Evolutionary Origins of Transcription Factor Binding Site Clusters

Gene Expression Noise in Spatial Patterning: hunchback Promoter Structure Affects Noise Amplitude and Distribution in Drosophila Segmentation

(2011) David M. Holloway et al.   PLoS Computational Biology

The Bicoid Morphogen System

(2010) Aude Porcher et al.   CURRENT BIOLOGY

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

(2010) V. Gotea et al.   GENOME RESEARCH

Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers

(2010) Justin Crocker et al.   Nature Communications

Quantitative Analysis of the Drosophila Segmentation Regulatory Network Using Pattern Generating Potentials

(2010) Majid Kazemian et al.   PLOS BIOLOGY

Redundancy and the Evolution of Cis-Regulatory Element Multiplicity

(2010) Tiago Paixão et al.   PLoS Computational Biology

Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression

(2010) Xin He et al.   PLoS Computational Biology

Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers

(2010) Richard W. Lusk et al.   PLoS Genetics

The Fitness Landscapes of cis-Acting Binding Sites in Different Promoter and Environmental Contexts

(2010) Ryan K. Shultzaberger et al.   PLoS Genetics

A Biophysical Model for Analysis of Transcription Factor Interaction and Binding Site Arrangement from Genome-Wide Binding Data

(2009) Xin He et al.   PLoS One

Statistical mechanics of convergent evolution in spatial patterning

(2009) B. S. Khatri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Regulatory Sequences in 12 Drosophila Species

(2009) Jaebum Kim et al.   PLoS Genetics

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

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

Systematic functional characterization of cis-regulatory motifs in human core promoters

(2008) S. Sinha et al.   GENOME RESEARCH

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE

Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites

(2008) V. Mustonen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA