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Items: 18

1.

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

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

Proc Natl Acad Sci U S A. 2019 Nov 26;116(48):23891-23893. doi: 10.1073/pnas.1915108116. Epub 2019 Nov 11.

2.

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, Razavi P, Lowe SW, Mok SC, Chiosis G, Levine DA, Leslie CS.

Nat Commun. 2019 Sep 25;10(1):4369. doi: 10.1038/s41467-019-12291-6.

3.

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

Moiseeva TN, Yin Y, Calderon MJ, Qian C, Schamus-Haynes S, Sugitani N, Osmanbeyoglu HU, Rothenberg E, Watkins SC, Bakkenist CJ.

Proc Natl Acad Sci U S A. 2019 Jul 2;116(27):13374-13383. doi: 10.1073/pnas.1903418116. Epub 2019 Jun 17.

4.

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 Discov. 2018 Dec;8(12):1548-1565. doi: 10.1158/2159-8290.CD-18-0804. Epub 2018 Oct 15.

5.

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 Syst. 2018 Oct 24;7(4):422-437.e7. doi: 10.1016/j.cels.2018.08.010. Epub 2018 Sep 26.

6.

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.

Nat Commun. 2017 Oct 20;8(1):1062. doi: 10.1038/s41467-017-01020-6.

7.

SWI/SNF tumor suppressor gene PBRM1/BAF180 in human clear cell kidney cancer.

Nargund AM, Osmanbeyoglu HU, Cheng EH, Hsieh JJ.

Mol Cell Oncol. 2017 Jun 19;4(4):e1342747. doi: 10.1080/23723556.2017.1342747. eCollection 2017.

8.

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;355(6331):1324-1330. doi: 10.1126/science.aah6893. Erratum in: Science. 2019 Jan 25;363(6425):.

9.

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. 2017 Jun 15;448:21-27. doi: 10.1016/j.mce.2017.03.005. Epub 2017 Mar 7.

PMID:
28286232
10.

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

Osmanbeyoglu HU, Toska E, Chan C, Baselga J, Leslie CS.

Nat Commun. 2017 Jan 31;8:14249. doi: 10.1038/ncomms14249.

11.

A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance.

Feng Y, van der Veeken J, Shugay M, Putintseva EV, Osmanbeyoglu HU, Dikiy S, Hoyos BE, Moltedo B, Hemmers S, Treuting P, Leslie CS, Chudakov DM, Rudensky AY.

Nature. 2015 Dec 3;528(7580):132-136. doi: 10.1038/nature16141. Epub 2015 Nov 25.

12.

Linking signaling pathways to transcriptional programs in breast cancer.

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

Genome Res. 2014 Nov;24(11):1869-80. doi: 10.1101/gr.173039.114. Epub 2014 Sep 2.

13.

Estrogen represses gene expression through reconfiguring chromatin structures.

Osmanbeyoglu HU, Lu KN, Oesterreich S, Day RS, Benos PV, Coronnello C, Lu X.

Nucleic Acids Res. 2013 Sep;41(17):8061-71. doi: 10.1093/nar/gkt586. Epub 2013 Jul 1.

14.

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

Osmanbeyoglu HU, Hartmaier RJ, Oesterreich S, Lu X.

BMC Genomics. 2012;13 Suppl 1:S1. doi: 10.1186/1471-2164-13-S1-S1. Epub 2012 Jan 17.

15.

Evaluating the barriers to point-of-care documentation for nursing staff.

Kohle-Ersher A, Chatterjee P, Osmanbeyoglu HU, Hochheiser H, Bartos C.

Comput Inform Nurs. 2012 Mar;30(3):126-33. doi: 10.1097/NCN.0b013e3182343f14.

PMID:
22024972
16.

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

Osmanbeyoglu HU, Ganapathiraju MK.

BMC Bioinformatics. 2011 Jan 10;12:12. doi: 10.1186/1471-2105-12-12.

17.

PLoS Computational Biology conference postcards from ISMB 2010.

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

PLoS Comput Biol. 2010 Nov 11;6(11):e1002000. doi: 10.1371/journal.pcbi.1002000. No abstract available.

18.

Active machine learning for transmembrane helix prediction.

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

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S58. doi: 10.1186/1471-2105-11-S1-S58.

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