Insect herbivory elicits genome-wide alternative splicing responses inNicotiana attenuata

Polyribosomal RNA-Seq Reveals the Decreased Complexity and Diversity of the Arabidopsis Translatome

(2015) Xingtan Zhang et al.   PLoS One

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

(2014) Feng Ding et al.   BMC GENOMICS

Abscisic Acid (ABA) Regulation of Arabidopsis SR Protein Gene Expression

(2014) Tiago Cruz et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Cytokinin levels and signaling respond to wounding and the perception of herbivore elicitors inNicotiana attenuata

(2014) Martin Schäfer et al.   Journal of Integrative Plant Biology

Root jasmonic acid synthesis and perception regulate folivore-induced shoot metabolites and increaseNicotiana attenuataresistance

(2014) Variluska Fragoso et al.   NEW PHYTOLOGIST

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

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

Global Dissection of Alternative Splicing in Paleopolyploid Soybean

(2014) Yanting Shen et al.   PLANT CELL

The roots of plant defenses: integrative multivariate analyses uncover dynamic behaviors of gene and metabolic networks of roots elicited by leaf herbivory

(2014) Jyotasana Gulati et al.   PLANT JOURNAL

Root Starch Reserves Are Necessary for Vigorous Re-Growth following Cutting Back in Lotus japonicus

(2014) Cécile Vriet et al.   PLoS One

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

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

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

(2014) Peng Cui et al.   GENOME BIOLOGY

A new perspective of phytohormones in salinity tolerance: Regulation of proline metabolism

(2013) Noushina Iqbal et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

RuBPCase activase (RCA) mediates growth-defense trade-offs: silencing RCA redirects jasmonic acid (JA) flux from JA-isoleucine to methyl jasmonate (MeJA) to attenuate induced defense responses inNicotiana attenuata

(2013) Sirsha Mitra et al.   NEW PHYTOLOGIST

Leaf-herbivore attack reduces carbon reserves and regrowth from the roots via jasmonate and auxin signaling

(2013) Ricardo A. R. Machado et al.   NEW PHYTOLOGIST

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

(2013) W. Li et al.   PLANT PHYSIOLOGY

Deciphering Herbivory-Induced Gene-to-Metabolite Dynamics in Nicotiana attenuata Tissues Using a Multifactorial Approach

(2013) J. Gulati et al.   PLANT PHYSIOLOGY

The HERBIVORE ELICITOR-REGULATED1 Gene Enhances Abscisic Acid Levels and Defenses against Herbivores in Nicotiana attenuata Plants

(2013) S. T. Dinh et al.   PLANT PHYSIOLOGY

A Jasmonate ZIM-Domain Protein NaJAZd Regulates Floral Jasmonic Acid Levels and Counteracts Flower Abscission in Nicotiana attenuata Plants

(2013) Youngjoo Oh et al.   PLoS One

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

(2013) Noam Leviatan et al.   PLoS One

High-Throughput RNA Sequencing of Pseudomonas-Infected Arabidopsis Reveals Hidden Transcriptome Complexity and Novel Splice Variants

(2013) Brian E. Howard et al.   PLoS One

Role of Tomato Lipoxygenase D in Wound-Induced Jasmonate Biosynthesis and Plant Immunity to Insect Herbivores

(2013) Liuhua Yan et al.   PLoS Genetics

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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

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

Jasmonoyl-l-isoleucine hydrolase 1 (JIH1) regulates jasmonoyl-l-isoleucine levels and attenuates plant defenses against herbivores

(2012) Melkamu G. Woldemariam et al.   PLANT JOURNAL

Identification of an intronic splicing regulatory element involved in auto-regulation of alternative splicing ofSCL33pre-mRNA

(2012) Julie Thomas et al.   PLANT JOURNAL

Empoasca leafhoppers attack wild tobacco plants in a jasmonate-dependent manner and identify jasmonate mutants in natural populations

(2012) M. Kallenbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Role of phytohormones in insect-specific plant reactions

(2012) Matthias Erb et al.   TRENDS IN PLANT SCIENCE

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A simple and efficient micrografting method for stably transformed Nicotiana attenuata plants to examine shoot-root signaling

(2011) Variluska Fragoso et al.   Plant Methods

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

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

Tissue Specific Diurnal Rhythms of Metabolites and Their Regulation during Herbivore Attack in a Native Tobacco, Nicotiana attenuata

(2011) Sang-Gyu Kim et al.   PLoS One

Jasmonate-induced defenses: a tale of intelligence, collaborators and rascals

(2011) Carlos L. Ballaré   TRENDS IN PLANT SCIENCE

Plant serine/arginine-rich proteins: roles in precursor messenger RNA splicing, plant development, and stress responses

(2011) Anireddy S. N. Reddy et al.   Wiley Interdisciplinary Reviews-RNA

New Insights into Plant Responses to the Attack from Insect Herbivores

(2010) Jianqiang Wu et al.   Annual Review of Genetics

SuperSAGE analysis of the Nicotiana attenuata transcriptome after fatty acid-amino acid elicitation (FAC): identification of early mediators of insect responses

(2010) Paola A Gilardoni et al.   BMC PLANT BIOLOGY

A rational nomenclature for serine/arginine-rich protein splicing factors (SR proteins)

(2010) J. L. Manley et al.   GENES & DEVELOPMENT

Conservation of an RNA regulatory map between Drosophila and mammals

(2010) A. N. Brooks 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

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Andrea Barta et al.   PLANT CELL

Biotic stress globally downregulates photosynthesis genes

(2010) DAMLA D. BILGIN et al.   PLANT CELL AND ENVIRONMENT

A splice variant of Arabidopsis mitogen-activated protein kinase and its regulatory function in the MKK6–MPK13 pathway

(2010) Wen-Yong Lin et al.   PLANT SCIENCE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Spliceosome Structure and Function

(2010) C. L. Will et al.   Cold Spring Harbor Perspectives in Biology

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay

(2009) Zhenguo Zhang et al.   BMC BIOLOGY

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

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

The underestimated role of roots in defense against leaf attackers

(2009) Matthias Erb et al.   TRENDS IN PLANT SCIENCE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Silencing two herbivory-activated MAP kinases, SIPK and WIPK, does not increase Nicotiana attenuata 's susceptibility to herbivores in the glasshouse and in nature

(2008) Stefan Meldau et al.   NEW PHYTOLOGIST

 -AMYLASE4, a Noncatalytic Protein Required for Starch Breakdown, Acts Upstream of Three Active  -Amylases in Arabidopsis Chloroplasts

(2008) D. C. Fulton et al.   PLANT CELL

Regulation and Function of Arabidopsis JASMONATE ZIM-Domain Genes in Response to Wounding and Herbivory

(2008) H. S. Chung et al.   PLANT PHYSIOLOGY

Independently Silencing Two Photosynthetic Proteins in Nicotiana attenuata Has Different Effects on Herbivore Resistance

(2008) S. Mitra et al.   PLANT PHYSIOLOGY

Why Does Herbivore Attack Reconfigure Primary Metabolism?

(2008) J. Schwachtje et al.   PLANT PHYSIOLOGY

Jasmonate Signaling: Toward an Integrated View

(2008) K. Kazan et al.   PLANT PHYSIOLOGY

Methyl jasmonate-elicited herbivore resistance: does MeJA function as a signal without being hydrolyzed to JA?

(2008) Jinsong Wu et al.   PLANTA

Herbivory-induced changes in the small-RNA transcriptome and phytohormone signaling in Nicotiana attenuata

(2008) S. P. Pandey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA