(Q38635802)

5 September 2017

phydms: software for phylogenetic analyses informed by deep mutational scanning (English)

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5 September 2017

1 reference

deep mutational scanning

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author name string

Sarah K Hilton

series ordinal

1

1 reference

5 September 2017

Michael B Doud

series ordinal

2

1 reference

5 September 2017

Jesse D Bloom

series ordinal

3

1 reference

5 September 2017

31 July 2017

1 reference

5 September 2017

1 reference

5 September 2017

5

1 reference

5 September 2017

e3657

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Creative Commons Attribution 4.0 International

5 September 2017

start time

31 July 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Functional Segregation of Overlapping Genes in HIV.

6 September 2017

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Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV's Envelope Protein on Viral Replication in Cell Culture

6 September 2017

1 reference

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Phenotypic Characterization of a Comprehensive Set of MAPK1/ERK2 Missense Mutants

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Prospective functional classification of all possible missense variants in PPARG.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Systematic Mutant Analyses Elucidate General and Client-Specific Aspects of Hsp90 Function

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

The relationship between dN/dS and scaled selection coefficients

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Massively parallel single-amino-acid mutagenesis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Modeling evolution using the probability of fixation: history and implications

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Deep mutational scanning: a new style of protein science

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

An experimentally determined evolutionary model dramatically improves phylogenetic fit.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

A comprehensive, high-resolution map of a gene's fitness landscape

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Bio++: efficient extensible libraries and tools for computational molecular evolution.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

The spatial architecture of protein function and adaptation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Correcting the bias of empirical frequency parameter estimators in codon models

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Mechanistic approaches to the study of evolution: the functional synthesis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

PAML 4: phylogenetic analysis by maximum likelihood

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Not so different after all: a comparison of methods for detecting amino acid sites under selection

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

HyPhy: hypothesis testing using phylogenies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

WebLogo: A Sequence Logo Generator

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Codon-substitution models for heterogeneous selection pressure at amino acid sites

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

A codon-based model of nucleotide substitution for protein-coding DNA sequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Evolutionary trees from DNA sequences: A maximum likelihood approach

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Hessian calculation for phylogenetic likelihood based on the pruning algorithm and its applications.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Evolvability as a function of purifying selection in TEM-1 β-lactamase.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5541924

A Limited Memory Algorithm for Bound Constrained Optimization

31 August 2018

1 reference

https://api.crossref.org/works/10.7717%2FPEERJ.3657

Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters

21 January 2018

1 reference

https://api.crossref.org/works/10.7717%2FPEERJ.3657

Remark on “algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound constrained optimization”

21 January 2018

1 reference

https://api.crossref.org/works/10.7717%2FPEERJ.3657

Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.7717%2FPEERJ.3657

21 January 2018

Identifiers

DOI

10.7717/PEERJ.3657

1 reference

5 September 2017

1 reference

5 September 2017

PubMed publication ID

28785526

1 reference