Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations (Q34044256)

30 July 2017

Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations (English)

1 reference

30 July 2017

18

Niko Beerenwinkel

0 references

Martin Däumer

12

Martin Däumer

1 reference

30 July 2017

Francesca Di Giallonardo

1

Francesca Di Giallonardo

0 references

Karin J Metzner

Karin J Metzner

19

0 references

Alexandra Trkola

Alexandra Trkola

15

0 references

Huldrych F Günthard

Huldrych F Günthard

16

0 references

Peter Rusert

14

Peter Rusert

1 reference

30 July 2017

Armin Töpfer

2

1 reference

30 July 2017

Melanie Rey

3

1 reference

30 July 2017

Sandhya Prabhakaran

4

1 reference

30 July 2017

Yannick Duport

5

1 reference

30 July 2017

Christine Leemann

6

1 reference

30 July 2017

Stefan Schmutz

7

1 reference

30 July 2017

Nottania K Campbell

8

1 reference

30 July 2017

Beda Joos

9

1 reference

30 July 2017

Maria Rita Lecca

10

1 reference

30 July 2017

Andrea Patrignani

11

1 reference

30 July 2017

Christian Beisel

13

1 reference

30 July 2017

Volker Roth

17

1 reference

30 July 2017

language of work or name

English

0 references

publication date

27 June 2014

1 reference

30 July 2017

Nucleic Acids Research

1 reference

30 July 2017

42

1 reference

30 July 2017

14

1 reference

30 July 2017

e115

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

30 July 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Origin of minority drug-resistant HIV-1 variants in primary HIV-1 infection

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Probabilistic inference of viral quasispecies subject to recombination

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Read length versus depth of coverage for viral quasispecies reconstruction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Single cell genomics: an individual look at microbes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Viral quasispecies evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Characterization of human immunodeficiency virus type 1 (HIV-1) diversity and tropism in 145 patients with primary HIV-1 infection

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

A maraviroc-resistant HIV-1 with narrow cross-resistance to other CCR5 antagonists depends on both N-terminal and extracellular loop domains of drug-bound CCR5

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Sequencing technologies - the next generation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Real-time DNA sequencing from single polymerase molecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Accurate whole human genome sequencing using reversible terminator chemistry

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

MetaSim: a sequencing simulator for genomics and metagenomics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

In vivo and in vitro escape from neutralizing antibodies 2G12, 2F5, and 4E10.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Bias and artifacts in multitemplate polymerase chain reactions (PCR).

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

Genome sequencing in microfabricated high-density picolitre reactors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

5 July 2018

What is a quasispecies?

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKU537

HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model

21 January 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132706

28 October 2018

https://pubmed.ncbi.nlm.nih.gov/24972832

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A patient with HIV-1 superinfection

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24972832

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKU537

1 reference

30 July 2017

1 reference

30 July 2017

1 reference