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Aedín Culhane

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Maria Prencipe; Aedín C Culhane; William M Gallagher; Elaine W Kay; Helmut Klocker; Stephen F Madden; Darran O'Connor; Gillian O'Hurley; Amanda O'Neill; William R Watson
Identification of transcription factors associated with castration-resistance: is the serum responsive factor a potential therapeutic target?
Markus S Schröder; John Quackenbush; Aedín C Culhane; Daniel Gusenleitner; Benjamin Haibe-Kains
RamiGO: an R/Bioconductor package providing an AmiGO visualize interface.
Matthew Schwede; Dimitrios Spentzos; Stefan Bentink; Benjamin Haibe-Kains; David Harrington; Oliver Hofmann; John Quackenbush; Aedín C Culhane
Stem cell-like gene expression in ovarian cancer predicts type II subtype and prognosis.

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All Publications

2013: Maria Prencipe; Aedín C Culhane; William M Gallagher; Elaine W Kay; Helmut Klocker; Stephen F Madden; Darran O'Connor; Gillian O'Hurley; Amanda O'Neill; William R Watson
Identification of transcription factors associated with castration-resistance: is the serum responsive factor a potential therapeutic target?
The Prostate 2013;73(7):743-53.
2013: Markus S Schröder; John Quackenbush; Aedín C Culhane; Daniel Gusenleitner; Benjamin Haibe-Kains
RamiGO: an R/Bioconductor package providing an AmiGO visualize interface.
Bioinformatics (Oxford, England) 2013;29(5):666-8.
2013: Matthew Schwede; Dimitrios Spentzos; Stefan Bentink; Benjamin Haibe-Kains; David Harrington; Oliver Hofmann; John Quackenbush; Aedín C Culhane
Stem cell-like gene expression in ovarian cancer predicts type II subtype and prognosis.
PloS one 2013;8(3):e57799.
2012: Zhigang C Wang; alexander miron; Gillian Mitchell; Huiying Piao; John Quackenbush; Helga B Salvesen; Matthew Schwede; Ruiyang Tian; Kathryn Alsop; Ross S Berkowitz; Nicolai Juul Birkbak; David D L Bowtell; Aedín C Culhane; Kathryn E Daniels; Anna deFazio; Ronny Drapkin; Dariush Etemadmoghadam; Aquila Fatima; J Dirk Iglehart; Joyce Liu; Ursula Matulonis
Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome.
Clinical cancer research : an official journal of the American Association for Cancer Research 2012;18(20):5806-15.
2012: Daniel Gusenleitner; Eleanor A Howe; John Quackenbush; Stefan Bentink; Aedín C Culhane
iBBiG: iterative binary bi-clustering of gene sets.
Bioinformatics (Oxford, England) 2012;28(19):2484-92.
2012: Donal J Brennan; J P Crown; Aedín C Culhane; M J Duffy; R Bernards; S M Hewitt; Karin Jirström; M J Kuhar; Göran Landberg; H Laursen; F M Martin; S McCarthy; S F McGee; Robert C Millikan; Darran P O'Connor; E Rexhepaj; L Ryden; Radoslaw Zagozdzon; William M Gallagher
The cocaine- and amphetamine-regulated transcript mediates ligand-independent activation of ERα, and is an independent prognostic factor in node-negative breast cancer.
Oncogene 2012;31(30):3483-94.
2012: Benjamin Haibe-Kains; Sherene Loi; John Quackenbush; Gianluca Bontempi; Aedín C Culhane; Christine Desmedt; C Sotiriou
A three-gene model to robustly identify breast cancer molecular subtypes.
Journal of the National Cancer Institute 2012;104(4):311-25.
2012: Stefan Bentink; Jing Chen; Aedín C Culhane; Ronny Drapkin; Jian-Bing Fan; Benjamin Haibe-Kains; Michelle S Hirsch; Kristina Holton; Joyce Liu; John Quackenbush; Thomas Risch; Renee Rubio; Eliza Wickham-Garcia; Craig April; Ursula Matulonis
Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer.
PloS one 2012;7(2):e30269.
2012: Shannan J Ho Sui; Oliver Hofmann; Andrei V Krivtsov; Eamonn Maguire; Ray McGovern; Dorothy Reilly; Philippe Rocca-Sera; Susanna-Assunta Sansone; Ramesh A Shivdasani; Ramakrishna Sompallae; Gabriel M Altschuler; Scott A Armstrong; Kimberly Begley; Brad Chapman; Mick Correll; Aedín C Culhane; Terah A A Hansen; Winston Hide
The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons.
Nucleic acids research 2012;40(Database issue):D984-91.
2011: Markus Schröder; John Quackenbush; Aedín C Culhane; Benjamin Haibe-Kains
survcomp: an R/Bioconductor package for performance assessment and comparison of survival models.
Bioinformatics (Oxford, England) 2011;27(22):3206-8.
2010: Aedín C Culhane; Thomas Schwarzl; Razvan Sultana; Kermshlise C Picard; Shaita C Picard; Tim H Lu; Katherine R Franklin; Simon J French; Gerald Papenhausen; Mick Correll; John Quackenbush
GeneSigDB--a curated database of gene expression signatures.
Nucleic acids research 2010;38(Database issue):D716-25.
2009: Aedín C Culhane; John Quackenbush
Confounding effects in "A six-gene signature predicting breast cancer lung metastasis".
Cancer research 2009;69(18):7480-5.
2009: myles smith; Aedín C Culhane; M Donovan; J C Coffey; BD Barry; M A Kelly; Desmond G Higgins; Jiang Huai Wang; William O Kirwan; Thomas G Cotter; H Paul Redmond
Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification.
British journal of cancer 2009;100(9):1452-64.
2009: John Ioannidis; David Allison; Catherine A Ball; Issa Coulibaly; Xiangqin Cui; Aedín C Culhane; Mario Falchi; Cesare Furlanello; Laurence Game; Giuseppe Jurman; Jon Mangion; Tapan Mehta; Michael Nitzberg; Grier P Page; Enrico Petretto; Vera van Noort
Repeatability of published microarray gene expression analyses.
Nature genetics 2009;41(2):149-55.
2008: myles smith; Aedín C Culhane; Shane Killeen; Maura A Kelly; Jiang H Wang; Thomas G Cotter; Henry P Redmond
Mechanisms driving local breast cancer recurrence in a model of breast-conserving surgery.
Annals of surgical oncology 2008;15(10):2954-64.
2008: Donal J Brennan; Elton Rexhepaj; Sallyann L O'Brien; Elaine McSherry; Darran P O'Connor; Ailís Fagan; Aedín C Culhane; Desmond G Higgins; Karin Jirstrom; Robert C Millikan; Göran Landberg; Michael J Duffy; Stephen M Hewitt; William M Gallagher
Altered cytoplasmic-to-nuclear ratio of survivin is a prognostic indicator in breast cancer.
Clinical cancer research : an official journal of the American Association for Cancer Research 2008;14(9):2681-9.
2008: Alfred S L Cheng; Aedín C Culhane; Michael W Y Chan; Chinnambally R Venkataramu; Mathias Ehrich; Aejaz Nasir; Benjamin A T Rodriguez; Joseph Liu; Pearlly S Yan; John Quackenbush; Kenneth P Nephew; Timothy J Yeatman; Hui-Ming (Tim) Huang
Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome.
Cancer research 2008;68(6):1786-96.
2007: Ailís Fagan; Aedín C Culhane; Desmond G Higgins
A multivariate analysis approach to the integration of proteomic and gene expression data.
Proteomics 2007;7(13):2162-71.
2007: Bijan Sobhian; Genze Shao; Dana R Lilli; Aedín C Culhane; Lisa A Moreau; Bing Xia; David M Livingston; Roger A. Greenberg
RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites.
Science (New York, N.Y.) 2007;316(5828):1198-202.
2007: Sallyann L O'Brien; Ailís Fagan; Edward J P Fox; Robert C Millikan; Aedín C Culhane; Donal J Brennan; Amanda McCann; Shauna Hegarty; Siobhan Moyna; Michael J Duffy; Desmond G Higgins; Karin Jirström; Göran Landberg; William M Gallagher
CENP-F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer.
International journal of cancer. Journal international du cancer 2007;120(7):1434-43.
2007: Ian B Jeffery; Stephen F Madden; Paul A McGettigan; Guy Perrière; Aedín C Culhane; Desmond G Higgins
Integrating transcription factor binding site information with gene expression datasets.
Bioinformatics (Oxford, England) 2007;23(3):298-305.
2006: Ian B Jeffery; Desmond G Higgins; Aedín C Culhane
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data.
BMC bioinformatics 2006;7():359.
2005: William M Gallagher; Orla E Bergin; Mairin Rafferty; Zoë D Kelly; Ilse-Maria Nolan; Edward J P Fox; Aedín C Culhane; Linda McArdle; Mario F Fraga; Linda Hughes; Caroline A Currid; Fiona O'Mahony; Aileen Byrne; Alison A Murphy; Catherine Moss; Susan McDonnell; Raymond L Stallings; Jane A Plumb; Manel Esteller; Robert Brown; Peter A Dervan; David J Easty
Multiple markers for melanoma progression regulated by DNA methylation: insights from transcriptomic studies.
Carcinogenesis 2005;26(11):1856-67.
2005: Donal J Brennan; Sallyann L O'Brien; Ailís Fagan; Aedín C Culhane; Desmond G Higgins; Michael J Duffy; William M Gallagher
Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response.
Expert opinion on biological therapy 2005;5(8):1069-83.
2005: Aedín C Culhane; Jean Thioulouse; Guy Perrière; Desmond G Higgins
MADE4: an R package for multivariate analysis of gene expression data.
Bioinformatics (Oxford, England) 2005;21(11):2789-90.
2005: Florent Baty; Michel P Bihl; Guy Perrière; Aedín C Culhane; Martin H Brutsche
Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data.
BMC bioinformatics 2005;6():239.
2004: Linda McArdle; M McDermott; Robert Purcell; D Grehan; Anne O'Meara; Finn Breatnach; Daniel Catchpoole; Aedín C Culhane; Ian B Jeffery; William M Gallagher; Raymond L Stallings
Oligonucleotide microarray analysis of gene expression in neuroblastoma displaying loss of chromosome 11q.
Carcinogenesis 2004;25(9):1599-609.
2004: Misha Kapushesky; Patrick Kemmeren; Aedín C Culhane; Steffen Durinck; Jan Ihmels; Christine Körner; Meelis Kull; Aurora Torrente; Ugis Sarkans; Jaak Vilo; Alvis Brazma
Expression Profiler: next generation--an online platform for analysis of microarray data.
Nucleic acids research 2004;32(Web Server issue):W465-70.
2003: Aedín C Culhane; Guy Perrière; Desmond G Higgins
Cross-platform comparison and visualisation of gene expression data using co-inertia analysis.
BMC bioinformatics 2003;4():59.
2002: Aedín C Culhane; Guy Perrière; Elizabeth C Considine; Thomas G Cotter; Desmond G Higgins
Between-group analysis of microarray data.
Bioinformatics (Oxford, England) 2002;18(12):1600-8.