Next-Generation Sequencing of Genomic DNA Fragments Bound to a Transcription Factor in Vitro Reveals Its Regulatory Potential

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Arabidopsis Phytochrome A Directly Targets Numerous Promoters for Individualized Modulation of Genes in a Wide Range of Pathways

(2014) F. Chen 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

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

ppdb: plant promoter database version 3.0

(2013) Ayaka Hieno et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis B-BOX Protein BBX25 Interacts with HY5, Negatively Regulating BBX22 Expression to Suppress Seedling Photomorphogenesis

(2013) S. N. Gangappa et al.   PLANT CELL

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis

(2013) Katherine Noelani Chang et al.   eLife

Molecular Interactions of GBF1 with HY5 and HYH Proteins during Light-mediated Seedling Development inArabidopsis thaliana

(2012) Aparna Singh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A novel role for the floral homeotic gene APETALA2 during Arabidopsis fruit development

(2011) J. J. Ripoll et al.   DEVELOPMENT

Genome-Wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL3 Reveals Its Novel Function in Arabidopsis Development

(2011) X. Ouyang et al.   PLANT CELL

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

(2010) A. Jolma et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Practical cell-free protein synthesis system using purified wheat embryos

(2010) Kazuyuki Takai et al.   Nature Protocols

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

GADEM: A Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an EM Algorithm for Motif Discovery

(2009) Leping Li   JOURNAL OF COMPUTATIONAL BIOLOGY

Functional Analysis of Transcription Factors in Arabidopsis

(2009) Nobutaka Mitsuda et al.   PLANT AND CELL PHYSIOLOGY

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

LZF1, a HY5-regulated transcriptional factor, functions in Arabidopsis de-etiolation

(2008) Chiung-swey Joanne Chang et al.   PLANT JOURNAL

DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins

(2008) Y. H. Song et al.   PLANT PHYSIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY