COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

A poor man's BLASTX--high-throughput metagenomic protein database search using PAUDA

(2013) D. H. Huson et al.   BIOINFORMATICS

FANTOM: Functional and taxonomic analysis of metagenomes

(2013) Kemal Sanli et al.   BMC BIOINFORMATICS

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Construction of Customized Sub-Databases from NCBI-nr Database for Rapid Annotation of Huge Metagenomic Datasets Using a Combined BLAST and MEGAN Approach

(2013) Ke Yu et al.   PLoS One

Co-occurrence of anaerobic bacteria in colorectal carcinomas

(2013) René L Warren et al.   Microbiome

Functional assignment of metagenomic data: challenges and applications

(2012) T. Prakash et al.   BRIEFINGS IN BIOINFORMATICS

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

RAPSearch: a fast protein similarity search tool for short reads

(2011) Yuzhen Ye et al.   BMC BIOINFORMATICS

The oral metagenome in health and disease

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

IMG/M: the integrated metagenome data management and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

iPath2.0: interactive pathway explorer

(2011) Takuji Yamada et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

CoMet—a web server for comparative functional profiling of metagenomes

(2011) Thomas Lingner et al.   NUCLEIC ACIDS RESEARCH

Metagenome of the gut of a malnourished child

(2011) Sourav Gupta et al.   Gut Pathogens

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics

(2010) Johannes Goll et al.   BIOINFORMATICS

A new bioinformatics analysis tools framework at EMBL-EBI

(2010) M. Goujon et al.   NUCLEIC ACIDS RESEARCH

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

(2010) S. Sun et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

(2009)   PLoS Computational Biology

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE