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Aedin Culhane, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. 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, Livingston DM. BRCA1-IRIS promotes human tumor progression through PTEN blockade and HIF-1a activation. Proc Natl Acad Sci U S A. 2018 10 09; 115(41):E9600-E9609. PMID: 30254159.
    Citations:    Fields:    Translation:HumansAnimalsCells
  2. 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. Enter the Matrix: Factorization Uncovers Knowledge from Omics. Trends Genet. 2018 10; 34(10):790-805. PMID: 30143323.
    Citations:    Fields:    
  3. 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, 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 CE, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L. The Immune Landscape of Cancer. Immunity. 2018 04 17; 48(4):812-830.e14. PMID: 29628290.
    Citations: 17     Fields:    Translation:HumansCells
  4. 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. Software for the Integration of Multiomics Experiments in Bioconductor. Cancer Res. 2017 11 01; 77(21):e39-e42. PMID: 29092936.
    Citations: 3     Fields:    Translation:Humans
  5. Meng C, Culhane A. Integrative Exploratory Analysis of Two or More Genomic Datasets. Methods Mol Biol. 2016; 1418:19-38. PMID: 27008008.
    Citations: 2     Fields:    Translation:HumansCells
  6. 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. PMID: 26546296.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  7. 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; 10(10):e0140243. PMID: 26460486.
    Citations: 3     Fields:    Translation:HumansCells
  8. 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 Apr 03; 106(5). PMID: 24700803.
    Citations: 38     Fields:    Translation:HumansCells
  9. 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 Feb; 124(2):859-70. PMID: 24463450.
    Citations: 64     Fields:    Translation:HumansCells
  10. 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 May 21; 110(21):8632-7. PMID: 23657012.
    Citations: 17     Fields:    Translation:HumansAnimals
  11. Prencipe M, Madden SF, O'Neill A, O'Hurley G, Culhane A, O'Connor D, Klocker H, Kay EW, Gallagher WM, Watson WR. Identification of transcription factors associated with castration-resistance: is the serum responsive factor a potential therapeutic target? Prostate. 2013 May; 73(7):743-53. PMID: 23359479.
    Citations: 5     Fields:    Translation:Humans
  12. 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(1):e1002875. PMID: 23365551.
    Citations: 14     Fields:    Translation:Humans
  13. 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. MicroRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32. Genome Med. 2013; 5(1):2. PMID: 23339462.
    Citations: 19     Fields:    
  14. Bentink S, Haibe-Kains B, Risch T, Fan JB, Hirsch MS, Holton K, Rubio R, April C, Chen J, Wickham-Garcia E, Liu J, Culhane A, Drapkin R, Quackenbush J, Matulonis UA. Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer. PLoS One. 2012; 7(2):e30269. PMID: 22348002.
    Citations: 33     Fields:    Translation:HumansCells
  15. 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. J Natl Cancer Inst. 2012 Feb 22; 104(4):311-25. PMID: 22262870.
    Citations: 92     Fields:    Translation:Humans
  16. 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. The cocaine- and amphetamine-regulated transcript mediates ligand-independent activation of ERa, and is an independent prognostic factor in node-negative breast cancer. Oncogene. 2012 Jul 26; 31(30):3483-94. PMID: 22139072.
    Citations: 2     Fields:    Translation:HumansCells
  17. 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. The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. Nucleic Acids Res. 2012 Jan; 40(Database issue):D984-91. PMID: 22121217.
    Citations: 11     Fields:    Translation:HumansAnimalsCells
  18. 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. 2012 Jan; 40(Database issue):D1060-6. PMID: 22110038.
    Citations: 43     Fields:    Translation:HumansAnimals
  19. 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. Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Res. 2012 Jan; 40(Database issue):D1077-81. PMID: 22064864.
    Citations: 77     Fields:    Translation:Humans
  20. Schröder MS, Culhane AC, Quackenbush J, Haibe-Kains B. survcomp: an R/Bioconductor package for performance assessment and comparison of survival models. Bioinformatics. 2011 Nov 15; 27(22):3206-8. PMID: 21903630.
    Citations: 60     Fields:    Translation:Humans
  21. 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. Integrated analysis of multiple microarray datasets identifies a reproducible survival predictor in ovarian cancer. PLoS One. 2011 Mar 29; 6(3):e18202. PMID: 21479231.
    Citations: 13     Fields:    Translation:HumansCells
  22. 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. Therapeutic implications of GIPC1 silencing in cancer. PLoS One. 2010 Dec 30; 5(12):e15581. PMID: 21209904.
    Citations: 12     Fields:    Translation:HumansCells
  23. Culhane AC, Schwarzl T, Sultana R, Picard KC, Picard SC, Lu TH, Franklin KR, French SJ, Papenhausen G, Correll M, Quackenbush J. GeneSigDB--a curated database of gene expression signatures. Nucleic Acids Res. 2010 Jan; 38(Database issue):D716-25. PMID: 19934259.
    Citations: 51     Fields:    Translation:HumansCells
  24. Speers C, Tsimelzon A, Sexton K, Herrick AM, Gutierrez C, Culhane A, Quackenbush J, Hilsenbeck S, Chang J, Brown P. Identification of novel kinase targets for the treatment of estrogen receptor-negative breast cancer. Clin Cancer Res. 2009 Oct 15; 15(20):6327-40. PMID: 19808870.
