A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data

A visual framework for sequence analysis using n-grams and spectral rearrangement

(2010) Stefan R. Maetschke et al.   BIOINFORMATICS

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments

(2010) Emily B Hollister et al.   ISME Journal

Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community

(2010) Christopher L Hemme et al.   ISME Journal

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

(2010) Jenna L. Morgan et al.   PLoS One

Metagenomic signatures of 86 microbial and viral metagenomes

(2009) Dana Willner et al.   ENVIRONMENTAL MICROBIOLOGY

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

(2009) Dana Willner et al.   PLoS One

Quantifying environmental adaptation of metabolic pathways in metagenomics

(2009) T. A. Gianoulis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

An Invitation to the Marriage of Metagenomics and Metabolomics

(2008) Peter J. Turnbaugh et al.   CELL

Multiway Spectral Clustering with Out-of-Sample Extensions through Weighted Kernel PCA

(2008) C. Alzate et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

Biodiversity and biogeography of phages in modern stromatolites and thrombolites

(2008) Christelle Desnues et al.   NATURE

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology

(2008) Karthik Devarajan   PLoS Computational Biology