List of Publications

WEE1 kinase inhibitor AZD1775 induces CDK1 kinase-dependent origin firing in unperturbed G1 and S phase cells. 

Moiseeva TN, Qian C, Chiba N, Osmanbeyoglu HU, Bakkenist CJ. 

Proc Natl Acad Sci2019 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 

An ATR and CHK1 kinase signaling mechanism that limits origin firing during unperturbed DNA replication

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

A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily

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 

PI3K pathway regulates ER-dependent transcription in breast cancer through the epigenetic regulator KMT2D

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

Pancancer modeling predicts the context-specific impact of somatic mutations on transcriptional programs

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

Improving ChIP-seq peak-calling for functional indirect co-regulator binding by integrating multiple sources of biological information

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

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