, working group PNSMCM, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L, Consortium P. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun 11(1):4748, 2020. e-Pub 2020. PMID: 32958763.
- Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, Clinical Translation PTSA, Boutros PC, Consortium P. Sex differences in oncogenic mutational processes. Nat Commun 11(1):4330, 2020. e-Pub 2020. PMID: 32859912.
- Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN, Xu Y, Han L, Kim HL, Nakagawa H, Park K, Campbell PJ, Liang H, Consortium P. Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat Genet 52(3):342-352, 2020. e-Pub 2020. PMID: 32024997.
- Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA, Working Group PSV, Consortium P. Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nat Genet 52(3):294-305, 2020. e-Pub 2020. PMID: 32024999.
- Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, Working Group PSV, Park PJ, Consortium P. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet 52(3):331-341, 2020. e-Pub 2020. PMID: 32025003.
- Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PAW, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine K, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH, Working Group PSV, Campbell PJ, Tubio JMC, Consortium P. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet 52(3):306-319, 2020. e-Pub 2020. PMID: 32024998.
- Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M, Working Group PV, Brors B, Rippe K, Jones DTW, Feuerbach L, Consortium P. Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun 11(1):733, 2020. e-Pub 2020. PMID: 32024817.
- Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M, Working Group PSV, Weischenfeldt J, Beroukhim R, Campbell PJ, Consortium P. Patterns of somatic structural variation in human cancer genomes. Nature 578(7793):112-121, 2020. e-Pub 2020. PMID: 32025012.
- Genomes Consortium IPAOW. Pan-cancer analysis of whole genomes. Nature 578(7793):82-93, 2020. e-Pub 2020. PMID: 32025007.
- Fiziev P, Akdemir KC, Miller JP, Keung EZ, Samant NS, Sharma S, Natale CA, Terranova CJ, Maitituoheti M, Amin SB, Martinez-Ledesma E, Dhamdhere M, Axelrad JB, Shah A, Cheng CS, Mahadeshwar H, Seth S, Barton MC, Protopopov A, Tsai KY, Davies MA, Garcia BA, Amit I, Chin L, Ernst J, Rai K. Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression. Cell Rep 19(4):875-889, 2017. e-Pub 2017. PMID: 28445736.
- Barthel FP, Wei W, Tang M, Martinez-Ledesma E, Hu X, Amin SB, Akdemir KC, Seth S, Song X, Wang Q, Lichtenberg T, Hu J, Zhang J, Zheng S, Verhaak RG. Systematic analysis of telomere length and somatic alterations in 31 cancer types. Nat Genet 49(3):349-357, 2017. e-Pub 2017. PMID: 28135248.
- Smyk M, Akdemir KC, Stankiewicz P. SOX9 chromatin folding domains correlate with its real and putative distant cis-regulatory elements. Nucleus 8(2):182-187, 2017. e-Pub 2017. PMID: 28085555.
- Genovese G, Carugo A, Tepper J, Robinson FS, Li L, Svelto M, Nezi L, Corti D, Minelli R, Pettazzoni P, Gutschner T, Wu CC, Seth S, Akdemir KC, Leo E, Amin S, Molin MD, Ying H, Kwong LN, Colla S, Takahashi K, Ghosh P, Giuliani V, Muller F, Dey P, Jiang S, Garvey J, Liu CG, Zhang J, Heffernan TP, Toniatti C, Fleming JB, Goggins MG, Wood LD, Sgambato A, Agaimy A, Maitra A, Roberts CW, Wang H, Viale A, DePinho RA, Draetta GF, Chin L. Synthetic vulnerabilities of mesenchymal subpopulations in pancreatic cancer. Nature 542(7641):362-366, 2017. e-Pub 2017. PMID: 28178232.
- Jain AK, Xi Y, McCarthy R, Allton K, Akdemir KC, Patel LR, Aronow B, Lin C, Li W, Yang L, Barton MC. LncPRESS1 Is a p53-Regulated LncRNA that Safeguards Pluripotency by Disrupting SIRT6-Mediated De-acetylation of Histone H3K56. Mol Cell 64(5):967-981, 2016. e-Pub 2016. PMID: 27912097.
