Positional distribution of transcription factor binding sites in Arabidopsis thaliana

RNA-seq analysis of an apical meristem time series reveals a critical point in Arabidopsis thaliana flower initiation

(2015) Anna V. Klepikova et al.   BMC GENOMICS

Transcriptome Dynamics of the Stomatal Lineage: Birth, Amplification, and Termination of a Self-Renewing Population

(2015) Jessika Adrian et al.   DEVELOPMENTAL CELL

Transcriptome dynamics of developing maize leaves and genomewide prediction ofciselements and their cognate transcription factors

(2015) Chun-Ping Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor

(2014) Martiniano M Ricardi et al.   BMC PLANT BIOLOGY

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

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

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

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

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

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

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis

(2012) W. Zhang et al.   PLANT CELL

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

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

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation

(2010) Zhenguo Lin et al.   BMC GENOMICS

Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

(2010) Yuling Jiao et al.   Molecular Systems Biology

Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)

(2010) Kerstin Kaufmann et al.   Nature Protocols

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Positional distribution of human transcription factor binding sites

(2008) Mark Koudritsky et al.   NUCLEIC ACIDS RESEARCH