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

Journal Publications

Aurora B Kinase Prevents and Overcomes Resistance to EGFR Inhibitors in Lung Cancer by Enhancing BIM- and PUMA-mediated Apoptosis 

Tanaka K, Han S, Yang S, Kim K, Selcuklu SD, Ganesan YT, Moyer A, Sinha S,

Ramani S, Xie Y, Ishizawa K, Osmanbeyoglu HU, Yu HA, Kris MG, Hsieh JJ, Cheng EH. Targeting

Cancer Cell  2021, in press

Recurrent human papillomavirus-related head and neck cancer undergoes metabolic re-programming and is driven by oxidative phosphorylation

Vyas A, Harbison RA, Faden D, Kubik M, Palmer D, Zhang Q, Osmanbeyoglu HU, Méndez E, Duvvuri U.

Clinical Cancer Research  2021, in press

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  

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

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 

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 

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 

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 

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 

Computational methods to dissect gene regulatory networks in cancer

Iyer A, Osmanbeyoglu HU, Leslie CS.

Current Opinion in Systems Biology 2017

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 

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 Endocrinology 2017

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

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

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

Linking signaling pathways to transcriptional programs in breast cancer

Osmanbeyoglu HU, Pelossof R, Bromberg JF, Leslie CS. 

Genome Research 2014

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

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 

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

N-gram analysis of 970 microbial organisms reveals presence of biological language models

Osmanbeyoglu HU, Ganapathiraju MK. 

BMC Bioinformatics  2011 

Rapid Deployment of Viral-Human Interactome Prediction for New Viruses

Osmanbeyoglu H, Ganapathiraju M.

AMIA Translational Bioinformatics Summit 2011 

PLoS Computational Biology conference postcards from ISMB

Chalancon G, Kosloff M, Osmanbeyoglu HU, Saraswathi S.

PLoS Computational Biology 2010 

Active machine learning for transmembrane helix prediction

Osmanbeyoglu HU, Wehner JA, Carbonell JG, Ganapathiraju MK.

BMC Bioinformatics 2010 

Thin alumina nanoporous membranes for similar size biomolecule separation

Osmanbeyoglu HU, Hur TB, Kim HK. 

Journal of Membrane Science 2009