(Q34174981)

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Transition between stochastic evolution and deterministic evolution in the presence of selection: general theory and application to virology.

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scholarly article

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Europe PubMed Central

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5 November 2019

1 reference

Europe PubMed Central

Transition between stochastic evolution and deterministic evolution in the presence of selection: general theory and application to virology (English)

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11238990%20AND%20SRC:MED&resulttype=core&format=json

5 November 2019

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Allen Gerard Rodrigo

2

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5 November 2019

author name string

I M Rouzine

1

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5 November 2019

J M Coffin

3

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5 November 2019

publication date

1 March 2001

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5 November 2019

Microbiology and Molecular Biology Reviews

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5 November 2019

65

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5 November 2019

151-185

1 reference

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5 November 2019

1

1 reference

Europe PubMed Central

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5 November 2019

The Average Number of Generations until Fixation of a Mutant Gene in a Finite Population.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Process Leading to Quasi-Fixation of Genes in Natural Populations Due to Random Fluctuation of Selection Intensities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

EVOLUTION IN MENDELIAN POPULATIONS

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

SOLUTION OF A PROCESS OF RANDOM GENETIC DRIFT WITH A CONTINUOUS MODEL.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

The Differential Equation of the Distribution of Gene Frequencies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

On the probability of fixation of mutant genes in a population

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Linkage disequilibrium test implies a large effective population number for HIV in vivo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Search for the mechanism of genetic variation in the pro gene of human immunodeficiency virus.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Population biology of HIV-1 infection: viral and CD4+ T cell demographics and dynamics in lymphatic tissues

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Coalescent estimates of HIV-1 generation time in vivo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Multiple molecular pathways for fitness recovery of an RNA virus debilitated by operation of Muller's ratchet

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Rapid clearance of simian immunodeficiency virus particles from plasma of rhesus macaques

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Tracking members of the simian immunodeficiency virus deltaB670 quasispecies population in vivo at single-cell resolution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Ancestral Processes with Selection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Divergent patterns of progression to AIDS after infection from the same source: human immunodeficiency virus type 1 evolution and antiviral responses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

The genealogy of samples in models with selection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Intrapatient sequence variation of the gag gene of human immunodeficiency virus type 1 plasma virions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Quantitative image analysis of HIV-1 infection in lymphoid tissue.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Large-population passages of vesicular stomatitis virus in interferon-treated cells select variants of only limited resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

In vivo sequence diversity of the protease of human immunodeficiency virus type 1: presence of protease inhibitor-resistant variants in untreated subjects.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Human immunodeficiency virus type 1 evolution in vivo tracked by DNA heteroduplex mobility assays.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Sequence constraints and recognition by CTL of an HLA-B27-restricted HIV-1 gag epitope

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Size of genetic bottlenecks leading to virus fitness loss is determined by mean initial population fitness.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

In vivo emergence of HIV-1 variants resistant to multiple protease inhibitors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Viral dynamics in human immunodeficiency virus type 1 infection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Envelope sequence variation, neutralizing antibodies, and primate lentivirus persistence.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Recovery of virtually full-length HIV-1 provirus of diverse subtypes from primary virus cultures using the polymerase chain reaction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Intrahost human immunodeficiency virus type 1 evolution is related to length of the immunocompetent period

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Extreme fitness differences in mammalian and insect hosts after continuous replication of vesicular stomatitis virus in sandfly cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

The evolutionary advantage of recombination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Evolution in bacteria: evidence for a universal substitution rate in cellular genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

The neutral theory of molecular evolution and the world view of the neutralists

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Structural requirements for class I MHC molecule-mediated antigen presentation and cytotoxic T cell recognition of an immunodominant determinant of the human immunodeficiency virus envelope protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Fitness of RNA virus decreased by Muller's ratchet

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Concurrent evolution of human immunodeficiency virus type 1 in patients infected from the same source: rate of sequence change and low frequency of inactivating mutations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Characterization of genetic variation and 3'-azido-3'-deoxythymidine- resistance mutations of human immunodeficiency virus by the RNase A mismatch cleavage method

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Selection of genetic variants of simian immunodeficiency virus in persistently infected rhesus monkeys

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Muller's ratchet and flu virus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Evolution of sequences encoding the principal neutralization epitope of human immunodeficiency virus 1 is host dependent, rapid, and continuous

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Naturally occurring mutations within HIV-1 V3 genomic RNA lead to antigenic variation dependent on a single amino acid substitution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

RNA virus populations as quasispecies.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

A statistical test for detecting geographic subdivision

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Phenotype-associated env gene variation among eight related human immunodeficiency virus type 1 clones: evidence for in vivo recombination and determinants of cytotropism outside the V3 domain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Characterization of HIV isolates arising after prolonged zidovudine therapy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Rapid fitness losses in mammalian RNA virus clones due to Muller's ratchet

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

On the number of segregating sites in genetical models without recombination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

5 July 2018

Evolution of zidovudine resistance-associated genotypes in human immunodeficiency virus type 1-infected patients

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

28 October 2018

V3 sequences of paired HIV-1 isolates from blood and cerebrospinal fluid cluster according to host and show variation related to the clinical stage of disease.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

28 October 2018

Molecular determinants of the V3 loop of human immunodeficiency virus type 1 glycoprotein gp120 responsible for controlling cell tropism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

28 October 2018

Causes of HIV diversity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

28 October 2018

Natural selection on the gag, pol, and env genes of human immunodeficiency virus 1 (HIV-1).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=99023

28 October 2018

A general theory of the distribution of gene frequencies. I. Overlapping generations

1 reference

https://pubmed.ncbi.nlm.nih.gov/11238990

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Stochastic processes and distribution of gene frequencies under natural selection

1 reference

https://pubmed.ncbi.nlm.nih.gov/11238990

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The effect of recombination on background selection

1 reference

https://pubmed.ncbi.nlm.nih.gov/11238990

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

What use is sex?

1 reference

https://pubmed.ncbi.nlm.nih.gov/11238990

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations

1 reference

https://pubmed.ncbi.nlm.nih.gov/11238990

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Sequence variation: looking for effects of genetic linkage

1 reference

https://pubmed.ncbi.nlm.nih.gov/11238990

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1128/MMBR.65.1.151-185.2001

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11238990%20AND%20SRC:MED&resulttype=core&format=json

5 November 2019

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11238990%20AND%20SRC:MED&resulttype=core&format=json

5 November 2019

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11238990%20AND%20SRC:MED&resulttype=core&format=json

5 November 2019

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