Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems
暂无分享,去创建一个
[1] Li Yang,et al. Conservation of an RNA regulatory map between Drosophila and mammals. , 2011, Genome research.
[2] Yamile Marquez,et al. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis , 2012, Genome research.
[3] Yufeng Liu,et al. FDM: a graph-based statistical method to detect differential transcription using RNA-seq data , 2011, Bioinform..
[4] V. Brendel,et al. Genomewide comparative analysis of alternative splicing in plants. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[5] B. Graveley. The developmental transcriptome of Drosophila melanogaster , 2010, Nature.
[6] Liang Chen. Statistical and Computational Methods for High-Throughput Sequencing Data Analysis of Alternative Splicing , 2013, Statistics in biosciences.
[7] J. Mathieu,et al. Temperature-dependent regulation of flowering by antagonistic FLM variants , 2013, Nature.
[8] Sandrine Dudoit,et al. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments , 2010, BMC Bioinformatics.
[9] A. Barta,et al. Implementing a Rational and Consistent Nomenclature for Serine/Arginine-Rich Protein Splicing Factors (SR Proteins) in Plants , 2010, Plant Cell.
[10] Colin N. Dewey,et al. Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs , 2013, Bioinform..
[11] L. Pachter. Models for transcript quantification from RNA-Seq , 2011, 1104.3889.
[12] A. Reddy. Alternative splicing of pre-messenger RNAs in plants in the genomic era. , 2007, Annual review of plant biology.
[13] Derek Y. Chiang,et al. DiffSplice: the genome-wide detection of differential splicing events with RNA-seq , 2012, Nucleic acids research.
[14] Ann E. Loraine,et al. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets , 2009, Bioinform..
[15] Gunnar Rätsch,et al. Accurate detection of differential RNA processing , 2013, Nucleic acids research.
[16] Anireddy S N Reddy,et al. Localization and Dynamics of Nuclear Speckles in Plants1 , 2011, Plant Physiology.
[17] Roland Eils,et al. SplicingCompass: differential splicing detection using RNA-Seq data , 2013, Bioinform..
[18] Stephen M. Mount,et al. Two Alternatively Spliced Isoforms of the Arabidopsis SR45 Protein Have Distinct Roles during Normal Plant Development1[W][OA] , 2009, Plant Physiology.
[19] G. Ast,et al. Alternative splicing and evolution: diversification, exon definition and function , 2010, Nature Reviews Genetics.
[20] S. Brenner,et al. The evolving roles of alternative splicing. , 2004, Current opinion in structural biology.
[21] Xuegong Zhang,et al. Identifying differentially spliced genes from two groups of RNA-seq samples. , 2013, Gene.
[22] Tanya Z. Berardini,et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools , 2011, Nucleic Acids Res..
[23] Hiral Vora,et al. Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a. , 2012, American journal of botany.
[24] Asa Ben-Hur,et al. Comparative Analysis of Serine/Arginine-Rich Proteins across 27 Eukaryotes: Insights into Sub-Family Classification and Extent of Alternative Splicing , 2011, PloS one.
[25] Stephen M. Mount,et al. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis , 2006, BMC Genomics.
[26] Wing Hung Wong,et al. Statistical inferences for isoform expression in RNA-Seq , 2009, Bioinform..
[27] Cole Trapnell,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.
[28] J. Harrow,et al. Assessment of transcript reconstruction methods for RNA-seq , 2013, Nature Methods.
[29] Dale N. Richardson,et al. Deciphering the Plant Splicing Code: Experimental and Computational Approaches for Predicting Alternative Splicing and Splicing Regulatory Elements , 2012, Front. Plant Sci..
[30] M. Stephens,et al. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. , 2008, Genome research.
[31] Peng Liu,et al. Stress-induced alternative splicing provides a mechanism for the regulation of microRNA processing in Arabidopsis thaliana. , 2012, Molecular cell.
[32] Masakazu Satou,et al. RIKEN Arabidopsis full-length (RAFL) cDNA and its applications for expression profiling under abiotic stress conditions. , 2003, Journal of experimental botany.
[33] Christopher D Town,et al. Analysis of the cDNAs of Hypothetical Genes on Arabidopsis Chromosome 2 Reveals Numerous Transcript Variants1[w] , 2005, Plant Physiology.
[34] E. Wang,et al. Analysis and design of RNA sequencing experiments for identifying isoform regulation , 2010, Nature Methods.
[35] T. Juenger,et al. Intron-mediated alternative splicing of Arabidopsis P5CS1 and its association with natural variation in proline and climate adaptation , 2012, Proceedings of the National Academy of Sciences.
[36] Serban Nacu,et al. Fast and SNP-tolerant detection of complex variants and splicing in short reads , 2010, Bioinform..
[37] John W. S. Brown,et al. Alternative Splicing Mediates Responses of the Arabidopsis Circadian Clock to Temperature Changes[W] , 2012, Plant Cell.
[38] Jie Wu,et al. SpliceTrap: a method to quantify alternative splicing under single cellular conditions , 2011, Bioinform..
[39] Anireddy S. N. Reddy,et al. Localization and dynamics of plant splicing regulators , 2011 .
[40] Gregory R. Grant,et al. Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data , 2015, Bioinform..
[41] W. Huber,et al. Detecting differential usage of exons from RNA-seq data , 2012, Genome research.
[42] Gael P. Alamancos,et al. Methods to study splicing from high-throughput RNA sequencing data. , 2013, Methods in molecular biology.
[43] Noriaki Tanabe,et al. Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, atSR30 and atSR45a, in response to environmental stress. , 2007, Plant & cell physiology.
[44] Juw Won Park,et al. MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data , 2012, Nucleic acids research.
[45] R. Guigó,et al. Modelling and simulating generic RNA-Seq experiments with the flux simulator , 2012, Nucleic acids research.
[46] Xi Wang,et al. Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing , 2013, BMC Bioinformatics.
[47] Yamile Marquez,et al. Alternative splicing in plants – coming of age , 2012, Trends in plant science.
[48] D. Black. Mechanisms of alternative pre-messenger RNA splicing. , 2003, Annual review of biochemistry.