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Estimation of alternative splicing isoform frequencies from RNA-Seq data

Authors: Marius Nicolae, Serghei Mangul, Ion Mandoiu, and Alex Zelikovsky

Published in: Dagstuhl Seminar Proceedings, Volume 10231, Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010)

Abstract

We present a novel expectation-maximization algorithm for inference of alternative splicing isoform frequencies from high-throughput transcriptome sequencing (RNA-Seq) data. Our algorithm exploits largely ignored disambiguation information provided by the distribution of insert sizes generated during sequencing library preparation, and takes advantage of base quality scores, strand and read pairing information if available. Empirical experiments on synthetic datasets show that the algorithm significantly outperforms existing methods of isoform and gene expression level estimation from RNA-Seq data.

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Marius Nicolae, Serghei Mangul, Ion Mandoiu, and Alex Zelikovsky. Estimation of alternative splicing isoform frequencies from RNA-Seq data. In Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings, Volume 10231, pp. 1-3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InProceedings{nicolae_et_al:DagSemProc.10231.5,
  author =	{Nicolae, Marius and Mangul, Serghei and Mandoiu, Ion and Zelikovsky, Alex},
  title =	{{Estimation of alternative splicing isoform frequencies from RNA-Seq data}},
  booktitle =	{Structure Discovery in Biology: Motifs, Networks \& Phylogenies},
  pages =	{1--3},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2010},
  volume =	{10231},
  editor =	{Alberto Apostolico and Andreas Dress and Laxmi Parida},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10231.5},
  URN =		{urn:nbn:de:0030-drops-26876},
  doi =		{10.4230/DagSemProc.10231.5},
  annote =	{Keywords: RNA-Seq, alternative splicing isoforms, expectation maximization}
}

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Estimation of alternative splicing isoform frequencies from RNA-Seq data

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