A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory (Q34864202)

5 August 2017

title

A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory (English)

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5 August 2017

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5

Niko Beerenwinkel

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Francesca Di Giallonardo

2

Francesca Di Giallonardo

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David Seifert

David Seifert

1

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Karin J Metzner

Karin J Metzner

3

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Huldrych F Günthard

Huldrych F Günthard

4

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language of work or name

English

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publication date

17 November 2014

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5 August 2017

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5 August 2017

volume

199

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5 August 2017

issue

1

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5 August 2017

page(s)

191-203

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Mutational and fitness landscapes of an RNA virus revealed through population sequencing

5 August 2017

cites work

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The individualized genetic barrier predicts treatment response in a large cohort of HIV-1 infected patients

8 July 2018

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Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design

8 July 2018

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Probabilistic inference of viral quasispecies subject to recombination

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

The peaks and geometry of fitness landscapes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

8 July 2018

1 reference

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Viral quasispecies evolution

8 July 2018

1 reference

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Exploring the complexity of the HIV-1 fitness landscape

8 July 2018

1 reference

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Landscape of next-generation sequencing technologies.

8 July 2018

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vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments

8 July 2018

1 reference

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Quasispecies theory for finite populations

8 July 2018

1 reference

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Fast and accurate long-read alignment with Burrows-Wheeler transform

8 July 2018

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Parallel tempering: theory, applications, and new perspectives

8 July 2018

1 reference

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Competition between recombination and epistasis can cause a transition from allele to genotype selection

8 July 2018

1 reference

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Analysis of epistatic interactions and fitness landscapes using a new geometric approach

8 July 2018

1 reference

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Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population

8 July 2018

1 reference

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Quasispecies theory in the context of population genetics

8 July 2018

1 reference

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Viral error catastrophe by mutagenic nucleosides

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

Nucleoside-analog resistance mutations in HIV-1 reverse transcriptase and their influence on polymerase fidelity and viral mutation rates

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

Fitness of drug resistant HIV-1: methodology and clinical implications

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

Evolvability of an RNA virus is determined by its mutational neighbourhood

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

Rapid production and clearance of HIV-1 and hepatitis C virus assessed by large volume plasma apheresis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

HIV evolutionary genetics.

8 July 2018

1 reference

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Rapid evolution of RNA viruses

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

The NK model of rugged fitness landscapes and its application to maturation of the immune response

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

RNA virus quasispecies populations can suppress vastly superior mutant progeny

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

Nucleotide sequence heterogeneity of an RNA phage population.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

The hypercycle. A principle of natural self-organization. Part A: Emergence of the hypercycle

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

On the Relation Between the Eigen Model and the Asexual Wright–Fisher Model

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

Cohort profile: the Swiss HIV Cohort study

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

Minority quasispecies of drug-resistant HIV-1 that lead to early therapy failure in treatment-naive and -adherent patients

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

Quasispecies and recombination

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

Relating HIV-1 sequence variation to replication capacity via trees and forests

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4286684

9 December 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/25406469

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1534/GENETICS.114.172312

1 reference

5 August 2017

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5 August 2017

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