A Modified RNA-Seq Approach for Whole Genome Sequencing of RNA Viruses from Faecal and Blood Samples

De novo assembly of highly diverse viral populations

(2012) Xiao Yang et al.   BMC GENOMICS

Field Monitoring of Avian Influenza Viruses: Whole-Genome Sequencing and Tracking of Neuraminidase Evolution Using 454 Pyrosequencing

(2012) G. Croville et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Analysis of Hepatitis C Virus Intrahost Diversity across the Coding Region by Ultradeep Pyrosequencing

(2012) M. Lauck et al.   JOURNAL OF VIROLOGY

Constraints on Viral Evolution during Chronic Hepatitis C Virus Infection Arising from a Common-Source Exposure

(2012) J. R. Bailey et al.   JOURNAL OF VIROLOGY

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

(2012) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Oxford Nanopore announcement sets sequencing sector abuzz

(2012) Michael Eisenstein   NATURE BIOTECHNOLOGY

Genome sequencing in clinical microbiology

(2012) Jacqueline Z-M Chan et al.   NATURE BIOTECHNOLOGY

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification

(2012) Christine M. Malboeuf et al.   NUCLEIC ACIDS RESEARCH

A pilot study of rapid benchtop sequencing ofStaphylococcus aureusandClostridium difficilefor outbreak detection and surveillance

(2012) David W Eyre et al.   BMJ Open

Insights from Genomics into Bacterial Pathogen Populations

(2012) Daniel J. Wilson   PLoS Pathogens

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

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

(2011) Mattia CF Prosperi et al.   BMC BIOINFORMATICS

Inferring viral quasispecies spectra from 454 pyrosequencing reads

(2011) Irina Astrovskaya et al.   BMC BIOINFORMATICS

A Viral Discovery Methodology for Clinical Biopsy Samples Utilising Massively Parallel Next Generation Sequencing

(2011) Gordon M. Daly et al.   PLoS One

Specific Capture and Whole-Genome Sequencing of Viruses from Clinical Samples

(2011) Daniel P. Depledge et al.   PLoS One

Mechanisms of GII.4 norovirus evolution

(2011) Rowena A. Bull et al.   TRENDS IN MICROBIOLOGY

PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes

(2010) Qing Yu et al.   BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

The Origin of the Haitian Cholera Outbreak Strain

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

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

(2010) Osvaldo Zagordi et al.   NUCLEIC ACIDS RESEARCH

Development of a Low Bias Method for Characterizing Viral Populations Using Next Generation Sequencing Technology

(2010) Stephanie M. Willerth et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Full-Length Characterization of Hepatitis C Virus Subtype 3a Reveals Novel Hypervariable Regions under Positive Selection during Acute Infection

(2009) I. Humphreys et al.   JOURNAL OF VIROLOGY

Evolutionary analysis of the dynamics of viral infectious disease

(2009) Oliver G. Pybus et al.   NATURE REVIEWS GENETICS

Direct Metagenomic Detection of Viral Pathogens in Nasal and Fecal Specimens Using an Unbiased High-Throughput Sequencing Approach

(2009) Shota Nakamura et al.   PLoS One

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

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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses

(2008) Peter Simmonds et al.   NUCLEIC ACIDS RESEARCH

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE