Preprints
SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators
X Ma, A Somasundaram, Z Qi, H Singh, Osmanbeyoglu HU
bioRxiv. 2020
Avani Vyas, R Alex Harbison, Daniel Faden, Mark Kubik, Drake Palmer, Qing Zhang, Osmanbeyoglu HU, Eduardo Méndez, Umamaheswar Duvvuri
bioRxiv. 2020
Journal Publications
Moiseeva TN, Qian C, Chiba N, Osmanbeyoglu HU, Bakkenist CJ.
Proc Natl Acad Sci. 2019 Nov 11
Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers.
Osmanbeyoglu HU#, Shimizu F*, Rynne-Vidal A*, Alonso-Curbelo D*, Chen HA, Wen HY, Yeung TL, Jelinic P, Ravazi P, Lowe SW, Mok SC, Chiosis G, Levine DA, Leslie CS#. (#=co-corresponding authors)
Nature Communications. 2019 Sep 25
Moiseeva NT, Yin Y, Calderon MJ, Qian C, Schamus-Haynes S, Sugitani N, Osmanbeyoglu HU, Rothenberg E, Watkins SC, Bakkenist CJ.
Proc Natl Acad Sci. 2019 Jun 17
Integrative Molecular Characterization of Malignant Pleural Mesothelioma
Hmeljak J, Sanchez-Vega F, Hoadley KA, Shih J, Stewart C, Heiman D, Tarpey P, Danilova L, Drill E, Gibb EA, Bowlby R, Kanchi R, Osmanbeyoglu HU, Sekido Y, Takeshita J, Newton Y, Graim K, Gupta M, Gay CM, Diao L, Gibbs DL, Thorsson V, Iype L, Kantheti H, Severson DT, Ravegnini G, Desmeules P, Jungbluth AA, Travis WD, Dacic S, Chirieac LR, Galateau-Sallé F, Fujimoto J, Husain AN, Silveira HC, Rusch VW, Rintoul RC, Pass H, Kindler H, Zauderer MG, Kwiatkowski DJ, Bueno R, Tsao AS, Creaney J, Lichtenberg T, Leraas K, Bowen J; TCGA Research Network, Felau I, Zenklusen JC, Akbani R, Cherniack AD, Byers LA, Noble MS, Fletcher JA, Robertson AG, Shen R, Aburatani H, Robinson BW, Campbell P, Ladanyi M.
Cancer Discovery. 2018 Dec. 8
Korkut A, Zaidi S, Kanchi RS, Rao S, Gough NR, Schultz A, Li X, Lorenzi PL, Berger AC, Robertson G, Kwong LN, 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 JB, O'Rourke CJ, Ohshiro K, Jogunoori W, Nguyen BN, Li S, Osmanbeyoglu HU, Ajani JA, Mani SA, Houseman A, Wiznerowicz M, Chen J, Gu S, Ma W, Zhang J, Tong P, Cherniack AD, Deng C, Resar L.,Cancer Genome Atlas Research Network, Weinstein JN, Mishra L, Akbani R.
Cell Systems. 2018 Oct 24
Ets transcription factor GABP controls T cell homeostasis and immunity
Luo CT, Osmanbeyoglu HU, Do MH, Bivona MR, Toure A, Kang D, Xie Y, Leslie CS, Li MO.
Nature Communications. 2017 Oct 20
SWI/SNF tumor suppressor gene PBRM1/BAF180 in human clear cell kidney cancer
Nargund AM, Osmanbeyoglu HU, Cheng EH, Hsieh JJ.
Molecular & Cellular Oncology. 2017 Jun 15
Computational methods to dissect gene regulatory networks in cancer
Iyer A, Osmanbeyoglu HU, Leslie CS.
Current Opinion in Systems Biology 2. 2017 Apr 17
The SWI/SNF Protein PBMR1 Restrains VHL Loss-Driven Clear Cell Kidney Cancer
Nargund AM, Pham CG, Dong Y, Wang PI, Osmanbeyoglu HU, Xie Y, Aras O, Han S, Oyama T, Takeda S, Ray CE, Dong Z, Berge M, Hakimi AA, Monetta S, Lekaye CL, Koutcher JA, Leslie CS, Creighton CJ, Weinhold N, Lee W, Tickoo SK, Wang Z, Cheng EH, Hsieh JJ.
Cell Reports. 2017 Mar 21
Steroid receptor coactivator-1 can regulate osteoblastogenesis independently of estrogen
Watters RJ, Hartmaier RJ, Osmanbeyoglu HU, Gillihan RM, Rae JM, Liao L, Chen K, Li W, Lu X, Oesterreich S.
Mol Cell Endocrinol. 2017Jun 15
Toska E, Osmanbeyoglu HU, Castel P, Chan C, Hendrickson RC, Elkabets M, Dickler MN, Scaltriti M, Leslie CS, Armstrong SA, Baselga J.
Science. 2017 Mar 24
Osmanbeyoglu HU, Toska E, Chan C, Baselga J, Leslie CS.
Nat Communications. 2017 Jan 31
A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance
Feng Y, Veeken J, Shugay M, Putintseva EV, Osmanbeyoglu HU, Dikiy S, Hoyos BE, Moltedo B, Hemmers S, Treuting P, Leslie CS, Chudakov M, Rudensky AY.
Nature. 2015 Dec 3
Linking signaling pathways to transcriptional programs in breast cancer
Osmanbeyoglu HU, Pelossof R, Bromberg JF, Leslie CS.
Genome Research. 2014 Nov
Estrogen represses gene expression through reconfiguring chromatin structures
Osmanbeyoglu HU, Lu KN, Oesterreich S, Day RS, Benos PV, Coronnello C, Lu X.
Nucleic Acids Research. 2013 Sep
Osmanbeyoglu HU, Hartmaier RJ, Oesterreich S, Lu X.
BMC Genomics. 2012 Jan 17
Evaluating the Barriers to Point-of-Care Documentation for Nursing Staff
Kohle-Ersher A, Chatterjee P, Osmanbeyoglu HU, Hochheiser H, Bartos CE.
Computers, Informatics, Nursing. 2012 Mar
N-gram analysis of 970 microbial organisms reveals presence of biological language models
Osmanbeyoglu HU, Ganapathiraju MK.
BMC Bioinformatics. 2011 Jan 10
Rapid Deployment of Viral-Human Interactome Prediction for New Viruses
Osmanbeyoglu H, Ganapathiraju M.
AMIA Translational Bioinformatics Summit. 2011 March 7
PLoS Computational Biology conference postcards from ISMB
Chalancon G, Kosloff M, Osmanbeyoglu HU, Saraswathi S.
PLoS computational biology 2010 Nov 11
Active machine learning for transmembrane helix prediction
Osmanbeyoglu HU, Wehner JA, Carbonell JG, Ganapathiraju MK.
BMC Bioinformatics. 2010 Jan 18
Thin alumina nanoporous membranes for similar size biomolecule separation
Osmanbeyoglu HU, Hur TB, Kim HK.
Journal of Membrane Science. 2009 Nov 1