ArticleAlgorithms for molecular biology : AMB2011
Estimation of alternative splicing isoform frequencies from RNA-Seq data.
Article in Algorithms for molecular biology : AMB, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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83 citing papers in PubMed.
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- LIQA: long-read isoform quantification and analysis.Genome biology · 2021Article
- HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets.Nucleic acids research · 2021Article
- T Cell Epitope Prediction and Its Application to Immunotherapy.Frontiers in immunology · 2021Review
- Factorial study of the RNA-seq computational workflow identifies biases as technical gene signatures.NAR genomics and bioinformatics · 2020Article
- Handling multi-mapped reads in RNA-seq.Computational and structural biotechnology journal · 2020Review
- Benchmark of long non-coding RNA quantification for RNA sequencing of cancer samples.GigaScience · 2019Article
- Locality Sensitive Imputation for Single Cell RNA-Seq Data.Journal of computational biology : a journal of computational molecular cell biology · 2019Article
- Systematic benchmarking of omics computational tools.Nature communications · 2019Review
- A discriminative learning approach to differential expression analysis for single-cell RNA-seq.Nature methods · 2019Article
- Dosage Compensation and Gene Expression of the X Chromosome in Sheep.G3 (Bethesda, Md.) · 2019Article
- Methylome Dynamics of Bovine Gametes andFrontiers in genetics · 2019Article
- Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans.PloS one · 2019Article
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4 authors.
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Abstract
backgroundMassively 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.
resultsIn this paper we present a novel expectation-maximization algorithm for inference of isoform- and gene-specific 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 when available. The open source Java implementation of IsoEM is freely available at http://dna.engr.uconn.edu/software/IsoEM/.
conclusionsEmpirical experiments on both synthetic and real RNA-Seq datasets show that IsoEM has scalable running time and outperforms existing methods of isoform and gene expression level estimation. Simulation experiments confirm previous findings that, for a fixed sequencing cost, using reads longer than 25-36 bases does not necessarily lead to better accuracy for estimating expression levels of annotated isoforms and genes.
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