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Publications/Preprints

Spatial landscape of malignant pleural and peritoneal mesothelioma tumor immune microenvironment

Ma X, Lembersky D, Kim ES, Bruno TC, Testa JR, Osmanbeyoglu HU

bioRxiv  2023.09.06.556559 2023

Clinical and biomarker results from a phase II trial of combined cabozantinib and durvalumab in patients with chemotherapy-refractory colorectal cancer (CRC): CAMILLA CRC cohort

Saeed A, Park R, Pathak H, Al-Bzour AN, Dai J, Phadnis M, Al-Rajabi R, Kasi A, Baranda J, SUn W, Williamson S, Chiu Y, Osmanbeyoglu HU, Madan R, Abushukair H, Mulvaney K, Godwin AK, Saeed A

Nature Communications 2024

Single-cell analysis reveals the stromal dynamics and tumor-specific characteristics in the microenvironment of ovarian cancer

Zhang L, Cascio S, Mellors JW, Buckanovich RJ, Osmanbeyoglu HU

Communications Biology  2024

Genomic and transcriptomic analysis of cutaneous squamous cell carcinoma arising in immunocompetent and immunosuppressed patients

Bibee KP, Kulkarni A, Lee S, Ho J, Osmanbeyoglu HU, Ferris RL, Zandberg DP
Oral Oncology  2023

Vascular endothelial profilin-1 drives a pro-tumorigenic tumor microenvironment and tumor progression in renal cancer

Gau D, Daoud A, Allen A, Joy M, Sagan A, Lee S, Lucas PC, Duensing S, Boone D, Osmanbeyoglu HU, Roy P

Journal of Biological Chemistry 2023

COVID-19db linkage maps of cell surface proteins and transcription factors in immune cells

Ramjattun K*, Ma X*, Gao SJ, Singh H, Osmanbeyoglu HU

Journal of Medical Virology  2023

Linking Expression of Cell-Surface Receptors with Transcription Factors by Computational Analysis of Paired Single-Cell Proteomes and Transcriptomes

Sagan AMa XRamjattun K, Osmanbeyoglu HU

Springer Protocol 2023

Immune landscape in estrogen receptor-positive breast cancer reveals divergent macrophage-driven microenvironment

Onkar S, Cui J, Zou J, Cardello C, Cillo AR, Uddin MR, Sagan A, Joy M, Osmanbeyoglu HU, Pogue-Geile K, McAuliffe PF, Lucas PC, Tseng GC, Lee AV, Bruno TC, Oesterreich S, Vignali DA

Nature Cancer  2023

Isolated BAP1 loss in malignant pleural mesothelioma predicts immunogenicity with implications for immunotherapeutic response

Osmanbeyoglu HU#, Palmer D, Sagan A, Sementino E,  Becich MJ, Testa JR

Cancers  2022 (#corresponding author)

Interpretable deep learning for chromatin-informed inference of transcriptional programs driven by somatic alterations across cancers

Tao Y*, Ma X*, Palmer D, Schwartz R, Lu X, Osmanbeyoglu HU.

Nucleic Acids Research  2022

Thymidine rescues ATR kinase inhibitor-induced deoxyuridine contamination in genomic DNA, cell death, and interferon-α/β expression

Sugitani N, Vendetti FP, Cipriano AJ, Deppas JJ, Moiseeva TN, Haynes SS, Wang Y, Palmer D, Osmanbeyoglu HU, Bostwick A, Snyder NW, Gong Y, Aird KM, Delgoffe GM, Beumer JH, Bakkenist CJ.

Cell Reports  2022

Chromatin accessibility and active transcription factors in primary human invasive lobular and ductal breast carcinomas

Lee S, Osmanbeyoglu HU

Breast Cancer Research  2022

Cancer-associated MSC drive tumor immune exclusion and resistance to immunotherapy, which can be overcome by Hedgehog inhibition

Cascio S, Chandler C, Zhang L, Sinno S, Gao B, Onkar S, Bruno T, Vignali D, Mahdi H, Osmanbeyoglu HU, Vlad A, Coffman L, Buckanovich RJ

Science Advances 2021

SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators

Ma X, Somasundaram A, Qi Z, Hartman D, Singh H, Osmanbeyoglu HU. 

Nucleic Acids Research  2021

Targeting 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. 

Cancer Cell  2021

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

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 Sci. 2019 

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

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