A Case Study for Large-Scale Human Microbiome Analysis Using JCVI’s Metagenomics Reports (METAREP)

Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics

(2011) Philippe N Bertin et al.   ISME Journal

Protein-Protein Interactions in Assembly of Lipoic Acid on the 2-Oxoacid Dehydrogenases of Aerobic Metabolism

(2011) Bachar H. Hassan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project

(2011) Jack A. Gilbert et al.   Standards in Genomic Sciences

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach

(2010) E. Cardenas et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2010) Johannes Goll et al.   BIOINFORMATICS

Ergatis: a web interface and scalable software system for bioinformatics workflows

(2010) J. Orvis et al.   BIOINFORMATICS

Pyruvate Formate Lyase Acts as a Formate Supplier for Metabolic Processes during Anaerobiosis in Staphylococcus aureus

(2010) M. Leibig et al.   JOURNAL OF BACTERIOLOGY

The Human Oral Microbiome

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

Metabolic Flux Analysis of the Mixotrophic Metabolisms in the Green Sulfur BacteriumChlorobaculum tepidum

(2010) Xueyang Feng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data

(2010) David M. Tanenbaum et al.   Standards in Genomic Sciences

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology