ThePopulusARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function

Detecting clustering and ordering binding patterns among transcription factors via point process models

(2014) Maria Cha et al.   BIOINFORMATICS

Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees

(2014) Lijun Liu et al.   BMC GENOMICS

Coherent Functional Modules Improve Transcription Factor Target Identification, Cooperativity Prediction, and Disease Association

(2014) Konrad J. Karczewski et al.   PLoS Genetics

Comparative study of RNA-seq- and Microarray-derived coexpression networks in Arabidopsis thaliana

(2013) Federico M. Giorgi et al.   BIOINFORMATICS

PtrHB7, a class III HD-Zip Gene, Plays a Critical Role in Regulation of Vascular Cambium Differentiation in Populus

(2013) Yingying Zhu et al.   Molecular Plant

Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets

(2013) Li Teng 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 F-Box Protein CORONATINE INSENSITIVE1 Is Stabilized by SCFCOI1 and Degraded via the 26S Proteasome Pathway

(2013) J. Yan et al.   PLANT CELL

A Quartet of PIF bHLH Factors Provides a Transcriptionally Centered Signaling Hub That Regulates Seedling Morphogenesis through Differential Expression-Patterning of Shared Target Genes in Arabidopsis

(2013) Yu Zhang et al.   PLoS Genetics

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Unraveling the KNOTTED1 regulatory network in maize meristems

(2012) N. Bolduc et al.   GENES & DEVELOPMENT

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

(2012) C. Cheng et al.   GENOME RESEARCH

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

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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

A combinatorial TIR1/AFB–Aux/IAA co-receptor system for differential sensing of auxin

(2012) Luz Irina A Calderón Villalobos et al.   Nature Chemical Biology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs

(2012) Morgane Thomas-Chollier et al.   Nature Protocols

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

Genome-wide binding-site analysis of REVOLUTA reveals a link between leaf patterning and light-mediated growth responses

(2012) Ronny Brandt et al.   PLANT JOURNAL

The Vascular Pathogen Verticillium longisporum Requires a Jasmonic Acid-Independent COI1 Function in Roots to Elicit Disease Symptoms in Arabidopsis Shoots

(2012) A. Ralhan et al.   PLANT PHYSIOLOGY

Histidine Kinase Activity of the Ethylene Receptor ETR1 Facilitates the Ethylene Response in Arabidopsis

(2012) B. P. Hall et al.   PLANT PHYSIOLOGY

Arabidopsis ETR1 and ERS1 Differentially Repress the Ethylene Response in Combination with Other Ethylene Receptor Genes

(2012) Q. Liu et al.   PLANT PHYSIOLOGY

Genome-Wide Location Analysis Reveals Distinct Transcriptional Circuitry by Paralogous Regulators Foxa1 and Foxa2

(2012) Irina M. Bochkis et al.   PLoS Genetics

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Brassinosteroid Signaling Network and Regulation of Photomorphogenesis

(2011) Zhi-Yong Wang et al.   Annual Review of Genetics

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

RETRACTED: The AFB4 Auxin Receptor Is a Negative Regulator of Auxin Signaling in Seedlings

(2011) Katie Greenham et al.   CURRENT BIOLOGY

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus

(2011) E. Rodgers-Melnick et al.   GENOME RESEARCH

RSAT 2011: regulatory sequence analysis tools

(2011) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

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

(2011) X. Ouyang et al.   PLANT CELL

A Mechanistic Link between STM and CUC1 during Arabidopsis Development

(2011) S. V. Spinelli et al.   PLANT PHYSIOLOGY

The Populus Class III HD ZIP Transcription Factor POPCORONA Affects Cell Differentiation during Secondary Growth of Woody Stems

(2011) Juan Du et al.   PLoS One

Genome-Wide Tissue-Specific Occupancy of the Hox Protein Ultrabithorax and Hox Cofactor Homothorax in Drosophila

(2011) Matthew Slattery et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

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

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Integration of Brassinosteroid Signal Transduction with the Transcription Network for Plant Growth Regulation in Arabidopsis

(2010) Yu Sun et al.   DEVELOPMENTAL CELL

The Role of Two F-Box Proteins, SLEEPY1 and SNEEZY, in Arabidopsis Gibberellin Signaling

(2010) T. Ariizumi et al.   PLANT PHYSIOLOGY

The Populus Class III HD ZIP, popREVOLUTA, Influences Cambium Initiation and Patterning of Woody Stems

(2010) M. Robischon et al.   PLANT PHYSIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Polyploidy and angiosperm diversification

(2009) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

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

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

The Maize Transcription Factor KNOTTED1 Directly Regulates the Gibberellin Catabolism Gene ga2ox1

(2009) N. Bolduc et al.   PLANT CELL

The Populus homeobox gene ARBORKNOX2 regulates cell differentiation during secondary growth

(2009) Juan Du et al.   PLANT JOURNAL

Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis

(2009) A. Mustroph et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Systems Approach Reveals Regulatory Circuitry for Arabidopsis Trichome Initiation by the GL3 and GL1 Selectors

(2009) Kengo Morohashi et al.   PLoS Genetics

RSAT: regulatory sequence analysis tools

(2008) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

BSKs Mediate Signal Transduction from the Receptor Kinase BRI1 in Arabidopsis

(2008) W. Tang et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY