Towards reliable isoform quantification using RNA-SEQ data
نویسندگان
چکیده
منابع مشابه
Efficient RNA isoform identification and quantification from RNA-Seq data with network flows
MOTIVATION Several state-of-the-art methods for isoform identification and quantification are based on [Formula: see text]-regularized regression, such as the Lasso. However, explicitly listing the-possibly exponentially-large set of candidate transcripts is intractable for genes with many exons. For this reason, existing approaches using the [Formula: see text]-penalty are either restricted to...
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Acknowledgments First and foremost, I want to thank my advisor Dr. Dongxiao Zhu. His endless support and wisdom helped me to finish this thesis. His enthusiasm for Bioinformatics was contagious—and I definitely caught it. His depth of knowledge and very precise academic guidance brought me to develop a computational pipeline for characterizing human transcriptome using RNA-seq. I would like to ...
متن کاملWemIQ: an accurate and robust isoform quantification method for RNA-seq data
MOTIVATION The deconvolution of isoform expression from RNA-seq remains challenging because of non-uniform read sampling and subtle differences among isoforms. RESULTS We present a weighted-log-likelihood expectation maximization method on isoform quantification (WemIQ). WemIQ integrates an effective bias removal with a weighted expectation maximization (EM) algorithm to distribute reads amon...
متن کاملGene expression WemIQ: an accurate and robust isoform quantification method for RNA-seq data
Motivation: The deconvolution of isoform expression from RNA-seq remains challenging because of non-uniform read sampling and subtle differences among isoforms. Results: We present a weighted-log-likelihood expectation maximization method on isoform quantification (WemIQ). WemIQ integrates an effective bias removal with a weighted expectation maximization (EM) algorithm to distribute reads amon...
متن کاملNetwork-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis
High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we propose to explore protein domain-domain interactions as prior knowledge for integrative analysis with RNA-Seq data. We introduce a Network-based method for RNA-S...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2010
ISSN: 1471-2105
DOI: 10.1186/1471-2105-11-s3-s6