FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares

Parallel-META: efficient metagenomic data analysis based on high-performance computation

(2013) Xiaoquan Su et al.   BMC Systems Biology

Genomes from Metagenomics

(2013) I. Sharon et al.   SCIENCE

Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution

(2013) Rogan Carr et al.   PLoS Computational Biology

GemSIM: general, error-model based simulator of next-generation sequencing data

(2012) Kerensa E McElroy et al.   BMC GENOMICS

Classification of metagenomic sequences: methods and challenges

(2012) S. S. Mande et al.   BRIEFINGS IN BIOINFORMATICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Metagenomic abundance estimation and diagnostic testing on species level

(2012) Martin S. Lindner et al.   NUCLEIC ACIDS RESEARCH

Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis

(2012) Amaro E. Trindade-Silva et al.   PLoS One

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

(2012) Ramy K. Aziz et al.   PLoS One

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Mixture models for analysis of the taxonomic composition of metagenomes

(2011) Peter Meinicke et al.   BIOINFORMATICS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles

(2011) Ozkan U Nalbantoglu et al.   BMC BIOINFORMATICS

The oral metagenome in health and disease

(2011) Pedro Belda-Ferre et al.   ISME Journal

PhymmBL expanded: confidence scores, custom databases, parallelization and more

(2011) Arthur Brady et al.   NATURE METHODS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS