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Hatice Osmanbeyoglu

Assistant Professor

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Ma, X., Somasundaram, A., Qi, Z., Hartman, D.J., Singh, H., & Osmanbeyoglu, H.U. (2021). SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators. Nucleic Acids Res.Oxford University Press (OUP). doi: 10.1093/nar/gkab745.

Vyas, A., Harbison, R.A., Faden, D.L., Kubik, M., Palmer, D., Zhang, Q., Osmanbeyoglu, H.U., Duvvuri, U., & Méndez, E. (2021). Recurrent human papillomavirus-related head and neck cancer undergoes metabolic re-programming and is driven by oxidative phosphorylation. Clin Cancer Res, clincanres.4789.2020.American Association for Cancer Research (AACR). doi: 10.1158/1078-0432.CCR-20-4789.

Moiseeva, T.N., Qian, C., Sugitani, N., Osmanbeyoglu, H.U., & Bakkenist, C.J. (2019). WEE1 kinase inhibitor AZD1775 induces CDK1 kinase-dependent origin firing in unperturbed G1-and S-phase cells. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 116(48), 23891-23893.Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1915108116.

Moiseeva, T.N., Yin, Y., Calderon, M.J., Qian, C., Schamus-Haynes, S., Sugitani, N., Osmanbeyoglu, H.U., Rothenberg, E., Watkins, S.C., & Bakkenist, C.J. (2019). An ATR and CHK1 kinase signaling mechanism that limits origin firing during unperturbed DNA replication. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 116(27), 13374-13383.Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1903418116.

Osmanbeyoglu, H.U., Shimizu, F., Rynne-Vidal, A., Alonso-Curbelo, D., Chen, H.A., Wen, H.Y., Yeung, T.L., Jelinic, P., Razavi, P., Lowe, S.W., Mok, S.C., Chiosis, G., Levine, D.A., & Leslie, C.S. (2019). Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers. NATURE COMMUNICATIONS, 10(1), 4369.Springer Science and Business Media LLC. doi: 10.1038/s41467-019-12291-6.

Toska, E., Osmanbeyoglu, H.U., Castel, P., Chan, C., Hendrickson, R.C., Elkabets, M., Dickler, M.N., Scaltriti, M., Leslie, C.S., Armstrong, S.A., & Baselga, J. (2019). "PI3K pathway regulates ER-dependent transcription in breast cancer through the epigenetic regulator KMT2D" (vol 363, eaaw7574, 2019). SCIENCE, 363(6425), eaaw7574.American Association for the Advancement of Science (AAAS). doi: 10.1126/science.aaw7574.

Hmeljaki, J., Sanchez-Vega, F., Hoadley, K.A., Shih, J., Stewart, C., Heiman, D., Tarpeyg, P., Danitova, L., Drill, E., Gibb, E.A., Bowlby, R., Kanchil, R., Osmanbeyoglull, H.U., Sekido, Y., Takeshita, J., Newton, Y., Graim, K., Gupta, M., Gaylg, C.M., Diaol, L., Gibbs, D.L., Thorsson, V., Lype, L., Kanthetir, H., Severson, D.T., Ravegnini, G., Desrneules, P., Jungbluth, A.A., Travis, W.D., Dacic, S., Chirieac, L.R., Galateau-Salle, F., Fujimoto, J., Husain, A.N., Silveira, H.C., Rusch, V.W., Rintoul, R.C., Pass, H., Kindler, H., Zauderer, M.G., Kwiatkowski, D.J., Bueno, R., Tsaols, A.S., Creaney, J., Lichtenberg, T., Leraas, K., Bowen, J., Felau, I., Zenklusen, J.C., Akbanil, R., Cherniack, A.D., Byers, L.A., Noble, M.S., Fletcher, J.A., Robertsong, A.G., Shen, R., Aburatani, H., Robinson, B.W., Campbells, P., Ladanyi, M., & Network, T.C.G.A.R. (2018). Integrative Molecular Characterization of Malignant Pleural Mesothelioma. CANCER DISCOVERY, 8(12), 1548-1565.American Association for Cancer Research (AACR). doi: 10.1158/2159-8290.CD-18-0804.

Korkut, A., Zaidi, S., Kanchi, R.S., Rao, S., Gough, N.R., Schultz, A., Li, X., Lorenzi, P.L., Berger, A.C., Robertson, G., Kwong, L.N., 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, J.B., O'Rourke, C.J., Ohshiro, K., Jogunoori, W., Nguyen, B.N., Li, S., Osmanbeyoglu, H.U., Ajani, J.A., Mani, S.A., Houseman, A., Wiznerowicz, M., Chen, J., Gu, S., Ma, W., Zhang, J., Tong, P., Cherniack, A.D., Deng, C., Resar, L., Weinstein, J.N., Mishra, L., Akbani, R., & Network, C.G.A.R. (2018). A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-beta Superfamily. CELL SYSTEMS, 7(4), 422-+.Elsevier BV. doi: 10.1016/j.cels.2018.08.010.

Iyer, A.S., Osmanbeyoglu, H.U., & Leslie, C.S. (2017). Computational methods to dissect gene regulatory networks in cancer. Current Opinion in Systems Biology, 2, 115-122.Elsevier BV. doi: 10.1016/j.coisb.2017.04.004.

Luo, C.T., Osmanbeyoglu, H.U., Do, M.H., Bivona, M.R., Toure, A., Kang, D., Xie, Y., Leslie, C.S., & Li, M.O. (2017). Ets transcription factor GABP controls T cell homeostasis and immunity. NATURE COMMUNICATIONS, 8(1), 1062.Springer Science and Business Media LLC. doi: 10.1038/s41467-017-01020-6.

