Transcriptional regulatory networks inArabidopsis thalianaduring single and combined stresses

ArabidopsisTOE proteins convey a photoperiodic signal to antagonize CONSTANS and regulate flowering time

(2015) Bailong Zhang et al.   GENES & DEVELOPMENT

Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature

(2015) D. D. Seaton et al.   Molecular Systems Biology

The MYB96-HHP module integrates cold and abscisic acid signaling to activate the CBF-COR pathway in Arabidopsis

(2015) Hong Gil Lee et al.   PLANT JOURNAL

CYCLIN-DEPENDENT KINASE G2 regulates salinity stress response and salt mediated flowering in Arabidopsis thaliana

(2015) Xiaoyan Ma et al.   PLANT MOLECULAR BIOLOGY

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Multidimensional approaches for studying plant defence against insects: from ecology to omics and synthetic biology

(2014) P. Barah et al.   JOURNAL OF EXPERIMENTAL BOTANY

Natural Variation in Abiotic Stress Responsive Gene Expression and Local Adaptation to Climate in Arabidopsis thaliana

(2014) Jesse R. Lasky et al.   MOLECULAR BIOLOGY AND EVOLUTION

Abiotic and biotic stress combinations

(2014) Nobuhiro Suzuki et al.   NEW PHYTOLOGIST

The EC Night-Time Repressor Plays a Crucial Role in Modulating Circadian Clock Transcriptional Circuitry by Conservatively Double-Checking Both Warm-Night and Night-Time-Light Signals in a Synergistic Manner in Arabidopsis thaliana

(2014) Takeshi Mizuno et al.   PLANT AND CELL PHYSIOLOGY

Arabidopsis miR156 Regulates Tolerance to Recurring Environmental Stress through SPL Transcription Factors

(2014) A. Stief et al.   PLANT CELL

Fast Retrograde Signaling in Response to High Light Involves Metabolite Export, MITOGEN-ACTIVATED PROTEIN KINASE6, and AP2/ERF Transcription Factors inArabidopsis

(2014) Marc Oliver Vogel et al.   PLANT CELL

A Functional and Evolutionary Perspective on Transcription Factor Binding in Arabidopsis thaliana

(2014) K. S. Heyndrickx et al.   PLANT CELL

ArabidopsisEnsemble Reverse-Engineered Gene Regulatory Network Discloses Interconnected Transcription Factors in Oxidative Stress

(2014) Vanessa Vermeirssen et al.   PLANT CELL

The Positive Regulatory Roles of the TIFY10 Proteins in Plant Responses to Alkaline Stress

(2014) Dan Zhu et al.   PLoS One

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

Applying evolutionary biology to address global challenges

(2014) S. P. Carroll et al.   SCIENCE

Variation in Arabidopsis flowering time associated with cis-regulatory variation in CONSTANS

(2014) Ulises Rosas et al.   Nature Communications

Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana

(2014) Alessandra M. Sullivan et al.   Cell Reports

The Membrane-Associated Transcription Factor NAC089 Controls ER-Stress-Induced Programmed Cell Death in Plants

(2014) Zheng-Ting Yang et al.   PLoS Genetics

Enhancing crop resilience to combined abiotic and biotic stress through the dissection of physiological and molecular crosstalk

(2014) Christos Kissoudis et al.   Frontiers in Plant Science

Regulation of primary plant metabolism during plant-pathogen interactions and its contribution to plant defense

(2014) Clemencia M. Rojas et al.   Frontiers in Plant Science

Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

(2013) Pankaj Barah et al.   BMC GENOMICS

Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome

(2013) Hume Stroud et al.   CELL

The Arabidopsis thaliana MYB60 promoter provides a tool for the spatio-temporal control of gene expression in stomatal guard cells

(2013) Fabio Rusconi et al.   JOURNAL OF EXPERIMENTAL BOTANY

Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics

(2013) Mahantesha Naika et al.   Molecular BioSystems

PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

(2013) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

STIFDB2: An Updated Version of Plant Stress-Responsive TranscrIption Factor DataBase with Additional Stress Signals, Stress-Responsive Transcription Factor Binding Sites and Stress-Responsive Genes in Arabidopsis and Rice

(2013) Mahantesha Naika et al.   PLANT AND CELL PHYSIOLOGY

Multisite Light-Induced Phosphorylation of the Transcription Factor PIF3 Is Necessary for Both Its Rapid Degradation and Concomitant Negative Feedback Modulation of Photoreceptor phyB Levels in Arabidopsis

(2013) W. Ni et al.   PLANT CELL

Interaction between salt and heat stress: when two wrongs make a right

(2013) JOSÉ M. COLMENERO-FLORES et al.   PLANT CELL AND ENVIRONMENT

Divergent DNA-Binding Specificities of a Group of ETHYLENE RESPONSE FACTOR Transcription Factors Involved in Plant Defense

(2013) T. Shoji et al.   PLANT PHYSIOLOGY

Identification of Genes Involved in the Response of Arabidopsis to Simultaneous Biotic and Abiotic Stresses

(2013) N. J. Atkinson et al.   PLANT PHYSIOLOGY

Cross-Repressive Interactions between SOC1 and the GATAs GNC and GNL/CGA1 in the Control of Greening, Cold Tolerance, and Flowering Time in Arabidopsis

(2013) R. Richter 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

Transcriptome Responses to Combinations of Stresses in Arabidopsis

(2013) S. Rasmussen et al.   PLANT PHYSIOLOGY

The Impact of Gene Expression Variation on the Robustness and Evolvability of a Developmental Gene Regulatory Network

(2013) David A. Garfield et al.   PLOS BIOLOGY

Conserved versatile master regulators in signalling pathways in response to stress in plants

(2013) V. E. Balderas-Hernandez et al.   AoB Plants

Genome scale transcriptional response diversity among ten ecotypes of Arabidopsis thaliana during heat stress

(2013) Pankaj Barah et al.   Frontiers in Plant Science

Towards understanding how molecular networks evolve in plants

(2012) Lee Chae et al.   CURRENT OPINION IN PLANT BIOLOGY

The interaction of plant biotic and abiotic stresses: from genes to the field

(2012) N. J. Atkinson et al.   JOURNAL OF EXPERIMENTAL BOTANY

Molecular Crosstalk Between PAMP-Triggered Immunity and Photosynthesis

(2012) Vera Göhre et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Reverse engineering and analysis of large genome-scale gene networks

(2012) Maneesha Aluru et al.   NUCLEIC ACIDS RESEARCH

Systems Analysis of Plant Functional, Transcriptional, Physical Interaction, and Metabolic Networks

(2012) George W. Bassel et al.   PLANT CELL

ArabidopsisMYC2 Interacts with DELLA Proteins in Regulating Sesquiterpene Synthase Gene Expression

(2012) Gao-Jie Hong et al.   PLANT CELL

DELLA Signaling Mediates Stress-Induced Cell Differentiation in Arabidopsis Leaves through Modulation of Anaphase-Promoting Complex/Cyclosome Activity

(2012) H. Claeys et al.   PLANT PHYSIOLOGY

ERF5 and ERF6 Play Redundant Roles as Positive Regulators of JA/Et-Mediated Defense against Botrytis cinerea in Arabidopsis

(2012) Caroline S. Moffat et al.   PLoS One

CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses

(2012) A. G. Lai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator

(2012) W. Huang et al.   SCIENCE

WRKY Transcription Factors Involved in Activation of SA Biosynthesis Genes

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

Partially observed bipartite network analysis to identify predictive connections in transcriptional regulatory networks

