Replaying the tape of life: quantification of the predictability of evolution (Q34504896)

2 August 2017

1 reference

title

Replaying the tape of life: quantification of the predictability of evolution (English)

1 reference

2 August 2017

Eugene V Koonin

1 reference

2 August 2017

author name string

Alexander E Lobkovsky

series ordinal

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2 August 2017

publication date

26 November 2012

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2 August 2017

published in

Frontiers in Genetics

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2 August 2017

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2 August 2017

page(s)

246

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Interactions between evolutionary processes at high mutation rates

2 August 2017

cites work

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Repeatability and contingency in the evolution of a key innovation in phage lambda

7 July 2018

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Predictability of evolutionary trajectories in fitness landscapes

7 July 2018

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Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

7 July 2018

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Evolutionary Accessibility of Mutational Pathways

7 July 2018

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The evolutionary landscape of antifolate resistance in Plasmodium falciparum

7 July 2018

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Systems-biology approaches for predicting genomic evolution

7 July 2018

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Fitness Trade-Offs in the Evolution of Dihydrofolate Reductase and Drug Resistance in Plasmodium falciparum

7 July 2018

1 reference

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Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape

7 July 2018

1 reference

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Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations

7 July 2018

1 reference

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Initial Mutations Direct Alternative Pathways of Protein Evolution

7 July 2018

1 reference

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Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes.

7 July 2018

1 reference

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Mutational effects and population dynamics during viral adaptation challenge current models

7 July 2018

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Pervasive Cryptic Epistasis in Molecular Evolution

7 July 2018

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Compensatory mutations restore fitness during the evolution of dihydrofolate reductase

7 July 2018

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The neutral theory of molecular evolution in the genomic era

7 July 2018

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Constraints and plasticity in genome and molecular-phenome evolution

7 July 2018

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High-throughput DNA sequencing--concepts and limitations

7 July 2018

1 reference

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Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution

7 July 2018

1 reference

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High-resolution mapping of evolutionary trajectories in a phage

7 July 2018

1 reference

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Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Fitness flux and ubiquity of adaptive evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Universal distribution of protein evolution rates as a consequence of protein folding physics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Evolutionary trajectories of beta-lactamase CTX-M-1 cluster enzymes: predicting antibiotic resistance

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Sequencing technologies - the next generation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Exploring protein fitness landscapes by directed evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

The dynamics of adaptation on correlated fitness landscapes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Colloquium papers: Adaptive landscapes and protein evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

The genetics of adaptation for eight microvirid bacteriophages

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Stepwise acquisition of pyrimethamine resistance in the malaria parasite

7 July 2018

1 reference

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Revealing evolutionary pathways by fitness landscape reconstruction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Directed enzyme evolution: climbing fitness peaks one amino acid at a time

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

A framework for evolutionary systems biology

7 July 2018

1 reference

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The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast

7 July 2018

1 reference

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Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae

7 July 2018

1 reference

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Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape

7 July 2018

1 reference

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Clonal interference, multiple mutations and adaptation in large asexual populations

7 July 2018

1 reference

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Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Constructing and analyzing the fitness landscape of an experimental evolutionary process

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

The ascent of the abundant: how mutational networks constrain evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Analysis of epistatic interactions and fitness landscapes using a new geometric approach

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Empirical fitness landscapes reveal accessible evolutionary paths

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Experimental rugged fitness landscape in protein sequence space

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Direct demonstration of an adaptive constraint

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Tests of parallel molecular evolution in a long-term experiment with Escherichia coli

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Darwinian evolution can follow only very few mutational paths to fitter proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Defining the sequence-recognition profile of DNA-binding molecules

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Orthologs, paralogs, and evolutionary genomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

The biochemical architecture of an ancient adaptive landscape

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Perspective: Sign epistasis and genetic constraint on evolutionary trajectories

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Microbial genetics: Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Different trajectories of parallel evolution during viral adaptation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Overdominant alleles in a population of variable size.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Parallel and divergent genotypic evolution in experimental populations of Ralstonia sp

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Evolution and dissemination of beta-lactamases accelerated by generations of beta-lactam antibiotics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Episodic adaptive evolution of primate lysozymes

7 July 2018

1 reference

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The interaction of genetic drift and mutation with selection in a fluctuating environment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Towards a general theory of adaptive walks on rugged landscapes

7 July 2018

1 reference

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DNA and the neutral theory

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

The NK model of rugged fitness landscapes and its application to maturation of the immune response

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Stomach lysozyme gene of the langur monkey: tests for convergence and positive selection

7 July 2018

1 reference

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Ordered appearance of zidovudine resistance mutations during treatment of 18 human immunodeficiency virus-positive subjects

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

The molecular diversity of adaptive convergence.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Predictive models for population performance on real biological fitness landscapes

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Multiple peaks and reciprocal sign epistasis in an empirically determined genotype-phenotype landscape.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Phylogenomics of C(4) photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence.

27 October 2018

1 reference

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Exploring the effect of sex on empirical fitness landscapes

27 October 2018

1 reference

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Compensatory mutations are repeatable and clustered within proteins.

27 October 2018

1 reference

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The genetic basis of parallel and divergent phenotypic responses in evolving populations of Escherichia coli.

27 October 2018

1 reference

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C4 Photosynthesis evolved in grasses via parallel adaptive genetic changes.

27 October 2018

1 reference

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Distributions of epistasis in microbes fit predictions from a fitness landscape model.

27 October 2018

1 reference

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Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Zidovudine treatment results in the selection of human immunodeficiency virus type 1 variants whose genotypes confer increasing levels of drug resistance.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509945

Parallel Genetic and Phenotypic Evolution of DNA Superhelicity in Experimental Populations of Escherichia coli

27 October 2018

1 reference

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Adaptive evolution in the stomach lysozymes of foregut fermenters

9 December 2018

1 reference

PubMed

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12 December 2020

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Analysis of a local fitness landscape with a model of the rough Mt. Fuji-type landscape: application to prolyl endopeptidase and thermolysin

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23226153

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.3389/FGENE.2012.00246

1 reference

2 August 2017

1 reference

2 August 2017

1 reference