Massive metagenomic data analysis using abundance-based machine learning

MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs

(2018) Daniel H. Huson et al.   Biology Direct

Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia

(2018) Loes M. Olde Loohuis et al.   Translational Psychiatry

MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms

(2018) Yuyang Qiao et al.   Biology Direct

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

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Strain profiling and epidemiology of bacterial species from metagenomic sequencing

(2017) Davide Albanese et al.   Nature Communications

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease

(2016) Timothy R. Sampson et al.   CELL

The Human Microbiome during Bacterial Vaginosis

(2016) Andrew B. Onderdonk et al.   CLINICAL MICROBIOLOGY REVIEWS

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

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

(2016) Edoardo Pasolli et al.   PLoS Computational Biology

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

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

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

(2016)   Microbiome

ConStrains identifies microbial strains in metagenomic datasets

(2015) Chengwei Luo et al.   NATURE BIOTECHNOLOGY

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

The microbiome of the built environment and mental health

(2015) Andrew J. Hoisington et al.   Microbiome

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

(2015) Ebrahim Afshinnekoo et al.   Cell Systems

Indoor-Air Microbiome in an Urban Subway Network: Diversity and Dynamics

(2014) Marcus H. Y. Leung et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

(2014) Tae-Hyuk Ahn et al.   BIOINFORMATICS

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

Airborne Bacterial Communities in Residences: Similarities and Differences with Fungi

(2014) Rachel I. Adams et al.   PLoS One

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

(2014) Yu-Wei Wu et al.   Microbiome

Vaginal Microbiome: Rethinking Health and Disease

(2012) Bing Ma et al.   Annual Review of Microbiology

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Architectural design influences the diversity and structure of the built environment microbiome

(2012) Steven W Kembel et al.   ISME Journal

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

Adaptive seeds tame genomic sequence comparison

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

Vaginal microbiome of reproductive-age women

(2010) J. Ravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Diversity and seasonal dynamics of bacterial community in indoor environment

(2008) Helena Rintala et al.   BMC MICROBIOLOGY

Decreased Diversity of the Fecal Microbiome in RecurrentClostridium difficile–Associated Diarrhea

(2008) Ju Young Chang et al.   JOURNAL OF INFECTIOUS DISEASES

The Airborne Metagenome in an Indoor Urban Environment

(2008) Susannah G. Tringe et al.   PLoS One