Physical Sciences and Mathematics Commons^™

Trip: A Method For Novel Transcript Reconstruction From Paired-End Rna-Seq Reads, Serghei Mangul, Adrian Caciula, Dumitru Brinza, Ion I. Măndoiu, Alexander Zelikovskiy

Computer Science Faculty Publications

Preliminary experimental results on synthetic datasets generated with various sequencing parameters and distribution assumptions show that TRIP has increased transcriptome reconstruction accuracy compared to previous methods that ignore fragment length distribution information.

Estimation Of Alternative Splicing Isoform Frequencies From Rna-Seq Data, Marius Nicolae, Serghei Mangul, Ion I. Măndoiu, Alexander Zelikovskiy

Computer Science Faculty Publications

Background: Massively parallel whole transcriptome sequencing, commonly referred as RNA-Seq, is quickly becoming the technology of choice for gene expression profiling. However, due to the short read length delivered by current sequencing technologies, estimation of expression levels for alternative splicing gene isoforms remains challenging.

Results: In this paper we present a novel expectation-maximization algorithm for inference of isoform- and genespecific expression levels from RNA-Seq data. Our algorithm, referred to as IsoEM, is based on disambiguating 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 …