Nargund, A.M., Osmanbeyoglu, H.U., Cheng, E.H., & Hsieh, J.J. (2017). SWI/SNF tumor suppressor gene PBRM1/BAF180 in human clear cell kidney cancer. Mol Cell Oncol, 4(4), e1342747.Informa UK Limited. doi: 10.1080/23723556.2017.1342747.

Osmanbeyoglu, H.U., Toska, E., Chan, C., Baselga, J., & Leslie, C.S. (2017). Pancancer modelling predicts the context-specific impact of somatic mutations on transcriptional programs. NATURE COMMUNICATIONS, 8(1), 14249.Springer Science and Business Media LLC. doi: 10.1038/ncomms14249.

Toska, E., Osmanbeyoglu, H.U., Castel, P., Chan, C., Hendrickson, R.C., & Elkabets, M. (2017). PI3K SIGNALING REGULATES ER ACTIVITY VIA KMT2D IN ER+ BREAST CANCER. CANCER DISCOVERY, 7(5), 455.

Toska, E., Osmanbeyoglu, H.U., Castel, P., Chan, C., Hendrickson, R.C., Elkabets, M., Dickler, M.N., Scaltriti, M., Leslie, C.S., Armstrong, S.A., & Baselga, J. (2017). CANCER THERAPY PI3K pathway regulates ER-dependent transcription in breast cancer through the epigenetic regulator KMT2D. SCIENCE, 355(6331), 1324-1329.American Association for the Advancement of Science (AAAS). doi: 10.1126/science.aah6893.

Watters, R.J., Hartmaier, R.J., Osmanbeyoglu, H.U., Gillihan, R.M., Rae, J.M., Liao, L., Chen, K., Li, W., Lu, X., & Oesterreich, S. (2017). Steroid receptor coactivator-1 can regulate osteoblastogenesis independently of estrogen. MOLECULAR AND CELLULAR ENDOCRINOLOGY, 448(C), 21-27.Elsevier BV. doi: 10.1016/j.mce.2017.03.005.

Feng, Y., van der Veeken, J., Shugay, M., Putintseva, E.V., Osmanbeyoglu, H.U., Dikiy, S., Hoyos, B.E., Moltedo, B., Hemmers, S., Treuting, P., Leslie, C.S., Chudakov, D.M., & Rudensky, A.Y. (2015). A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance. NATURE, 528(7580), 132-+.Springer Science and Business Media LLC. doi: 10.1038/nature16141.

Osmanbeyoglu, H.U., Pelossof, R., Bromberg, J.F., & Leslie, C.S. (2014). Linking signaling pathways to transcriptional programs in breast cancer. GENOME RESEARCH, 24(11), 1869-1880.Cold Spring Harbor Laboratory. doi: 10.1101/gr.173039.114.

Osmanbeyoglu, H.U., Lu, K.N., Oesterreich, S., Day, R.S., Benos, P.V., Coronnello, C., & Lu, X. (2013). Estrogen represses gene expression through reconfiguring chromatin structures. NUCLEIC ACIDS RESEARCH, 41(17), 8061-8071.Oxford University Press (OUP). doi: 10.1093/nar/gkt586.

Kohle-Ersher, A., Chatterjee, P., Osmanbeyoglu, H.U., Hochheiser, H., & Bartos, C. (2012). Evaluating the Barriers to Point-of-Care Documentation for Nursing Staff. CIN-COMPUTERS INFORMATICS NURSING, 30(3), 126-133.Ovid Technologies (Wolters Kluwer Health). doi: 10.1097/NCN.0b013e3182343f14.

Osmanbeyoglu, H.U., Hartmaier, R.J., Oesterreich, S., & Lu, X. (2012). Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information. BMC GENOMICS, 13(S1), S1.Springer Science and Business Media LLC. doi: 10.1186/1471-2164-13-S1-S1.

Osmanbeyoglu, H.U., & Ganapathiraju, M.K. (2011). N-gram analysis of 970 microbial organisms reveals presence of biological language models. BMC BIOINFORMATICS, 12(1), 12.Springer Science and Business Media LLC. doi: 10.1186/1471-2105-12-12.

Chalancon, G., Kosloff, M., Osmanbeyoglu, H.U., & Saraswathi, S. (2010). PLoS Computational Biology Conference Postcards from ISMB 2010. PLOS COMPUTATIONAL BIOLOGY, 6(11), e1002000.Public Library of Science (PLoS). doi: 10.1371/journal.pcbi.1002000.

Osmanbeyoglu, H.U., Wehner, J.A., Carbonell, J.G., & Ganapathiraju, M.K. (2010). Active machine learning for transmembrane helix prediction. BMC BIOINFORMATICS, 11(S1), S58.Springer Science and Business Media LLC. doi: 10.1186/1471-2105-11-S1-S58.

Osmanbeyoglu, H.U., Hur, T.B., & Kim, H.K. (2009). Thin alumina nanoporous membranes for similar size biomolecule separation. JOURNAL OF MEMBRANE SCIENCE, 343(1-2), 1-6.Elsevier BV. doi: 10.1016/j.memsci.2009.07.027.

Osmanbeyoglu, H.U., & Leslie, C. (2017). Modeling the impact of mutations in ubiquitin pathway genes across human cancers. In CANCER RESEARCH, 77.American Association for Cancer Research. doi: 10.1158/1538-7445.AM2017-LB-010.

Osmanbeyoglu, H.U., Toska, E., Baselga, J., & Leslie, C. (2016). Modeling the impact of somatic alterations across human cancers. In CANCER RESEARCH, 76.American Association for Cancer Research. doi: 10.1158/1538-7445.AM2016-781.