Gimeno-Valiente F, Castignani C, Larose Cadieux E, …,Deniz Ö, Jamal-Hanjani M, McGranahan N, TRACERx Consortium Beck S, Demeulemeester J, Tani M, Swanton C, Van Loo P, Kanu N. DNA methylation cooperates with genomic alterations during non-small cell lung cancer evolution. Nat Genet. 2025;57(9):2226-2237. [Link]
Tunbak H, Deniz Ö. Reawakening retrotransposons: immune modulation in normal and malignant hematopoiesis. Trends Cancer. Published online August 29, 2025. [Link]
Prokopov D, Tunbak H, Leddy E, Drylie B, Camera F, Deniz Ö Transposable elements as genome regulators in normal and malignant haematopoiesis. Blood Cancer J. 15, 87 (2025). [Link]
Kaya F, Bewicke-Copley F, Miettinen JJ, Casado P, Leddy E, Deniz Ö, et al. DEK::NUP214 acts as an XPO1-dependent transcriptional activator of essential leukemia genes Leukemia (2025). [Link]
Ng HL, Glaser TL, Robinson ME, Cosgun NK, Malysheva V, Zhu J., Deniz O, Crump NT, Helian K, Innes AJ, Sun L, Spivakov M, Mueschen M, Feldhahn F. Unraveling BCR::ABL1-driven enhancer activation and transcriptional reprogramming in Ph B-ALL (2024). Preprint [Link]
Grillo, G., Nadorp, B., Qamra, A., Mitchell, A., Arlidge, C., Nand, A., Takayama, N., Murison, A., Tonekaboni, S. A. M., Arruda, A., Wang, J. C. Y., Minden, M. D., Deniz, Ö., Boutzen, H., Dick, J. E., & Lupien, M. (2024). Transposable Elements Shape Stemness in Normal and Leukemic Hematopoiesis. BioRxiv (2024), 2021.02.16.431334. [Link]
Deniz Ö†, Ahmed M, Todd CD, Rio-Machin A, Dawson MA, Branco MR†. Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukemia. Nature Communications, 11 (1): 3506 (2020). † corresponding author. [PubMed]
Carrillo-Jimenez A*, Deniz Ö*, Niklison-Chirou M*, Bezerra-Salomao K, Stratoulias V, Amoroux VR, Ruiz R, Yip PK, Vilalta A, Cheray M, Scott-Egerton AM, Rivas E, Tayara K, Espinosa-Oliva AM, Shen X, Brown GC, Hajkova P, Joseph B, Venero JL, Branco MR, Burguillos MA. TET2 regulates the neuroinflammatory response in microglia. Cell Reports,15;29(3):697-713 (2019). * equal contribution [PubMed]
Deniz Ö, Frost JM, Branco MR. Regulation of transposable elements by DNA modifications. Nature Reviews Genetics, 20(7):417-431 (2019). [PubMed]
Todd CD, Deniz Ö, Taylor D, Branco MR. Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells. eLife, Apr 23;8 (2019). [PubMed]
Deniz Ö, de la Rica L, Cheng KC, Spensberger D, Branco MR. SETDB1 prevents TET2-dependent activation of IAP retroelements in na ve embryonic stem cells. Genome Biology, 19(1):6 (2018). [PubMed]
de la Rica L, Deniz Ö, Cheng KC, Todd CD, Cruz C, Houseley J, Branco MR. TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells. Genome Biology, 17:234 (2016). [PubMed]
Deniz Ö*, Flores O*, Aldea M, Soler-López M, Orozco M. Nucleosome architecture throughout the cell cycle. Sci. Rep., 6, 19729 (2016). * equal contribution [PubMed]
Flores O*, Deniz Ö*, Soler-López M, Orozco M. Fuzziness and noise in nucleosomal architecture. Nucleic Acids Res., 42, 4934–46 (2014). * equal contribution [PubMed]
Pérez A, Castellazzi CL, Battistini F, Collinet K, Flores O, Deniz Ö, Ruiz ML, Torrents D, Eritja R, Soler-López M, Orozco M. Impact of methylation on the physical properties of DNA. Biophys. J., 102, 2140–8 (2012). [PubMed]
Deniz Ö*, Flores O*, Battistini F, Pérez A, Soler-López M, Orozco M. Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. BMC Genomics, 12, 489 (2011). * equal contribution [PubMed]
Deniz lab 