Viral Quasispecies Assembly via Maximal Clique Enumeration

MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels

(2013) Tobias Marschall et al.   BIOINFORMATICS

Haplotype assembly in polyploid genomes and identical by descent shared tracts

(2013) Derek Aguiar et al.   BIOINFORMATICS

Probabilistic Inference of Viral Quasispecies Subject to Recombination

(2013) Armin Töpfer et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Sequencing approach to analyze the role of quasispecies for classical swine fever

(2013) Armin Töpfer et al.   VIROLOGY

Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges

(2013) Mattia C. F. Prosperi et al.   Scientific Reports

CLEVER: clique-enumerating variant finder

(2012) Tobias Marschall et al.   BIOINFORMATICS

Efficient error correction for next-generation sequencing of viral amplicons

(2012) Pavel Skums et al.   BMC BIOINFORMATICS

Haplotype and minimum-chimerism consensus determination using short sequence data

(2012) Shawn T O'Neil et al.   BMC GENOMICS

HapCompass: A Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data

(2012) Derek Aguiar et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Viral Quasispecies Evolution

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

Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing

(2012) Karen E. Ocwieja et al.   NUCLEIC ACIDS RESEARCH

Read length versus Depth of Coverage for Viral Quasispecies Reconstruction

(2012) Osvaldo Zagordi 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

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

Inferring viral quasispecies spectra from 454 pyrosequencing reads

(2011) Irina Astrovskaya 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

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase

(2011) Trevor Hinkley et al.   NATURE GENETICS

Sequential Bottlenecks Drive Viral Evolution in Early Acute Hepatitis C Virus Infection

(2011) Rowena A. Bull et al.   PLoS Pathogens

Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction

(2010) Osvaldo Zagordi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

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

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem

(2008) V. Bansal et al.   BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Viral Population Estimation Using Pyrosequencing

(2008) Nicholas Eriksson et al.   PLoS Computational Biology