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Items: 1 to 50 of 53

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, Mokrab Y, Newman AM, 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 CS; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I.

Immunity. 2019 Aug 20;51(2):411-412. doi: 10.1016/j.immuni.2019.08.004. No abstract available.

2.

MOGSA: Integrative Single Sample Gene-set Analysis of Multiple Omics Data.

Meng C, Basunia A, Peters B, Gholami AM, Kuster B, Culhane AC.

Mol Cell Proteomics. 2019 Aug 9;18(8 suppl 1):S153-S168. doi: 10.1074/mcp.TIR118.001251. Epub 2019 Jun 26.

3.

BRCA1-IRIS promotes human tumor progression through PTEN blockade and HIF-1α activation.

Li AG, Murphy EC, Culhane AC, Powell E, Wang H, Bronson RT, Von T, Giobbie-Hurder A, Gelman RS, Briggs KJ, Piwnica-Worms H, Zhao JJ, Kung AL, Kaelin WG Jr, Livingston DM.

Proc Natl Acad Sci U S A. 2018 Oct 9;115(41):E9600-E9609. doi: 10.1073/pnas.1807112115. Epub 2018 Sep 25.

4.

Enter the Matrix: Factorization Uncovers Knowledge from Omics.

Stein-O'Brien GL, Arora R, Culhane AC, Favorov AV, Garmire LX, Greene CS, Goff LA, Li Y, Ngom A, Ochs MF, Xu Y, Fertig EJ.

Trends Genet. 2018 Oct;34(10):790-805. doi: 10.1016/j.tig.2018.07.003. Epub 2018 Aug 22. Review.

5.

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, Mokrab Y, Newman AM, 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 CS; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I.

Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5. Erratum in: Immunity. 2019 Aug 20;51(2):411-412.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons.

Ho Sui SJ, Begley K, Reilly D, Chapman B, McGovern R, Rocca-Sera P, Maguire E, Altschuler GM, Hansen TA, Sompallae R, Krivtsov A, Shivdasani RA, Armstrong SA, Culhane AC, Correll M, Sansone SA, Hofmann O, Hide W.

Nucleic Acids Res. 2012 Jan;40(Database issue):D984-91. doi: 10.1093/nar/gkr1051. Epub 2011 Nov 24.

26.

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures.

Culhane AC, Schröder MS, Sultana R, Picard SC, Martinelli EN, Kelly C, Haibe-Kains B, Kapushesky M, St Pierre AA, Flahive W, Picard KC, Gusenleitner D, Papenhausen G, O'Connor N, Correll M, Quackenbush J.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1060-6. doi: 10.1093/nar/gkr901. Epub 2011 Nov 21.

27.

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models.

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

Bioinformatics. 2011 Nov 15;27(22):3206-8. doi: 10.1093/bioinformatics/btr511. Epub 2011 Sep 7.

28.

GeneSigDB--a curated database of gene expression signatures.

Culhane AC, Schwarzl T, Sultana R, Picard KC, Picard SC, Lu TH, Franklin KR, French SJ, Papenhausen G, Correll M, Quackenbush J.

Nucleic Acids Res. 2010 Jan;38(Database issue):D716-25. doi: 10.1093/nar/gkp1015. Epub 2009 Nov 24.

29.

Confounding effects in "A six-gene signature predicting breast cancer lung metastasis".

Culhane AC, Quackenbush J.

Cancer Res. 2009 Sep 15;69(18):7480-5. doi: 10.1158/0008-5472.CAN-08-3350. Epub 2009 Sep 1.

30.

Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification.

Smith MJ, Culhane AC, Donovan M, Coffey JC, Barry BD, Kelly MA, Higgins DG, Wang JH, Kirwan WO, Cotter TG, Redmond HP.

Br J Cancer. 2009 May 5;100(9):1452-64. doi: 10.1038/sj.bjc.6604931.

31.

Repeatability of published microarray gene expression analyses.

Ioannidis JP, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, Falchi M, Furlanello C, Game L, Jurman G, Mangion J, Mehta T, Nitzberg M, Page GP, Petretto E, van Noort V.

Nat Genet. 2009 Feb;41(2):149-55. doi: 10.1038/ng.295. Epub 2008 Jan 28.

PMID:
19174838
32.

Mechanisms driving local breast cancer recurrence in a model of breast-conserving surgery.

Smith MJ, Culhane AC, Killeen S, Kelly MA, Wang JH, Cotter TG, Redmond HP.

Ann Surg Oncol. 2008 Oct;15(10):2954-64. doi: 10.1245/s10434-008-0037-5. Epub 2008 Jul 12.

PMID:
18622646
33.

Altered cytoplasmic-to-nuclear ratio of survivin is a prognostic indicator in breast cancer.

Brennan DJ, Rexhepaj E, O'Brien SL, McSherry E, O'Connor DP, Fagan A, Culhane AC, Higgins DG, Jirstrom K, Millikan RC, Landberg G, Duffy MJ, Hewitt SM, Gallagher WM.

