(Q33517082)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19955476%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

title

Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1 (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19955476%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

1 reference

1

1 reference

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13 February 2020

Luke Swenson

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19955476%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

Zabrina L Brumme

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19955476%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

Simon Frost

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19955476%20AND%20SRC:MED&resulttype=core&format=json

Sergei L. Kosakovsky Pond

13 February 2020

5

object named as

Sergei L Kosakovsky Pond

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19955476%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

7

James I Mullins

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19955476%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

author name string

Winnie W Y Dong

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19955476%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

Wenjie Deng

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19955476%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

Douglas D Richman

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19955476%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

P Richard Harrigan

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19955476%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

publication date

2 December 2009

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19955476%20AND%20SRC:MED&resulttype=core&format=json

Molecular Biology and Evolution

13 February 2020

published in

1 reference

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13 February 2020

volume

27

1 reference

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13 February 2020

issue

4

1 reference

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13 February 2020

page(s)

819-832

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19955476%20AND%20SRC:MED&resulttype=core&format=json

Architecture and secondary structure of an entire HIV-1 RNA genome

13 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=2877536

Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy 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=2877536

Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Next-generation sequencing: from basic research to diagnostics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-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=2877536

Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Lysine 144, a ubiquitin attachment site in HIV-1 Nef, is required for Nef-mediated CD4 down-regulation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Parallel tagged sequencing on the 454 platform

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Alignment uncertainty and genomic analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Quality scores and SNP detection in sequencing-by-synthesis systems

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Accounting for bias from sequencing error in population genetic estimates

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Nef-mediated enhancement of virion infectivity and stimulation of viral replication are fundamental properties of primate lentiviruses

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Accuracy and quality of massively parallel DNA pyrosequencing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes 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=2877536

Leveraging hierarchical population structure in discrete association studies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B*5703-restricted Gag epitope in chronic human immunodeficiency virus type 1 infection

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

HIV-1 subtype B protease and reverse transcriptase amino acid covariation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Maintenance of Nef-mediated modulation of major histocompatibility complex class I and CD4 after sexual transmission of human immunodeficiency virus type 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=2877536

HIV evolutionary dynamics within and among hosts

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

A Phylogenetic Method for Detecting Positive Epistasis in Gene Sequences and Its Application to RNA Virus Evolution

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Human immunodeficiency virus type 1 Nef: adapting to intracellular trafficking pathways

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Dynamic evolution of the human immunodeficiency virus type 1 pathogenic factor, Nef.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Genome sequencing in microfabricated high-density picolitre reactors

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Perspective: Sign epistasis and genetic constraint on evolutionary trajectories

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Joint Bayesian Estimation of Alignment and Phylogeny

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

The rate of compensatory mutation in the DNA bacteriophage phiX174

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

The coupon collector and the suppressor mutation: estimating the number of compensatory mutations 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=2877536

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=2877536

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=2877536

Disruption of the actin cytoskeleton can complement the ability of Nef to enhance human immunodeficiency virus type 1 infectivity

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

14 July 2018

HIV sequence databases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Sources and magnitude of intralaboratory variability in a sequence-based genotypic assay for human immunodeficiency virus type 1 drug resistance

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Human immunodeficiency virus type 1 recombination: rate, fidelity, and putative hot spots

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

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=2877536

Implications of antiretroviral resistance on viral fitness

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

The effect of recombination on the accuracy of phylogeny estimation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

A fast algorithm for joint reconstruction of ancestral amino acid sequences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

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=2877536

Sequence variations in human immunodeficiency virus type 1 Nef are associated with different stages of disease

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Grossly defective nef gene sequences in a human immunodeficiency virus type 1-seropositive long-term nonprogressor

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Theoretical uncertainty of measurements using quantitative polymerase chain reaction.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

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=2877536

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=2877536

Optimal alignments in linear space

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Kinetics of early HIV-1 gene expression in infected H9 cells assessed by PCR

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Six epitopes reacting with human cytotoxic CD8+ T cells in the central region of the HIV-1 NEF protein

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

HIV protease and reverse transcriptase variation and therapy outcome in antiretroviral-naive individuals from a large North American cohort.

14 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP289

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/10.1093%2FMOLBEV%2FMSP289

HIV-1 Nef is preferentially recognized by CD8 T cells in primary HIV-1 infection despite a relatively high degree of genetic diversity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP289

Optimal alignments in linear space

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP289

A simple hierarchical approach to modeling distributions of substitution rates.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Covariation of amino acid positions in HIV-1 protease

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877536

Covariability of selected amino acid positions for HIV type 1 subtypes C and B

31 October 2018

1 reference

12 December 2020

Characterization of intramolecular interactions of HIV-1 accessory protein Nef by differential scanning calorimetry

1 reference

12 December 2020

Rates of disease progression by baseline CD4 cell count and viral load after initiating triple-drug therapy

1 reference

12 December 2020

Consensus and Ancestral State HIV Vaccines

1 reference

12 December 2020

HIV-1 Nef leads to inhibition or activation of T cells depending on its intracellular localization

1 reference

12 December 2020

Identifiers

DOI

10.1093/MOLBEV/MSP289

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19955476%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19955476%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

PubMed publication ID

19955476

1 reference