Publications - Working papers

Please find below working papers of our group. Currently, we list 47 working papers. In the list are only not published papers present. If you look for a preprint of an already published paper you must look in the "Published papers" section. If you have problems accessing electronic information, please let us know:

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Ryūtō: A Framework for Network-Flow based Transcriptome Reconstruction of RNA-seq Data

Gatter, Thomas and Stadler, Peter F.

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Abstract


Despite the rapid increase in RNA-seq data the complete and accurate annotation of the complex transcriptional output of the human genome has remained elusive. One of the critical bottlenecks in this endevour is the computational reconstruction of transcript structures of high throughout sequencing data. Here we introduce an extension of the common splice graph framework that combines aspects of overlap and bin graphs and makes it possible to efficiently use both multi-splice and paired-end information to the fullest extent. The decomposition of read coverage patterns is modeled as a minimum-cost flow problem to account for the unavoidable non-uniformities of RNA-seq data. The method is implemented in the Ryūtō package. Its performance compares favourably to state of the art of methods on both simulated and real-life datasets.

Keywords


RNA-seq, Transcript reconstruction, splice graph, exon bins, bin graph, minimum-cost flow