Evolutionary potential of transcription factors for gene regulatory rewiring

Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels

(2016) Arno Steinacher et al.   PLoS One

Epistasis in protein evolution

(2016) Tyler N. Starr et al.   PROTEIN SCIENCE

Intrinsic limits to gene regulation by global crosstalk

(2016) Tamar Friedlander et al.   Nature Communications

Dynamics of Transcription Factor Binding Site Evolution

(2015) Murat Tuğrul et al.   PLoS Genetics

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

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

The Robustness and Evolvability of Transcription Factor Binding Sites

(2014) J. L. Payne et al.   SCIENCE

A Promiscuous Intermediate Underlies the Evolution of LEAFY DNA Binding Specificity

(2014) C. Sayou et al.   SCIENCE

Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network

(2014) Ksenia Pougach et al.   Nature Communications

Simulations of Enhancer Evolution Provide Mechanistic Insights into Gene Regulation

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

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

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

(2013) Mario Pujato et al.   PLoS Computational Biology

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

(2012) Yue Zhao et al.   GENETICS

The role of robustness in phenotypic adaptation and innovation

(2012) A. Wagner   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

(2011) Patricia J. Wittkopp et al.   NATURE REVIEWS GENETICS

Accurate Prediction of Gene Expression by Integration of DNA Sequence Statistics with Detailed Modeling of Transcription Regulation

(2010) Jose M.G. Vilar   BIOPHYSICAL JOURNAL

Evolution of Transcription Networks — Lessons from Yeasts

(2010) Hao Li et al.   CURRENT BIOLOGY

Mutational robustness can facilitate adaptation

(2010) Jeremy A. Draghi et al.   NATURE

Determining the specificity of protein–DNA interactions

(2010) Gary D. Stormo et al.   NATURE REVIEWS GENETICS

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

Degeneracy: a link between evolvability, robustness and complexity in biological systems

(2010) James M Whitacre   Theoretical Biology and Medical Modelling

Experimental determination of the evolvability of a transcription factor

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

Epistasis in a quantitative trait captured by a molecular model of transcription factor interactions

(2009) Jason Gertz et al.   THEORETICAL POPULATION BIOLOGY

P22 c2 Repressor−Operator Complex:  Mechanisms of Direct and Indirect Readout‡

(2008) Derrick Watkins et al.   BIOCHEMISTRY

Evolvability and hierarchy in rewired bacterial gene networks

(2008) Mark Isalan 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

Growth-rate-dependent partitioning of RNA polymerases in bacteria

(2008) S. Klumpp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Eukaryotic Transcription Circuits

(2008) B. B. Tuch et al.   SCIENCE

The gene regulatory logic of transcription factor evolution

(2008) Günter P. Wagner et al.   TRENDS IN ECOLOGY & EVOLUTION

Is evolvability evolvable?

(2007) Massimo Pigliucci   NATURE REVIEWS GENETICS