Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites

How do regulatory networks evolve and expand throughout evolution?

(2015) Karin Voordeckers et al.   CURRENT OPINION IN BIOTECHNOLOGY

Pervasive degeneracy and epistasis in a protein-protein interface

(2015) A. I. Podgornaia et al.   SCIENCE

Using ancient protein kinases to unravel a modern cancer drug's mechanism

(2015) C. Wilson et al.   SCIENCE

Topological features of rugged fitness landscapes in sequence space

(2015) Dmitry A. Kondrashov et al.   TRENDS IN GENETICS

Spec-seq: determining protein-DNA-binding specificity by sequencing

(2014) G. D. Stormo et al.   Briefings in Functional Genomics

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

(2014) Alesia N. McKeown et al.   CELL

A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain

(2014) C. Anders Olson et al.   CURRENT BIOLOGY

How duplicated transcription regulators can diversify to govern the expression of nonoverlapping sets of genes

(2014) J. C. Perez et al.   GENES & DEVELOPMENT

A Systematic Survey of an Intragenic Epistatic Landscape

(2014) Claudia Bank et al.   MOLECULAR BIOLOGY AND EVOLUTION

Epistasis Constrains Mutational Pathways of Hemoglobin Adaptation in High-Altitude Pikas

(2014) Danielle M. Tufts et al.   MOLECULAR BIOLOGY AND EVOLUTION

Historical contingency and its biophysical basis in glucocorticoid receptor evolution

(2014) Michael J. Harms et al.   NATURE

Inferring fitness landscapes by regression produces biased estimates of epistasis

(2014) J. Otwinowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2014) Ksenia Pougach et al.   Nature Communications

Epistatic Adaptive Evolution of Human Color Vision

(2014) Shozo Yokoyama et al.   PLoS Genetics

Exploitation of Latent Allostery Enables the Evolution of New Modes of MAP Kinase Regulation

(2013) Scott M. Coyle et al.   CELL

Evolutionary biochemistry: revealing the historical and physical causes of protein properties

(2013) Michael J. Harms et al.   NATURE REVIEWS GENETICS

Capturing the mutational landscape of the beta-lactamase TEM-1

(2013) H. Jacquier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein

(2013) D. Melamed et al.   RNA

Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin

(2013) C. Natarajan et al.   SCIENCE

Stability-mediated epistasis constrains the evolution of an influenza protein

(2013) Lizhi Ian Gong et al.   eLife

Disentangling the Many Layers of Eukaryotic Transcriptional Regulation

(2012) Katherine M. Lelli et al.   Annual Review of Genetics

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

(2012) Yue Zhao et al.   GENETICS

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Epistasis as the primary factor in molecular evolution

(2012) Michael S. Breen et al.   NATURE

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

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

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

(2012) C. L. Araya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme

(2012) Nobuhiko Tokuriki et al.   Nature Communications

Coevolution within and between Regulatory Loci Can Preserve Promoter Function Despite Evolutionary Rate Acceleration

(2012) Antoine Barrière et al.   PLoS Genetics

Evolution of Minimal Specificity and Promiscuity in Steroid Hormone Receptors

(2012) Geeta N. Eick et al.   PLoS Genetics

Maximally Efficient Modeling of DNA Sequence Motifs at All Levels of Complexity

(2011) G. D. Stormo   GENETICS

Synthesis and Crystal Structure of a Pr5Ni19Superlattice Alloy and Its Hydrogen Absorption–Desorption Property

(2011) Kenji Iwase et al.   INORGANIC CHEMISTRY

Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB

(2011) Vincent J. Lynch et al.   NATURE

A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase

(2011) Trevor Hinkley et al.   NATURE GENETICS

Prediction of Regulatory Interactions from Genome Sequences Using a Biophysical Model for theArabidopsisLEAFY Transcription Factor

(2011) Edwige Moyroud et al.   PLANT CELL

Extensive DNA-binding specificity divergence of a conserved transcription regulator

(2011) C. R. Baker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Second-Order Selection for Evolvability in a Large Escherichia coli Population

(2011) R. J. Woods et al.   SCIENCE

Initial Mutations Direct Alternative Pathways of Protein Evolution

(2011) Merijn L. M. Salverda et al.   PLoS Genetics

Bis{2-[3-(dimethylamino)propyliminomethyl]-6-methoxyphenolato}-κ3N,N′,O1;κ2N,O1-zinc(II) dihydrate

(2010) Hong Lin et al.   ACTA CRYSTALLOGRAPHICA SECTION E-STRUCTURE REPORTS ONLINE

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

Analyzing protein structure and function using ancestral gene reconstruction

(2010) Michael J Harms et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

Determining the specificity of protein–DNA interactions

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

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building

(2010) François-Yves Dupradeau et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Permissive Secondary Mutations Enable the Evolution of Influenza Oseltamivir Resistance

(2010) J. D. Bloom et al.   SCIENCE

Genomic actions of estrogen receptor α: what are the targets and how are they regulated?

(2009) Willem-Jan Welboren et al.   ENDOCRINE-RELATED CANCER

Retracing Evolution of Red Fluorescence in GFP-Like Proteins from Faviina Corals

(2009) S. F. Field et al.   MOLECULAR BIOLOGY AND EVOLUTION

An epistatic ratchet constrains the direction of glucocorticoid receptor evolution

(2009) Jamie T. Bridgham et al.   NATURE

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

In the light of directed evolution: Pathways of adaptive protein evolution

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

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Protein kinase R reveals an evolutionary model for defeating viral mimicry

(2008) Nels C. Elde et al.   NATURE

Neutralism and selectionism: a network-based reconciliation

(2008) Andreas Wagner   NATURE REVIEWS GENETICS

Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems

(2008) Patrick C. Phillips   NATURE REVIEWS GENETICS

Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals

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

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

(2008) Xiao-yong Li et al.   PLOS BIOLOGY

Evolution of a New Function by Degenerative Mutation in Cephalochordate Steroid Receptors

(2008) Jamie T. Bridgham et al.   PLoS Genetics