(Q34205837)

31 July 2017

title

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

1 reference

31 July 2017

13

Gregory D Ebel

1 reference

31 July 2017

2

Michael C Zody

1 reference

31 July 2017

10

Doug E Brackney

1 reference

31 July 2017

author name string

Alexander R Macalalad

1

1 reference

31 July 2017

Patrick Charlebois

3

1 reference

31 July 2017

Niall J Lennon

4

1 reference

31 July 2017

Ruchi M Newman

5

1 reference

31 July 2017

Christine M Malboeuf

6

1 reference

31 July 2017

Elizabeth M Ryan

7

1 reference

31 July 2017

Christian L Boutwell

8

1 reference

31 July 2017

Karen A Power

9

1 reference

31 July 2017

Kendra N Pesko

11

1 reference

31 July 2017

Joshua Z Levin

12

1 reference

31 July 2017

Todd M Allen

14

1 reference

31 July 2017

Bruce W Birren

15

1 reference

31 July 2017

Matthew R Henn

16

1 reference

31 July 2017

publication date

15 March 2012

1 reference

PLOS Computational Biology

31 July 2017

published in

1 reference

31 July 2017

volume

8

1 reference

31 July 2017

issue

3

1 reference

31 July 2017

page(s)

e1002417

1 reference

Creative Commons Attribution 4.0 International

31 July 2017

copyright license

start time

15 March 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305335

QuRe: software for viral quasispecies reconstruction 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=3305335

Inferring viral quasispecies spectra from 454 pyrosequencing reads.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305335

ShoRAH: estimating the genetic diversity of a mixed sample 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=3305335

A framework for variation discovery and genotyping using next-generation DNA 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=3305335

Removing noise from pyrosequenced amplicons

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305335

The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time--an ultra-deep approach

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305335

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=3305335

Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep 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=3305335

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305335

Optimization of allele-specific PCR using patient-specific HIV consensus sequences for primer design

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305335

SNP detection for massively parallel whole-genome resequencing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305335

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305335

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=3305335

Mapping short DNA sequencing reads and calling variants using mapping quality scores

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305335

Viral population estimation using 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=3305335

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=3305335

Quality scores and SNP detection in sequencing-by-synthesis systems

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305335

Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305335

DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305335

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=3305335

Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305335

An SNP map of the human genome generated by reduced representation shotgun 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=3305335

Genotypic and phenotypic characterization of HIV-1 patients with primary 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=3305335

Detection, quantification and sequencing of HIV-1 from the plasma of seropositive individuals and from factor VIII concentrates

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305335

Comparative performance of high-density oligonucleotide sequencing and dideoxynucleotide sequencing of HIV type 1 pol from clinical samples.

5 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002417

Slider--maximum use of probability information for alignment of short sequence reads and SNP detection

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002417

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/22438797

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1002417

1 reference

journals/ploscb/MacalaladZCLNMRBPBPLEABH12

31 July 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

31 July 2017

1 reference