The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities

(2013) Sharon Greenblum et al.   CURRENT OPINION IN BIOTECHNOLOGY

Diet Alters Both the Structure and Taxonomy of the Ovine Gut Microbial Ecosystem

(2013) M. J. Ellison et al.   DNA RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi 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

High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing

(2012) Elizabeth M Ross et al.   BMC GENETICS

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

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes

(2012) P. Jeraldo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Network-based approaches for linking metabolism with environment

(2012) Sarath Janga et al.   GENOME BIOLOGY

Expression level, cellular compartment and metabolic network position all influence the average selective constraint on mammalian enzymes

(2011) Corey M Hudson et al.   BMC EVOLUTIONARY BIOLOGY

Status of the phylogenetic diversity census of ruminal microbiomes

(2011) Minseok Kim et al.   FEMS MICROBIOLOGY ECOLOGY

Patterns of indirect protein interactions suggest a spatial organization to metabolism

(2011) Åsa Pérez-Bercoff et al.   Molecular BioSystems

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

(2011) S. Greenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) M. Hess et al.   SCIENCE

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

Host specificity of the ruminal bacterial community in the dairy cow following near-total exchange of ruminal contents1

(2010) P.J. Weimer et al.   JOURNAL OF DAIRY SCIENCE

Copy Number Alterations among Mammalian Enzymes Cluster in the Metabolic Network

(2010) M. Bekaert et al.   MOLECULAR BIOLOGY AND EVOLUTION

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Testing the functional significance of microbial community composition

(2009) Michael S. Strickland et al.   ECOLOGY

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

(2009) Jennifer M. Brulc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neutral evolution on mammalian protein surfaces

(2009) Gavin C. Conant   TRENDS IN GENETICS

Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks

(2009) João F. Matias Rodrigues et al.   PLoS Computational Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

SeqAn An efficient, generic C++ library for sequence analysis

(2008) Andreas Döring et al.   BMC BIOINFORMATICS

Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiency

(2008) Le Luo Guan et al.   FEMS MICROBIOLOGY LETTERS

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Molecular eco-systems biology: towards an understanding of community function

(2008) Jeroen Raes et al.   NATURE REVIEWS MICROBIOLOGY

Worlds within worlds: evolution of the vertebrate gut microbiota

(2008) Ruth E. Ley et al.   NATURE REVIEWS MICROBIOLOGY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH