Publications

Publications

(my publication with citations on Google Scholar)

    1. deVelasco G, Culhane AC, Fay AP, Hakimi AA, Voss MH, Tannir NM, Tamboli P, Appleman LJ, Bellmunt J, Rathmell WK, Albiges L, Hsieh JJ, Heng DYC, Signoretti S, Choueiri Prognostic value of genomic signatures in metastatic Clear Cell Renal Cell Carcinoma (mRCC) using The Cancer Genome Atlas (TCGA) data. The Oncologist, 2017. 22(3):286-292
      • de Velasco G, Culhane AC, Heng DYC, Signoretti S, Choueiri TK. In Reply.Oncologist. 2017 Sep 11.doi: 10.1634/theoncologist.2017-0283.

    2. Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez Cabrera C, Chan T, Chapman P, Davis S, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, Mer AS, Riester M, Morgan M, Carey V, Waldron L. Software for the integration of multi-omics experiments in Bioconductor. Cancer Research. In Press  biorxiv
    3. Meng C, Kuster B , Peters B, Culhane AC, Gholami AM. moGSA: a multivariate approach for integrative gene-set analysis of multiple omics data. 
    4. 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. Cancer Discov. 2016 Jan;6(1):45-58.
    5. Zeleznik 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)
    6. 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. PLoS One. 2015 Oct 13;10(10):e0140243. doi: 10.1371/journal.pone.0140243
    7. 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
    8. Meng C, Kuster B, Culhane AC, Gholami AM, A multivariate approach to the integration of multi-omics datasets. BMC Bioinformatics, 2014 15:162.(BMC highly accessed manuscript)
    9. 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).
    10. Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer MJ. Risk Prediction for Late-Stage Ovarian Cancer by Meta-analysis of 1525 Patient Samples. J Natl Cancer Inst. 2014. 106(5)
    11. 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 R, Ince TA. Taxonomy of Breast Cancers Based on Normal Cell Phenotype and Ontology. J Clin Invest. 2014 124(2):859-70.
    12. 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. 110(21):8632-7
    13. 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
    14. Schröder M, Gusenleitner D, Quackenbush J, Culhane AC, Haibe-Kains B (2013) RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface. Bioinformatics 29(5):666-8. Supplement, Supplement R Code (Joint Last Author)
    15. Beck AH, Knoblauch NM, Hefti MH, Kaplan J, Schnitt SJ, Culhane AC, Schroeder M, Risch T, Quackenbush J, Haibe-Kains B. (2013) Significance Analysis of Prognostic Signatures PLoS Computational Biology. 9(1):e1002875
    16. Kelly AD, Haibe-Kains B, Janeway KA, Hill KE, Howe E, Goldsmith J, Kurek K,
      Perez-Atayde AR, Francoeur N, Fan JB, April C, Schneider H, Gebhardt MC, Culhane
      A
      , Quackenbush J, Spentzos D. (2013) MicroRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32. Genome Med. 2013
      5(1):2.
    17. Prencipe M, Madden SF. O’Neill A, O’Hurely G, Culhane AC, O’Connor D, Klocker H, Gallagher W, Watson W. (2013) Identification of transcription factors associated with castration-resistance: is the Serum Responsive Factor a potential therapeutic target? Clinical Cancer Research. In Press
    18. Gusenleitner D, Howe EA, Bentink S, Quackenbush J,  Culhane AC (2012) Iterative Binary Bi-clustering of Gene Sets. Bioinformatics. 28(19):2484-92 Supplement  Bioconductor Package
    19. Wang ZC , Birkbak NJ, Culhane AC, Drapkin RI, 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, Bowtell DD, Matulonis UA. (2012) Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome. Clinical Cancer Research. 18(20):5806-15
    20. Haibe-Kains B, Desmedt C, Loi S, Culhane A, Bontempi G, Quackenbush J, Sotiriou C (2012) A Three-Gene Model to Robustly Identify Breast Cancer Molecular Subtypes (2012) JNCI. 104(4):311-25
    21. 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. (2012) GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Res. 40(Database issue):D1060-6. GeneSigDB website
    22. Bentink S, Haibe-Kains B, Risch T, Fan J-B, Hirsch MS, Holton K, Rubio R, Aprils C, Chen J, Wickham-Garcia E, Liu J, Culhane AC, Drapkin R, Quackenbush J, Matulonis UA. (2012) Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancerPLoS One, 7(2):e30269
    23. Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A. (2012) Gene Expression Atlas update – a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Research. 40(Database issue):D1077-81 GXA website
    24. 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. (2012) The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. Nucleic Acids Res. 40(D1):D984-D991.  SCDE website
    25. 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. (2011) The cocaine- and amphetamine-regulated transcript mediates ligand-independent activation of ER?, and is an independent prognostic factor in node-negative breast cancer. Oncogene. [Epub ahead of print]
    26. Schröder M, Culhane AC, Quackenbush J, Haibe-Kains B (2011) SurvComp: an R/Bioconductor package for performance assessment and comparison for survival analysis. Bioinformatics 27(22):3206-8  Supplement
    27. Konstantinopoulos PA, Cannistra SA, Fountzilas H, Culhane A, Pillay K, Rueda B, Cramer D, Seiden M, Birrer M, Coukos G, Zhang L, Quackenbush J, Spentzos D. (2011) Integrated analysis of multiple microarray datasets identifies a reproducible survival predictor in ovarian cancer. PLoS One. 6(3):e18202.
    28. Culhane AC, Schwarzl T, Sultana R, Picard KC, Picard SC, Lu TH, Franklin K, French SJ, Papenhausen J, Correll M, Quackenbush J. (2010) GeneSigDB – a curated database of gene expression signatures. Nucleic Acids Research 38: D716-D725; GeneSigDB website
