Gunes Gundem, PhD

Principal Computational Biologist

Gunes Gundem, PhD

Principal Computational Biologist
Gunes Gundem

Gunes Gundem’s research focuses on the study of tumor genome from the point of view of understanding subclonal structure and how it changes across time and space. She is particularly interested in the study of advanced stages of the neoplastic process such as metastasis or when patients relapse in response to therapy and how changes in clonal dynamics is related to these transitions. With an undergraduate background in molecular biology and genetics, Gunes has been developing strong computational and bioinformatic skills for high-throughput data analysis with a special focus in next-generation sequencing data. She completed her undergraduate degree in Middle East Technical University in Ankara, Turkey. After finishing a Master’s degree in computational science in Koc University in Istanbul, she did her graduate studies under the supervision of Dr. Nuria Lopez Bigas in Barcelona. She later on moved to Cambridge, U.K., where she spent more than three years working as a postdoctoral scientist as part of the ICGC UK Prostate project in Wellcome Trust Sanger Institute, one of the leading genome centers in the world. Gunes has recently joined the Papaemmanouil Lab as a postdoctoral fellow.


Diolaiti D, Dela Cruz FS, Gundem G, et al. A recurrent novel MGA-NUTM1 fusion identifies a new subtype of high-grade spindle cell sarcoma. Cold Spring Harb Mol Case Stud. 2018;4(6):a003194. Published 2018 Dec 17. doi:10.1101/mcs.a003194

Wedge DC, Gundem G, Mitchell T, et al. Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets. Nat Genet. 2018;50(5):682-692. doi:10.1038/s41588-018-0086-z

Grinfeld J, Nangalia J, Baxter EJ, et al. Classification and Personalized Prognosis in Myeloproliferative Neoplasms. N Engl J Med. 2018;379(15):1416-1430. doi:10.1056/NEJMoa1716614

Casuscelli J, Weinhold N, Gundem G, et al. Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma. JCI Insight. 2017;2(12):e92688. Published 2017 Jun 15. doi:10.1172/jci.insight.92688

Behjati S, Gundem G, Wedge DC, et al. Mutational signatures of ionizing radiation in second malignancies. Nat Commun. 2016;7:12605. Published 2016 Sep 12. doi:10.1038/ncomms12605

Desmedt C, Zoppoli G, Gundem G, et al. Genomic Characterization of Primary Invasive Lobular Breast Cancer. J Clin Oncol. 2016;34(16):1872-1881. doi:10.1200/JCO.2015.64.0334

Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JM, Papaemmanouil E, Brewer DS, Kallio HM, Högnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O’Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC; ICGC Prostate UK Group, Neal DE, Cooper CS, Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC, Bova GS. The evolutionary history of lethal metastatic prostate cancer. Nature. 2015 Apr 16;520(7547):353-7. doi: 10.1038/nature14347. Epub 2015 Apr 1. PubMed Central PMCID: PMC4413032. PubMed

Manson-Bahr D, Ball R, Gundem G, Sethia K, Mills R, Rochester M, Goody V, Anderson E, O’Meara S, Flather M, Keeling M, Yazbek-Hanna M, Hurst R, Curley H, Clark J, Brewer DS, McDermott U, Cooper C. Mutation detection in formalin-fixed prostate cancer biopsies taken at the time of diagnosis using next-generation DNA sequencing. J Clin Pathol. 2015 Mar;68(3):212-7. doi: 10.1136/jclinpath-2014-202754. Epub 2015 Jan 13. PubMed

Furney SJ, Gundem G, Lopez-Bigas N. Oncogenomics methods and resources. Cold Spring Harb Protoc. 2012 May 1;2012(5). pii: pdb.top069229. doi: 10.1101/pdb.top069229. PubMed

Gundem G, Lopez-Bigas N. Sample-level enrichment analysis unravels shared stress phenotypes among multiple cancer types. Genome Med. 2012 Mar 29;4(3):28. PubMed Central PMCID: PMC3446278. PubMed


Gundem G, Perez-Llamas C, Jene-Sanz A, Kedzierska A, Islam A, Deu-Pons J, Furney SJ, Lopez-Bigas N. IntOGen: integration and data mining of multidimensional oncogenomic data. Nat Methods. 2010 Feb;7(2):92-3. doi: 10.1038/nmeth0210-92. PubMed


View a full listing of Gunes Gundem’s journal articles.