(2011) Angel Alvarez et al.   BMC Systems Biology

Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network

(2011) Taewoo Ryu et al.   BMC Systems Biology

Evolutionary Origins of Transcription Factor Binding Site Clusters

(2011) Xin He et al.   MOLECULAR BIOLOGY AND EVOLUTION

Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis

(2011) K. Klopffleisch et al.   Molecular Systems Biology

WRKY22 transcription factor mediates dark-induced leaf senescence in Arabidopsis

(2011) Xiang Zhou et al.   MOLECULES AND CELLS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

HsfA1d and HsfA1e Involved in the Transcriptional Regulation of HsfA2 Function as Key Regulators for the Hsf Signaling Network in Response to Environmental Stress

(2011) Ayako Nishizawa-Yokoi et al.   PLANT AND CELL PHYSIOLOGY

TheArabidopsisbHLH Transcription Factors MYC3 and MYC4 Are Targets of JAZ Repressors and Act Additively with MYC2 in the Activation of Jasmonate Responses

(2011) Patricia Fernández-Calvo et al.   PLANT CELL

Identification of the MBF1 heat-response regulon of Arabidopsis thaliana

(2011) Nobuhiro Suzuki et al.   PLANT JOURNAL

The ethylene response factor AtERF11 that is transcriptionally modulated by the bZIP transcription factor HY5 is a crucial repressor for ethylene biosynthesis in Arabidopsis

(2011) Zhuofu Li et al.   PLANT JOURNAL

The TOPLESS Interactome: A Framework for Gene Repression in Arabidopsis

(2011) B. Causier et al.   PLANT PHYSIOLOGY

Characterization of constricted fruit (ctf) Mutant Uncovers a Role for AtMYB117/LOF1 in Ovule and Fruit Development in Arabidopsis thaliana

(2011) Maria Dolores Gomez et al.   PLoS One

Integration of low temperature and light signaling during cold acclimation response in Arabidopsis

(2011) R. Catala et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana

(2011) C. Zou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for Network Evolution in an Arabidopsis Interactome Map

(2011) et al.   SCIENCE

BioMart Central Portal: an open database network for the biological community

(2011) J. M. Guberman et al.   Database-The Journal of Biological Databases and Curation

PRR5 regulates phosphorylation, nuclear import and subnuclear localization of TOC1 in the Arabidopsis circadian clock

(2010) Lei Wang et al.   EMBO JOURNAL

NINJA connects the co-repressor TOPLESS to jasmonate signalling

(2010) Laurens Pauwels et al.   NATURE

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

Regulation of transcription in plants: mechanisms controlling developmental switches

(2010) Kerstin Kaufmann et al.   NATURE REVIEWS GENETICS

AGRIS: the Arabidopsis Gene Regulatory Information Server, an update

(2010) A. Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis shoot organogenesis is enhanced by an amino acid change in the ATHB15 transcription factor

(2010) J. Duclercq et al.   PLANT BIOLOGY

Natural Variation of Transcriptional Auxin Response Networks in Arabidopsis thaliana

(2010) C. Delker et al.   PLANT CELL

PSEUDO-RESPONSE REGULATORS 9, 7, and 5 Are Transcriptional Repressors in the Arabidopsis Circadian Clock

(2010) N. Nakamichi et al.   PLANT CELL

NF-YC3, NF-YC4 and NF-YC9 are required for CONSTANS-mediated, photoperiod-dependent flowering in Arabidopsis thaliana

(2010) Roderick W. Kumimoto et al.   PLANT JOURNAL

Genome-Wide Analysis of Ethylene-Responsive Element Binding Factor-Associated Amphiphilic Repression Motif-Containing Transcriptional Regulators in Arabidopsis

(2010) S. Kagale et al.   PLANT PHYSIOLOGY

Plant molecular stress responses face climate change

(2010) Ishita Ahuja et al.   TRENDS IN PLANT SCIENCE

Arabidopsis gene co-expression network and its functional modules

(2009) Linyong Mao et al.   BMC BIOINFORMATICS

Detection of in vivo interactions between Arabidopsis class A-HSFs, using a novel BiFC fragment, and identification of novel class B-HSF interacting proteins

