A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation

(2016) Song Li et al.   DEVELOPMENTAL CELL

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Mechanism and regulation of the nonsense-mediated decay pathway

(2016) Nele Hug et al.   NUCLEIC ACIDS RESEARCH

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

(2015) Yeon Lee et al.   Annual Review of Biochemistry

Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress

(2015) Sergei Filichkin et al.   CURRENT OPINION IN PLANT BIOLOGY

Phenotypic evolution through variation in splicing of the noncoding RNACOOLAIR

(2015) Peijin Li et al.   GENES & DEVELOPMENT

Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity

(2015) Yamile Marquez et al.   GENOME RESEARCH

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

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

(2015) Runxuan Zhang et al.   NEW PHYTOLOGIST

Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts

(2015) John W.S. Brown et al.   PLANT CELL

Leveraging transcript quantification for fast computation of alternative splicing profiles

(2015) Gael P. Alamancos et al.   RNA

Seed Dormancy in Arabidopsis Requires Self-Binding Ability of DOG1 Protein and the Presence of Multiple Isoforms Generated by Alternative Splicing

(2015) Kazumi Nakabayashi et al.   PLoS Genetics

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data

(2015) Alexander Kanitz et al.   GENOME BIOLOGY

MAF2 Is Regulated by Temperature-Dependent Splicing and Represses Flowering at Low Temperatures in Parallel with FLM

(2015) Chiara A. Airoldi et al.   PLoS One

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

(2014) Ruolin Liu et al.   BMC BIOINFORMATICS

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

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Paired-End Analysis of Transcription Start Sites inArabidopsisReveals Plant-Specific Promoter Signatures

(2014) Taj Morton et al.   PLANT CELL

Phytochrome controls alternative splicing to mediate light responses inArabidopsis

(2014) Hiromasa Shikata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Chloroplast Retrograde Signal Regulates Nuclear Alternative Splicing

(2014) E. Petrillo et al.   SCIENCE

Epigenetic Regulation in Plant Responses to the Environment

(2014) D. C. Baulcombe et al.   Cold Spring Harbor Perspectives in Biology

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

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

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

Nonsense-Mediated Decay of Alternative Precursor mRNA Splicing Variants Is a Major Determinant of the Arabidopsis Steady State Transcriptome

(2013) G. Drechsel et al.   PLANT CELL

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

Genome-Wide Survey of Cold Stress Regulated Alternative Splicing in Arabidopsis thaliana with Tiling Microarray

(2013) Noam Leviatan et al.   PLoS One

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Using Tablet for visual exploration of second-generation sequencing data

(2012) I. Milne et al.   BRIEFINGS IN BIOINFORMATICS

Function of alternative splicing

(2012) Olga Kelemen et al.   GENE

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation

(2012) Alexander Sherstnev et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

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

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

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

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

(2011) Maria Kalyna et al.   NUCLEIC ACIDS RESEARCH

Alternative splicing: Enhancing ability to cope with stress via transcriptome plasticity

(2011) Anna M. Mastrangelo et al.   PLANT SCIENCE

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Cutting the nonsense: the degradation of PTC-containing mRNAs

(2010) Pamela Nicholson et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

Single amino acid change alters the ability to specify male or female organ identity

(2010) C. A. Airoldi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

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

Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs

(2009) Bogna Szarzynska et al.   NUCLEIC ACIDS 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

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY