AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression inArabidopsis thaliana

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions inBrachypodium distachyon

(2015) Kranthi K. Mandadi et al.   PLANT CELL

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

(2014) Ruolin Liu et al.   BMC BIOINFORMATICS

Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis

(2014) Feng Ding et al.   BMC GENOMICS

Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis

(2014) Florian Bardou et al.   DEVELOPMENTAL CELL

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

Genome-Wide Analysis of Alternative Splicing in Zea mays: Landscape and Genetic Regulation

(2014) S. R. Thatcher et al.   PLANT CELL

A Chloroplast Retrograde Signal Regulates Nuclear Alternative Splicing

(2014) E. Petrillo et al.   SCIENCE

Intron Retention in the 5′UTR of the Novel ZIF2 Transporter Enhances Translation to Promote Zinc Tolerance in Arabidopsis

(2014) Estelle Remy et al.   PLoS Genetics

Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens

(2014) Hshin-Ping Wu et al.   GENOME BIOLOGY

Nonsense-mediated mRNA decay — Mechanisms of substrate mRNA recognition and degradation in mammalian cells

(2013) Christoph Schweingruber et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations

(2013) Gordon Gremme et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Temperature-dependent regulation of flowering by antagonistic FLM variants

(2013) David Posé et al.   NATURE

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

(2013) D. Staiger et al.   PLANT CELL

Complexity of the Alternative Splicing Landscape in Plants

(2013) A. S. N. Reddy et al.   PLANT CELL

MIR846 and MIR842 comprise a cistronic MIRNA pair that is regulated by abscisic acid by alternative splicing in roots of Arabidopsis

(2013) Fan Jia et al.   PLANT MOLECULAR BIOLOGY

Genome-Wide Detection of Condition-Sensitive Alternative Splicing in Arabidopsis Roots

(2013) W. Li et al.   PLANT PHYSIOLOGY

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

Gene Duplication and the Evolution of Plant MADS-box Transcription Factors

(2012) Chiara A. Airoldi et al.   Journal of Genetics and Genomics

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana

(2012) Corinna Streitner et al.   NUCLEIC ACIDS RESEARCH

Mutation ofArabidopsis SPLICEOSOMAL TIMEKEEPER LOCUS1Causes Circadian Clock Defects

(2012) Matthew A. Jones et al.   PLANT CELL

Polypyrimidine Tract Binding Protein Homologs from Arabidopsis Are Key Regulators of Alternative Splicing with Implications in Fundamental Developmental Processes

(2012) C. Ruhl et al.   PLANT CELL

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

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

Alternative splicing of the auxin biosynthesis gene YUCCA4 determines its subcellular compartmentation

(2012) Verena Kriechbaumer et al.   PLANT JOURNAL

On the physiological significance of alternative splicing events in higher plants

(2012) Raquel F. Carvalho et al.   PROTOPLASMA

Alternative splicing in plants – coming of age

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

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

(2011) Maria Kalyna et al.   NUCLEIC ACIDS RESEARCH

Cutting the nonsense: the degradation of PTC-containing mRNAs

(2010) Pamela Nicholson et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen 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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

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

Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabidopsis thaliana

(2009) Katarzyna Dorota Raczynska et al.   NUCLEIC ACIDS RESEARCH

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

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