Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems

SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing

(2014) Xi Wang et al.   BIOINFORMATICS

Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs

(2013) Laura H. LeGault et al.   BIOINFORMATICS

SplicingCompass: differential splicing detection using RNA-Seq data

(2013) Moritz Aschoff et al.   BIOINFORMATICS

Temperature-dependent regulation of flowering by antagonistic FLM variants

(2013) David Posé et al.   NATURE

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Accurate detection of differential RNA processing

(2013) Philipp Drewe et al.   NUCLEIC ACIDS RESEARCH

Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a

(2012) Alyssa A. Gulledge et al.   AMERICAN JOURNAL OF BOTANY

Identifying differentially spliced genes from two groups of RNA-seq samples

(2012) Weichen Wang et al.   GENE

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Stress-Induced Alternative Splicing Provides a Mechanism for the Regulation of MicroRNA Processing in Arabidopsis thaliana

(2012) Kang Yan et al.   MOLECULAR CELL

Modelling and simulating generic RNA-Seq experiments with the flux simulator

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq

(2012) Yin Hu et al.   NUCLEIC ACIDS RESEARCH

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

Alternative Splicing Mediates Responses of the Arabidopsis Circadian Clock to Temperature Changes

(2012) A. B. James et al.   PLANT CELL

Intron-mediated alternative splicing of Arabidopsis P5CS1 and its association with natural variation in proline and climate adaptation

(2012) R. Kesari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alternative splicing in plants – coming of age

(2012) Naeem H. Syed et al.   TRENDS IN PLANT SCIENCE

Deciphering the Plant Splicing Code: Experimental and Computational Approaches for Predicting Alternative Splicing and Splicing Regulatory Elements

(2012) Anireddy S. N. Reddy et al.   Frontiers in Plant Science

FDM: a graph-based statistical method to detect differential transcription using RNA-seq data

(2011) Darshan Singh et al.   BIOINFORMATICS

SpliceTrap: a method to quantify alternative splicing under single cellular conditions

(2011) Jie Wu et al.   BIOINFORMATICS

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Localization and Dynamics of Nuclear Speckles in Plants

(2011) A. S. N. Reddy et al.   PLANT PHYSIOLOGY

Comparative Analysis of Serine/Arginine-Rich Proteins across 27 Eukaryotes: Insights into Sub-Family Classification and Extent of Alternative Splicing

(2011) Dale N. Richardson et al.   PLoS One

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Conservation of an RNA regulatory map between Drosophila and mammals

(2010) A. N. Brooks et al.   GENOME RESEARCH

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

Implementing a Rational and Consistent Nomenclature for Serine/Arginine-Rich Protein Splicing Factors (SR Proteins) in Plants

(2010) Andrea Barta et al.   PLANT CELL

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

Two Alternatively Spliced Isoforms of the Arabidopsis SR45 Protein Have Distinct Roles during Normal Plant Development

(2009) X.-N. Zhang et al.   PLANT PHYSIOLOGY

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH