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Items: 1 to 20 of 49

1.

The Immune Landscape of Cancer.

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CE; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L.

Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5.

2.

Software for the Integration of Multiomics Experiments in Bioconductor.

Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, Chan T, Chapman P, Davis SR, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, Mer AS, Riester M, Morgan M, Carey V, Waldron L.

Cancer Res. 2017 Nov 1;77(21):e39-e42. doi: 10.1158/0008-5472.CAN-17-0344.

PMID:
29092936
3.

In Reply.

de Velasco G, Culhane AC, Heng DYC, Signoretti S, Choueiri TK.

Oncologist. 2017 Dec;22(12):1561. doi: 10.1634/theoncologist.2017-0283. Epub 2017 Sep 11. No abstract available.

4.

Molecular Subtypes Improve Prognostic Value of International Metastatic Renal Cell Carcinoma Database Consortium Prognostic Model.

de Velasco G, Culhane AC, Fay AP, Hakimi AA, Voss MH, Tannir NM, Tamboli P, Appleman LJ, Bellmunt J, Kimryn Rathmell W, Albiges L, Hsieh JJ, Heng DY, Signoretti S, Choueiri TK.

Oncologist. 2017 Mar;22(3):286-292. doi: 10.1634/theoncologist.2016-0078. Epub 2017 Feb 20.

5.

Dimension reduction techniques for the integrative analysis of multi-omics data.

Meng C, Zeleznik OA, Thallinger GG, Kuster B, Gholami AM, Culhane AC.

Brief Bioinform. 2016 Jul;17(4):628-41. doi: 10.1093/bib/bbv108. Epub 2016 Mar 11. Review.

6.

MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy.

Neupane M, Clark AP, Landini S, Birkbak NJ, Eklund AC, Lim E, Culhane AC, Barry WT, Schumacher SE, Beroukhim R, Szallasi Z, Vidal M, Hill DE, Silver DP.

Cancer Discov. 2016 Jan;6(1):45-58. doi: 10.1158/2159-8290.CD-15-0341. Epub 2015 Nov 6.

7.

Public data and open source tools for multi-assay genomic investigation of disease.

Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DM, Davis S, Gomez-Cabrero D, Castelo R, Hansen KD, Carey VJ, Morgan M, Culhane AC, Haibe-Kains B, Waldron L.

Brief Bioinform. 2016 Jul;17(4):603-15. doi: 10.1093/bib/bbv080. Epub 2015 Oct 12. Review.

8.

RelA-Induced Interferon Response Negatively Regulates Proliferation.

Kochupurakkal BS, Wang ZC, Hua T, Culhane AC, Rodig SJ, Rajkovic-Molek K, Lazaro JB, Richardson AL, Biswas DK, Iglehart JD.

PLoS One. 2015 Oct 13;10(10):e0140243. doi: 10.1371/journal.pone.0140243. eCollection 2015.

9.

A multivariate approach to the integration of multi-omics datasets.

Meng C, Kuster B, Culhane AC, Gholami AM.

BMC Bioinformatics. 2014 May 29;15:162. doi: 10.1186/1471-2105-15-162.

10.

Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples.

Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer MJ.

J Natl Cancer Inst. 2014 Apr 3;106(5). pii: dju048. doi: 10.1093/jnci/dju048.

11.

Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer.

Waldron L, Haibe-Kains B, Culhane AC, Riester M, Ding J, Wang XV, Ahmadifar M, Tyekucheva S, Bernau C, Risch T, Ganzfried BF, Huttenhower C, Birrer M, Parmigiani G.

J Natl Cancer Inst. 2014 Apr 3;106(5). pii: dju049. doi: 10.1093/jnci/dju049. Review.

12.

Taxonomy of breast cancer based on normal cell phenotype predicts outcome.

Santagata S, Thakkar A, Ergonul A, Wang B, Woo T, Hu R, Harrell JC, McNamara G, Schwede M, Culhane AC, Kindelberger D, Rodig S, Richardson A, Schnitt SJ, Tamimi RM, Ince TA.

J Clin Invest. 2014 Feb;124(2):859-70. doi: 10.1172/JCI70941. Epub 2014 Jan 27.

13.

Palb2 synergizes with Trp53 to suppress mammary tumor formation in a model of inherited breast cancer.

Bowman-Colin C, Xia B, Bunting S, Klijn C, Drost R, Bouwman P, Fineman L, Chen X, Culhane AC, Cai H, Rodig SJ, Bronson RT, Jonkers J, Nussenzweig A, Kanellopoulou C, Livingston DM.

Proc Natl Acad Sci U S A. 2013 May 21;110(21):8632-7. doi: 10.1073/pnas.1305362110. Epub 2013 May 8.

14.

Stem cell-like gene expression in ovarian cancer predicts type II subtype and prognosis.

Schwede M, Spentzos D, Bentink S, Hofmann O, Haibe-Kains B, Harrington D, Quackenbush J, Culhane AC.

PLoS One. 2013;8(3):e57799. doi: 10.1371/journal.pone.0057799. Epub 2013 Mar 11.

15.

Significance analysis of prognostic signatures.

Beck AH, Knoblauch NW, Hefti MM, Kaplan J, Schnitt SJ, Culhane AC, Schroeder MS, Risch T, Quackenbush J, Haibe-Kains B.

PLoS Comput Biol. 2013;9(1):e1002875. doi: 10.1371/journal.pcbi.1002875. Epub 2013 Jan 24.

16.

RamiGO: an R/Bioconductor package providing an AmiGO visualize interface.

Schröder MS, Gusenleitner D, Quackenbush J, Culhane AC, Haibe-Kains B.

Bioinformatics. 2013 Mar 1;29(5):666-8. doi: 10.1093/bioinformatics/bts708. Epub 2013 Jan 6.

17.

Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome.

Wang ZC, Birkbak NJ, Culhane AC, Drapkin R, Fatima A, Tian R, Schwede M, Alsop K, Daniels KE, Piao H, Liu J, Etemadmoghadam D, Miron A, Salvesen HB, Mitchell G, DeFazio A, Quackenbush J, Berkowitz RS, Iglehart JD, Bowtell DD; Australian Ovarian Cancer Study Group, Matulonis UA.

Clin Cancer Res. 2012 Oct 15;18(20):5806-15. doi: 10.1158/1078-0432.CCR-12-0857. Epub 2012 Aug 21.

18.

iBBiG: iterative binary bi-clustering of gene sets.

Gusenleitner D, Howe EA, Bentink S, Quackenbush J, Culhane AC.

Bioinformatics. 2012 Oct 1;28(19):2484-92. Epub 2012 Jul 12.

19.

A three-gene model to robustly identify breast cancer molecular subtypes.

Haibe-Kains B, Desmedt C, Loi S, Culhane AC, Bontempi G, Quackenbush J, Sotiriou C.

J Natl Cancer Inst. 2012 Feb 22;104(4):311-25. doi: 10.1093/jnci/djr545. Epub 2012 Jan 18.

20.

The cocaine- and amphetamine-regulated transcript mediates ligand-independent activation of ERα, and is an independent prognostic factor in node-negative breast cancer.

Brennan DJ, O'Connor DP, Laursen H, McGee SF, McCarthy S, Zagozdzon R, Rexhepaj E, Culhane AC, Martin FM, Duffy MJ, Landberg G, Ryden L, Hewitt SM, Kuhar MJ, Bernards R, Millikan RC, Crown JP, Jirström K, Gallagher WM.

Oncogene. 2012 Jul 26;31(30):3483-94. doi: 10.1038/onc.2011.519. Epub 2011 Dec 5.

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