(2009) Ming Li et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

Molecular Basis of Disease Resistance Acquired through Cold Acclimation in Overwintering Plants

(2009) Chikako Kuwabara et al.   JOURNAL OF PLANT BIOLOGY

Primary Metabolism and Plant Defense—Fuel for the Fire

(2009) Melvin D. Bolton   MOLECULAR PLANT-MICROBE INTERACTIONS

Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture

(2009) Raja Jothi et al.   Molecular Systems Biology

The Cytosolic Protein Response as a Subcomponent of the Wider Heat Shock Response in Arabidopsis

(2009) A. Sugio et al.   PLANT CELL

The High Light Response in Arabidopsis Involves ABA Signaling between Vascular and Bundle Sheath Cells

(2009) G. Galvez-Valdivieso et al.   PLANT CELL

What Has Natural Variation Taught Us about Plant Development, Physiology, and Adaptation?

(2009) C. Alonso-Blanco et al.   PLANT CELL

Crosstalk between Cold Response and Flowering in Arabidopsis Is Mediated through the Flowering-Time Gene SOC1 and Its Upstream Negative Regulator FLC

(2009) E. Seo et al.   PLANT CELL

Reactive oxygen species homeostasis and signalling during drought and salinity stresses

(2009) GAD MILLER et al.   PLANT CELL AND ENVIRONMENT

A role for circadian evening elements in cold-regulated gene expression in Arabidopsis

(2009) Michael D. Mikkelsen et al.   PLANT JOURNAL

Transcriptional Regulatory Networks in Response to Abiotic Stresses in Arabidopsis and Grasses

(2009) K. Nakashima et al.   PLANT PHYSIOLOGY

Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks

(2009) K. Vandepoele et al.   PLANT PHYSIOLOGY

Over-expression of CONSTANS-LIKE 5 can induce flowering in short-day grown Arabidopsis

(2009) Miriam Hassidim et al.   PLANTA

A Functional Genomics Approach Reveals CHE as a Component of the Arabidopsis Circadian Clock

(2009) J. L. Pruneda-Paz et al.   SCIENCE

Evolving gene expression: from G to E to G×E

(2009) Andrea Hodgins-Davis et al.   TRENDS IN ECOLOGY & EVOLUTION

Evolution of Stress-Regulated Gene Expression in Duplicate Genes of Arabidopsis thaliana

(2009) Cheng Zou et al.   PLoS Genetics

Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions

(2009) Javier Carrera et al.   GENOME BIOLOGY

Systems Approaches to Identifying Gene Regulatory Networks in Plants

(2008) Terri A. Long et al.   Annual Review of Cell and Developmental Biology

Role of Stomata in Plant Innate Immunity and Foliar Bacterial Diseases

(2008) Maeli Melotto et al.   Annual Review of Phytopathology

Light has a specific role in modulating Arabidopsis gene expression at low temperature

(2008) Arto J Soitamo et al.   BMC PLANT BIOLOGY

The Transcriptional Co-activator MBF1c Is a Key Regulator of Thermotolerance inArabidopsis thaliana

(2008) Nobuhiro Suzuki et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The future of biocuration

(2008) Doug Howe et al.   NATURE

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

(2008) Luis López-Maury et al.   NATURE REVIEWS GENETICS

The Arabidopsis NFYA5 Transcription Factor Is Regulated Transcriptionally and Posttranscriptionally to Promote Drought Resistance

(2008) W.-X. Li et al.   PLANT CELL

MYBL2 is a new regulator of flavonoid biosynthesis inArabidopsis thaliana

(2008) Christian Dubos et al.   PLANT JOURNAL

BTB and TAZ domain scaffold proteins perform a crucial function in Arabidopsis development

(2008) Hélène S. Robert et al.   PLANT JOURNAL

Inferring Condition-Specific Modulation of Transcription Factor Activity in Yeast through Regulon-Based Analysis of Genomewide Expression

(2008) André Boorsma et al.   PLoS One