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Nacu","year":"2011","journal-title":"BMC Med Genomics"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"133","DOI":"10.5483\/BMBRep.2012.45.3.133","article-title":"Chimeric RNAs as potential biomarkers for tumor diagnosis","volume":"45","author":"J Zhou","year":"2012","journal-title":"BMB Rep"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists","volume":"37","author":"DW Huang","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"DW Huang","year":"2009","journal-title":"Nat 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Goya","year":"2010","journal-title":"Bioinformatics"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"e58815","DOI":"10.1371\/journal.pone.0058815","article-title":"Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data","volume":"8","author":"EM Quinn","year":"2013","journal-title":"PLoS ONE"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"2315","DOI":"10.1101\/gr.140988.112","article-title":"Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events","volume":"22","author":"J Liu","year":"2012","journal-title":"Genome Res"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1126\/science.1210557","article-title":"Mutations in CIC and FUBP1 contribute to human oligodendroglioma","volume":"333","author":"C 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Cycle"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"MD Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1038\/nature08712","article-title":"The transcriptional network for mesenchymal transformation of brain tumours","volume":"463","author":"MS Carro","year":"2010","journal-title":"Nature"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1038\/nature07638","article-title":"Transcriptome sequencing to detect gene fusions in cancer","volume":"458","author":"CA Maher","year":"2009","journal-title":"Nature"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"e6","DOI":"10.1093\/nar\/gks816","article-title":"Exome RNA sequencing reveals rare and novel alternative 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Roberts","year":"2011","journal-title":"Bioinformatics"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"A Subramanian","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"JT Robinson","year":"2011","journal-title":"Nature Biotechnology"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"W597","DOI":"10.1093\/nar\/gks400","article-title":"ExPASy: SIB bioinformatics resource portal","volume":"40","author":"P Artimo","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"5857","DOI":"10.1073\/pnas.95.11.5857","article-title":"SMART, a simple modular architecture research 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