Articles

  1. Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors.
    Herschkowitz JI, Simin K, Weigman VJ, Mikaelian I, Usary J, Hu Z, Rasmussen KE, Jones LP, Assefnia S, Chandrasekharan S, Backlund MG, Yin Y, Khramtsov AI, Bastein R, Quackenbush J, Glazer RI, Brown PH, Green JE, Kopelovich L, Furth PA, Palazzo JP, Olopade OI, Bernard PS, Churchill GA, Van Dyke T, Perou CM. Genome Biol. 2007;8(5):R76.
    http://genomebiology.com/2007/8/5/R76/abstract
  2. Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage
    Min Zhu, Ming Yi, Chang-Hee Kim, Chuxia Deng, Yi Li, Daniel Medina, Robert Stephen and Jeffrey E Green
    Genome Biology 2011, 12:R77 doi:10.1186/gb-2011-12-8-r77
    http://genomebiology.com/2011/12/8/R77/abstract
  3. Sex differences in disease risk from reported genome-wide association study findings.
    Liu LY, Schaub MA, Sirota M, Butte AJ.
    Human Genetics. 2011 Aug 20
    http://www.springerlink.com/content/a8m4l35368124785/
  4. Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data
    Marina Sirota, Joel T. Dudley, Jeewon Kim, Annie P. Chiang, Alex A. Morgan, Alejandro Sweet-Cordero, Julien Sage and Atul J. Butte
    Sci Transl Med 17 August 2011
    http://stm.sciencemag.org/content/3/96/96ra77.short
  5. Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases
    Lopes, T. J. S., Schaefer, M., Shoemaker, J., Matsuoka, Y., Fontaine, J.-F., Neumann, G., Andrade-Navarro, M. A., Kawaoka, Y., Kitano, H. Bionformatics
    http://bioinformatics.oxfordjournals.org/cgi/content/short/27/17/2414
  6. OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes
    ou, J. S., Kelly, T. K., De Carvalho, D. D., Taberlay, P. C., Liang, G., Jones, P. A.
    http://www.pnas.org/content/108/35/14497.short
  7. Tissue-specific prediction of directly regulated genes
    McLeay, R. C., Leat, C. J., Bailey, T. L.
    http://bioinformatics.oxfordjournals.org/cgi/content/short/27/17/2354
  8. The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes, Matthew N. McCall et al.(pdf)
  9. Stage prediction of embryonic stem cell differentiation from genome-wide expression data
    Zagar, L., Mulas, F., Garagna, S., Zuccotti, M., Bellazzi, R., Zupan, B
    http://bioinformatics.oxfordjournals.org/cgi/content/short/27/18/2546
  10. A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction
    Arunachalam Vinayagam1*, Ulrich Stelzl1,2*, Raphaele Foulle1, Stephanie Plassmann1, Martina Zenkner1, Jan Timm1, Heike E. Assmus3, Miguel A. Andrade-Navarro1, and Erich E. Wanker1
    http://stke.sciencemag.org/cgi/content/full/sigtrans;4/189/rs8
  11. The PathOlogist: an automated tool for pathway-centric analysis
    Sharon I Greenblum, Sol Efroni, Carl F Schaefer and Ken H Buetow
    http://www.biomedcentral.com/1471-2105/12/133
  12. A high-resolution map of human evolutionary constraint using 29 mammals
    Lindblad-Toh...Kellis
    Nature Published online 12 October 2011
    http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10530.html
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