CIDANE: Comprehensive Isoform Discovery and Abundance Estimation
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High-throughput sequencing of cellular RNA (RNA-seq) allows to assess the set of all RNA molecules, the transcriptome, produced by a cell at a high resolution, under various conditions. The assembly of short sequencing reads to full-length transcripts, however, poses profound challenges to bioinformatics tools.
KeywordsInteger Linear Programming Abundance Estimation Result Optimization Problem Lasso Regression Regularization Path
- 3.Li, J.J., Jiang, C.R., Brown, J.B., Huang, H., Bickel, P.J.: Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proceedings of the National Academy of Sciences 108(50), 19867–19872 (2011). http://www.pnas.org/content/108/50/19867.abstract CrossRefGoogle Scholar