4.0 Article

Quantifying the impact of changes in effective population size and expression level on the rate of coding sequence evolution

Related references

Note: Only part of the references are listed.
Article Evolutionary Biology

Reconstructing the History of Variation in Effective Population Size along Phylogenies

Mathieu Brevet et al.

Summary: The study introduces an integrative framework for reconstructing the phylogenetic history of Ne, allowing for testing the nearly neutral theory and estimating the evolution of genetic variation patterns. The results show that both Ne and u play important roles in modulating patterns of genetic variation, with opposing trends observed in their variations.

GENOME BIOLOGY AND EVOLUTION (2021)

Article Evolutionary Biology

An Overexpression Experiment Does Not Support the Hypothesis That Avoidance of Toxicity Determines the Rate of Protein Evolution

Magdalena K. Biesiadecka et al.

GENOME BIOLOGY AND EVOLUTION (2020)

Article Biochemistry & Molecular Biology

Substitution Rates Predicted by Stability-Constrained Models of Protein Evolution Are Not Consistent with Empirical Data

Maria Jose Jimenez et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

Protein Stability and Avoidance of Toxic Misfolding Do Not Explain the Sequence Constraints of Highly Expressed Proteins

German Plata et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

Estimating the contribution of folding stability to nonspecific epistasis in protein evolution

Pouria Dasmeh et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2018)

Article Ecology

Sequence entropy of folding and the absolute rate of amino acid substitutions

Richard A. Goldstein et al.

NATURE ECOLOGY & EVOLUTION (2017)

Article Biochemistry & Molecular Biology

What evolution tells us about protein physics, and protein physics tells us about evolution

Ugo Bastolla et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes

Emeric Figuet et al.

MOLECULAR BIOLOGY AND EVOLUTION (2016)

Review Biochemistry & Molecular Biology

Epistasis in protein evolution

Tyler N. Starr et al.

PROTEIN SCIENCE (2016)

Article Biochemistry & Molecular Biology

The tangled bank of amino acids

Richard A. Goldstein et al.

PROTEIN SCIENCE (2016)

Article Biochemistry & Molecular Biology

The Relationship between dN/dS and Scaled Selection Coefficients

Stephanie J. Spielman et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Review Genetics & Heredity

Determinants of the rate of protein sequence evolution

Jianzhi Zhang et al.

NATURE REVIEWS GENETICS (2015)

Article Multidisciplinary Sciences

Protein folding and binding can emerge as evolutionary spandrels through structural coupling

Michael Manhart et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Biochemistry & Molecular Biology

Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics

Adrian W. R. Serohijos et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2014)

Article Evolutionary Biology

The Influence of Selection for Protein Stability on dN/dS Estimations

Pouria Dasmeh et al.

GENOME BIOLOGY AND EVOLUTION (2014)

Review Biology

MODELING EVOLUTION USING THE PROBABILITY OF FIXATION: HISTORY AND IMPLICATIONS

David M. McCandlish et al.

QUARTERLY REVIEW OF BIOLOGY (2014)

Review Ecology

Population size and the rate of evolution

Robert Lanfear et al.

TRENDS IN ECOLOGY & EVOLUTION (2014)

Article Biophysics

Highly Abundant Proteins Favor More Stable 3D Structures in Yeast

Adrian W. R. Serohijos et al.

BIOPHYSICAL JOURNAL (2013)

Article Biochemistry & Molecular Biology

Evolution of protein structures and interactions from the perspective of residue contact networks

Xiuwei Zhang et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2013)

Article Biochemistry & Molecular Biology

The Rate of Molecular Adaptation in a Changing Environment

Joao M. Lourenco et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemical Research Methods

Evolutionary Capacitance and Control of Protein Stability in Protein-Protein Interaction Networks

Purushottam D. Dixit et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Article Multidisciplinary Sciences

Amino acid coevolution induces an evolutionary Stokes shift

David D. Pollock et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

Protein misinteraction avoidance causes highly expressed proteins to evolve slowly

Jian-Rong Yang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemistry & Molecular Biology

Sequence determinants of protein folding rates: Positive correlation between contact energy and contact range indicates selection for fast folding

Ugo Bastolla et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2012)

Article Cell Biology

Protein Biophysics Explains Why Highly Abundant Proteins Evolve Slowly

Adrian W. R. Serohijos et al.

CELL REPORTS (2012)

Article Biochemistry & Molecular Biology

A Phylogenetic Model for Investigating Correlated Evolution of Substitution Rates and Continuous Phenotypic Characters

Nicolas Lartillot et al.

MOLECULAR BIOLOGY AND EVOLUTION (2011)

Article Biochemistry & Molecular Biology

The evolution and evolutionary consequences of marginal thermostability in proteins

Richard A. Goldstein

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)

Article Evolutionary Biology

Expression Level, Evolutionary Rate, and the Cost of Expression

Joshua L. Cherry

GENOME BIOLOGY AND EVOLUTION (2010)

Article Multidisciplinary Sciences

Mutation rate is linked to diversification in birds

Robert Lanfear et al.

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

Article Multidisciplinary Sciences

Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles

Nicolas Rodrigue et al.

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

Review Genetics & Heredity

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

Ville Mustonen et al.

TRENDS IN GENETICS (2009)

Article Biochemistry & Molecular Biology

Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution

D. Allan Drummond et al.

Article Biochemistry & Molecular Biology

Divergence and Polymorphism Under the Nearly Neutral Theory of Molecular Evolution

John J. Welch et al.

JOURNAL OF MOLECULAR EVOLUTION (2008)

Article Biochemistry & Molecular Biology

Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size

Jingshan Zhang et al.

MOLECULAR SYSTEMS BIOLOGY (2008)

Article Multidisciplinary Sciences

Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements

Sergey I. Nikolaev et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Multidisciplinary Sciences

Protein stability imposes limits on organism complexity and speed of molecular evolution

Konstantin B. Zeldovich et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Multidisciplinary Sciences

Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals

Konstantin Popadin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Genetics & Heredity

Thermodynamics of neutral protein evolution

Jesse D. Bloom et al.

GENETICS (2007)

Article Biochemical Research Methods

Assessing the accuracy of ancestral protein reconstruction methods

Paul D. Williams et al.

PLOS COMPUTATIONAL BIOLOGY (2006)

Article Genetics & Heredity

Population genetics of translational robustness

CO Wilke et al.

GENETICS (2006)

Article Biochemistry & Molecular Biology

Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level

JZ Zhang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2005)

Article Multidisciplinary Sciences

Why highly expressed proteins evolve slowly

DA Drummond et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Multidisciplinary Sciences

The application of statistical physics to evolutionary biology

G Sella et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemistry & Molecular Biology

An analysis of determinants of amino acids substitution rates in bacterial proteins

EPC Rocha et al.

MOLECULAR BIOLOGY AND EVOLUTION (2004)

Article Biochemistry & Molecular Biology

Why are proteins marginally stable?

DM Taverna et al.

PROTEINS-STRUCTURE FUNCTION AND GENETICS (2002)

Article Biochemistry & Molecular Biology

Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate

L Duret et al.

MOLECULAR BIOLOGY AND EVOLUTION (2000)