Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection

An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing

(2014) Birgitte B. Simen et al.   JOURNAL OF VIROLOGICAL METHODS

Detecting ultralow-frequency mutations by Duplex Sequencing

(2014) Scott R Kennedy et al.   Nature Protocols

Selection bias at the heterosexual HIV-1 transmission bottleneck

(2014) J. M. Carlson et al.   SCIENCE

Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data

(2013) Wenjie Deng et al.   BIOINFORMATICS

PCR-Induced Transitions Are the Major Source of Error in Cleaned Ultra-Deep Pyrosequencing Data

(2013) Johanna Brodin et al.   PLoS One

Quality Score Based Identification and Correction of Pyrosequencing Errors

(2013) Shyamala Iyer et al.   PLoS One

Improved Detection of Rare HIV-1 Variants using 454 Pyrosequencing

(2013) Brendan B. Larsen et al.   PLoS One

Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA

(2013) Wei Shao et al.   Retrovirology

Experimental Analysis of Sources of Error in Evolutionary Studies Based on Roche/454 Pyrosequencing of Viral Genomes

(2012) E. A. Becker et al.   Genome Biology and Evolution

Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities

(2012) Juan M. Gonzalez et al.   PLoS One

K65R in Subtype C HIV-1 Isolates from Patients Failing on a First-Line Regimen Including d4T or AZT: Comparison of Sanger and UDP Sequencing Data

(2012) Patricia Recordon-Pinson et al.   PLoS One

Implications of Pyrosequencing Error Correction for Biological Data Interpretation

(2012) Matthew G. Bakker et al.   PLoS One

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

(2012) Ameet J. Pinto et al.   PLoS One

Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing

(2012) Charles K. Lee et al.   PLoS One

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data

(2012) Alexander R. Macalalad et al.   PLoS Computational Biology

Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

(2012) Matthew R. Henn et al.   PLoS Pathogens

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

(2011) Mattia C. F. Prosperi et al.   BIOINFORMATICS

Correcting errors in short reads by multiple alignments

(2011) L. Salmela et al.   BIOINFORMATICS

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

(2011) Mattia CF Prosperi et al.   BMC BIOINFORMATICS

pcrEfficiency: a Web tool for PCR amplification efficiency prediction

(2011) Izaskun Mallona et al.   BMC BIOINFORMATICS

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

(2011) Osvaldo Zagordi et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

(2011) André Gilles et al.   BMC GENOMICS

Low-Frequency HIV-1 Drug Resistance Mutations and Risk of NNRTI-Based Antiretroviral Treatment Failure

(2011) Jonathan Z. Li   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

HIV-1 nucleotide mixture detection in the virco®TYPE HIV-1 genotyping assay: A comparison between Sanger sequencing and 454 pyrosequencing

(2011) Hans De Wolf et al.   JOURNAL OF VIROLOGICAL METHODS

Human immunodeficiency virus type 1 drug resistance testing: Evaluation of a new ultra-deep sequencing-based protocol and comparison with the TRUGENE HIV-1 Genotyping Kit

(2011) Evelyn Stelzl et al.   JOURNAL OF VIROLOGICAL METHODS

Detection of Minority Resistance during Early HIV-1 Infection: Natural Variation and Spurious Detection rather than Transmission and Evolution of Multiple Viral Variants

(2011) S. Gianella et al.   JOURNAL OF VIROLOGY

Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial

(2011) Morgane Rolland et al.   NATURE MEDICINE

Systematic Comparison of Three Methods for Fragmentation of Long-Range PCR Products for Next Generation Sequencing

(2011) Ellen Knierim et al.   PLoS One

A Comparison of Parallel Pyrosequencing and Sanger Clone-Based Sequencing and Its Impact on the Characterization of the Genetic Diversity of HIV-1

(2011) Binhua Liang et al.   PLoS One

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

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

(2011) C. B. Jabara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultra-deep sequencing for the analysis of viral populations

(2011) Niko Beerenwinkel et al.   Current Opinion in Virology

Analysis of Low-Frequency Mutations Associated with Drug Resistance to Raltegravir before Antiretroviral Treatment

(2010) Jia Liu et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites

(2010) Wenjie Deng et al.   BIOTECHNIQUES

Vaccine-Induced HIV Seropositivity/Reactivity in Noninfected HIV Vaccine Recipients

(2010) Cristine J. Cooper   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Whole-Genome Characterization of Human and Simian Immunodeficiency Virus Intrahost Diversity by Ultradeep Pyrosequencing

(2010) B. N. Bimber et al.   JOURNAL OF VIROLOGY

Mathematical Modeling of Ultradeep Sequencing Data Reveals that Acute CD8+ T-Lymphocyte Responses Exert Strong Selective Pressure in Simian Immunodeficiency Virus-Infected Macaques but Still Fail To Clear Founder Epitope Sequences

(2010) T. M. T. Love et al.   JOURNAL OF VIROLOGY

HIV Drug Resistance Surveillance Using Pooled Pyrosequencing

(2010) Hezhao Ji et al.   PLoS One

Nucleic Acid Template and the Risk of a PCR-Induced HIV-1 Drug Resistance Mutation

(2010) Vici Varghese et al.   PLoS One

Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing

(2010) Charlotte Hedskog et al.   PLoS One

Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing

(2010) Will Fischer et al.   PLoS One

The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time—An Ultra-Deep Approach

(2010) John Archer et al.   PLoS Computational Biology

Minority Variants Associated with Transmitted and Acquired HIV-1 Nonnucleoside Reverse Transcriptase Inhibitor Resistance: Implications for the Use of Second-Generation Nonnucleoside Reverse Transcriptase Inhibitors

(2009) Vici Varghese et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Ultradeep Pyrosequencing Detects Complex Patterns of CD8+ T-Lymphocyte Escape in Simian Immunodeficiency Virus-Infected Macaques

(2009) B. N. Bimber et al.   JOURNAL OF VIROLOGY

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

HIV-1 vaccine-induced immunity in the test-of-concept Step Study: a case–cohort analysis

(2008) M Juliana McElrath et al.   LANCET

Efficacy assessment of a cell-mediated immunity HIV-1 vaccine (the Step Study): a double-blind, randomised, placebo-controlled, test-of-concept trial

(2008) Susan P Buchbinder et al.   LANCET

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

(2008) B. F. Keele et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA