Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization

Genome-Wide Screens for In Vivo Tinman Binding Sites Identify Cardiac Enhancers with Diverse Functional Architectures

(2013) Hong Jin et al.   PLoS Genetics

Interpreting the regulatory genome: the genomics of transcription factor function in Drosophila melanogaster

(2012) M. Slattery et al.   Briefings in Functional Genomics

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

A System of Repressor Gradients Spatially Organizes the Boundaries of Bicoid-Dependent Target Genes

(2012) Hongtao Chen et al.   CELL

crinkled reveals a new role for Wingless signaling in Drosophila denticle formation

(2012) A. Bejsovec et al.   DEVELOPMENT

Thecis-regulatory code of Hox function inDrosophila

(2012) Sebastian Sorge et al.   EMBO JOURNAL

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

(2012) Carl Herrmann et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Effectors of tridimensional cell morphogenesis and their evolution

(2012) Hélène Chanut-Delalande et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Deciphering the transcriptional cis-regulatory code

(2012) J. Omar Yáñez-Cuna et al.   TRENDS IN GENETICS

Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules

(2011) Marc S Halfon et al.   BMC GENOMICS

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

(2011) Matthew Slattery et al.   CELL

High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation

(2011) A. Ozdemir et al.   GENOME RESEARCH

Morphological evolution caused by many subtle-effect substitutions in regulatory DNA

(2011) Nicolás Frankel et al.   NATURE

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

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

(2011) Qiye He et al.   NATURE GENETICS

Deciphering the genome's regulatory code: The many languages of DNA

(2010) Jens Rister et al.   BIOESSAYS

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

A cis-Regulatory Signature in Ascidians and Flies, Independent of Transcription Factor Binding Sites

(2010) Pierre Khoueiry et al.   CURRENT BIOLOGY

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

(2010) Michael W. Perry et al.   CURRENT BIOLOGY

Zona Pellucida Domain Proteins Remodel the Apical Compartment for Localized Cell Shape Changes

(2010) Isabelle Fernandes et al.   DEVELOPMENTAL CELL

Structural Rules and Complex Regulatory Circuitry Constrain Expression of a Notch- and EGFR-Regulated Eye Enhancer

(2010) Christina I. Swanson et al.   DEVELOPMENTAL CELL

Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity

(2010) S. Rowan et al.   GENES & DEVELOPMENT

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

(2010) Lihua Julie Zhu et al.   NUCLEIC ACIDS RESEARCH

Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny

(2010) H. Rouault et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE

Robust Target Gene Discovery through Transcriptome Perturbations and Genome-Wide Enhancer Predictions in Drosophila Uncovers a Regulatory Basis for Sensory Specification

(2010) Stein Aerts et al.   PLOS BIOLOGY

Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances

(2010) Jaebum Kim et al.   PLoS Computational Biology

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

Organization of developmental enhancers in the Drosophila embryo

(2009) Dmitri Papatsenko 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

Expression of theDrosophilasecreted cuticle protein 73 (dsc73) requires shavenbaby

(2008) Deborah J. Andrew et al.   DEVELOPMENTAL DYNAMICS

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE

Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts

(2008) Justin Crocker et al.   PLOS BIOLOGY

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

(2008) Xiao-yong Li et al.   PLOS BIOLOGY

A Closer Look at the eve Stripe 2 Enhancers of Drosophila and Themira

(2008) Justin Crocker et al.   PLoS Genetics