BibSonomy publications for /author/LapukThu Jun 23 00:00:00 CEST 2011Bioinformatics [ISMB/ECCB]13205-213Optimally discriminative subnetwork markers predict response to chemotherapy.272011dblp Tue May 31 00:00:00 CEST 2011Bioinformatics111481-1488Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.272011dblp Tue Jan 26 20:35:53 CET 2010Cancer Cell6515-27A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.102006imported Tue Jun 30 00:00:00 CEST 2009Bioinformatics151707-1714FIRMA: a method for detection of alternative splicing from exon array data.242008dblp Fri Oct 17 17:04:38 CEST 2008Cancer Cell6515--527A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes102006imported Recent studies suggest that thousands of genes may contribute to breast cancer pathophysiologies when deregulated by genomic or epigenomic events. Here, we describe a model ``system'' to appraise the functional contributions of these genes to breast cancer subsets. In general, the recurrent genomic and transcriptional characteristics of 51 breast cancer cell lines mirror those of 145 primary breast tumors, although some significant differences are documented. The cell lines that comprise the system also exhibit the substantial genomic, transcriptional, and biological heterogeneity found in primary tumors. We show, using Trastuzumab (Herceptin) monotherapy as an example, that the system can be used to identify molecular features that predict or indicate response to targeted therapies or other physiological perturbations.