Clin Cancer Res. 2008 May 1;14(9):2681-9. doi: 10.1158/1078-0432.CCR-07-1760.

34.

Functional classification analysis of somatically mutated genes in human breast and colorectal cancers.

Chittenden TW, Howe EA, Culhane AC, Sultana R, Taylor JM, Holmes C, Quackenbush J.

Genomics. 2008 Jun;91(6):508-11. doi: 10.1016/j.ygeno.2008.03.002. Epub 2008 Apr 22.

35.

Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome.

Cheng AS, Culhane AC, Chan MW, Venkataramu CR, Ehrich M, Nasir A, Rodriguez BA, Liu J, Yan PS, Quackenbush J, Nephew KP, Yeatman TJ, Huang TH.

Cancer Res. 2008 Mar 15;68(6):1786-96. doi: 10.1158/0008-5472.CAN-07-5547.

36.

Molecular profiling of breast cancer: transcriptomic studies and beyond.

Culhane AC, Howlin J.

Cell Mol Life Sci. 2007 Dec;64(24):3185-200. Review.

PMID:
17957338
37.

A multivariate analysis approach to the integration of proteomic and gene expression data.

Fagan A, Culhane AC, Higgins DG.

Proteomics. 2007 Jun;7(13):2162-71.

PMID:
17549791
38.

RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites.

Sobhian B, Shao G, Lilli DR, Culhane AC, Moreau LA, Xia B, Livingston DM, Greenberg RA.

Science. 2007 May 25;316(5828):1198-202.

39.

CENP-F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer.

O'Brien SL, Fagan A, Fox EJ, Millikan RC, Culhane AC, Brennan DJ, McCann AH, Hegarty S, Moyna S, Duffy MJ, Higgins DG, Jirström K, Landberg G, Gallagher WM.

Int J Cancer. 2007 Apr 1;120(7):1434-43.

40.

Integrating transcription factor binding site information with gene expression datasets.

Jeffery IB, Madden SF, McGettigan PA, Perrière G, Culhane AC, Higgins DG.

Bioinformatics. 2007 Feb 1;23(3):298-305. Epub 2006 Nov 24.

PMID:
17127681
41.
42.

Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data.

Baty F, Bihl MP, Perrière G, Culhane AC, Brutsche MH.

BMC Bioinformatics. 2005 Sep 28;6:239.

43.

Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response.

Brennan DJ, O'Brien SL, Fagan A, Culhane AC, Higgins DG, Duffy MJ, Gallagher WM.

Expert Opin Biol Ther. 2005 Aug;5(8):1069-83. Review.

PMID:
16050784
44.

Multiple markers for melanoma progression regulated by DNA methylation: insights from transcriptomic studies.

Gallagher WM, Bergin OE, Rafferty M, Kelly ZD, Nolan IM, Fox EJ, Culhane AC, McArdle L, Fraga MF, Hughes L, Currid CA, O'Mahony F, Byrne A, Murphy AA, Moss C, McDonnell S, Stallings RL, Plumb JA, Esteller M, Brown R, Dervan PA, Easty DJ.

Carcinogenesis. 2005 Nov;26(11):1856-67. Epub 2005 Jun 15.

PMID:
15958521
45.

MADE4: an R package for multivariate analysis of gene expression data.

Culhane AC, Thioulouse J, Perrière G, Higgins DG.

Bioinformatics. 2005 Jun 1;21(11):2789-90. Epub 2005 Mar 29.

PMID:
15797915
46.

Expression Profiler: next generation--an online platform for analysis of microarray data.

Kapushesky M, Kemmeren P, Culhane AC, Durinck S, Ihmels J, Körner C, Kull M, Torrente A, Sarkans U, Vilo J, Brazma A.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W465-70.

47.

Oligonucleotide microarray analysis of gene expression in neuroblastoma displaying loss of chromosome 11q.

McArdle L, McDermott M, Purcell R, Grehan D, O'Meara A, Breatnach F, Catchpoole D, Culhane AC, Jeffery I, Gallagher WM, Stallings RL.

Carcinogenesis. 2004 Sep;25(9):1599-609. Epub 2004 Apr 16. Review.

PMID:
15090470
48.

Cross-platform comparison and visualisation of gene expression data using co-inertia analysis.

Culhane AC, Perrière G, Higgins DG.

BMC Bioinformatics. 2003 Nov 21;4:59.

49.

Between-group analysis of microarray data.

Culhane AC, Perrière G, Considine EC, Cotter TG, Higgins DG.

Bioinformatics. 2002 Dec;18(12):1600-8.

PMID:
12490444
50.

Detection of the interleukin 18 family in rat brain by RT-PCR.

Wheeler RD, Culhane AC, Hall MD, Pickering-Brown S, Rothwell NJ, Luheshi GN.

Brain Res Mol Brain Res. 2000 May 5;77(2):290-3.

PMID:
10837926

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