Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism

Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.

(2012) John Archer et al.   BMC BIOINFORMATICS

Cancer Genomics: Technology, Discovery, and Translation

(2012) Ben Tran et al.   JOURNAL OF CLINICAL ONCOLOGY

Study of Genotypic and Phenotypic HIV-1 Dynamics of Integrase Mutations During Raltegravir Treatment: A Refined Analysis by Ultra-Deep 454 Pyrosequencing

(2012) Daniele Armenia et al.   JOURNAL OF INFECTIOUS DISEASES

Discordance in HIV-1 Co-receptor use prediction by different genotypic algorithms and phenotype assay: Intermediate profile in relation to concordant predictions

(2012) Mary-Anne Trabaud et al.   JOURNAL OF MEDICAL VIROLOGY

Complete Genome Sequence of the Giant Pseudomonas Phage Lu11

(2012) E. M. Adriaenssens et al.   JOURNAL OF VIROLOGY

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting

(2012) Hirokazu Matsushita et al.   NATURE

Ultra-Deep Sequencing of HIV-1 Reverse Transcriptase Before Start of an NNRTI-based Regimen in Treatment-naive Patients

(2012) Peter Messiaen et al.   VIROLOGY

Frequency of CXCR4-using viruses in primary HIV-1 infections using ultra-deep pyrosequencing

(2011) Stéphanie Raymond et al.   AIDS

Switching between raltegravir resistance pathways analyzed by deep sequencing

(2011) Rithun Mukherjee et al.   AIDS

Correlation of the Virological Response to Short-Term Maraviroc Monotherapy with Standard and Deep-Sequencing-Based Genotypic Tropism Prediction Methods

(2011) A. Gonzalez-Serna et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Concordance between Two Phenotypic Assays and Ultradeep Pyrosequencing for Determining HIV-1 Tropism

(2011) Adrien Saliou et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Deep V3 Sequencing for HIV Type 1 Tropism in Treatment-Naive Patients: A Reanalysis of the MERIT Trial of Maraviroc

(2011) Luke C. Swenson et al.   CLINICAL INFECTIOUS DISEASES

Improved V3 genotyping with duplicate PCR amplification for determining HIV-1 tropism

(2011) S. Raymond et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

High Concordance between the Position-Specific Scoring Matrix and Geno2pheno Algorithms for Genotypic Interpretation of HIV-1 Tropism: V3 Length as the Major Cause of Disagreement: Table 1.

(2011) Eduardo Seclén et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Genome-Wide Analysis of the 5' and 3' Ends of Vaccinia Virus Early mRNAs Delineates Regulatory Sequences of Annotated and Anomalous Transcripts

(2011) Z. Yang et al.   JOURNAL OF VIROLOGY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

(2011) David A. Rasko et al.   NEW ENGLAND JOURNAL OF MEDICINE

“Dynamic Range” of Inferred Phenotypic HIV Drug Resistance Values in Clinical Practice

(2011) Luke C. Swenson et al.   PLoS One

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

(2011) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Multidrug Resistance during Staphylococcus aureus Infection Involves Mutation of the Essential Two Component Regulator WalKR

(2011) Benjamin P. Howden et al.   PLoS Pathogens

Detection of Inferred CCR5- and CXCR4-Using HIV-1 Variants and Evolutionary Intermediates Using Ultra-Deep Pyrosequencing

(2011) Evelien M. Bunnik et al.   PLoS Pathogens

Deep Molecular Characterization of HIV-1 Dynamics under Suppressive HAART

(2011) Maria J. Buzón et al.   PLoS Pathogens

A vertebrate case study of the quality of assemblies derived from next-generation sequences

(2011) Liang Ye et al.   GENOME BIOLOGY

Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection

(2010) Isabella Abbate et al.   AIDS

Evaluation of the Genotypic Prediction of HIV-1 Coreceptor Use versus a Phenotypic Assay and Correlation with the Virological Response to Maraviroc: the ANRS GenoTropism Study

(2010) P. Recordon-Pinson et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

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

Prevalence of CCR5-tropic HIV-1 Among Treatment-Experienced Individuals in Spain

(2010) S. Moreno et al.   HIV CLINICAL TRIALS

Improved Detection of CXCR4-Using HIV by V3 Genotyping: Application of Population-Based and “Deep” Sequencing to Plasma RNA and Proviral DNA

(2010) Luke C Swenson et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Deep Sequencing to Infer HIV-1 Co-Receptor Usage: Application to Three Clinical Trials of Maraviroc in Treatment-Experienced Patients

(2010) L. C. Swenson et al.   JOURNAL OF INFECTIOUS DISEASES

The Origin of the Haitian Cholera Outbreak Strain

(2010) Chen-Shan Chin et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

HIV-1 V3 envelope deep sequencing for clinical plasma specimens failing in phenotypic tropism assays

(2010) Ina Vandenbroucke et al.   AIDS Research and Therapy

Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing

(2009) John Archer et al.   AIDS

Entry inhibitors in the treatment of HIV-1 infection

(2009) John C. Tilton et al.   ANTIVIRAL RESEARCH

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

Development and performance of a new recombinant virus phenotypic entry assay to determine HIV-1 coreceptor usage

(2009) Stéphanie Raymond et al.   JOURNAL OF CLINICAL VIROLOGY

Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment–Naive Patients Significantly Impact Treatment Outcomes

(2009) Birgitte B. Simen et al.   JOURNAL OF INFECTIOUS DISEASES

A Double‐Blind, Placebo‐Controlled Trial of Maraviroc in Treatment‐Experienced Patients Infected with Non‐R5 HIV‐1

(2009) Michael Saag et al.   JOURNAL OF INFECTIOUS DISEASES

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Tropism testing in the clinical management of HIV-1 infection

(2009) Nina H Lin et al.   Current Opinion in HIV and AIDS

Correlation between genotypic predictions based on V3 sequences and phenotypic determination of HIV-1 tropism

(2008) Stéphanie Raymond et al.   AIDS

The Genome Sequencer FLX™ System—Longer reads, more applications, straight forward bioinformatics and more complete data sets

(2008) Marcus Droege et al.   JOURNAL OF BIOTECHNOLOGY

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY