An integrated view of protein evolution (Q22122015)

Dimensions Publication ID

Dimensions

25 September 2022

Balázs Papp

Balázs

Papp

1 reference

Dimensions Publication ID

Dimensions

25 September 2022

Martin J. Lercher

Martin J.

Lercher

1 reference

Dimensions Publication ID

Dimensions

1040006009

Molecular phylogenies link rates of evolution and speciation

25 September 2022

language of work or name

English

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publication date

May 2006

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published in

Nature Reviews Genetics

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volume

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issue

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page(s)

337-348

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cites work

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The hitch-hiking effect of a favourable gene

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The genomic rate of adaptive amino acid substitution in Drosophila.

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Recombination enhances protein adaptation in Drosophila melanogaster

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Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome

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Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata.

21 January 2018

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

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Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae

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Does the Recombination Rate Affect the Efficiency of Purifying Selection? The Yeast Genome Provides a Partial Answer

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Evidence that positive selection drives Y-chromosome degeneration in Drosophila miranda.

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Evolutionary processes and evolutionary noise at the molecular level. I. Functional density in proteins

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Why highly expressed proteins evolve slowly

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Missense meanderings in sequence space: a biophysical view of protein evolution

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The coupon collector and the suppressor mutation: estimating the number of compensatory mutations by maximum likelihood.

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Protein dispensability and rate of evolution

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Essential genes are more evolutionarily conserved than are nonessential genes in bacteria

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Molecular correlates of genes exhibiting RNAi phenotypes in Caenorhabditis elegans

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Genomic function (communication arising): Rate of evolution and gene dispensability

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Functional genomic analysis of the rates of protein evolution

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Significant impact of protein dispensability on the instantaneous rate of protein evolution

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Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast

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Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution

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Do essential genes evolve slowly?

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Sex-specific functional specialization and the evolutionary rates of essential fertility genes.

21 January 2018

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Genetic analysis of protein stability and function

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Protein tolerance to random amino acid change

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Principles of protein folding, misfolding and aggregation

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Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species

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Thermophilic adaptation of proteins

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Generality of the structurally constrained protein evolution model: assessment on representatives of the four main fold classes.

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The pattern of amino acid replacements in alpha/beta-barrels

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Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica.

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Protein topology and stability define the space of allowed sequences.

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Evolutionary rate in the protein interaction network

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Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets

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Molecular evolution in large genetic networks: does connectivity equal constraint?

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No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly

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Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks

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The constraints protein-protein interactions place on sequence divergence

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Structure, function, and evolution of transient and obligate protein-protein interactions

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Modularity and evolutionary constraint on proteins

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The Effect of Multifunctionality on the Rate of Evolution in Yeast

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Constrained evolution with respect to gene overlap of hepatitis B virus

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Protein evolution in the context of Drosophila development

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In search of the vertebrate phylotypic stage: a molecular examination of the developmental hourglass model and von Baer's third law.

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The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint

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Rates of protein evolution are positively correlated with developmental timing of expression during mouse spermatogenesis.

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Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences

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Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis

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Testing the neutral theory of molecular evolution with genomic data from Drosophila.

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Robustness, evolvability, and neutrality

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A scan for positively selected genes in the genomes of humans and chimpanzees

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Adaptive molecular evolution for 13,000 phage generations: a possible arms race

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The rate of compensatory mutation in the DNA bacteriophage phiX174

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Adaptive evolution in GroEL from distantly related endosymbiotic bacteria of insects.

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The eloquent ape: genes, brains and the evolution of language

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Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens.

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Natural selection on protein-coding genes in the human genome

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Systemic determinants of gene evolution and function

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Understanding protein dispensability through machine-learning analysis of high-throughput data

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Bioinformatical assay of human gene morbidity

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Accurate multiplex polony sequencing of an evolved bacterial genome

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Horizontal gene transfer among genomes: the complexity hypothesis

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Molecular phylogenetics: state-of-the-art methods for looking into the past

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Understanding human disease mutations through the use of interspecific genetic variation

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Human non-synonymous SNPs: server and survey

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Assessing the function of genetic variants in candidate gene association studies

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Estimating the distribution of fitness effects from DNA sequence data: implications for the molecular clock

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Estimating selection on nonsynonymous mutations

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An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus

21 January 2018

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The 'evolvability' of promiscuous protein functions

21 January 2018

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Preferential duplication of conserved proteins in eukaryotic genomes

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Duplicated genes evolve slower than singletons despite the initial rate increase

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Changes in Alternative Splicing of Human and Mouse Genes Are Accompanied by Faster Evolution of Constitutive Exons

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The cost of inbreeding in Arabidopsis.

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Dissecting the regulatory circuitry of a eukaryotic genome

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Evidence for co-evolution of gene order and recombination rate

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Comparative assessment of large-scale data sets of protein-protein interactions

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Lethality and centrality in protein networks

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Gene essentiality and the topology of protein interaction networks.

21 January 2018

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The Evolutionary Rate of a Protein Is Influenced by Features of the Interacting Partners

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The proteins of linked genes evolve at similar rates

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Exploiting the co-evolution of interacting proteins to discover interaction specificity

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A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate

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A single determinant dominates the rate of yeast protein evolution

31 March 2020

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Conservation and coevolution in the scale-free human gene coexpression network

31 March 2020

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Molecular evolution in the yeast transcriptional regulation network

31 March 2020

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

31 March 2020

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Molecular evolution of sex-biased genes in Drosophila

31 March 2020

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Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis

31 March 2020

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Unifying measures of gene function and evolution

31 March 2020

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Selection in the evolution of gene duplications

31 March 2020

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