Dr. Aedin Culhane

Harvard University, USA

Professional Preparation

Research Scientist Biostatistics & Computational Biology, Dana-Farber Cancer Institute, MA Biostatistics, Harvard School of Public Health, MA, 2011-present

Instructor, Adjunct Rabb School of Continuing Studies, Brandeis University, MA. 2008-2010

Research Associate Biostatistics & Computational Biology, Dana-Farber Cancer Institute, MABiostatistics, Harvard School of Public Health, MA. 2005-2011

Postdoctoral Fellow. Conway Institute, University College Dublin, Ireland. 2003-2005

Postdoctoral Researcher. Dept of Biochemistry, University College Cork, Ireland. 2001-2003

Ph.D.in Neuro-Immunology. University of Manchester, UK. 2000

B.Sc in Industrial Biochemistry (highest honors), University of Limerick, Ireland. 1994

Selected Publications

Meng C, Kuster B , Peters B, Culhane AC, Gholami AM. moGSA: a multivariate approach for integrative gene-set analysis of multiple omics data. http://biorxiv.org/content/early/2016/04/03/046904

eleznik OA,, Thallinger GG, Platig J, Culhane AC. Topological pathway enrichment analysis of gene expression in high grade serous ovarian cancer reveals tumor-stoma cross-talk. Birkhäuser's series Trends in Mathematics Research Perspectives CRM Barcelona Guillamon T, Ventura E (Eds)

Kochupurakkal BS, Wang ZC, Hua T, Culhane AC, Rodig SJ, Rajkovic-Molek K, Lazaro JB, Richardson AL, Biswas DK, Iglehart JD. RelA-Induced Interferon Response Negatively Regulates Proliferation. PLoSOne. 2015 Oct 13;10(10):e0140243. doi: 10.1371/journal.pone.0140243

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. Public data and open source tools for multi-assay genomic investigation of disease. Brief Bioinform. 2015 Oct 12. pii: bbv080

Meng C, Kuster B, Culhane AC, Gholami AM, A multivariate approach to the integration of multi-omics datasets. BMC Bioinformatics, 2014 15:162.

Waldron L, Haibe-Kains B, Culhane AC, Riester M, Ding J, Wang V, Tyekucheva S, Bernau C, Risch T, Ganzfried B, Huttenhower C, Birrer M, Parmigiani G. Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer. J Natl Cancer Inst. 2014. 106(5).

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. Palb2 synergizes with Trp53 to suppress mammary tumor formation in a model of inherited breast cancer. Proc Natl Acad Sci U S A. 2013. 110(21):8632-7.

Schröder M, Gusenleitner D, Quackenbush J, Culhane AC, Haibe-Kains B. RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface. Bioinformatics 2013 29(5):666-8

Schwede M, Spentzos D, Bentink S, Hofmann O, Haibe-Kains B, Harrington D, Quackenbush J, Culhane AC. Stem cell-like gene expression in ovarian cancer is prognostic and associated with Type II tumor characteristics. PLoS One. 2013 8(3):e57799

Beck AH, Knoblauch NM, Hefti MH, Kaplan J, Schnitt SJ, Culhane AC, Schroeder M, Risch T, Quackenbush J, Haibe-Kains B. Significance Analysis of Prognostic Signatures. PLoS Computational Biology. 2013. 9 (1): e1002875

Kelly AD, Haibe-Kains B, Janeway KA, Howe EA, Goldsmith J, Kurek K, Perez-Atayde AR, Francoeur N, Fan JB, Craig A, Schneider H, Gebhardt MC, Culhane AC, Quackenbush J, Spentzos D. MicroRNA and mRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32 Genome Medicine. 2013.

Gusenleitner D, Howe EA, Bentink S, Quackenbush J, Culhane AC. iBBiG: Iterative Binary Bi-clustering of Gene Sets. Bioinformatics. 2012. 28(19):2484-92.

Schröder MS, Culhane AC, Quackenbush J, Haibe-Kains B. survcomp: an R/Bioconductor package for performance assessment and comparison of survival models. Bioinformatics. 2011;27(22):3206-8.

Culhane AC, Schwarzl T, Sultana R, Picard KC, Picard SC, Lu TH, Franklin K, French SJ, Papenhausen J,Correll M, Quackenbush J. GeneSigDB - a curated database of gene expression signatures. Nucleic Acids Research; 2010. D716-25.

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. Repeatability of published microarray gene expression analyses. Nature Genetics. 2009; 41(2):149-155.

Fagan A, Culhane AC, Higgins DG. A multivariate analysis approach to the integration of proteomic and gene expression data. Proteomics. 2007; 7(13):2162-71.

Culhane AC, Thioulouse J A multivariate approach to integrating datasets using made4 and ade4. R News. Special Issue on Bioconductor 2006; 6(5) 54:58.

Culhane AC, Thioulouse J, Perriére G, Higgins DG. MADE4: An R package for multivariate analysis of gene expression data. Bioinformatics.2005; 21(11):2789-90

Culhane AC, Perriére G, Higgins DG. Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. BMC Bioinformatics 2003; 4(1):59

Culhane AC, Perriére G, Considine EC, Cotter TG, Higgins DG. Between-group analysis of microarray data. Bioinformatics.2002; 18: 1600-1608 (Recommended by Faculty of 1000.

Book Chapters

Meng C, Gholami AM, Culhane AC (2014) Integrative exploratory analysis of two or more genomic data. in Statistical Genomics: Methods and Protocols. Davis S (Editor). Methods Mol Biol. 2016;1418:19-38.

De Troyer E, Sengupta E, Otava M, Zhang JD, Kaiser S, Culhane AC, Gusenleitner D, Gestraud P, Csardi G, Hochreiter S, Klambauer G, Clevert DA, Perualila NJ, Kasim A, Verbeke T and Shkedy Z. (2016) The biclustGUI Shiny App. Biclustering. In Applied Biclustering Methods for Big and High-Dimensional Data Using R Kasim A, Shkedy Z, Kaiser S, Hochreiter S, Talloen W (Editors) Chapman & Hall/CRC Press.

De Troyer E, Otava M, Zhang JD, Pramana S, Khamiakova T, Kaiser S, Culhane AC, Gusenleitner D, Gestraud P, Csardi G, Aregay M, Hochreiter S, Klambauer G, Clevert DA, Perualila NJ, Kasim A, Verbeke T and Shkedy Z. The BiclustGUI Package. In Applied Biclustering Methods for Big and High-Dimensional Data Using R Kasim A, Shkedy Z, Kaiser S, Hochreiter S, Talloen W (Editors) Chapman & Hall/CRC Press.

Djebbari A, Culhane AC, Armstrong AJ, Quackenbush J. (2008) Artificial intelligence methods for analyzing microarray data. In Encyclopedia of Artificial Intelligence. Rabuñal, JR, Dorado J & Pazos A (Editors)

Culhane AC and Brazma A. Mining of gene expression data. In In Silico technology in drug target identification and validation. León D, Markel S., editors. Marcel Dekker, Inc. New York. CRC Press, Drug Discovery Series. 2006 p123-13

Brazma A., and Culhane AC. Algorithms for gene expression analysis. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Jorde LB., Little PFR, Dunn MJ., Subramaniam S, editors. John Wiley & Sons. London. 2005, p 3148 -3159. John Quackenbush, editor. Computational Methods for Highthroughput Genetic Analysis: Expression Profiling; vol. 7(5)