    Citations: 39     Fields:    Translation:HumansCells
  25. Culhane AC, Quackenbush J. Confounding effects in "A six-gene signature predicting breast cancer lung metastasis". Cancer Res. 2009 Sep 15; 69(18):7480-5. PMID: 19723662.
    Citations: 14     Fields:    Translation:Humans
  26. Smith MJ, Culhane AC, Donovan M, Coffey JC, Barry BD, Kelly MA, Higgins DG, Wang JH, Kirwan WO, Cotter TG, Redmond HP. Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification. Br J Cancer. 2009 May 05; 100(9):1452-64. PMID: 19401702.
    Citations: 9     Fields:    Translation:HumansCells
  27. Chen DT, Nasir A, Culhane A, Venkataramu C, Fulp W, Rubio R, Wang T, Agrawal D, McCarthy SM, Gruidl M, Bloom G, Anderson T, White J, Quackenbush J, Yeatman T. Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue. Breast Cancer Res Treat. 2010 Jan; 119(2):335-46. PMID: 19266279.
    Citations: 67     Fields:    Translation:Humans
  28. 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 Oct; 15(10):2954-64. PMID: 18622646.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  29. 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. Altered cytoplasmic-to-nuclear ratio of survivin is a prognostic indicator in breast cancer. Clin Cancer Res. 2008 May 01; 14(9):2681-9. PMID: 18451232.
    Citations: 30     Fields:    Translation:HumansCells
  30. Chittenden TW, Howe EA, Culhane AC, Sultana R, Taylor JM, Holmes C, Quackenbush J. Functional classification analysis of somatically mutated genes in human breast and colorectal cancers. Genomics. 2008 Jun; 91(6):508-11. PMID: 18434084.
    Citations: 28     Fields:    Translation:Humans
  31. 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 Mar 15; 68(6):1786-96. PMID: 18339859.
    Citations: 58     Fields:    Translation:HumansCells
  32. 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 Feb; 41(2):149-55. PMID: 19174838.
    Citations: 150     Fields:    Translation:HumansAnimals
  33. Culhane AC, Howlin J. Molecular profiling of breast cancer: transcriptomic studies and beyond. Cell Mol Life Sci. 2007 Dec; 64(24):3185-200. PMID: 17957338.
    Citations: 3     Fields:    Translation:HumansAnimals
  34. Fagan A, Culhane AC, Higgins DG. A multivariate analysis approach to the integration of proteomic and gene expression data. Proteomics. 2007 Jun; 7(13):2162-71. PMID: 17549791.
    Citations: 26     Fields:    Translation:HumansAnimalsCells
  35. 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 May 25; 316(5828):1198-202. PMID: 17525341.
    Citations: 282     Fields:    Translation:HumansAnimalsCells
  36. 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. CENP-F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer. Int J Cancer. 2007 Apr 01; 120(7):1434-43. PMID: 17205517.
    Citations: 26     Fields:    Translation:HumansCells
  37. Jeffery IB, Madden SF, McGettigan PA, Perrière G, Culhane AC, Higgins DG. Integrating transcription factor binding site information with gene expression datasets. Bioinformatics. 2007 Feb 01; 23(3):298-305. PMID: 17127681.
    Citations: 15     Fields:    Translation:HumansCells
  38. Jeffery IB, Higgins DG, Culhane AC. Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics. 2006 Jul 26; 7:359. PMID: 16872483.
    Citations: 102     Fields:    Translation:HumansCells
  39. Baty F, Bihl MP, Perrière G, Culhane AC, Brutsche MH. Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data. BMC Bioinformatics. 2005 Sep 28; 6:239. PMID: 16191195.
    Citations: 2     Fields:    
  40. Brennan DJ, O'Brien SL, Fagan A, Culhane AC, Higgins DG, Duffy MJ, Gallagher WM. Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response. Expert Opin Biol Ther. 2005 Aug; 5(8):1069-83. PMID: 16050784.
    Citations: 14     Fields:    Translation:Humans
  41. 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. Multiple markers for melanoma progression regulated by DNA methylation: insights from transcriptomic studies. Carcinogenesis. 2005 Nov; 26(11):1856-67. PMID: 15958521.
    Citations: 33     Fields:    Translation:HumansAnimalsCells
  42. Culhane AC, Thioulouse J, Perrière G, Higgins DG. MADE4: an R package for multivariate analysis of gene expression data. Bioinformatics. 2005 Jun 01; 21(11):2789-90. PMID: 15797915.
    Citations: 95     Fields:    Translation:Cells
  43. 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 Jul 01; 32(Web Server issue):W465-70. PMID: 15215431.
    Citations: 42     Fields:    
  44. Culhane AC, Perrière G, Higgins DG. Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. BMC Bioinformatics. 2003 Nov 21; 4:59. PMID: 14633289.
    Citations: 34     Fields:    Translation:HumansCells
  45. Culhane AC, Perrière G, Considine EC, Cotter TG, Higgins DG. Between-group analysis of microarray data. Bioinformatics. 2002 Dec; 18(12):1600-8. PMID: 12490444.
    Citations: 48     Fields:    Translation:HumansCells
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Funded by the NIH/NCATS Clinical and Translational Science Award (CTSA) program, grant number UL1TR001102, and through institutional support from Harvard University, Harvard Medical School, Harvard T.H. Chan School of Public Health, Beth Israel Deaconess Medical Center, Boston Children's Hospital, Brigham and Women's Hospital, Massachusetts General Hospital and the Dana Farber Cancer Institute.