ArticleNucleic acids research2017
Information transduction capacity reduces the uncertainties in annotation-free isoform discovery and quantification.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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8 authors.
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Abstract
The automated transcript discovery and quantification of high-throughput RNA sequencing (RNA-seq) data are important tasks of next-generation sequencing (NGS) research. However, these tasks are challenging due to the uncertainties that arise in the inference of complete splicing isoform variants from partially observed short reads. Here, we address this problem by explicitly reducing the inherent uncertainties in a biological system caused by missing information. In our approach, the RNA-seq procedure for transforming transcripts into short reads is considered an information transmission process. Consequently, the data uncertainties are substantially reduced by exploiting the information transduction capacity of information theory. The experimental results obtained from the analyses of simulated datasets and RNA-seq datasets from cell lines and tissues demonstrate the advantages of our method over state-of-the-art competitors. Our algorithm is an open-source implementation of MaxInfo.
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