- Carugo A, Genovese G, Seth S, Nezi L, Rose JL, Bossi D, Cicalese A, Shah PK, Viale A, Pettazzoni PF, Akdemir KC, Bristow CA, Robinson FS, Tepper J, Sanchez N, Gupta S, Estecio MR, Giuliani V, Dellino GI, Riva L, Yao W, Di Francesco ME, Green T, D'Alesio C, Corti D, Kang Y, Jones P, Wang H, Fleming JB, Maitra A, Pelicci PG, Chin L, DePinho RA, Lanfrancone L, Heffernan TP, Draetta GF. In Vivo Functional Platform Targeting Patient-Derived Xenografts Identifies WDR5-Myc Association as a Critical Determinant of Pancreatic Cancer. Cell Rep 16(1):133-147, 2016. e-Pub 2016. PMID: 27320920.
- Szafranski P, Gambin T, Dharmadhikari AV, Akdemir KC, Jhangiani SN, Schuette J, Godiwala N, Yatsenko SA, Sebastian J, Madan-Khetarpal S, Surti U, Abellar RG, Bateman DA, Wilson AL, Markham MH, Slamon J, Santos-Simarro F, Palomares M, Nevado J, Lapunzina P, Chung BH, Wong WL, Chu YWY, Mok GTK, Kerem E, Reiter J, Ambalavanan N, Anderson SA, Kelly DR, Shieh J, Rosenthal TC, Scheible K, Steiner L, Iqbal MA, McKinnon ML, Hamilton SJ, Schlade-Bartusiak K, English D, Hendson G, Roeder ER, DeNapoli TS, Littlejohn RO, Wolff DJ, Wagner CL, Yeung A, Francis D, Fiorino EK, Edelman M, Fox J, Hayes DA, Janssens S, De Baere E, Menten B, Loccufier A, Vanwalleghem L, Moerman P, Sznajer Y, Lay AS, Kussmann JL, Chawla J, Payton DJ, Phillips GE, Brosens E, Tibboel D, de Klein A, Maystadt I, Fisher R, Sebire N, Male A, Chopra M, Pinner J, Malcolm G, Peters G, Arbuckle S, Lees M, Mead Z, Quarrell O, Sayers R, Owens M, Shaw-Smith C, Lioy J, McKay E, de Leeuw N, Feenstra I, Spruijt L, Elmslie F, Thiruchelvam T, Bacino CA, Langston C, Lupski JR, Sen P, Popek E, Stankiewicz P. Pathogenetics of alveolar capillary dysplasia with misalignment of pulmonary veins. Hum Genet 135(5):569-586, 2016. e-Pub 2016. PMID: 27071622.
- Lissanu Deribe Y, Shi Y, Rai K, Nezi L, Amin SB, Wu CC, Akdemir KC, Mahdavi M, Peng Q, Chang QE, Hornigold K, Arold ST, Welch HC, Garraway LA, Chin L. Truncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanoma. Proc Natl Acad Sci U S A 113(9):E1296-305, 2016. e-Pub 2016. PMID: 26884185.
- Rai K, Akdemir KC, Kwong LN, Fiziev P, Wu CJ, Keung EZ, Sharma S, Samant NS, Williams M, Axelrad JB, Shah A, Yang D, Grimm EA, Barton MC, Milton DR, Heffernan TP, Horner JW, Ekmekcioglu S, Lazar AJ, Ernst J, Chin L. Dual Roles of RNF2 in Melanoma Progression. Cancer Discov 5(12):1314-27, 2015. e-Pub 2015. PMID: 26450788.
- Akdemir KC, Chin L. HiCPlotter integrates genomic data with interaction matrices. Genome Biol 16:198, 2015. e-Pub 2015. PMID: 26392354.
- Keung EZ, Akdemir KC, Al Sannaa GA, Garnett J, Lev D, Torres KE, Lazar AJ, Rai K, Chin L. Increased H3K9me3 drives dedifferentiated phenotype via KLF6 repression in liposarcoma. J Clin Invest 125(8):2965-78, 2015. e-Pub 2015. PMID: 26193637.
- Akdemir KC, Jain AK, Allton K, Aronow B, Xu X, Cooney AJ, Li W, Barton MC. Genome-wide profiling reveals stimulus-specific functions of p53 during differentiation and DNA damage of human embryonic stem cells. Nucleic Acids Res 42(1):205-23, 2014. e-Pub 2014. PMID: 24078252.
