(Q33247450)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16789820%20AND%20SRC:MED&resulttype=core&format=json

25 December 2019

title

Adaptation to different human populations by HIV-1 revealed by codon-based analyses (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16789820%20AND%20SRC:MED&resulttype=core&format=json

Sergei L. Kosakovsky Pond

25 December 2019

author

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16789820%20AND%20SRC:MED&resulttype=core&format=json

25 December 2019

Simon Frost

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16789820%20AND%20SRC:MED&resulttype=core&format=json

25 December 2019

6

Andrew J Leigh Brown

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16789820%20AND%20SRC:MED&resulttype=core&format=json

25 December 2019

author name string

Zehava Grossman

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16789820%20AND%20SRC:MED&resulttype=core&format=json

25 December 2019

Michael B Gravenor

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16789820%20AND%20SRC:MED&resulttype=core&format=json

25 December 2019

Douglas D Richman

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16789820%20AND%20SRC:MED&resulttype=core&format=json

25 December 2019

publication date

23 June 2006

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16789820%20AND%20SRC:MED&resulttype=core&format=json

PLOS Computational Biology

25 December 2019

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16789820%20AND%20SRC:MED&resulttype=core&format=json

25 December 2019

volume

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16789820%20AND%20SRC:MED&resulttype=core&format=json

25 December 2019

page(s)

e62

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16789820%20AND%20SRC:MED&resulttype=core&format=json

25 December 2019

issue

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16789820%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

25 December 2019

copyright license

start time

23 June 2006

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Genetics of natural populations; altitudinal and seasonal changes produced by natural selection in certain populations of Drosophila persimilis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Inefficient cytotoxic T lymphocyte-mediated killing of HIV-1-infected cells in vivo

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Site-to-site variation of synonymous substitution rates

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Divergent and convergent evolution after a common-source outbreak of hepatitis C virus

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Rapid viral escape at an immunodominant simian-human immunodeficiency virus cytotoxic T-lymphocyte epitope exacts a dramatic fitness cost

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

HyPhy: hypothesis testing using phylogenies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

New Methods for Detecting Positive Selection at Single Amino Acid Sites

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Mapping sites of positive selection and amino acid diversification in the HIV genome: an alternative approach to vaccine design?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Patterns of Intra- and Interhost Nonsynonymous Variation Reveal Strong Purifying Selection in Dengue Virus

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Determinant of HIV-1 mutational escape from cytotoxic T lymphocytes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Molecular characteristics of human immunodeficiency virus type 1 subtype C viruses from KwaZulu-Natal, South Africa: implications for vaccine and antiretroviral control strategies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

MRBAYES: Bayesian inference of phylogenetic trees

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

The origins of acquired immune deficiency syndrome viruses: where and when?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Analysis of the distribution of HLA-B alleles in populations from five continents

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Clustered mutations in HIV-1 gag are consistently required for escape from HLA-B27-restricted cytotoxic T lymphocyte responses.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Analysis of the distribution of HLA-A alleles in populations from five continents

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Origins of Falasha Jews studied by haplotypes of the Y chromosome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Genealogical evidence for positive selection in the nef gene of HIV-1

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Phylogenetic evidence for recombination in dengue virus

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

HLA class II allele and haplotype frequencies in Ethiopian Amhara and Oromo populations

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Antiviral pressure exerted by HIV-1-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Evolutionary trees from DNA sequences: A maximum likelihood approach

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

A new method for calculating evolutionary substitution rates

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Isozyme variability in species of the genus Drosophila. VII. Genotype-environment relationships in populations of D. melanogaster from the Eastern United States.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Accelerated evolution in the reactive centre regions of serine protease inhibitors.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

The neighbor-joining method: a new method for reconstructing phylogenetic trees

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

HLA-A and B polymorphisms predate the divergence of humans and chimpanzees

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Update of the drug resistance mutations in HIV-1: Fall 2005.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Detecting amino acid sites under positive selection and purifying selection

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Column sorting: rapid calculation of the phylogenetic likelihood function.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

A simple hierarchical approach to modeling distributions of substitution rates.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

RDP2: recombination detection and analysis from sequence alignments.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Reversion of CTL escape–variant immunodeficiency viruses in vivo

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

HIV evolution: CTL escape mutation and reversion after transmission.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Acute phase cytotoxic T lymphocyte escape is a hallmark of simian immunodeficiency virus infection

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Evolution and transmission of stable CTL escape mutations in HIV infection

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480537

Genotypic variation of HIV-1 reverse transcriptase and protease: comparative analysis of clade C and clade B

31 October 2018

1 reference

12 December 2020

HIV/AIDS. HLA leaves its footprints on HIV

1 reference

12 December 2020

Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level

1 reference

12 December 2020

Potential impact of recombination on sitewise approaches for detecting positive natural selection

1 reference

12 December 2020

Frequent false detection of positive selection by the likelihood method with branch-site models

1 reference

12 December 2020

ALCOHOL DEHYDROGENASE AND GLYCEROL-3-PHOSPHATE DEHYDROGENASE CLINES IN DROSOPHILA MELANOGASTER ON DIFFERENT CONTINENTS

1 reference

12 December 2020

Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.0020062

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16789820%20AND%20SRC:MED&resulttype=core&format=json

journals/ploscb/PondFGGRB06

25 December 2019

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16789820%20AND%20SRC:MED&resulttype=core&format=json

25 December 2019

1 reference