A transcription factor hierarchy defines an environmental stress response network

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

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

cDREM: Inferring Dynamic Combinatorial Gene Regulation

(2015) Aaron Wise et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Agrochemical control of plant water use using engineered abscisic acid receptors

(2015) Sang-Youl Park et al.   NATURE

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana

(2015) Jason S. Cumbie et al.   Plant Methods

Transcriptional control of tissue formation throughout root development

(2015) M. A. Moreno-Risueno et al.   SCIENCE

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

(2014) S. Anders et al.   BIOINFORMATICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

A Mesoscale Abscisic Acid Hormone Interactome Reveals a Dynamic Signaling Landscape in Arabidopsis

(2014) Shelley Lumba et al.   DEVELOPMENTAL CELL

Histone-Fold Domain Protein NF-Y Promotes Chromatin Accessibility for Cell Type-Specific Master Transcription Factors

(2014) Andrew J. Oldfield et al.   MOLECULAR CELL

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

A Chloroplast Retrograde Signal Regulates Nuclear Alternative Splicing

(2014) E. Petrillo et al.   SCIENCE

RDAVIDWebService: a versatile R interface to DAVID

(2013) C. Fresno et al.   BIOINFORMATICS

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

bHLH122is important for drought and osmotic stress resistance inArabidopsisand in the repression of ABA catabolism

(2013) Wenwen Liu et al.   NEW PHYTOLOGIST

Ensembl Genomes 2013: scaling up access to genome-wide data

(2013) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Functional characterization ofArabidopsis HsfA6a as a heat-shock transcription factor under high salinity and dehydration conditions

(2013) SUNG MIN HWANG et al.   PLANT CELL AND ENVIRONMENT

ABA and the ubiquitin E3 ligase KEEP ON GOING affect proteolysis of theArabidopsis thalianatranscription factors ABF1 and ABF3

(2013) Yi-Tze Chen et al.   PLANT JOURNAL

NUCLEAR FACTOR Y Transcription Factors Have Both Opposing and Additive Roles in ABA-Mediated Seed Germination

(2013) Roderick W. Kumimoto et al.   PLoS One

Quantitative phosphoproteomics identifies SnRK2 protein kinase substrates and reveals the effectors of abscisic acid action

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

bHLH Transcription Factors That Facilitate K+ Uptake During Stomatal Opening Are Repressed by Abscisic Acid Through Phosphorylation

(2013) Y. Takahashi et al.   Science Signaling

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

ATAF1 transcription factor directly regulates abscisic acid biosynthetic gene NCED3 in Arabidopsis thaliana

(2013) Michael Krogh Jensen et al.   FEBS Open Bio

Phosphorylation of the zinc finger transcriptional regulator ZAT6 by MPK6 regulates Arabidopsis seed germination under salt and osmotic stress

(2012) Xiao-Min Liu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

DAVID-WS: a stateful web service to facilitate gene/protein list analysis

(2012) X. Jiao et al.   BIOINFORMATICS

Genome-wide in silico prediction of gene expression

(2012) Robert C. McLeay et al.   BIOINFORMATICS

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

(2012) Marcel H Schulz et al.   BMC Systems Biology

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Functional roles of the protein phosphatase 2C, AtAIP1, in abscisic acid signaling and sugar tolerance in Arabidopsis

(2012) Chae Woo Lim et al.   PLANT SCIENCE

Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development

(2012) C. Smaczniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Prioritizing candidate disease genes by network-based boosting of genome-wide association data

(2011) I. Lee et al.   GENOME RESEARCH

Ectopic expression of different cytokinin-regulated transcription factor genes of Arabidopsis thaliana alters plant growth and development

(2011) Ireen Köllmer et al.   JOURNAL OF PLANT PHYSIOLOGY

ABA-mediated transcriptional regulation in response to osmotic stress in plants

(2011) Yasunari Fujita et al.   JOURNAL OF PLANT RESEARCH

Auxin-nonresponsive grape Aux/IAA19 is a positive regulator of plant growth

(2011) Minako Kohno et al.   MOLECULAR BIOLOGY REPORTS

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Age-Dependent Action of an ABA-Inducible Receptor Kinase, RPK1, as a Positive Regulator of Senescence in Arabidopsis Leaves

(2011) In Chul Lee et al.   PLANT AND CELL PHYSIOLOGY

The TOPLESS Interactome: A Framework for Gene Repression in Arabidopsis

(2011) B. Causier et al.   PLANT PHYSIOLOGY

SCARECROW-LIKE 3 promotes gibberellin signaling by antagonizing master growth repressor DELLA in Arabidopsis

(2011) Zhong-Lin Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Abscisic Acid: Emergence of a Core Signaling Network

(2010) Sean R. Cutler et al.   Annual Review of Plant Biology

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

DREB2C Interacts with ABF2, a bZIP Protein Regulating Abscisic Acid-Responsive Gene Expression, and Its Overexpression Affects Abscisic Acid Sensitivity

(2010) S.-j. Lee et al.   PLANT PHYSIOLOGY

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

Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice

(2010) K. Sugimoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

TheArabidopsis thalianaNAC transcription factor family: structure–function relationships and determinants of ANAC019 stress signalling

(2009) Michael K. Jensen et al.   BIOCHEMICAL JOURNAL

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

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

In vitro reconstitution of an abscisic acid signalling pathway

(2009) Hiroaki Fujii et al.   NATURE

The abscisic acid receptor PYR1 in complex with abscisic acid

(2009) Julia Santiago et al.   NATURE

Modulation of drought resistance by the abscisic acid receptor PYL5 through inhibition of clade A PP2Cs

(2009) Julia Santiago et al.   PLANT JOURNAL

AREB1, AREB2, and ABF3 are master transcription factors that cooperatively regulate ABRE-dependent ABA signaling involved in drought stress tolerance and require ABA for full activation

(2009) Takuya Yoshida et al.   PLANT JOURNAL

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

(2009) Z. Ouyang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulators of PP2C Phosphatase Activity Function as Abscisic Acid Sensors

(2009) Y. Ma et al.   SCIENCE

Abscisic Acid Inhibits Type 2C Protein Phosphatases via the PYR/PYL Family of START Proteins

(2009) S.-Y. Park et al.   SCIENCE

The zinc finger network of plants

(2008) S. Ciftci-Yilmaz et al.   CELLULAR AND MOLECULAR LIFE SCIENCES