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

Astrovirus VA1/HMO-C: An Increasingly Recognized Neurotropic Pathogen in Immunocompromised Patients

(2015) Julianne R. Brown et al.   CLINICAL INFECTIOUS DISEASES

Diagnosis of Neuroinvasive Astrovirus Infection in an Immunocompromised Adult With Encephalitis by Unbiased Next-Generation Sequencing

(2015) Samia N. Naccache et al.   CLINICAL INFECTIOUS DISEASES

A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012–14): a retrospective cohort study

(2015) Alexander L Greninger et al.   LANCET INFECTIOUS DISEASES

Successful test launch for nanopore sequencing

(2015) Nicholas J Loman et al.   NATURE METHODS

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

(2015) Nicholas J Loman et al.   NATURE METHODS

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

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

(2015) Andy Kilianski et al.   GigaScience

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

(2014) S. N. Naccache et al.   GENOME RESEARCH

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

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

Emergence of Zaire Ebola Virus Disease in Guinea

(2014) Sylvain Baize et al.   NEW ENGLAND JOURNAL OF MEDICINE

Ebola Virus Disease in the Democratic Republic of Congo

(2014) Gaël D. Maganga et al.   NEW ENGLAND JOURNAL OF MEDICINE

Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing

(2014) Michael R. Wilson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections

(2014) M. J. PALLEN   PARASITOLOGY

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

Clinical detection and characterization of bacterial pathogens in the genomics era

(2014) Pierre-Edouard Fournier et al.   Genome Medicine

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

(2014) Joshua Quick et al.   GigaScience

Viral pathogen discovery

(2013) Charles Y Chiu   CURRENT OPINION IN MICROBIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metagenomics for pathogen detection in public health

(2013) Ruth R Miller et al.   Genome Medicine

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Parameters for accurate genome alignment

(2012) Martin C Frith et al.   BMC BIOINFORMATICS

Using a Pan-Viral Microarray Assay (Virochip) to Screen Clinical Samples for Viral Pathogens

(2011) Eunice C. Chen et al.   Jove-Journal of Visualized Experiments

Comprehensive Panel of Real-Time TaqMan™ Polymerase Chain Reaction Assays for Detection and Absolute Quantification of Filoviruses, Arenaviruses, and New World Hantaviruses

(2010) Adrienne R. Trombley et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

Evaluation of the Analytical Performance of the Xpert MTB/RIF Assay

(2010) R. Blakemore et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America

(2010) Alexander L. Greninger et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Detection and Characterization of Lujo Virus, a New Hemorrhagic Fever–Associated Arenavirus from Southern Africa

(2009) Thomas Briese et al.   PLoS Pathogens

A Bioinformatician's Guide to Metagenomics

(2008) V. Kunin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases

(2008) Gustavo Palacios et al.   NEW ENGLAND JOURNAL OF MEDICINE