(Q28471994)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

title

An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1 (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

1 reference

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

Art Poon

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

Andrew J Leigh Brown

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%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:19956739%20AND%20SRC:MED&resulttype=core&format=json

Sergei L. Kosakovsky Pond

13 February 2020

1

object named as

Sergei L Kosakovsky Pond

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

7

Esther Fearnhill

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

author name string

Eric Stawiski

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

Colombe Chappey

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

Gareth Hughes

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

Mike B Gravenor

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

language of work or name

English

0 references

publication date

26 November 2009

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

PLOS Computational Biology

13 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

volume

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

page(s)

e1000581

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

issue

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

13 February 2020

copyright license

start time

26 November 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update

1 reference

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Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes

19 March 2017

1 reference

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A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

A fast algorithm for joint reconstruction of ancestral amino acid sequences

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Evolutionary trees from DNA sequences: A maximum likelihood approach

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

A general method applicable to the search for similarities in the amino acid sequence of two proteins

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

HyPhy: hypothesis testing using phylogenies

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Datamonkey: rapid detection of selective pressure on individual sites of codon alignments

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Update of the Drug Resistance Mutations in HIV-1.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Reliability of rapid subtyping tools compared to that of phylogenetic analysis for characterization of human immunodeficiency virus type 1 non-B subtypes and recombinant forms

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

An exploratory algorithm to identify intra-host recombinant viral sequences

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Discrepancies in assignment of subtype/recombinant forms by genotyping programs for HIV type 1 drug resistance testing may falsely predict superinfection.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

The HIV type 1 epidemic in Bulgaria involves multiple subtypes and is sustained by continuous viral inflow from West and East European countries

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

HIV subtypes induce distinct profiles of HIV-specific CD8(+) T cell responses

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Effect of human immunodeficiency virus Type 1 (HIV-1) subtype on disease progression in persons from Rakai, Uganda, with incident HIV-1 infection

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Protein stability imposes limits on organism complexity and speed of molecular evolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

HIV-specific probabilistic models of protein evolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Nucleotide composition string selection in HIV-1 subtyping using whole genomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

HIV-1 subtypes: epidemiology and significance for HIV management

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Identification of a novel HIV-1 circulating ADG intersubtype recombinant form (CRF19_cpx) in Cuba.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

In-depth analysis of a heterosexually acquired human immunodeficiency virus type 1 superinfection: evolution, temporal fluctuation, and intercompartment dynamics from the seronegative window period through 30 months postinfection

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

An automated genotyping system for analysis of HIV-1 and other microbial sequences

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

A web-based genotyping resource for viral sequences

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

High rates of human immunodeficiency virus type 1 recombination: near-random segregation of markers one kilobase apart in one round of viral replication

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Evolution and diversity of HIV-1 in Africa--a review.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Among 46 near full length HIV type 1 genome sequences from Rakai District, Uganda, subtype D and AD recombinants predominate

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Diversity considerations in HIV-1 vaccine selection

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Evaluation of methods for detecting recombination from DNA sequences: empirical data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Evaluation of methods for detecting recombination from DNA sequences: computer simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Re-analysis of human immunodeficiency virus type 1 isolates from Cyprus and Greece, initially designated 'subtype I', reveals a unique complex A/G/H/K/? mosaic pattern.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

HIV type 1 A/J recombinant with a pronounced pol gene mosaicism

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

An isolate of human immunodeficiency virus type 1 originally classified as subtype I represents a complex mosaic comprising three different group M subtypes (A, G, and I)

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Alignment uncertainty and genomic analysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

Robust inference of positive selection from recombining coding sequences

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

The effect of recombination on the accuracy of phylogeny estimation.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

At least five HIV-1 sequence subtypes (A, B, C, D, A/E) occur in England

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2776870

HIV-1 nomenclature proposal.

2 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

Near-full-length genome sequencing of divergent African HIV type 1 subtype F viruses leads to the identification of a new HIV type 1 subtype designated K.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

Drug resistance testing provides evidence of the globalization of HIV type 1: a new circulating recombinant form.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

A Modified Bootscan Algorithm for Automated Identification of Recombinant Sequences and Recombination Breakpoints

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

A statistical model for HIV-1 sequence classification using the subtype analyser (STAR).

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

Dual multiple change-point model leads to more accurate recombination detection.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

Automated phylogenetic detection of recombination using a genetic algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

A simple hierarchical approach to modeling distributions of substitution rates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

Estimating the Dimension of a Model

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

A new look at the statistical model identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

Further analysts of the data by akaike' s information criterion and the finite corrections

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

Antiretroviral-drug resistance among patients recently infected with HIV.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

Tracking the prevalence of transmitted antiretroviral drug-resistant HIV-1: a decade of experience

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

Identification of two new CRF_BF in Rio de Janeiro State, Brazil.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

Unveiling the Molecular Clock in the Presence of Recombination

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

Effect of HIV-1 subtype on virologic and immunologic response to starting highly active antiretroviral therapy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000581

Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19956739

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1000581

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

journals/ploscb/PondPSCPHFGBF09

13 February 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19956739%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

2 references