(Q43110160)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25415964%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

title

A model of substitution trajectories in sequence space and long-term protein evolution (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25415964%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

0 references

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25415964%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

Luca Ferretti

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25415964%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

5

Fyodor A Kondrashov

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25415964%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

author name string

Dinara R Usmanova

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25415964%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

Peter K Vlasov

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25415964%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

language of work or name

1 reference

17 November 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25415964%20AND%20SRC:MED&resulttype=core&format=json

Molecular Biology and Evolution

23 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25415964%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

volume

32

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25415964%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25415964%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

page(s)

542-554

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25415964%20AND%20SRC:MED&resulttype=core&format=json

The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

23 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Empirical fitness landscapes and the predictability of evolution

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Mechanisms of protein sequence divergence and incompatibility

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Experiments on the role of deleterious mutations as stepping stones in adaptive evolution

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Stability-mediated epistasis constrains the evolution of an influenza protein

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Quantifying the similarity of monotonic trajectories in rough and smooth fitness landscapes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Emerging methods in protein co-evolution

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Analyses of the effects of all ubiquitin point mutants on yeast growth rate

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Estimating the rate of irreversibility in protein evolution.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

The spatial architecture of protein function and adaptation

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

The peaks and geometry of fitness landscapes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Fitness conferred by replaced amino acids declines with time

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

25 May 2018

The causes of epistasis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Molecular mechanisms of epistasis within and between genes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Evolutionary innovations and the organization of protein functions in genotype space

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Pervasive cryptic epistasis in molecular evolution

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Sequence space and the ongoing expansion of the protein universe

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Rate of sequence divergence under constant selection

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Exploring protein fitness landscapes by directed evolution

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

An epistatic ratchet constrains the direction of glucocorticoid receptor evolution

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Stepwise acquisition of pyrimethamine resistance in the malaria parasite

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Extensive parallelism in protein evolution

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Percolation on fitness landscapes: effects of correlation, phenotype, and incompatibilities

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Protein tolerance to random amino acid change

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

An in silico Exploration of the Neutral Network in Protein Sequence Space

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Dobzhansky-Muller incompatibilities in protein evolution

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Multidimensional epistasis and the disadvantage of sex.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Early fixation of an optimal genetic code

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Neutral evolution of mutational robustness

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Modeling the covarion hypothesis of nucleotide substitution.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Percolation on the fitness hypercube and the evolution of reproductive isolation

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Testing the covarion hypothesis of molecular evolution

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Evolutionary trees from DNA sequences: A maximum likelihood approach

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Natural Selection and the Concept of a Protein Space

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Towards a general theory of adaptive walks on rugged landscapes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Protein evolution on rugged landscapes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Amino acid substitution matrices from protein blocks

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Why epistasis is important for selection and adaptation.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

The role of epistasis in protein evolution.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Epistasis as the primary factor in molecular evolution

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Negative epistasis between beneficial mutations in an evolving bacterial population

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Evolution and speciation on holey adaptive landscapes.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Functionally compensating coevolving positions are neither homoplasic nor conserved in clades

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Frequent and widespread parallel evolution of protein sequences

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Testing for covarion-like evolution in protein sequences

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Adaptive evolution of non-coding DNA in Drosophila

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

Maximum-likelihood phylogenetic analysis under a covarion-like model.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

15 August 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU318

Multidimensional epistasis and fitness landscapes in enzyme evolution

21 January 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4298177

3 November 2018

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU318

Evolutionary Inferences from Phylogenies: A Review of Methods

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU318

Testing a covariotide model of DNA substitution

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25415964

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Evolution by nearly-neutral mutations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25415964

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25415964

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/MOLBEV/MSU318

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25415964%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25415964%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

PubMed publication ID

25415964

1 reference