Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA

A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations

(2016) David Seifert et al.   JOURNAL OF MOLECULAR BIOLOGY

Primer ID Informs Next-Generation Sequencing Platforms and Reveals Preexisting Drug Resistance Mutations in the HIV-1 Reverse Transcriptase Coding Domain

(2015) Jessica R. Keys et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations

(2015) Shuntai Zhou et al.   JOURNAL OF VIROLOGY

Library preparation methods for next-generation sequencing: Tone down the bias

(2014) Erwin L. van Dijk et al.   EXPERIMENTAL CELL RESEARCH

Human Immunodeficiency Virus Reverse Transcriptase Displays Dramatically Higher Fidelity under Physiological Magnesium Conditions In Vitro

(2014) V. Achuthan et al.   JOURNAL OF VIROLOGY

Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing

(2014) Richard H. Liang et al.   NUCLEIC ACIDS RESEARCH

Extensive Recombination Due to Heteroduplexes Generates Large Amounts of Artificial Gene Fragments during PCR

(2014) Jia Liu et al.   PLoS One

Lack of Detectable HIV-1 Molecular Evolution during Suppressive Antiretroviral Therapy

(2014) Mary F. Kearney et al.   PLoS Pathogens

Homopolymer tail-mediated ligation PCR: a streamlined and highly efficient method for DNA cloning and library construction

(2013) David W. Lazinski et al.   BIOTECHNIQUES

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Restriction of V3 region sequence divergence in the HIV-1 envelope gene during antiretroviral treatment in a cohort of recent seroconverters

(2013) Astrid Gall et al.   Retrovirology

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

Optimal enzymes for amplifying sequencing libraries

(2011) Michael A Quail et al.   NATURE METHODS

A method for counting PCR template molecules with application to next-generation sequencing

(2011) J. A. Casbon et al.   NUCLEIC ACIDS RESEARCH

Counting individual DNA molecules by the stochastic attachment of diverse labels

(2011) G. K. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The impact of PCR-generated recombination on diversity estimation of mixed viral populations by deep sequencing

(2010) Irene Görzer et al.   JOURNAL OF VIROLOGICAL METHODS

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

Human Immunodeficiency Virus Type 1 Population Genetics and Adaptation in Newly Infected Individuals

(2008) M. Kearney et al.   JOURNAL OF VIROLOGY

Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing

(2008) J. F. Salazar-Gonzalez et al.   JOURNAL OF VIROLOGY

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