Subtle Changes in Motif Positioning Cause Tissue-Specific Effects on Robustness of an Enhancer's Activity

Phenotypic impact of genomic structural variation: insights from and for human disease

(2013) Joachim Weischenfeldt et al.   NATURE REVIEWS GENETICS

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

(2013) Hong Jin et al.   PLoS Genetics

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

(2012) Guillaume Junion et al.   CELL

Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing

(2012) T. Zichner et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network

(2012) B. W. Busser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

(2012) Andreas Massouras et al.   PLoS Genetics

Master Transcription Factors Determine Cell-Type-Specific Responses to TGF-β Signaling

(2011) Alan C. Mullen et al.   CELL

Lineage Regulators Direct BMP and Wnt Pathways to Cell-Specific Programs during Differentiation and Regeneration

(2011) Eirini Trompouki et al.   CELL

Paused RNA Polymerase II as a Developmental Checkpoint

(2011) Michael Levine   CELL

Building Enhancers from the Ground Up: A Synthetic Biology Approach

(2011) Roee Amit et al.   CELL

Mathematical modeling of gene expression: a guide for the perplexed biologist

(2011) Ahmet Ay et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Rapid Evolutionary Rewiring of a Structurally Constrained Eye Enhancer

(2011) Christina I. Swanson et al.   CURRENT BIOLOGY

Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer

(2011) P. Struffi et al.   DEVELOPMENT

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity

(2011) D. S. Parker et al.   Science Signaling

Consequences of Eukaryotic Enhancer Architecture for Gene Expression Dynamics, Development, and Fitness

(2011) Michael Z. Ludwig et al.   PLoS Genetics

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

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

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

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

Changes in Selective Effects Over Time Facilitate Turnover of Enhancer Sequences

(2010) K. Bullaughey   GENETICS

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo

(2010) Walid D Fakhouri et al.   Molecular Systems Biology

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

Emerging properties of animal gene regulatory networks

(2010) Eric H. Davidson   NATURE

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF-β effectors

(2010) Nithya BabuRajendran et al.   NUCLEIC ACIDS RESEARCH

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Conservation and divergence in developmental networks: a view from Drosophila myogenesis

(2009) Lucia Ciglar et al.   CURRENT OPINION IN CELL BIOLOGY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Synchronous and Stochastic Patterns of Gene Activation in theDrosophilaEmbryo

(2009) Alistair N. Boettiger et al.   SCIENCE

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

cis-Regulatory networks during development: a view of Drosophila

(2008) Stefan Bonn et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The words of the regulatory code are arranged in a variable manner in highly conserved enhancers

(2008) Sepand Rastegar et al.   DEVELOPMENTAL BIOLOGY

Design flexibility in cis-regulatory control of gene expression: Synthetic and comparative evidence

(2008) Louisa M. Liberman et al.   DEVELOPMENTAL BIOLOGY

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz 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