Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs
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[1] Tao Jiang,et al. IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly - (Extended Abstract) , 2011, RECOMB.
[2] K. Hansen,et al. Biases in Illumina transcriptome sequencing caused by random hexamer priming , 2010, Nucleic acids research.
[3] J. Rinn,et al. Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature Biotechnology.
[4] Brendan J. Frey,et al. Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data , 2012, BMC Bioinformatics.
[5] Tao Jiang,et al. IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly - (Extended Abstract) , 2011, RECOMB.
[6] K. Hansen,et al. Sequencing technology does not eliminate biological variability , 2011, Nature Biotechnology.
[7] D. Hanck,et al. Profiling the array of Cav3.1 variants from the human T‐type calcium channel gene CACNA1G: Alternative structures, developmental expression, and biophysical variations , 2006, Proteins.
[8] Xiaobo Zhou,et al. NSMAP: A method for spliced isoforms identification and quantification from RNA-Seq , 2011, BMC Bioinformatics.
[9] Wing Hung Wong,et al. Identifiability of isoform deconvolution from junction arrays and RNA-Seq , 2009, Bioinform..
[10] Tin Wee Tan,et al. ASGS: an alternative splicing graph web service , 2006, Nucleic Acids Res..
[11] J. Rinn,et al. Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature biotechnology.
[12] Cole Trapnell,et al. Improving RNA-Seq expression estimates by correcting for fragment bias , 2011, Genome Biology.
[13] Juan P Fededa,et al. A polar mechanism coordinates different regions of alternative splicing within a single gene. , 2005, Molecular cell.
[14] Walid S. Saba,et al. ANALYSIS AND DESIGN , 2000 .
[15] J. C. Clemens,et al. Drosophila Dscam Is an Axon Guidance Receptor Exhibiting Extraordinary Molecular Diversity , 2000, Cell.
[16] Gunnar Rätsch,et al. Transcript quantification with RNA-Seq data , 2009, BMC Bioinformatics.
[17] Steven J. M. Jones,et al. De novo assembly and analysis of RNA-seq data , 2010, Nature Methods.
[18] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[19] Yufeng Liu,et al. FDM: a graph-based statistical method to detect differential transcription using RNA-seq data , 2011, Bioinform..
[20] Lior Pachter,et al. Sequence Analysis , 2020, Definitions.
[21] C. Mungall,et al. The Release 5.1 Annotation of Drosophila melanogaster Heterochromatin , 2007, Science.
[22] E. Wang,et al. Analysis and design of RNA sequencing experiments for identifying isoform regulation , 2010, Nature Methods.
[23] Colin N. Dewey,et al. RNA-Seq gene expression estimation with read mapping uncertainty , 2009, Bioinform..
[25] Marcel H. Schulz,et al. Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments , 2010, Nucleic acids research.
[26] N. Proudfoot,et al. Exon tethering in transcription by RNA polymerase II. , 2006, Molecular cell.
[27] Mark Daly,et al. Stochastic yet biased expression of multiple Dscam splice variants by individual cells , 2004, Nature Genetics.
[28] Raymond K. Auerbach,et al. A User's Guide to the Encyclopedia of DNA Elements (ENCODE) , 2011, PLoS biology.
[29] Ion I. Mandoiu,et al. Estimation of alternative splicing isoform frequencies from RNA-Seq data , 2010, Algorithms for Molecular Biology.
[30] David G Hendrickson,et al. Differential analysis of gene regulation at transcript resolution with RNA-seq , 2012, Nature Biotechnology.
[31] W. Wong,et al. Modeling non-uniformity in short-read rates in RNA-Seq data , 2010, Genome Biology.
[32] N. Friedman,et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.
[33] M. Gerstein,et al. RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.
[34] F. Clark,et al. Understanding alternative splicing: towards a cellular code , 2005, Nature Reviews Molecular Cell Biology.
[35] Anne Bergeron,et al. Exact Transcriptome Reconstruction from Short Sequence Reads , 2008, WABI.
[36] B. Graveley. The developmental transcriptome of Drosophila melanogaster , 2010, Nature.
[37] James B. Brown,et al. Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation , 2011, Proceedings of the National Academy of Sciences.
[38] Yi Xing,et al. An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs , 2006, Nucleic acids research.
[39] Fang-Rong Hsu,et al. The application of alternative splicing graphs in quantitative analysis of alternative splicing form from EST database , 2004, Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering.
[40] Haixu Tang,et al. Splicing graphs and EST assembly problem , 2002, ISMB.
[41] A. Ben-Hur,et al. METHOD Open Access , 2014 .
[42] Eric T. Wang,et al. Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.
[43] Wing Hung Wong,et al. Statistical inferences for isoform expression in RNA-Seq , 2009, Bioinform..
[44] Cole Trapnell,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.
[45] JiangHui,et al. Identifiability of isoform deconvolution from junction arrays and RNA-Seq , 2009 .
[46] Li Yang,et al. The transcriptional diversity of 25 Drosophila cell lines. , 2011, Genome research.
[47] R. Guigó,et al. Transcriptome genetics using second generation sequencing in a Caucasian population , 2010, Nature.
[48] Paul Jenkins,et al. How Many Transcripts Does It Take to Reconstruct the Splice Graph? , 2006, WABI.
[49] David Haussler,et al. The UCSC Known Genes , 2006, Bioinform..