    29. Chittenden TW, Pak J, Rubio R, Cheng H, Holton K, Prendergast N, Glinskii V, Cai Y, Culhane A, Bentink S, Schwede M, Mar JC, Howe EA, Aryee M, Sultana R, Lanahan AA, Taylor JM, Holmes C, Hahn WC, Zhao JJ, Iglehart JD, Quackenbush J. (2010) Therapeutic implications of GIPC1 silencing in cancer. PLoS One. 5(12):e15581
    30. Chen D-T, Nasir A, Culhane AC, Venkataramu C, Fulp W, Rubio R, Wang T, Agrawal D, McCarthy S, Gruidl M, Bloom G, Anderson T, White J, Quackenbush J, Yeatman T. (2009) Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue. Breast Cancer Research and Treatment. 2010 Jan;119(2):335-46
    31. Culhane AC and Quackenbush J. (2009) Confounding Effects in “A Six-gene signature Predicting Breast Cancer Lung Metastasis” Cancer Research.  69(18):7480-5.
    32. Speers C, Tsimelzon A, Sexton K, Herrick AM, Gutierrez C, Culhane A, Quackenbush J, Hilsenbeck S, Chang J, Brown P. (2009) Indentification of novel kinase targets for the treatment of estrogen receptor-negative breast cancer. Clinical Cancer Research. 15(20):632740.
    33. 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. (2009) Repeatability of published microarray gene expression analyses.  Nat Genet. 41(2):149-155.   Accompanying editorial in Nature Genetics
    34. Smith MJ, Culhane AC, Donovan M, Coffey C, Barry B, Kelly M, Higgins DG, Wang JH, Kirwan WO, Cotter TG, Redmond HP (2009) Analysis of Differential Gene Expression in Colorectal Cancer and Stroma Using Flow Activated Cell Sorting Purification. British Journal of Cancer. 100(9):1452-64.
    35. Chittenden TW, Howe EA, Culhane AC,  Sultana R, Taylor JM, Holmes C, Quackenbush J. (2008) Functional classification analysis of somatically mutated genes in human breast and colorectal cancers. Genomics  91(6):508-11
    36. Cheng ASL, Culhane AC, Chan MWY, Chinnambally V, Ehrich M, Nasir A, Rodriguez BAT, Liu J, Yan PS, Quackenbush J, Nephew KP, Yeatman TJ, Huang TH-M. (2008) Epithelial Progeny of Estrogen-exposed Breast Progenitor Cells Display a Cancer-like Methylome. Cancer Res 68(6): 1786-96.
    37. Smith MJ, Culhane AC, Killeen S, Kelly MA, Wang JH, Cotter TG, Redmond HP. (2008)  Mechanisms Driving Local Breast Cancer Recurrence in a Model of Breast-Conserving Surgery. Ann Surg Oncol. 15(10):2954-64
    38. 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. (2008) Altered Cytoplasmic-to-Nuclear Ratio of Survivin Is a Prognostic Indicator in Breast Cancer. Clinical Cancer Res. 14(9):2681-9.
    39. Sobhian B, Shao G, Culhane AC, Moreau L, Xia B, Livingston DM, Greenberg RA. (2007) Rap80 targets BRCA1 to specific ubiquitin structures at DNA damage sites. Science. 316(5828):1198-202 Recommended by Faculty of 1000
    40. Fagan A, Culhane AC, Higgins DG. (2007) A multivariate analysis approach to the integration of proteomic and gene expression data. Proteomics. 7(13):2162-71.
    41. Jeffery IB,Madden SF,McGettigan PA,Perriere G, Culhane AC, Higgins DG (2007) Integrating transcription factor binding site information with gene expression datasets. Bioinformatics 23(3):298-305.
    42. O’Brien SL, Fagan A, Fox EJP, Millikan RC, Culhane AC, Brennan DJ, McCann AH, Hegarty S, Moyna S, Duffy MJ, Higgins DG, Jirstrom K,Landberg G,Gallagher WM. (2007) CENP-F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer. Int. J. Cancer 120(7):1426-35.
    43. Jeffery IB, Higgins DG, Culhane AC. (2006) Comparison and evaluation of microarray feature selection methods. BMC Bioinformatics 7:359. (Highly Accessed)
    44. Culhane AC, Thioulouse J (2006) A multivariate approach to integrating datasets using made4 and ade4. R News: Special Issue on Bioconductor Dec 2006 (http://cran.r-project.org/doc/Rnews/Rnews_2006-5.pdf)
    45. Gallagher WM, Orla E. Bergin OE, Rafferty M, Kelly ZD, Nolan IM, Fox EJP, Culhane AC et al., (2005) Multiple markers for melanoma progression regulated by DNA methylation: Insights from transcriptomic studies Carcinogenesis 26(11):1856-1867.
    46. Baty F, Bihl MP , Perriére G, Culhane AC, Brutsche MH. Optimization of the Between Group Analysis for disease class prediction based on gene expression data: a new jackknife based gene selection procedure. BMC Bioinformatics. 2005; 6: 239
    47. Culhane AC, Thioulouse J, Perriére G, Higgins DG. (2005) MADE4: An R package for multivariate analysis of gene expression data. Bioinformatics. 21(11):2789-90.  Bioconductor Package
    48. Kapushesky M, Kemmeren P, Culhane AC, Durinck S, Ihmels J, Körner C, Kull M, Torrente A, Sarkans U, Vilo J, Brazma A. (2004) Expression Profiler: next generation: an online platform for analysis of microarray data. Nucleic Acids Research. 32:W465-470
    49. McArdle L, McDermott M, Purcell R, Grehan D, O’Meara A, Breatnach F, Catchpoole D, Culhane AC, Jeffery I, Gallagher WM, Stallings RL. (2004). Oligonucleotide microarray analysis of gene expression in neuroblastoma displaying loss of chromosome 11q. Carcinogenesis 25:1599-1609
    50. Culhane AC, Perriére G, Higgins DG. (2003) Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. BMC Bioinformatics. 4(1):59
    51. Culhane AC, Perriére G, Considine EC, Cotter TG, Higgins DG. (2002) Between-group analysis of microarray data. Bioinformatics. 18:1600-1608. Recommended by Faculty of 1000 
    52. Wheeler RD, Culhane AC, Hall MD, Pickering-Brown S, Rothwell NJ, Luheshi GN. (2000) Detection of the interleukin 18 family in rat brain by RT-PCR. Brain Res Mol Brain Res. 77(2):290-3.
    53. Culhane AC, Hall MD, Rothwell NJ, Luheshi GN. (1998) Cloning of rat brain interleukin-18 cDNA. Mol Psychiatry. 3(4):362-6.

