Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing

Taxonomy of the order Mononegavirales: update 2018

(2018) Gaya K. Amarasinghe et al.   ARCHIVES OF VIROLOGY

Whole-genome sequencing of genotype VI Newcastle disease viruses from formalin-fixed paraffin-embedded tissues from wild pigeons reveals continuous evolution and previously unrecognized genetic diversity in the U.S.

(2018) Ying He et al.   Virology Journal

Illumina short-read and MinION long-read WGS to characterize the molecular epidemiology of an NDM-1 Serratia marcescens outbreak in Romania

(2017) H T T Phan et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates

(2017) Jamie K. Lemon et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

(2017) Joshua Quick et al.   Nature Protocols

A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses

(2017) Kiril M. Dimitrov et al.   Virology Journal

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

High Throughput Sequencing: An Overview of Sequencing Chemistry

(2016) Sheetal Ambardar et al.   INDIAN JOURNAL OF MICROBIOLOGY

Temporal, geographic, and host distribution of avian paramyxovirus 1 (Newcastle disease virus)

(2016) Kiril M. Dimitrov et al.   INFECTION GENETICS AND EVOLUTION

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

(2016) Patrick D. Schloss et al.   PeerJ

INC-Seq: accurate single molecule reads using nanopore sequencing

(2016) Chenhao Li et al.   GigaScience

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

(2015) Alexander L. Greninger et al.   Genome Medicine

Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer

(2015) Andy Kilianski et al.   GigaScience

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

Next generation sequencing of viral RNA genomes

(2013) Denise A Marston et al.   BMC GENOMICS

Viral pathogen discovery

(2013) Charles Y Chiu   CURRENT OPINION IN MICROBIOLOGY

Molecular epidemiology of viral diseases in the era of next generation sequencing

(2013) Mayra Cruz-Rivera et al.   JOURNAL OF CLINICAL VIROLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

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

Genetic diversity of avian paramyxovirus type 1: Proposal for a unified nomenclature and classification system of Newcastle disease virus genotypes

(2012) Diego G. Diel et al.   INFECTION GENETICS AND EVOLUTION

Avian paramyxovirus serotypes 2-9 (APMV-2-9) vary in the ability to induce protective immunity in chickens against challenge with virulent Newcastle disease virus (APMV-1)

(2012) Baibaswata Nayak et al.   VACCINE

Detection of a Broad Range of Class I and II Newcastle Disease Viruses Using a Multiplex Real-Time Reverse Transcription Polymerase Chain Reaction Assay

(2011) L. Mia Kim et al.   JOURNAL OF VETERINARY DIAGNOSTIC INVESTIGATION

Development of an L gene real-time reverse-transcription PCR assay for the detection of avian paramyxovirus type 1 RNA in clinical samples

(2010) Chad M. Fuller et al.   ARCHIVES OF VIROLOGY

Evolutionary Changes Affecting Rapid Identification of 2008 Newcastle Disease Viruses Isolated from Double-Crested Cormorants

(2010) C. A. Rue et al.   JOURNAL OF CLINICAL MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Biological and Phylogenetic Characterization of Pigeon Paramyxovirus Serotype 1 Circulating in Wild North American Pigeons and Doves

(2008) L. M. Kim et al.   JOURNAL OF CLINICAL MICROBIOLOGY