Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries (Vitis vinifera L.) Exposed to Water Deficit

Preveraison Water Deficit Accelerates Berry Color Change in Merlot Grapevines

(2016) J. C. Herrera et al.   AMERICAN JOURNAL OF ENOLOGY AND VITICULTURE

Distinct transcriptome responses to water limitation in isohydric and anisohydric grapevine cultivars

(2016) Silvia Dal Santo et al.   BMC GENOMICS

Transcriptomic network analyses of leaf dehydration responses identify highly connected ABA and ethylene signaling hubs in three grapevine species differing in drought tolerance

(2016) Daniel W. Hopper et al.   BMC PLANT BIOLOGY

ABA-mediated responses to water deficit separate grapevine genotypes by their genetic background

(2016) Landry Rossdeutsch et al.   BMC PLANT BIOLOGY

Transcriptome and metabolite profiling reveals that prolonged drought modulates the phenylpropanoid and terpenoid pathway in white grapes (Vitis vinifera L.)

(2016) Stefania Savoi et al.   BMC PLANT BIOLOGY

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

(2016) Ronan C. O’Malley et al.   CELL

A systems-oriented analysis of the grapevine R2R3-MYB transcription factor family uncovers new insights into the regulation of stilbene accumulation

(2016) Darren Chern Jan Wong et al.   DNA RESEARCH

Impact of Leaf Removal, Applied Before and After Flowering, on Anthocyanin, Tannin, and Methoxypyrazine Concentrations in ‘Merlot’ (Vitis vinifera L.) Grapes and Wines

(2016) Paolo Sivilotti et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Identification of (Z)-3:(E)-2-Hexenal Isomerases Essential to the Production of the Leaf Aldehyde in Plants

(2016) Mikiko Kunishima et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Effect of water deficit and severe shoot trimming on the composition ofVitis vinifera L. Merlot grapes and wines

(2015) J.C. Herrera et al.   AUSTRALIAN JOURNAL OF GRAPE AND WINE RESEARCH

Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit

(2015) Nina Opitz et al.   JOURNAL OF EXPERIMENTAL BOTANY

Molecular genetics of blood-fleshed peach reveals activation of anthocyanin biosynthesis by NAC transcription factors

(2015) Hui Zhou et al.   PLANT JOURNAL

A grapevine anthocyanin acyltransferase, transcriptionally regulated by VvMYBA, can produce most acylated anthocyanins present in grape skins

(2015) Amy Rinaldo et al.   PLANT PHYSIOLOGY

The Phenylpropanoid Pathway Is Controlled at Different Branches by a Set of R2R3-MYB C2 Repressors in Grapevine

(2015) Erika Cavallini et al.   PLANT PHYSIOLOGY

Cultivar specific metabolic changes in grapevines berry skins in relation to deficit irrigation and hydraulic behavior

(2015) Uri Hochberg et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Severe drought stress is affecting selected primary metabolites, polyphenols, and volatile metabolites in grapevine leaves (Vitis vinifera cv. Pinot noir)

(2015) Michaela Griesser et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Dynamic subnuclear relocalisation of WRKY40 in response to Abscisic acid in Arabidopsis thaliana

(2015) Katja Geilen et al.   Scientific Reports

Reactive short-chain leaf volatiles act as powerful inducers of abiotic stress-related gene expression

(2015) Yasuo Yamauchi et al.   Scientific Reports

Auxin Response Factor SlARF2 Is an Essential Component of the Regulatory Mechanism Controlling Fruit Ripening in Tomato

(2015) Yanwei Hao et al.   PLoS Genetics

Transcriptional regulation of drought response: a tortuous network of transcriptional factors

(2015) Dhriti Singh et al.   Frontiers in Plant Science

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Metabolite and transcript profiling of berry skin during fruit development elucidates differential regulation between Cabernet Sauvignon and Shiraz cultivars at branching points in the polyphenol pathway

(2014) Asfaw Degu et al.   BMC PLANT BIOLOGY

ABA-dependent and ABA-independent signaling in response to osmotic stress in plants

(2014) Takuya Yoshida et al.   CURRENT OPINION IN PLANT BIOLOGY

The role of abscisic acid in fruit ripening and responses to abiotic stress

(2014) Ping Leng et al.   JOURNAL OF EXPERIMENTAL BOTANY

Role of plant hormones and their interplay in development and ripening of fleshy fruits

(2014) Rahul Kumar et al.   JOURNAL OF EXPERIMENTAL BOTANY

Water shortage and quality of fleshy fruits—making the most of the unavoidable

(2014) Julie Ripoll et al.   JOURNAL OF EXPERIMENTAL BOTANY

A 13-lipoxygenase, TomloxC, is essential for synthesis of C5 flavour volatiles in tomato

(2014) Jiyuan Shen et al.   JOURNAL OF EXPERIMENTAL BOTANY

Transcriptional control of fleshy fruit development and ripening

(2014) Rumyana Karlova et al.   JOURNAL OF EXPERIMENTAL BOTANY

Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development

(2014) Maria Concetta Palumbo et al.   PLANT CELL

Global reprogramming of transcription and metabolism inMedicago truncatuladuring progressive drought and after rewatering

(2014) JI-YI ZHANG et al.   PLANT CELL AND ENVIRONMENT

Integrated Analysis of the Effects of Cold and Dehydration on Rice Metabolites, Phytohormones, and Gene Transcripts

(2014) K. Maruyama 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

DNA-binding specificities of plant transcription factors and their potential to define target genes

(2014) José M. Franco-Zorrilla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera)

(2014) Sushma Naithani et al.   Frontiers in Plant Science

The transcriptional regulatory network in the drought response and its crosstalk in abiotic stress responses including drought, cold, and heat

