Evolution of complex adaptations in molecular systems

The White-Knight Hypothesis, or Does the Environment Limit Innovations?

(2017) Andreas Wagner   TRENDS IN ECOLOGY & EVOLUTION

Evolutionary assembly patterns of prokaryotic genomes

(2016) Maximilian O. Press et al.   GENOME RESEARCH

On the Potential Origins of the High Stability of Reconstructed Ancestral Proteins

(2016) Devin L. Trudeau et al.   MOLECULAR BIOLOGY AND EVOLUTION

A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species

(2016) Ákos Nyerges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A global genetic interaction network maps a wiring diagram of cellular function

(2016) M. Costanzo et al.   SCIENCE

Adaptive evolution of complex innovations through stepwise metabolic niche expansion

(2016) Balázs Szappanos et al.   Nature Communications

Environmental changes bridge evolutionary valleys

(2016) B. Steinberg et al.   Science Advances

Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates

(2015) Christopher D. Aakre et al.   CELL

Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase

(2015) Michael A. Stiffler et al.   CELL

Estimating the mutation load in human genomes

(2015) Brenna M. Henn et al.   NATURE REVIEWS GENETICS

Breaking evolutionary constraint with a tradeoff ratchet

(2015) Marjon G. J. de Vos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pervasive degeneracy and epistasis in a protein-protein interface

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

An evolutionary biochemist's perspective on promiscuity

(2015) Shelley D. Copley   TRENDS IN BIOCHEMICAL SCIENCES

Evolution of Robustness to Protein Mistranslation by Accelerated Protein Turnover

(2015) Dorottya Kalapis et al.   PLOS BIOLOGY

The Evolutionary Potential of Phenotypic Mutations

(2015) Hayato Yanagida et al.   PLoS Genetics

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

(2015) Dave W Anderson et al.   eLife

A structural perspective of compensatory evolution

(2014) Dmitry N Ivankov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Limits of Neutral Drift: Lessons From the In Vitro Evolution of Two Ribozymes

(2014) Katherine L. Petrie et al.   JOURNAL OF MOLECULAR EVOLUTION

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Network-level architecture and the evolutionary potential of underground metabolism

(2014) R. A. Notebaart 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

Protein mistranslation: friend or foe?

(2014) Liuís Ribas de Pouplana et al.   TRENDS IN BIOCHEMICAL SCIENCES

Evolutionary constraints in variable environments, from proteins to networks

(2014) Katja M. Taute et al.   TRENDS IN GENETICS

Should evolutionary geneticists worry about higher-order epistasis?

(2013) Daniel M Weinreich et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

Cumulative Impact of Chaperone-Mediated Folding on Genome Evolution

(2012) David Bogumil et al.   BIOCHEMISTRY

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Evolution of increased complexity in a molecular machine

(2012) Gregory C. Finnigan et al.   NATURE

Environmental change exposes beneficial epistatic interactions in a catalytic RNA

(2012) E. J. Hayden et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

The Genomic Landscape and Evolutionary Resolution of Antagonistic Pleiotropy in Yeast

(2012) Wenfeng Qian et al.   Cell Reports

Pervasive Multinucleotide Mutational Events in Eukaryotes

(2011) Daniel R. Schrider et al.   CURRENT BIOLOGY

The Evolution of Multimeric Protein Assemblages

(2011) M. Lynch   MOLECULAR BIOLOGY AND EVOLUTION

Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme

(2011) Eric J. Hayden et al.   NATURE

Systems-biology approaches for predicting genomic evolution

(2011) Balázs Papp et al.   NATURE REVIEWS GENETICS

The aneuploidy paradox: costs and benefits of an incorrect karyotype

(2011) Jason M. Sheltzer et al.   TRENDS IN GENETICS

Formation of Regulatory Modules by Local Sequence Duplication

(2011) Armita Nourmohammad et al.   PLoS Computational Biology

Beyond directed evolution—semi-rational protein engineering and design

(2010) Stefan Lutz   CURRENT OPINION IN BIOTECHNOLOGY

Open issues in genetic programming

(2010) Michael O’Neill et al.   Genetic Programming and Evolvable Machines

The Rate of Fitness-Valley Crossing in Sexual Populations

(2010) D. B. Weissman et al.   GENETICS

The Rate of Establishment of Complex Adaptations

(2010) M. Lynch et al.   MOLECULAR BIOLOGY AND EVOLUTION

Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness

(2010) Margarita V. Meer et al.   NATURE

Scaling expectations for the time to establishment of complex adaptations

(2010) M. Lynch   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A time-invariant principle of genome evolution

(2010) S. De et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Increased Mutagenesis and Unique Mutation Signature Associated with Mitotic Gene Conversion

(2010) W. M. Hicks et al.   SCIENCE

Permissive Secondary Mutations Enable the Evolution of Influenza Oseltamivir Resistance

(2010) J. D. Bloom et al.   SCIENCE

Rapid Diversification of Cell Signaling Phenotypes by Modular Domain Recombination

(2010) S. G. Peisajovich et al.   SCIENCE

Stability effects of mutations and protein evolvability

(2009) Nobuhiko Tokuriki et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Chaperonin overexpression promotes genetic variation and enzyme evolution

(2009) Nobuhiko Tokuriki et al.   NATURE

An epistatic ratchet constrains the direction of glucocorticoid receptor evolution

(2009) Jamie T. Bridgham et al.   NATURE

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Evolution of biomolecular networks — lessons from metabolic and protein interactions

(2009) Takuji Yamada et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Exploring protein fitness landscapes by directed evolution

(2009) Philip A. Romero et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Fluctuating selection: the perpetual renewal of adaptation in variable environments

(2009) G. Bell   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Saltational evolution: hopeful monsters are here to stay

(2009) Günter Theißen   THEORY IN BIOSCIENCES

From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation

(2009) Ville Mustonen et al.   TRENDS IN GENETICS

Asymmetric relationships between proteins shape genome evolution

(2009) Richard A Notebaart et al.   GENOME BIOLOGY

The look-ahead effect of phenotypic mutations

(2008) Dion J Whitehead et al.   Biology Direct

Aneuploidy Underlies Rapid Adaptive Evolution of Yeast Cells Deprived of a Conserved Cytokinesis Motor

(2008) Giulia Rancati et al.   CELL

Intense Neutral Drifts Yield Robust and Evolvable Consensus Proteins

(2008) Shimon Bershtein et al.   JOURNAL OF MOLECULAR BIOLOGY

Ohno's Model Revisited: Measuring the Frequency of Potentially Adaptive Mutations under Various Mutational Drifts

(2008) Shimon Bershtein et al.   MOLECULAR BIOLOGY AND EVOLUTION

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

(2008) Z. D. Blount et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments

(2008) Merav Parter et al.   PLoS Computational Biology

A Catalog of Neutral and Deleterious Polymorphism in Yeast

(2008) Scott W. Doniger et al.   PLoS Genetics