Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution

Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinIONTM nanopore sequencer

(2019) Shinichi Kai et al.   FEBS Open Bio

The effect of 16S rRNA region choice on bacterial community metabarcoding results

(2019) Yu. S. Bukin et al.   Scientific Data

Clinical metagenomics

(2019) Charles Y. Chiu et al.   NATURE REVIEWS GENETICS

Nanopore sequencing: Review of potential applications in functional genomics

(2019) Nobuaki Kono et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

(2019) Jethro S. Johnson et al.   Nature Communications

Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens

(2019) Richard M. Leggett et al.   Nature Microbiology

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects

(2018) Tomohisa Takagi et al.   JOURNAL OF GASTROENTEROLOGY

Elucidation of the bacterial communities associated with the harmful microalgae Alexandrium tamarense and Cochlodinium polykrikoides using nanopore sequencing

(2018) HyeonSeok Shin et al.   Scientific Reports

A world of opportunities with nanopore sequencing

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

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

Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer

(2017) Alfonso Benítez-Páez et al.   GigaScience

Forensic SNP Genotyping using Nanopore MinION Sequencing

(2017) Senne Cornelis et al.   Scientific Reports

A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer

(2017) Satomi Mitsuhashi et al.   Scientific Reports

Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing

(2016) Jongoh Shin et al.   Scientific Reports

Gut Bifidobacteria Populations in Human Health and Aging

(2016) Silvia Arboleya et al.   Frontiers in Microbiology

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

Use of 16S rRNA Gene for Identification of a Broad Range of Clinically Relevant Bacterial Pathogens

(2015) Ramya Srinivasan et al.   PLoS One

Genomic Encyclopedia of Type Strains of the Genus Bifidobacterium

(2014) Christian Milani et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Robustness of Gut Microbiota of Healthy Adults in Response to Probiotic Intervention Revealed by High-Throughput Pyrosequencing

(2013) S.-W. Kim et al.   DNA RESEARCH

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

A framework for human microbiome research

(2012)   NATURE

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

A new repeat-masking method enables specific detection of homologous sequences

(2010) Martin C. Frith   NUCLEIC ACIDS RESEARCH