Protein signature-based estimation of metagenomic abundances including all domains of life and viruses

Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method

(2012) Melissa B. Duhaime et al.   ENVIRONMENTAL MICROBIOLOGY

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

Metagenomics and future perspectives in virus discovery

(2012) John L Mokili et al.   Current Opinion in Virology

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

(2012) Nicola Segata et al.   GENOME BIOLOGY

Mixture models for analysis of the taxonomic composition of metagenomes

(2011) Peter Meinicke et al.   BIOINFORMATICS

Classifying short genomic fragments from novel lineages using composition and homology

(2011) Donovan H Parks et al.   BMC BIOINFORMATICS

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments

(2011) Othilde Håvelsrud et al.   BMC MICROBIOLOGY

Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome

(2011) Margret E. Berg Miller et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2011) Arthur Brady et al.   NATURE METHODS

CoMet—a web server for comparative functional profiling of metagenomes

(2011) Thomas Lingner et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Treephyler: fast taxonomic profiling of metagenomes

(2010) F. Schreiber et al.   BIOINFORMATICS

NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads

(2010) G. L. Rosen et al.   BIOINFORMATICS

Predicting phenotypic traits of prokaryotes from protein domain frequencies

(2010) Thomas Lingner et al.   BMC BIOINFORMATICS

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

(2009) M. Monzoorul Haque et al.   BIOINFORMATICS

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

(2009) Naryttza N Diaz et al.   BMC BIOINFORMATICS

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

Phylogenetic classification of short environmental DNA fragments

(2008) Lutz Krause et al.   NUCLEIC ACIDS RESEARCH

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

(2008) Daniel C. Richter et al.   PLoS One