A human gut bacterial genome and culture collection for improved metagenomic analyses

Commensal Koch's postulates: establishing causation in human microbiota research

(2018) B Anne Neville et al.   CURRENT OPINION IN MICROBIOLOGY

Culturing of female bladder bacteria reveals an interconnected urogenital microbiota

(2018) Krystal Thomas-White et al.   Nature Communications

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

(2017) Supratim Mukherjee et al.   NATURE BIOTECHNOLOGY

Transmission of the gut microbiota: spreading of health

(2017) Hilary P. Browne et al.   NATURE REVIEWS MICROBIOLOGY

The European Nucleotide Archive in 2017

(2017) Nicole Silvester et al.   NUCLEIC ACIDS RESEARCH

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling

(2016) Jennifer T. Lau et al.   Genome Medicine

Culture of previously uncultured members of the human gut microbiota by culturomics

(2016) Jean-Christophe Lagier et al.   Nature Microbiology

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes

(2015) Samuel C. Forster et al.   NUCLEIC ACIDS RESEARCH

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Phylogeny, culturing, and metagenomics of the human gut microbiota

(2014) Alan W. Walker et al.   TRENDS IN MICROBIOLOGY

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

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

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

Control of pathogens and pathobionts by the gut microbiota

(2013) Nobuhiko Kamada et al.   NATURE IMMUNOLOGY

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

(2011) A. L. Goodman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

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

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