RevEcoR: an R package for the reverse ecology analysis of microbiomes

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation

(2015) Roie Levy et al.   BMC BIOINFORMATICS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

(2014) T.B.K. Reddy et al.   NUCLEIC ACIDS RESEARCH

IMG/M 4 version of the integrated metagenome comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment

(2012) R. Carr et al.   BIOINFORMATICS

Multispecies communities: interspecies interactions influence growth on saliva as sole nutritional source

(2011) Paul E Kolenbrander   International Journal of Oral Science

The Human Oral Microbiome

(2010) F. E. Dewhirst et al.   JOURNAL OF BACTERIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Mutualistic Biofilm Communities Develop with Porphyromonas gingivalis and Initial, Early, and Late Colonizers of Enamel

(2009) S. Periasamy et al.   JOURNAL OF BACTERIOLOGY

Large-scale reconstruction and phylogenetic analysis of metabolic environments

(2008) E. Borenstein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA