Select Publications
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. 2023 Dec 1;29(23):4844-4852. doi: 10.1158/1078-0432.CCR-23-1703.PMID: 37747813.
Li J, Lan Z, Liao W, Horner JW, Xu X, Liu J, Yoshihama Y, Jiang S, Shim HS, Slotnik M, LaBella KA, Wu CJ, Dunner K Jr, Hsu WH, Lee R, Khanduri I, Terranova C, Akdemir K, Chakravarti D, Shang X, Spring DJ, Wang YA, DePinho RA. Histone demethylase KDM5D upregulation drives sex differences in colon cancer. Nature. 2023 Jul;619(7970):632-639. doi: 10.1038/s41586-023-06254-7. Epub 2023 Jun 21.PMID: 37344599.
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. 2022 Dec;612(7940):564-572. doi: 10.1038/s41586-022-05504-4. Epub 2022 Dec 7. PubMed PMID: 36477537; PubMed Central PMCID: PMC9810360.
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. 2022 Dec 1;6(1):89. doi: 10.1038/s41698-022-00331-2. PubMed PMID: 36456685; PubMed Central PMCID: PMC9715662.
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. 2022 Oct 1;45(8):374-378. doi: 10.1097/CJI.0000000000000431. Epub 2022 Aug 4. PubMed PMID: 35943386; PubMed Central PMCID: PMC9452485.
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. 2021 Jul;161(1):196-210. doi: 10.1053/j.gastro.2021.03.022. Epub 2021 Mar 19. PubMed PMID: 33745946; PubMed Central PMCID: PMC8238881.
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. 2021 May 21;49(9):5084-5094. doi: 10.1093/nar/gkab276. PubMed PMID: 33877329; PubMed Central PMCID: PMC8136768.
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. 2020 Nov;52(11):1178-1188. doi: 10.1038/s41588-020-0708-0. Epub 2020 Oct 5. PubMed PMID: 33020667; PubMed Central PMCID: PMC8350746.
Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA. Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nat Genet. 2020 Mar;52(3):294-305. doi: 10.1038/s41588-019-0564-y. Epub 2020 Feb 5. PubMed PMID: 32024999; PubMed Central PMCID: PMC7058537.
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. 2017 Apr 25;19(4):875-889. doi: 10.1016/j.celrep.2017.03.078. PubMed PMID: 28445736; PubMed Central PMCID: PMC5473172.
Smyk M, Akdemir KC, Stankiewicz P. SOX9 chromatin folding domains correlate with its real and putative distant cis-regulatory elements. Nucleus. 2017 Mar 4;8(2):182-187. doi: 10.1080/19491034.2017.1279776. Epub 2017 Jan 13. PubMed PMID: 28085555; PubMed Central PMCID: PMC5403132.
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. 2017 Mar;49(3):349-357. doi: 10.1038/ng.3781. Epub 2017 Jan 30. PubMed PMID: 28135248; PubMed Central PMCID: PMC5571729.
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. 2017 Feb 16;542(7641):362-366. doi: 10.1038/nature21064. Epub 2017 Feb 8. PubMed PMID: 28178232; PubMed Central PMCID: PMC7609022.