ArticleGenome biology2008
SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays.
Article in Genome biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- An NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data.NAR genomics and bioinformatics · 2020Article
- EventPointer: an effective identification of alternative splicing events using junction arrays.BMC genomics · 2016Article
- NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq data.BMC genomics · 2016Article
- Seq-ing improved gene expression estimates from microarrays using machine learning.BMC bioinformatics · 2015Article
- Simultaneous isoform discovery and quantification from RNA-seq.Statistics in biosciences · 2013Article
- Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants.Nucleic acids research · 2011Article
- NSMAP: a method for spliced isoforms identification and quantification from RNA-Seq.BMC bioinformatics · 2011Article
- Estimation of alternative splicing isoform frequencies from RNA-Seq data.Algorithms for molecular biology : AMB · 2011Article
- Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays.BMC bioinformatics · 2011Article
- Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays.BMC bioinformatics · 2010Article
- Verifying expressed transcript variants by detecting and assembling stretches of consecutive exons.Nucleic acids research · 2010Article
- Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer.BMC genomics · 2010Article
- Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.Nucleic acids research · 2010Article
- Identifiability of isoform deconvolution from junction arrays and RNA-Seq.Bioinformatics (Oxford, England) · 2009Article
- Resolving deconvolution ambiguity in gene alternative splicing.BMC bioinformatics · 2009Article
- A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level.Nucleic acids research · 2009Article
Corrections and comments
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Authors and funding
9 authors.
Funding
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Abstract
Exon and exon+junction microarrays are promising tools for studying alternative splicing. Current analytical tools applied to these arrays lack two relevant features: the ability to predict unknown spliced forms and the ability to quantify the concentration of known and unknown isoforms. SPACE is an algorithm that has been developed to (1) estimate the number of different transcripts expressed under several conditions, (2) predict the precursor mRNA splicing structure and (3) quantify the transcript concentrations including unknown forms. The results presented here show its robustness and accuracy for real and simulated data.
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