Computational exploration of cis-regulatory modules in rhythmic expression data using the “Exploration of Distinctive CREs and CRMs” (EDCC) and “CRM Network Generator” (CNG) programs

LWD–TCP complex activates the morning gene CCA1 in Arabidopsis

(2016) Jing-Fen Wu et al.   Nature Communications

MYB96 shapes the circadian gating of ABA signaling in Arabidopsis

(2016) Hong Gil Lee et al.   Scientific Reports

Salt-Related MYB1 Coordinates Abscisic Acid Biosynthesis and Signaling during Salt Stress in Arabidopsis

(2015) Ting Wang et al.   PLANT PHYSIOLOGY

SRR1 is essential to repress flowering in non-inductive conditions in Arabidopsis thaliana

(2014) Mikael Johansson et al.   JOURNAL OF EXPERIMENTAL BOTANY

Differential Control of Pre-Invasive and Post-Invasive Antibacterial Defense by the Arabidopsis Circadian Clock

(2014) Christin Korneli et al.   PLANT AND CELL PHYSIOLOGY

A Genome-Scale Resource for the Functional Characterization of Arabidopsis Transcription Factors

(2014) Jose L. Pruneda-Paz et al.   Cell Reports

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation inSaccharomyces cerevisiae

(2013) Miguel Cacho Teixeira et al.   NUCLEIC ACIDS RESEARCH

Crosstalk between the Circadian Clock and Innate Immunity in Arabidopsis

(2013) Chong Zhang et al.   PLoS Pathogens

Diurnal Dependence of Growth Responses to Shade in Arabidopsis: Role of Hormone, Clock, and Light Signaling

(2012) Romina Sellaro et al.   Molecular Plant

Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor

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

Evolutionary artificial neural networks: a review

(2011) Shifei Ding et al.   ARTIFICIAL INTELLIGENCE REVIEW

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis

(2011) R. Yamashita et al.   GENOME RESEARCH

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

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Thousands of Cis-Regulatory Sequence Combinations Are Shared by Arabidopsis and Poplar

(2011) J. Ding et al.   PLANT PHYSIOLOGY

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

Circadian clock-dependent gating in ABA signalling networks

(2011) David Seung et al.   PROTOPLASMA

Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation

(2010) R. Yang et al.   BIOINFORMATICS

Discover regulatory DNA elements using chromatin signatures and artificial neural network

(2010) Hiram A. Firpi et al.   BIOINFORMATICS

Systematic identification of conserved motif modules in the human genome

(2010) Xiaohui Cai et al.   BMC GENOMICS

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

Early transcriptomic changes induced by magnesium deficiency in Arabidopsis thaliana reveal the alteration of circadian clock gene expression in roots and the triggering of abscisic acid-responsive genes

(2010) Christian Hermans et al.   NEW PHYTOLOGIST

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

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

(2010) N. Nakamichi et al.   PLANT CELL

TCP Transcription Factors Link the Regulation of Genes Encoding Mitochondrial Proteins with the Circadian Clock inArabidopsis thaliana

(2010) Estelle Giraud et al.   PLANT CELL

Circadian control of carbohydrate availability for growth in Arabidopsis plants at night

(2010) A. Graf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TOC1 functions as a molecular switch connecting the circadian clock with plant responses to drought

(2009) Tommaso Legnaioli et al.   EMBO JOURNAL

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

(2009) K. Vandepoele et al.   PLANT PHYSIOLOGY

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

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

The ‘ABC’ of MADS domain protein behaviour and interactions

(2009) Richard G.H. Immink et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

MOPAT: a graph-based method to predict recurrent cis -regulatory modules from known motifs

(2008) Jianfei Hu et al.   NUCLEIC ACIDS RESEARCH

Comparative Transcriptome of Diurnally Oscillating Genes and Hormone-Responsive Genes in Arabidopsis thaliana: Insight into Circadian Clock-Controlled Daily Responses to Common Ambient Stresses in Plants

(2008) Takeshi Mizuno et al.   PLANT AND CELL PHYSIOLOGY

The small glycine-rich RNA binding protein At GRP7 promotes floral transition in Arabidopsis thaliana

(2008) Corinna Streitner et al.   PLANT JOURNAL

Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules

(2008) Todd P. Michael et al.   PLoS Genetics

A Morning-Specific Phytohormone Gene Expression Program underlying Rhythmic Plant Growth

(2008) Todd P Michael et al.   PLOS BIOLOGY