Integrated omics analyses of retrograde signaling mutant delineate interrelated stress-response strata

Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies

(2016) Hendrik Treutler et al.   ANALYTICAL CHEMISTRY

Glutathione reductase gene expression depends on chloroplast signals in Arabidopsis thaliana

(2016) E. Yu. Garnik et al.   BIOCHEMISTRY-MOSCOW

More effort — more results: recent advances in integrative ‘omics’ data analysis

(2016) Dhivyaa Rajasundaram et al.   CURRENT OPINION IN PLANT BIOLOGY

The plastidial retrograde signal methyl erythritol cyclopyrophosphate is a regulator of salicylic acid and jasmonic acid crosstalk

(2016) Mark Lemos et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Plastidial metabolite MEcPP induces a transcriptionally centered stress-response hub via the transcription factor CAMTA3

(2016) Geoffrey Benn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Glutathione – linking cell proliferation to oxidative stress

(2015) Pedro Diaz-Vivancos et al.   FREE RADICAL BIOLOGY AND MEDICINE

Disruption of both chloroplastic and cytosolic FBPase genes results in a dwarf phenotype and important starch and metabolite changes in Arabidopsis thaliana

(2015) José A. Rojas-González et al.   JOURNAL OF EXPERIMENTAL BOTANY

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

(2015) Hiroshi Tsugawa et al.   NATURE METHODS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Integrated multi-omics analysis supports role of lysophosphatidylcholine and related glycerophospholipids in theLotus japonicus-Glomus intraradicesmycorrhizal symbiosis

(2015) Vinod Vijayakumar et al.   PLANT CELL AND ENVIRONMENT

The diversion of 2-C-methyl-d-erythritol-2,4-cyclodiphosphate from the 2-C-methyl-d-erythritol 4-phosphate pathway to hemiterpene glycosides mediates stress responses inArabidopsis thaliana

(2015) Diego González-Cabanelas et al.   PLANT JOURNAL

TCP transcription factors are critical for the coordinated regulation ofISOCHORISMATE SYNTHASE 1expression inArabidopsis thaliana

(2015) Xiaoyan Wang et al.   PLANT JOURNAL

Increased glutathione contributes to stress tolerance and global translational changes in Arabidopsis

(2015) Mei-Chun Cheng et al.   PLANT JOURNAL

Plastid-produced interorgannellar stress signal MEcPP potentiates induction of the unfolded protein response in endoplasmic reticulum

(2015) Justin Walley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial and temporal regulation of biosynthesis of the plant immune signal salicylic acid

(2015) Xiao-yu Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PathVisio 3: An Extendable Pathway Analysis Toolbox

(2015) Martina Kutmon et al.   PLoS Computational Biology

Salicylic acid and reactive oxygen species interplay in the transcriptional control of defense genes expression

(2015) Ariel Herrera-Vásquez et al.   Frontiers in Plant Science

Exploiting Natural Variation of Secondary Metabolism Identifies a Gene Controlling the Glycosylation Diversity of Dihydroxybenzoic Acids in Arabidopsis thaliana

(2014) X. Li et al.   GENETICS

Endoplasmic reticulum stress triggers ROS signalling, changes the redox state, and regulates the antioxidant defence of Arabidopsis thaliana

(2014) Rengin Ozgur et al.   JOURNAL OF EXPERIMENTAL BOTANY

Infection by a foliar endophyte elicits novel arabidopside-based plant defence reactions in its host,Cirsium arvense

(2014) Susan E. Hartley et al.   NEW PHYTOLOGIST

A key general stress response motif is regulated non-uniformly by CAMTA transcription factors

(2014) Geoffrey Benn et al.   PLANT JOURNAL

Distinct Roles for Mitogen-Activated Protein Kinase Signaling and CALMODULIN-BINDING TRANSCRIPTIONAL ACTIVATOR3 in Regulating the Peak Time and Amplitude of the Plant General Stress Response

(2014) M. Bjornson et al.   PLANT PHYSIOLOGY

Functional Convergence of Oxylipin and Abscisic Acid Pathways Controls Stomatal Closure in Response to Drought

(2014) T. Savchenko et al.   PLANT PHYSIOLOGY

De-novo RNA Sequencing and Metabolite Profiling to Identify Genes Involved in Anthocyanin Biosynthesis in Korean Black Raspberry (Rubus coreanus Miquel)

(2014) Tae Kyung Hyun et al.   PLoS One

Understanding the Relationship between Cotton Fiber Properties and Non-Cellulosic Cell Wall Polysaccharides

(2014) Dhivyaa Rajasundaram et al.   PLoS One

Network Analysis of the MVA and MEP Pathways for Isoprenoid Synthesis

(2013) Eva Vranová et al.   Annual Review of Plant Biology

Plastid-Localized Glutathione Reductase2-Regulated Glutathione Redox Status Is Essential for Arabidopsis Root Apical Meristem Maintenance

(2013) X. Yu et al.   PLANT CELL

Salicylic Acid Suppresses Jasmonic Acid Signaling Downstream of SCFCOI1-JAZ by Targeting GCC Promoter Motifs via Transcription Factor ORA59

(2013) D. Van der Does et al.   PLANT CELL

The α/β Hydrolase CGI-58 and Peroxisomal Transport Protein PXA1 Coregulate Lipid Homeostasis and Signaling inArabidopsis

(2013) Sunjung Park et al.   PLANT CELL

Integration of Transcriptome, Proteome and Metabolism Data Reveals the Alkaloids Biosynthesis in Macleaya cordata and Macleaya microcarpa

(2013) Jianguo Zeng et al.   PLoS One

Salicylic acid 3-hydroxylase regulatesArabidopsisleaf longevity by mediating salicylic acid catabolism

(2013) Kewei Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

(2013) P. Juntawong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Retrograde Signaling by the Plastidial Metabolite MEcPP Regulates Expression of Nuclear Stress-Response Genes

(2012) Yanmei Xiao et al.   CELL

Coronatine Promotes Pseudomonas syringae Virulence in Plants by Activating a Signaling Cascade that Inhibits Salicylic Acid Accumulation

(2012) Xiao-yu Zheng et al.   Cell Host & Microbe

Oxo-phytodienoic acid (OPDA) is formed on fatty acids esterified to galactolipids after tissue disruption inArabidopsis thaliana

(2012) Anders K. Nilsson et al.   FEBS LETTERS

Structure and Dynamics of the Isoprenoid Pathway Network

(2012) Eva Vranová et al.   Molecular Plant

Analysis of Arabidopsis glutathione-transferases in yeast

(2012) Matthias P. Krajewski et al.   PHYTOCHEMISTRY

A High-Throughput Method for Illumina RNA-Seq Library Preparation

(2012) Ravi Kumar et al.   Frontiers in Plant Science

WRKY Transcription Factors Involved in Activation of SA Biosynthesis Genes

(2011) Marcel C van Verk et al.   BMC PLANT BIOLOGY

Salicylic acid beyond defence: its role in plant growth and development

(2011) M. Rivas-San Vicente et al.   JOURNAL OF EXPERIMENTAL BOTANY

Glutathione in plants: an integrated overview

(2011) GRAHAM NOCTOR et al.   PLANT CELL AND ENVIRONMENT

Firefly Luciferase and Rluc8 Exhibit Differential Sensitivity to Oxidative Stress in Apoptotic Cells

(2011) Julie Czupryna et al.   PLoS One

Linking energy metabolism to dysfunctions in mitochondrial respiration – A metabolomics in vitro approach

(2011) G.U. Balcke et al.   TOXICOLOGY LETTERS

ROS signaling: the new wave?

(2011) Ron Mittler et al.   TRENDS IN PLANT SCIENCE

Accumulation of Isochorismate-derived 2,3-Dihydroxybenzoic 3-O-β-d-Xyloside inArabidopsisResistance to Pathogens and Ageing of Leaves

(2010) Michael Bartsch et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Effect of copper and salicylic acid on phenolic metabolites and free amino acids in Scenedesmus quadricauda (Chlorophyceae)

(2010) Jozef Kováčik et al.   PLANT SCIENCE

Control of salicylic acid synthesis and systemic acquired resistance by two members of a plant-specific family of transcription factors

(2010) Y. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Salicylic Acid, a Multifaceted Hormone to Combat Disease

(2009) A. Corina Vlot et al.   Annual Review of Phytopathology

GAGE: generally applicable gene set enrichment for pathway analysis

(2009) Weijun Luo et al.   BMC BIOINFORMATICS

H2O2-Activated Up-Regulation of Glutathione in Arabidopsis Involves Induction of Genes Encoding Enzymes Involved in Cysteine Synthesis in the Chloroplast

(2009) Guillaume Queval et al.   Molecular Plant

ETHYLENE INSENSITIVE3 and ETHYLENE INSENSITIVE3-LIKE1 Repress SALICYLIC ACID INDUCTION DEFICIENT2 Expression to Negatively Regulate Plant Innate Immunity in Arabidopsis

(2009) H. Chen et al.   PLANT CELL

The NADPH-dependent thioredoxin system constitutes a functional backup for cytosolic glutathione reductase in Arabidopsis

(2009) L. Marty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis

(2009) A. Mustroph et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Presenting and exploring biological pathways with PathVisio

(2008) Martijn P van Iersel et al.   BMC BIOINFORMATICS

Metabolism of salicylic acid in wild-type, ugt74f1 and ugt74f2 glucosyltransferase mutants of Arabidopsis thaliana

(2008) John V. Dean et al.   PHYSIOLOGIA PLANTARUM

Overexpression of AtSGT1, an Arabidopsis salicylic acid glucosyltransferase, leads to increased susceptibility to Pseudomonas syringae

(2008) Jong Tae Song et al.   PHYTOCHEMISTRY

The Arabidopsis glutathione transferase gene family displays complex stress regulation and co-silencing multiple genes results in altered metabolic sensitivity to oxidative stress

(2008) Pia G. Sappl et al.   PLANT JOURNAL

Oxylipins: Structurally diverse metabolites from fatty acid oxidation

(2008) Alina Mosblech et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY