Rapid phylogenetic analysis using open reading frame content patterns acquired by Oxford nanopore sequencing

Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care

(2021) Leah W. Roberts et al.   Microbial Genomics

Institutional outbreak involving multiple clades of IMP-producing Enterobacter cloacae complex sequence type 78 at a cancer center in Tokyo, Japan

(2021) Sohei Harada et al.   BMC INFECTIOUS DISEASES

Rapid Open-Source SNP-Based Clustering Offers an Alternative to Core Genome MLST for Outbreak Tracing in a Hospital Setting

(2021) Judit Szarvas et al.   Frontiers in Microbiology

Transmission of Vancomycin-Resistant Enterococci in the Hospital Setting: Uncovering the Patient–Environment Interplay

(2020) Carlos L. Correa-Martinez et al.   Microorganisms

Assessing Nanopore sequencing for clinical diagnostics: A comparison of NGS methods for Mycobacterium tuberculosis

(2020) Carol Smith et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Comparison of single-nucleotide variants identified by Illumina and Oxford Nanopore technologies in the context of a potential outbreak of Shiga toxin–producing Escherichia coli

(2019) David R Greig et al.   GigaScience

Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology

(2019) Tonya L. Taylor et al.   Scientific Reports

MinION sequencing of Streptococcus suis allows for functional characterization of bacteria by multilocus sequence typing and antimicrobial resistance profiling

(2019) Shaoyuan Tan et al.   JOURNAL OF MICROBIOLOGICAL METHODS

ORF-based binarized structure network analysis of plasmids (OSNAp), a novel approach to core gene-independent plasmid phylogeny

(2019) Masahiro Suzuki et al.   PLASMID

Molecular Characterization of IMP-1-Producing Enterobacter cloacae Complex Isolates in Tokyo

(2018) Kotaro Aoki et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Evaluation of Oxford Nanopore’s MinION Sequencing Device for Microbial Whole Genome Sequencing Applications

(2018) Andrea D. Tyler et al.   Scientific Reports

Emergence of NDM-7-Producing Multidrug-Resistant Enterobacter hormaechei sequence type ST78 in Spain, a high-risk international clone

(2018) Jennifer Villa et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer

(2018) Daniel Golparian et al.   Scientific Reports

Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review

(2017) F. Tagini et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

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

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

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Spread of Enterobacter cloacae carrying bla NDM-1 , bla CTX-M-15 , bla SHV-12 and plasmid-mediated quinolone resistance genes in a surgical intensive care unit in Croatia

(2016) N. Petrosillo et al.   Journal of Global Antimicrobial Resistance

Oxford Nanopore MinION Sequencing and Genome Assembly

(2016) Hengyun Lu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection

(2015) Angela J. Taylor et al.   JOURNAL OF CLINICAL MICROBIOLOGY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS