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

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

(2011) Joshua WK Ho et al.   BMC GENOMICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

GenomeView: a next-generation genome browser

(2011) T. Abeel et al.   NUCLEIC ACIDS RESEARCH

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions

(2011) Jose M Muiño et al.   Plant Methods

Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes

(2011) Rebecca M. Davidson et al.   Plant Genome

BamView: viewing mapped read alignment data in the context of the reference sequence

(2010) T. Carver et al.   BIOINFORMATICS

Savant: genome browser for high-throughput sequencing data

(2010) M. Fiume et al.   BIOINFORMATICS

Prevalence of alternative splicing choices in Arabidopsis thaliana

(2010) Adam C English et al.   BMC PLANT BIOLOGY

RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

(2010) Andrew J Severin et al.   BMC PLANT BIOLOGY

Alternative splicing: global insights

(2010) Martina Hallegger et al.   FEBS Journal

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

(2010) T. Lu et al.   GENOME RESEARCH

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

A methyl transferase links the circadian clock to the regulation of alternative splicing

(2010) Sabrina E. Sanchez et al.   NATURE

Conserved Alternative Splicing of Arabidopsis Transthyretin-Like Determines Protein Localization and S-Allantoin Synthesis in Peroxisomes

(2010) I. Lamberto et al.   PLANT CELL

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

(2010) Andrea Barta et al.   PLANT CELL

Characterization of Transcriptional Complexity during Berry Development in Vitis vinifera Using RNA-Seq

(2010) S. Zenoni et al.   PLANT PHYSIOLOGY

The Plant-Specific SR45 Protein Negatively Regulates Glucose and ABA Signaling during Early Seedling Development in Arabidopsis

(2010) R. F. Carvalho et al.   PLANT PHYSIOLOGY

Noisy Splicing Drives mRNA Isoform Diversity in Human Cells

(2010) Joseph K. Pickrell et al.   PLoS Genetics

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The Spliceosome: Design Principles of a Dynamic RNP Machine

(2009) Markus C. Wahl et al.   CELL

Assembly of ribosomes and spliceosomes: complex ribonucleoprotein machines

(2009) Jonathan P Staley et al.   CURRENT OPINION IN CELL BIOLOGY

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs

(2009) Giorgio Grillo et al.   NUCLEIC ACIDS RESEARCH

Stochastic noise in splicing machinery

(2009) Eugene Melamud et al.   NUCLEIC ACIDS RESEARCH

Plant-specific SR-related protein atSR45a interacts with spliceosomal proteins in plant nucleus

(2009) Noriaki Tanabe et al.   PLANT MOLECULAR BIOLOGY

Plant SMU-1 and SMU-2 Homologues Regulate Pre-mRNA Splicing and Multiple Aspects of Development

(2009) T. Chung et al.   PLANT PHYSIOLOGY

Consistency Analysis of Redundant Probe Sets on Affymetrix Three-Prime Expression Arrays and Applications to Differential mRNA Processing

(2009) Xiangqin Cui et al.   PLoS One

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The SR protein family of splicing factors: master regulators of gene expression

(2008) Jennifer C. Long et al.   BIOCHEMICAL JOURNAL

Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes

(2008) Stefanie Schindler et al.   BMC GENOMICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Changing transcriptional initiation sites and alternative 5′- and 3′-splice site selection of the first intron deploys Arabidopsis PROTEIN ISOASPARTYL METHYLTRANSFERASE2 variants to different subcellular compartments

(2008) Randy D. Dinkins et al.   PLANT JOURNAL