(2014) Kazuo Nakashima et al.   Frontiers in Plant Science

The Auxin Response Factor Transcription Factor Family in Soybean: Genome-Wide Identification and Expression Analyses During Development and Water Stress

(2013) C. Van Ha et al.   DNA RESEARCH

A negative MYB regulator of proanthocyanidin accumulation, identified through expression quantitative locus mapping in the grape berry

(2013) Yung-Fen Huang et al.   NEW PHYTOLOGIST

A New Tomato NAC (NAM/ATAF1/2/CUC2) Transcription Factor, SlNAC4, Functions as a Positive Regulator of Fruit Ripening and Carotenoid Accumulation

(2013) Mingku Zhu et al.   PLANT AND CELL PHYSIOLOGY

Functional Diversification of Grapevine MYB5a and MYB5b in the Control of Flavonoid Biosynthesis in a Petunia Anthocyanin Regulatory Mutant

(2013) Erika Cavallini et al.   PLANT AND CELL PHYSIOLOGY

The R2R3-MYB Transcription Factors MYB14 and MYB15 Regulate Stilbene Biosynthesis in Vitis vinifera

(2013) J. Holl et al.   PLANT CELL

The Basic Leucine Zipper Transcription Factor ABSCISIC ACID RESPONSE ELEMENT-BINDING FACTOR2 Is an Important Transcriptional Regulator of Abscisic Acid-Dependent Grape Berry Ripening Processes

(2013) P. Nicolas et al.   PLANT PHYSIOLOGY

The Arabidopsis ETHYLENE RESPONSE FACTOR1 Regulates Abiotic Stress-Responsive Gene Expression by Binding to Different cis-Acting Elements in Response to Different Stress Signals

(2013) M.-C. Cheng et al.   PLANT PHYSIOLOGY

Lipoxygenase6-Dependent Oxylipin Synthesis in Roots Is Required for Abiotic and Biotic Stress Resistance of Arabidopsis

(2013) W. Grebner et al.   PLANT PHYSIOLOGY

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

(2012) Cole Trapnell et al.   Nature Protocols

JUNGBRUNNEN1, a Reactive Oxygen Species-Responsive NAC Transcription Factor, Regulates Longevity in Arabidopsis

(2012) A. Wu et al.   PLANT CELL

The homeodomain-leucine zipper (HD-Zip) class I transcription factors ATHB7 and ATHB12 modulate abscisic acid signalling by regulating protein phosphatase 2C and abscisic acid receptor gene activities

(2012) Ana Elisa Valdés et al.   PLANT MOLECULAR BIOLOGY

Application of the Gini Correlation Coefficient to Infer Regulatory Relationships in Transcriptome Analysis

(2012) C. Ma et al.   PLANT PHYSIOLOGY

Integrative Comparative Analyses of Transcript and Metabolite Profiles from Pepper and Tomato Ripening and Development Stages Uncovers Species-Specific Patterns of Network Regulatory Behavior

(2012) S. Osorio et al.   PLANT PHYSIOLOGY

AP2/ERF family transcription factors in plant abiotic stress responses

(2011) Junya Mizoi et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Systems Biology of Tomato Fruit Development: Combined Transcript, Protein, and Metabolite Analysis of Tomato Transcription Factor ( nor, rin ) and Ethylene Receptor ( Nr ) Mutants Reveals Novel Regulatory Interactions

(2011) Sonia Osorio et al.   PLANT PHYSIOLOGY

Physiological mechanisms underlying OsNAC5-dependent tolerance of rice plants to abiotic stress

(2011) Shi-Yong Song et al.   PLANTA

Water Deficit Increases Stilbene Metabolism in Cabernet Sauvignon Berries

(2010) Laurent G. Deluc et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

The lipoxygenase-dependent oxygenation of lipid body membranes is promoted by a patatin-type phospholipase in cucumber cotyledons

(2010) Maike Rudolph et al.   JOURNAL OF EXPERIMENTAL BOTANY

Identification of Putative Stage-Specific Grapevine Berry Biomarkers and Omics Data Integration into Networks

(2010) A. Zamboni et al.   PLANT PHYSIOLOGY

Molecular and Physiological Analysis of Drought Stress in Arabidopsis Reveals Early Responses Leading to Acclimation in Plant Growth

(2010) A. Harb et al.   PLANT PHYSIOLOGY

Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay

(2009) Laurent G Deluc et al.   BMC GENOMICS

Evolution of Volatile Compounds during the Development of Cabernet Sauvignon Grapes (Vitis vinifera L.)

(2009) Curtis M. Kalua et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Overexpression of the soybean GmERF3 gene, an AP2/ERF type transcription factor for increased tolerances to salt, drought, and diseases in transgenic tobacco

(2009) G. Zhang et al.   JOURNAL OF EXPERIMENTAL BOTANY

A Visual Reporter System for Virus-Induced Gene Silencing in Tomato Fruit Based on Anthocyanin Accumulation

(2009) D. Orzaez et al.   PLANT PHYSIOLOGY

Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development

(2009) F. Mounet et al.   PLANT PHYSIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Biosynthesis of plant-derived flavor compounds

(2008) Wilfried Schwab et al.   PLANT JOURNAL

Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics

(2008) Kaoru Urano et al.   PLANT JOURNAL

The Transcription Factor VvMYB5b Contributes to the Regulation of Anthocyanin and Proanthocyanidin Biosynthesis in Developing Grape Berries

(2008) L. Deluc et al.   PLANT PHYSIOLOGY

Role of Arabidopsis RAP2.4 in Regulating Light- and Ethylene-Mediated Developmental Processes and Drought Stress Tolerance

(2007) Rong-Cheng Lin et al.   Molecular Plant