Photo of Aedin Culhane,  PhD

Aedin Culhane, PhD

Dana-Farber Cancer Institute

Dana-Farber Cancer Institute
Phone: (617) 632-2468


aedin@jimmy.harvard.edu

Aedin Culhane, PhD

Dana-Farber Cancer Institute

EDUCATIONAL TITLES

  • Senior Research Scientist, Biostatistics and Computational Biology, Dana-Farber Cancer Institute
  • Senior Research Scientist, Biostatistics, Harvard T.H. Chan School Of Public Health

DF/HCC PROGRAM AFFILIATION

Research Abstract

My research in bioinformatics and computational biology is focused on developing methods that leverage the growing public genomics resources from projects such as TCGA, ICGC and other large-scale genomic projects. I develop methods for integration of genomics data including DNA, RNA and proteomics data (Meng et al., 2014, Fagan et al., 2007, Culhane et al., 2003) and have developed a bi-clustering method called iBBiG, to analyze gene set enrichment analyses results across studies (Gusenleitner et al., 2012). I also led the GeneSigDB database, in which we curated over 5,000 gene signatures of cancer and disease from the published literature (Culhane et al., 2010, Culhane et al., 2012) which can be used for pathway based mining of cancer gene networks. I and my team have created several R packages for integrated exploratory data analysis of multiple genomics datasets including made4 [59] and omicade4 [28]. Our most recent R/Bioconductor package MOGSA includes methods for multi-way decomposition of multiple omics data including co-inertia analysis, multiple factor analysis, Generalized canonical correlations analysis and consensus principal component analysis. These transform multiple types of genomics data on the same scale, allowing one to extract correlated patterns between data sets, and integrate data for better performance in downstream pathway and geneset analysis. I am a member of biostatistician/bioinformatics core team for the DF/HCC Renal Cancer SPORE. I also work on women's cancer and am co-PI on a project to study the breast metastatic environment in ER+ breast cancer.

Publications

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  • 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. Molecular Subtypes Improve Prognostic Value of International Metastatic Renal Cell Carcinoma Database Consortium Prognostic Model. Oncologist 2017; 22:286-292. PubMed
  • Meng C, Zeleznik OA, Thallinger GG, Kuster B, Gholami AM, Culhane AC. Dimension reduction techniques for the integrative analysis of multi-omics data. 2016; 17:628-41. PubMed
  • 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. MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy. 2015. PubMed
  • 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. 2015. PubMed
  • Meng C, Kuster B, Culhane AC, Gholami AM. A multivariate approach to the integration of multi-omics datasets. BMC Bioinformatics 2014; 15:162. PubMed
  • 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. Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer. Journal of the National Cancer Institute 2014. PubMed
  • 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. Taxonomy of breast cancer based on normal cell phenotype predicts outcome. J Clin Invest 2014; 124:859-70. PubMed
  • 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. PubMed
  • Schröder MS, Gusenleitner D, Quackenbush J, Culhane AC, Haibe-Kains B. RamiGO: an R/Bioconductor package providing an AmiGO visualize interface. Bioinformatics 2013; 29:666-8. PubMed
  • 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 predicts type II subtype and prognosis. PLoS ONE 2013; 8:e57799. PubMed
  • Beck AH, Knoblauch NW, Hefti MM, Kaplan J, Schnitt SJ, Culhane AC, Schroeder MS, Risch T, Quackenbush J, Haibe-Kains B. Significance analysis of prognostic signatures. PLoS Comput. Biol. 2013; 9:e1002875. PubMed
  • 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, , Matulonis UA. Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome. Clin Cancer Res 2012; 18:5806-15. PubMed
  • Gusenleitner D, Howe EA, Bentink S, Quackenbush J, Culhane AC. iBBiG: iterative binary bi-clustering of gene sets. Bioinformatics 2012; 28:2484-92. PubMed
  • Haibe-Kains B, Desmedt C, Loi S, Culhane AC, Bontempi G, Quackenbush J, Sotiriou C. A three-gene model to robustly identify breast cancer molecular subtypes. Journal of the National Cancer Institute 2012; 104:311-25. PubMed
  • 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. GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Res 2011; 40:D1060-6. PubMed
  • Schröder MS, Culhane AC, Quackenbush J, Haibe-Kains B. survcomp: an R/Bioconductor package for performance assessment and comparison of survival models. Bioinformatics 2011. PubMed
  • Culhane AC, Quackenbush J. Confounding effects in "A six-gene signature predicting breast cancer lung metastasis". Cancer Res 2009; 69:7480-5. PubMed
  • 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. Nat Genet 2009; 41:149-55. PubMed
  • Smith MJ, Culhane AC, Killeen S, Kelly MA, Wang JH, Cotter TG, Redmond HP. Mechanisms driving local breast cancer recurrence in a model of breast-conserving surgery. Ann Surg Oncol 2008; 15:2954-64. PubMed
  • 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. Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome. Cancer Res 2008; 68:1786-96. PubMed
  • Fagan A, Culhane AC, Higgins DG. A multivariate analysis approach to the integration of proteomic and gene expression data. Proteomics 2007; 7:2162-71. PubMed
  • Sobhian B, Shao G, Lilli DR, Culhane AC, Moreau LA, Xia B, Livingston DM, Greenberg RA. RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites. Science 2007; 316:1198-202. PubMed
  • Jeffery IB, Madden SF, McGettigan PA, Perrière G, Culhane AC, Higgins DG. Integrating transcription factor binding site information with gene expression datasets. Bioinformatics 2007; 23:298-305. PubMed
  • Jeffery IB, Higgins DG, Culhane AC. Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics 2006; 7:359. PubMed
  • Culhane AC, Thioulouse J, Perrière G, Higgins DG. MADE4: an R package for multivariate analysis of gene expression data. Bioinformatics 2005; 21:2789-90. PubMed
  • Kapushesky M, Kemmeren P, Culhane AC, Durinck S, Ihmels J, Körner C, Kull M, Torrente A, Sarkans U, Vilo J, Brazma A. Expression Profiler: next generation--an online platform for analysis of microarray data. Nucleic Acids Res 2004; 32:W465-70. PubMed
  • Culhane AC, Perrière G, Higgins DG. Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. BMC Bioinformatics 2004; 4:59. PubMed
  • Culhane AC, Perrière G, Considine EC, Cotter TG, Higgins DG. Between-group analysis of microarray data. Bioinformatics 2002; 18:1600-8. PubMed
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