- Henry SP, Liang S, Akdemir KC, de Crombrugghe B. The postnatal role of Sox9 in cartilage. J Bone Miner Res 27(12):2511-25, 2012. e-Pub 2012. PMID: 22777888.
- Wilson MA, Koutelou E, Hirsch C, Akdemir K, Schibler A, Barton MC, Dent SY. Ubp8 and SAGA regulate Snf1 AMP kinase activity. Mol Cell Biol 31(15):3126-35, 2011. e-Pub 2011. PMID: 21628526.
- Tsai WW, Wang Z, Yiu TT, Akdemir KC, Xia W, Winter S, Tsai CY, Shi X, Schwarzer D, Plunkett W, Aronow B, Gozani O, Fischle W, Hung MC, Patel DJ, Barton MC. TRIM24 links a non-canonical histone signature to breast cancer. Nature 468(7326):927-32, 2010. e-Pub 2010. PMID: 21164480.
- Kurinna S, Stratton SA, Tsai WW, Akdemir KC, Gu W, Singh P, Goode T, Darlington GJ, Barton MC. Direct activation of forkhead box O3 by tumor suppressors p53 and p73 is disrupted during liver regeneration in mice. Hepatology 52(3):1023-32, 2010. e-Pub 2010. PMID: 20564353.
- Al-Swailem AM, Shehata MM, Abu-Duhier FM, Al-Yamani EJ, Al-Busadah KA, Al-Arawi MS, Al-Khider AY, Al-Muhaimeed AN, Al-Qahtani FH, Manee MM, Al-Shomrani BM, Al-Qhtani SM, Al-Harthi AS, Akdemir KC, Inan MS, Otu HH. Sequencing, analysis, and annotation of expressed sequence tags for Camelus dromedarius. PLoS One 5(5):e10720, 2010. e-Pub 2010. PMID: 20502665.
Invited Articles
- Sarabipour S, Wissink EM, Burgess SJ, Hensel Z, Debat H, Emmott E, Akay A, Akdemir K, Schwessinger B. Maintaining confidence in the reporting of scientific outputs. PeerJ Preprints 6(e27098v1), 2018. e-Pub 2018.
Review Articles
- Rubino F, Alvarez-Breckenridge C, Akdemir K, Conley AP, Bishop AJ, Wang WL, Lazar AJ, Rhines LD, DeMonte F, Raza SM. Prognostic molecular biomarkers in chordomas: A systematic review and identification of clinically usable biomarker panels. Front Oncol 12:997506, 2022. e-Pub 2022. PMID: 36248987.
Other Articles
- Yuan, Y, Ju, YS, Kim, Y, Li, J, Wang, Y, Yoon, CJ, Yang, Y, Martincorena, I, Creighton, CJ, Weinstein, JN, Xu, Y, Han, L, Kim, HL, Nakagawa, H, Park, K, Campbell, PJ, Liang, H, Aaltonen, LA, Abascal, F, Abeshouse, A, Aburatani, H, Adams, DJ, Agrawal, N, Ahn, KS, Ahn, SM, Aikata, H, Akbani, R, Akdemir, KC, Aldape, KD, Cao, S, Chakravarty, D, Chen, Y, Czerniak, BA, Eils, R, El-Naggar, AK, Fan, Y, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Langerod, A, Lazar, A, Lichter, P, Mills, GB, Myklebost, O, Sood, AK, Thompson, A, Van Loo, P, Wang, L Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nature Genetics 55(6):1078, 2023. PMID: 36944732.
- Cortés-Ciriano, I, Lee, JK, Xi, R, Jain, D, Jung, YL, Yang, L, Gordenin, D, Klimczak, LJ, Zhang, CZ, Pellman, D, Akdemir, KC, Alvarez, EG, Baez-Ortega, A, Beroukhim, R, Boutros, PC, Bowtell, DD, Brors, B, Burns, KH, Campbell, PJ, Chan, K, Chen, K, Cortés-Ciriano, I, Dueso-Barroso, A, Dunford, A, Edwards, PA, Estivill, X, Etemadmoghadam, D, Feuerbach, L, Fink, JL, Frenkel-Morgenstern, M, Garsed, DW, Gerstein, MB, Gordenin, DA, Haan, D, Haber, JE, Hess, J, Hutter, B, Imielinski, MB, Jones, DT, Ju, YS, Kazanov, MD, Klimczak, LJ, Koh, Y, Korbel, JO, Kumar, K, Lee, EA, Lee, JK, Li, Y, Lynch, AG, Macintyre, G Correction to Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nature Genetics 55(5):893, 2023. PMID: 32404988.
