Inference with viral quasispecies diversity indices: clonal and NGS approaches

Ultra-Deep Pyrosequencing (UDPS) Data Treatment to Study Amplicon HCV Minor Variants

(2014) Josep Gregori et al.   PLoS One

A comparative study of ultra-deep pyrosequencing and cloning to quantitatively analyze the viral quasispecies using hepatitis B virus infection as a model

(2013) Clara Ramírez et al.   ANTIVIRAL RESEARCH

Analysis of HCV quasispecies dynamic under selective pressure of combined therapy

(2013) Ana CG Jardim et al.   BMC INFECTIOUS DISEASES

Low-Level Persistence of Drug Resistance Mutations in Hepatitis B Virus-Infected Subjects with a Past History of Lamivudine Treatment

(2012) Severine Margeridon-Thermet et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Minor variant detection in amplicons using 454 massive parallel pyrosequencing: experiences and considerations for successful applications

(2012) Ina Vandenbroucke et al.   BIOTECHNIQUES

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

Increased viral quasispecies evolution in HBeAg seroconverter patients treated with oral nucleoside therapy

(2012) Yan Cheng et al.   JOURNAL OF HEPATOLOGY

Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages

(2012) R. K. Colwell et al.   Journal of Plant Ecology

Viral Quasispecies Evolution

(2012) E. Domingo et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Grinder: a versatile amplicon and shotgun sequence simulator

(2012) Florent E. Angly et al.   NUCLEIC ACIDS RESEARCH

Dynamics of Hepatitis B Virus Quasispecies in Association with Nucleos(t)ide Analogue Treatment Determined by Ultra-Deep Sequencing

(2012) Norihiro Nishijima et al.   PLoS One

Read length versus Depth of Coverage for Viral Quasispecies Reconstruction

(2012) Osvaldo Zagordi et al.   PLoS One

The impact of quasispecies dynamics on the use of therapeutics

(2012) Celia Perales et al.   TRENDS IN MICROBIOLOGY

Quasispecies dynamics in main core epitopes of hepatitis B virus by ultra-deep-pyrosequencing

(2012) Maria Homs   WORLD JOURNAL OF GASTROENTEROLOGY

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

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

(2012) Niko Beerenwinkel et al.   Frontiers in Microbiology

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

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

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

(2011) Mattia CF Prosperi et al.   BMC BIOINFORMATICS

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

(2011) André Gilles et al.   BMC GENOMICS

Evolutionary patterns of hepatitis B virus quasispecies under different selective pressures: correlation with antiviral efficacy

(2011) F. Liu et al.   GUT

Boceprevir for Untreated Chronic HCV Genotype 1 Infection

(2011) Fred Poordad et al.   NEW ENGLAND JOURNAL OF MEDICINE

Telaprevir for Previously Untreated Chronic Hepatitis C Virus Infection

(2011) Ira M. Jacobson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Ultrasensitive detection of rare mutations using next-generation targeted resequencing

(2011) Patrick Flaherty et al.   NUCLEIC ACIDS RESEARCH

Ultra-deep pyrosequencing analysis of the hepatitis B virus preCore region and main catalytic motif of the viral polymerase in the same viral genome

(2011) M. Homs et al.   NUCLEIC ACIDS RESEARCH

Performance of Ultra-Deep Pyrosequencing in Analysis of HIV-1 pol Gene Variation

(2011) Mattias Mild et al.   PLoS One

Genetic Heterogeneity of Hepatitis C Virus in Association with Antiviral Therapy Determined by Ultra-Deep Sequencing

(2011) Akihiro Nasu et al.   PLoS One

Contribution of a mutational bias in hepatitis C virus replication to the genetic barrier in the development of drug resistance

(2011) M. H. Powdrill 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

Viral quasispecies profiles as the result of the interplay of competition and cooperation

(2010) Juan Arbiza et al.   BMC EVOLUTIONARY BIOLOGY

Mutant spectra in virus behavior

(2010) Celia Perales et al.   Future Virology

A consistent terminology for quantifying species diversity? Yes, it does exist

(2010) Hanna Tuomisto   OECOLOGIA

Phylogenetic diversity measures based on Hill numbers

(2010) A. Chao et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Competition-colonization dynamics in an RNA virus

(2010) S. Ojosnegros et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sufficient sampling for asymptotic minimum species richness estimators

(2009) Anne Chao et al.   ECOLOGY

Resistance to Direct Antiviral Agents in Patients With Hepatitis C Virus Infection

(2009) Christoph Sarrazin et al.   GASTROENTEROLOGY

The quasispecies nature and biological implications of the hepatitis C virus

(2009) Sarah L. Fishman et al.   INFECTION GENETICS AND EVOLUTION

Ultra‐Deep Pyrosequencing of Hepatitis B Virus Quasispecies from Nucleoside and Nucleotide Reverse‐Transcriptase Inhibitor (NRTI)–Treated Patients and NRTI‐Naive Patients

(2009) Severine Margeridon‐Thermet et al.   JOURNAL OF INFECTIOUS DISEASES

Use of Massively Parallel Ultradeep Pyrosequencing To Characterize the Genetic Diversity of Hepatitis B Virus in Drug-Resistant and Drug-Naive Patients and To Detect Minor Variants in Reverse Transcriptase and Hepatitis B S Antigen

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