Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens

Sequencing-based methods and resources to study antimicrobial resistance

(2019) Manish Boolchandani et al.   NATURE REVIEWS GENETICS

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Ultra-deep, long-read nanopore sequencing of mock microbial community standards

(2019) Samuel M Nicholls et al.   GigaScience

NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes

(2019) G. A. Arango-Argoty et al.   Microbiome

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

The challenge of diagnostic metagenomics

(2018) Alexander L. Greninger   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

First WHO antimicrobial surveillance data reveal high levels of resistance globally

(2018) Susan Mayor   BMJ-British Medical Journal

First WHO antimicrobial surveillance data reveal high levels of resistance globally

(2018) Susan Mayor   BMJ-British Medical Journal

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms

(2018) Brandon Brooks et al.   Microbiome

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

A world of opportunities with nanopore sequencing

(2017) Richard M Leggett et al.   JOURNAL OF EXPERIMENTAL BOTANY

Brain Autoimmunity and Intestinal Microbiota: 100 Trillion Game Changers

(2017) Hartmut Wekerle   TRENDS IN IMMUNOLOGY

Gut microbiota dysbiosis associated with glucose metabolism disorders and the metabolic syndrome in older adults

(2017) K. Lippert et al.   Beneficial Microbes

MinION Nanopore Sequencing Enables Correlation between Resistome Phenotype and Genotype of Coliform Bacteria in Municipal Sewage

(2017) Yu Xia et al.   Frontiers in Microbiology

The antibiotic resistome: gene flow in environments, animals and human beings

(2017) Yongfei Hu et al.   Frontiers of Medicine

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach

(2017) Bonnie L. Brown et al.   GigaScience

The Role of Mucosal Immunity in the Pathogenesis of Necrotizing Enterocolitis

(2017) Zerina Hodzic et al.   Frontiers in Pediatrics

Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing

(2016) K. Schmidt et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Human gut microbes impact host serum metabolome and insulin sensitivity

(2016) Helle Krogh Pedersen et al.   NATURE

Understanding the mechanisms of faecal microbiota transplantation

(2016) Alexander Khoruts et al.   Nature Reviews Gastroenterology & Hepatology

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments

(2016) Ivan Yevshin et al.   NUCLEIC ACIDS RESEARCH

Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones

(2016) Kelly L. Wyres et al.   TRENDS IN MICROBIOLOGY

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

A Review of SHV Extended-Spectrum β-Lactamases: Neglected Yet Ubiquitous

(2016) Apostolos Liakopoulos et al.   Frontiers in Microbiology

An international legal framework to address antimicrobial resistance

(2015) Steven J Hoffman et al.   BULLETIN OF THE WORLD HEALTH ORGANIZATION

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

(2015) Nicholas J Loman et al.   NATURE METHODS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Dysbiosis Anticipating Necrotizing Enterocolitis in Very Premature Infants

(2014) K. Sim et al.   CLINICAL INFECTIOUS DISEASES

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

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The immune consequences of preterm birth

(2013) Jacqueline M. Melville et al.   Frontiers in Neuroscience

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Insights into Physiological and Genetic Mupirocin Susceptibility in Bifidobacteria

(2011) Fausta Serafini et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Identification of a novel fosfomycin resistance gene (fosA2) in Enterobacter cloacae from the Salmon River, Canada

(2011) H. Xu et al.   LETTERS IN APPLIED MICROBIOLOGY

Antimicrobial Susceptibility Testing: A Review of General Principles and Contemporary Practices

(2009) James H. Jorgensen et al.   CLINICAL INFECTIOUS DISEASES

Late-Onset Enterobacter cloacae Sepsis in Very-Low-Birth-Weight Neonates: Experience in a Medical Center

(2009) Hsiao-Neng Chen et al.   Pediatrics and Neonatology

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

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