Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies

(2012) C. Smaczniak et al.   DEVELOPMENT

Predicting cell-type-specific gene expression from regions of open chromatin

(2012) A. Natarajan et al.   GENOME 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

BASIC PENTACYSTEINE Proteins Mediate MADS Domain Complex Binding to the DNA for Tissue-Specific Expression of Target Genes inArabidopsis

(2012) Sara Simonini et al.   PLANT CELL

Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA

(2012) S. E. Wuest et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

(2011) Qiye He et al.   NATURE GENETICS

Overlapping and antagonistic activities of BASIC PENTACYSTEINE genes affect a range of developmental processes in Arabidopsis

(2011) Mona M. Monfared et al.   PLANT JOURNAL

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions

(2011) Jose M Muiño et al.   Plant Methods

FLOWERING LOCUS C (FLC) regulates development pathways throughout the life cycle of Arabidopsis

(2011) W. Deng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SHINE Transcription Factors Act Redundantly to Pattern the Archetypal Surface of Arabidopsis Flower Organs

(2011) Jian Xin Shi et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

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

Regulation of transcription in plants: mechanisms controlling developmental switches

(2010) Kerstin Kaufmann et al.   NATURE REVIEWS GENETICS

Arabidopsis Basic Leucine-Zipper Transcription Factors TGA9 and TGA10 Interact with Floral Glutaredoxins ROXY1 and ROXY2 and Are Redundantly Required for Anther Development

(2010) J. Murmu et al.   PLANT PHYSIOLOGY

Orchestration of Floral Initiation by APETALA1

(2010) K. Kaufmann et al.   SCIENCE

Control of cell proliferation in Arabidopsis thaliana by microRNA miR396

(2009) R. E. Rodriguez et al.   DEVELOPMENT

Regulation of Floral Patterning by Flowering Time Genes

(2009) Chang Liu et al.   DEVELOPMENTAL CELL

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

PlnTFDB: updated content and new features of the plant transcription factor database

(2009) Paulino Pérez-Rodríguez et al.   NUCLEIC ACIDS RESEARCH

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Dual Effects of miR156-Targeted SPL Genes and CYP78A5/KLUH on Plastochron Length and Organ Size in Arabidopsis thaliana

(2008) J.-W. Wang et al.   PLANT CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY