Dynamics of Transcription Factor Binding Site Evolution

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

What Does It Take to Evolve an Enhancer? A Simulation-Based Study of Factors Influencing the Emergence of Combinatorial Regulation

(2015) T. Duque et al.   Genome Biology and Evolution

Coexpression networks identify brain region–specific enhancer RNAs in the human brain

(2015) Pu Yao et al.   NATURE NEUROSCIENCE

Ancestral Alleles in the Human Genome Based on Population Sequencing Data

(2015) Leeyoung Park   PLoS One

Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module

(2014) Alesia N. McKeown et al.   CELL

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

(2014) Cosmas D Arnold et al.   NATURE GENETICS

Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation

(2014) Petter Hammar et al.   NATURE GENETICS

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

(2014) Diego Villar et al.   NATURE REVIEWS GENETICS

Comparison of the theoretical and real-world evolutionary potential of a genetic circuit

(2014) M Razo-Mejia et al.   PHYSICAL BIOLOGY

Scaling of Gene Expression with Transcription-Factor Fugacity

(2014) Franz M. Weinert et al.   PHYSICAL REVIEW LETTERS

Evolutionary meandering of intermolecular interactions along the drift barrier

(2014) Michael Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Robustness and Evolvability of Transcription Factor Binding Sites

(2014) J. L. Payne et al.   SCIENCE

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

Quantitative Modeling of a Gene's Expression from Its Intergenic Sequence

(2014) Md. Abul Hassan Samee et al.   PLoS Computational Biology

Biophysical Fitness Landscapes for Transcription Factor Binding Sites

(2014) Allan Haldane et al.   PLoS Computational Biology

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

(2013) Klara Stefflova et al.   CELL

Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila

(2013) A. A. Alekseyenko et al.   GENES & DEVELOPMENT

Compensatory Evolution and the Origins of Innovations

(2013) E. Rajon et al.   GENETICS

Simulations of Enhancer Evolution Provide Mechanistic Insights into Gene Regulation

(2013) Thyago Duque et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of complex gene regulation by low-specificity binding sites

(2013) A. J. Stewart et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Dosage Compensation via Transposable Element Mediated Rewiring of a Regulatory Network

(2013) C. E. Ellison et al.   SCIENCE

Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression

(2013) Mathilde Paris et al.   PLoS Genetics

Why Transcription Factor Binding Sites Are Ten Nucleotides Long

(2012) A. J. Stewart et al.   GENETICS

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing

(2012) H. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A universal scaling law determines time reversibility and steady state of substitutions under selection

(2012) Michael Manhart et al.   THEORETICAL POPULATION BIOLOGY

Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli

(2012) Robert C. Brewster et al.   PLoS Computational Biology

Regulatory Variation Within and Between Species

(2011) Wei Zheng et al.   Annual Review of Genomics and Human Genetics

Evolutionary Origins of Transcription Factor Binding Site Clusters

(2011) Xin He et al.   MOLECULAR BIOLOGY AND EVOLUTION

Formation of Regulatory Modules by Local Sequence Duplication

(2011) Armita Nourmohammad et al.   PLoS Computational Biology

Does Positive Selection Drive Transcription Factor Binding Site Turnover? A Test with Drosophila Cis-Regulatory Modules

(2011) Bin Z. He et al.   PLoS Genetics

Variable Tandem Repeats Accelerate Evolution of Coding and Regulatory Sequences

(2010) Rita Gemayel et al.   Annual Review of Genetics

Noncooperative Interactions between Transcription Factors and Clustered DNA Binding Sites Enable Graded Transcriptional Responses to Environmental Inputs

(2010) Luca Giorgetti et al.   MOLECULAR CELL

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

(2010) J. B. Kinney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Transcription factor binding variation in the evolution of gene regulation

(2010) Robin D. Dowell   TRENDS IN GENETICS

Combinatorial Gene Regulation Using Auto-Regulation

(2010) Rutger Hermsen et al.   PLoS Computational Biology

On the application of statistical physics to evolutionary biology

(2009) N.H. Barton et al.   JOURNAL OF THEORETICAL BIOLOGY

Variation in the Ratio of Nucleotide Substitution and Indel Rates across Genomes in Mammals and Bacteria

(2009) J.-Q. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Different gene regulation strategies revealed by analysis of binding motifs

(2009) Zeba Wunderlich et al.   TRENDS IN GENETICS

Inferring Binding Energies from Selected Binding Sites

(2009) Yue Zhao et al.   PLoS Computational Biology

Problems and Solutions for Estimating Indel Rates and Length Distributions

(2008) Reed A. Cartwright   MOLECULAR BIOLOGY AND EVOLUTION

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

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