Viral quasispecies assembly via maximal clique enumeration (Q28541589)

2

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Fabio Luciani

object named as

Fabio Luciani

4

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Rowena A Bull

object named as

Rowena A Bull

3

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author name string

Armin Töpfer

1

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Alexander Schönhuth

PLOS Computational Biology

5

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language of work or name

English

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publication date

March 2014

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published in

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volume

10

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issue

3

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page(s)

e1003515

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copyright license

Creative Commons Attribution 4.0 International

start time

27 March 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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Viral quasispecies evolution

19 March 2017

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ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

19 March 2017

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Removing noise from pyrosequenced amplicons

19 March 2017

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Viral population estimation using pyrosequencing

19 March 2017

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Velvet: algorithms for de novo short read assembly using de Bruijn graphs

19 March 2017

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Genetic variation, classification and 'race'

19 March 2017

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High-quality draft assemblies of mammalian genomes from massively parallel sequence data

19 March 2017

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Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population

7 April 2017

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MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels

7 April 2017

1 reference

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Haplotype assembly in polyploid genomes and identical by descent shared tracts

29 September 2017

1 reference

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Sequencing approach to analyze the role of quasispecies for classical swine fever

29 September 2017

1 reference

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Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes

29 September 2017

1 reference

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QColors: an algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads

29 September 2017

1 reference

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Read length versus depth of coverage for viral quasispecies reconstruction

29 September 2017

1 reference

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Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing.

29 September 2017

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Efficient error correction for next-generation sequencing of viral amplicons

29 September 2017

1 reference

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HapCompass: a fast cycle basis algorithm for accurate haplotype assembly of sequence data

29 September 2017

1 reference

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Haplotype and minimum-chimerism consensus determination using short sequence data

29 September 2017

1 reference

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Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence 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=3967922

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

29 September 2017

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GAGE: A critical evaluation of genome assemblies and assembly algorithms

29 September 2017

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QuRe: software for viral quasispecies reconstruction from next-generation sequencing 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=3967922

Inferring viral quasispecies spectra from 454 pyrosequencing reads.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967922

Assemblathon 1: a competitive assessment of de novo short read assembly methods

29 September 2017

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Sequential bottlenecks drive viral evolution in early acute hepatitis C virus 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=3967922

Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967922

Probabilistic inference of viral quasispecies subject to recombination

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967922

CLEVER: clique-enumerating variant finder

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967922

RNA-Seq gene expression estimation with read mapping uncertainty

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967922

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

3 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003515

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003515

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003515

Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24675810

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1003515

0 references

DBLP publication ID

journals/ploscb/TopferMBLSB14

1 reference