- Yakneen, S, Waszak, SM, Aminou, B, Bartolome, J, Boroevich, KA, Boyce, R, Brooks, AN, Buchanan, A, Buchhalter, I, Butler, A, Byrne, NJ, Cafferkey, A, Campbell, PJ, Chen, Z, Cho, S, Choi, W, Clapham, P, Davis-Dusenbery, BN, De La Vega, FM, Eils, R, Akbani, R, Akdemir, KC, Cao, S, Chakravarty, D, Chen, K, Chen, Y, Chong, Z, Czerniak, BA, El-Naggar, AK, Fan, Y, Futreal, A, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Lazar, A, Wang, L, Li, J, Liang, H, Lu, Y, Mills, GB, Park, K, Sood, AK, Su, X, Ueno, NT, Wang, L, Wang, W, Weinstein, JN, Yuan, Y Author Correction: Butler enables rapid cloud-based analysis of thousands of human genomes. Nature biotechnology 41(4):577, 2023. PMID: 36944844.
- Aaltonen, LA, Abascal, F, Abeshouse, A, Aburatani, H, Adams, D, Agrawal, N, Ahn, KS, Ahn, SM, Aikata, H, Akbani, R, Akdemir, KC, Al Ahmadie, H, Al-Sedairy, ST, Al-Shahrour, F, Alawi, M, Aldape, KD, Plass, C, Broaddus, R, Langerod, A, Cao, S, Chakravarty, D, Chen, K, Chen, Y, Chong, Z, Czerniak, BA, Eils, R, El-Naggar, AK, Fan, Y, Futreal, A, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Lazar, A, Li, J, Liang, H, Lichter, P, Lu, Y, Mills, GB, Park, K, Sood, AK, Su, X, Thompson, A, Ueno, NT, Van Loo, P, Wang, L, Weinstein, JN, Yuan, Y, Zhu, H Author Correction: Pan-cancer analysis of whole genomes. Nature 614(7948):E39, 2023. PMID: 36697834.
- Gerstung, M, Jolly, C, Leshchiner, I, Dentro, SC, Gonzalez, S, Rosebrock, D, Mitchell, TJ, Rubanova, Y, Anur, P, Yu, K, Tarabichi, M, Deshwar, A, Wintersinger, J, Kleinheinz, K, Vázquez-García, I, Haase, K, Jerman, L, Sengupta, S, Macintyre, G, Malikic, S, Donmez, N, Livitz, DG, Cmero, M, Demeulemeester, J, Schumacher, S, Fan, Y, Zhu, H, Wang, W, Van Loo, P, Fan, Y, Akbani, R, Akdemir, KC, Aldape, KD, Cao, S, Chakravarty, D, Chen, Y, Czerniak, BA, Eils, R, El-Naggar, AK, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Lazar, A, Lichter, P, Mills, GB, Sood, AK, Wang, L, Weinstein, JN Author Correction: The evolutionary history of 2,658 cancers. Nature 614(7948):E42, 2023. PMID: 36697833.
- Alexandrov, LB, Kim, J, Haradhvala, NJ, Huang, MN, Tian Ng, AW, Wu, Y, Boot, A, Covington, KR, Gordenin, DA, Bergstrom, EN, Islam, SM, Lopez-Bigas, N, Klimczak, LJ, McPherson, JR, Morganella, S, Sabarinathan, R, Wheeler, DA, Mustonen, V, Alexandrov, LB, Akbani, R, Akdemir, KC, Cao, S, Chakravarty, D, Chen, K, Chen, Y, Chong, Z, Czerniak, BA, Eils, R, El-Naggar, AK, Fan, Y, Futreal, A, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Lazar, A, Wang, L, Li, J, Liang, H, Lu, Y, Mills, GB, Park, K, Sood, AK, Su, X, Ueno, NT, Wang, W, Weinstein, JN, Yuan, Y, Zhu, H Author Correction: The repertoire of mutational signatures in human cancer. Nature 614(7948):E41, 2023. PMID: 36697836.
Patient Reviews
CV information above last modified March 26, 2026