Reviews

  1. Meng C, Zeleznik OA, Thallinger GG, Kuster B, Gholami AM, Culhane AC. Dimension reduction techniques for the integrative
    analysis of multi-omics data
    Brief Bioinform. 2016 Jul;17(4):628-41. doi: 10.1093/bib/bbv108. Supplement
  2. 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. Briefings in Bioinformatics. 2015 Oct 12. pii: bbv080.
  3. Culhane AC, Howlin J. (2007) Molecular profiling of breast cancer: transcriptomic studies and beyond. Cell Mol Life Sci. 64(24):3185-200..
  4. Brennan D, O’ Brien S, Fagan A, Culhane AC, Higgins DG, Duffy MJ, Gallagher WM. (2005) Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response. Expert Opinion on Biological Therapy 5(8):1069-83
  5. Duffy MJ, Kelly ZD, Culhane AC, O’ Brien S, Gallagher WM. (2005) DNA Microarray-Based Gene Expression profiling in cancer: Aiding cancer diagnosis, assessing prognosis and predicting response to therapy Current Pharmacogenomics 3(4):289-304.
  6. Hale AJ, Smith CA, Sutherland LC, Stoneman VE, Longthorne V, Culhane AC, Williams GT. Apoptosis: molecular regulation of cell death. J. Biochem. 1996; 236: 1-26

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) AI Methods for Analyzing Microarray Data. In Encyclopedia of Artificial Intelligence. Rabuñal Dopico JR, Dorado J or Pazos A (eds).Information Science Reference, IGI Global Publishing.

Culhane AC and Brazma A. (2006) Mining of gene expression data. In In Silico technology in drug target identification and validation. León D, Markel S. (eds) Marcel Dekker, Inc. New York

Brazma A., and Culhane AC. (2005) Algorithms for gene expression analysis. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Dunn MJ., Jorde LB., Little PFR, Subramaniam S. (eds) John Wiley & Sons. London