High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems (Q36491810)

14 August 2017

High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems (English)

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14 August 2017

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Li Yin

1

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14 August 2017

Li Liu

2

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14 August 2017

Yijun Sun

3

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14 August 2017

Wei Hou

4

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14 August 2017

Amanda C Lowe

5

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14 August 2017

Brent P Gardner

6

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14 August 2017

Marco Salemi

7

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14 August 2017

Wilton B Williams

8

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14 August 2017

William G Farmerie

9

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14 August 2017

John W Sleasman

10

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14 August 2017

Maureen M Goodenow

11

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14 August 2017

17 December 2012

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14 August 2017

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14 August 2017

9

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14 August 2017

108

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Creative Commons Attribution 2.0 Generic

14 August 2017

start time

1 December 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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April 2022 Public Data File from Crossref

exact match

https://scigraph.springernature.com/pub.10.1186/1742-4690-9-108

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cites work

Previously transmitted HIV-1 strains are preferentially selected during subsequent sexual transmissions

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Structure, function and diversity of the healthy human microbiome

30 September 2017

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Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection

30 September 2017

1 reference

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High-resolution phylogenetics and phylogeography of human immunodeficiency virus type 1 subtype C epidemic in South America

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Viral evolution and escape during acute HIV-1 infection

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Quasispecies theory and the behavior of RNA viruses

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

30 September 2017

1 reference

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Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing

30 September 2017

1 reference

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Evolutionary characterization of the West Nile Virus complete genome

30 September 2017

1 reference

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Clinical management of HIV-1 resistance

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Identifying genetic determinants needed to establish a human gut symbiont in its habitat

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Genetic determinants in HIV-1 Gag and Env V3 are related to viral response to combination antiretroviral therapy with a protease inhibitor

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

High-throughput sequencing of the zebrafish antibody repertoire

30 September 2017

1 reference

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ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Viral population estimation using pyrosequencing

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Phylodynamics of HIV-1 in lymphoid and non-lymphoid tissues reveals a central role for the thymus in emergence of CXCR4-using quasispecies

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Microbial diversity in the deep sea and the underexplored "rare biosphere"

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Complex determinants in human immunodeficiency virus type 1 envelope gp120 mediate CXCR4-dependent infection of macrophages

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Impact on genetic networks in human macrophages by a CCR5 strain of human immunodeficiency virus type 1

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Importance and detection of virus reservoirs and compartments of HIV infection

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

An index of substitution saturation and its application

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Genetic subtypes of HIV-1 in the Philippines

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

PAML: a program package for phylogenetic analysis by maximum likelihood

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

RNA virus mutations and fitness for survival

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Independent variation and positive selection in env V1 and V2 domains within maternal-infant strains of human immunodeficiency virus type 1 in vivo

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Persistence of multiple maternal genotypes of human immunodeficiency virus type I in infants infected by vertical transmission

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

HIV-1 isolates are rapidly evolving quasispecies: evidence for viral mixtures and preferred nucleotide substitutions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

The evolutionary dynamics of HIV-1 quasispecies and the development of immunodeficiency disease.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Selective transmission of human immunodeficiency virus type-1 variants from mothers to infants

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Pyrosequencing analysis of the oral microflora of healthy adults

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Characterization of minority subpopulations in the mutant spectrum of HIV-1 quasispecies by successive specific amplifications.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

On the nature of virus quasispecies

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531307

Save those molecules! Molecular biodiversity and life*

21 September 2018

1 reference

28 May 2022

https://opencitations.net/index/coci/api/v1/citations/10.1046/J.1365-2664.2003.00803.X

Identifiers

DOI

10.1186/1742-4690-9-108

1 reference

Dimensions Publication ID

14 August 2017

0 references

1 reference

14 August 2017

PubMed publication ID

23244298

1 reference