Simulations of Enhancer Evolution Provide Mechanistic Insights into Gene Regulation

Evaluating thermodynamic models of enhancer activity on cellular resolution gene expression data

(2013) Md. Abul Hassan Samee et al.   METHODS

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development

(2013) Majid Kazemian et al.   NUCLEIC ACIDS RESEARCH

The Underlying Molecular and Network Level Mechanisms in the Evolution of Robustness in Gene Regulatory Networks

(2013) Mario Pujato et al.   PLoS Computational Biology

Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA Occupancy

(2013) Qiong Cheng et al.   PLoS Genetics

The population genetics of cooperative gene regulation

(2012) Alexander J Stewart et al.   BMC EVOLUTIONARY BIOLOGY

Analysis of variation at transcription factor binding sites in Drosophila and humans

(2012) Mikhail Spivakov et al.   GENOME BIOLOGY

Shadow enhancers: Frequently asked questions about distributed cis-regulatory information and enhancer redundancy

(2011) Scott Barolo   BIOESSAYS

Modeling the evolution of a classic genetic switch

(2011) Christos Josephides et al.   BMC Systems Biology

Rapid Evolutionary Rewiring of a Structurally Constrained Eye Enhancer

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

Evolutionary Origins of Transcription Factor Binding Site Clusters

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

Microevolution of cis-Regulatory Elements: An Example from the Pair-Rule Segmentation Gene fushi tarazu in the Drosophila melanogaster Subgroup

(2011) Mohammed Bakkali   PLoS One

Formation of Regulatory Modules by Local Sequence Duplication

(2011) Armita Nourmohammad et al.   PLoS Computational Biology

Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development

(2011) Tommy Kaplan et al.   PLoS Genetics

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

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

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo

(2011) Chung-Yi Nien et al.   PLoS Genetics

Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition

(2011) Melissa M. Harrison et al.   PLoS Genetics

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

(2011) Xiao-Yong Li et al.   GENOME BIOLOGY

Towards realistic benchmarks for multiple alignments of non-coding sequences

(2010) Jaebum Kim et al.   BMC BIOINFORMATICS

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

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

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

(2010) Matthew T. Weirauch et al.   TRENDS IN GENETICS

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 evolutionary influence of binding site organisation on gene regulatory networks

(2009) Max B. Cooper et al.   BIOSYSTEMS

Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites

(2009) Alan M Moses   BMC EVOLUTIONARY BIOLOGY

Organization of developmental enhancers in the Drosophila embryo

(2009) Dmitri Papatsenko et al.   NUCLEIC ACIDS RESEARCH

LuMPIS – A modified luminescence-based mammalian interactome mapping pull-down assay for the investigation of protein–protein interactions encoded by GC-low ORFs

(2009) Maria Guadalupe Vizoso Pinto et al.   PROTEOMICS

Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution

(2009) Xin He et al.   PLoS Computational Biology

Evolutionary Triplet Models of Structured RNA

(2009) Robert K. Bradley et al.   PLoS Computational Biology

Evolution of Regulatory Sequences in 12 Drosophila Species

(2009) Jaebum Kim et al.   PLoS Genetics

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment

(2008) Benedict Paten et al.   BIOINFORMATICS

Multiple modular promoter elements drive graded brinker expression in response to the Dpp morphogen gradient

(2008) L.-C. Yao et al.   DEVELOPMENT

Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution

(2008) Rick Durrett et al.   GENETICS

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

(2008) Axel Visel et al.   NATURE GENETICS

Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation

(2008) Emily E. Hare et al.   PLoS Genetics