FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

(2013) Weijun Luo et al.   BIOINFORMATICS

The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification

(2013) Cyrus Afrasiabi et al.   NUCLEIC ACIDS RESEARCH

FunGene: the functional gene pipeline and repository

(2013) Jordan A. Fish et al.   Frontiers in Microbiology

Voronto: mapper for expression data to ontologies

(2012) Rodrigo Santamaría et al.   BIOINFORMATICS

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

(2012) Olivia U Mason et al.   ISME Journal

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

(2012) J. Pell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Omics for understanding microbial functional dynamics

(2011) Janet K. Jansson et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

(2011) Rachel Mackelprang et al.   NATURE

GLAMM: Genome-Linked Application for Metabolic Maps

(2011) J. T. Bates et al.   NUCLEIC ACIDS RESEARCH

iPath2.0: interactive pathway explorer

(2011) Takuji Yamada et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The Pfam protein families database

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

The metagenomics of disease-suppressive soils – experiences from the METACONTROL project

(2008) Jan Dirk van Elsas et al.   TRENDS IN BIOTECHNOLOGY