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

Investigating Bacterial-Animal Symbioses with Light Sheet Microscopy

(2016) Michael J. Taormina et al.   BIOLOGICAL BULLETIN

Computational systems biology and in silico modeling of the human microbiome

(2012) E. Borenstein   BRIEFINGS IN BIOINFORMATICS

Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species

(2012) Kevin R. Foster et al.   CURRENT BIOLOGY

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

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

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

Ecological Populations of Bacteria Act as Socially Cohesive Units of Antibiotic Production and Resistance

(2012) O. X. Cordero et al.   SCIENCE

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Network-based approaches for linking metabolism with environment

(2012) Sarath Janga et al.   GENOME BIOLOGY

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

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

Predicting a Human Gut Microbiota's Response to Diet in Gnotobiotic Mice

(2011) J. J. Faith et al.   SCIENCE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

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

(2011) Paul E Kolenbrander   International Journal of Oral Science

Systems approaches to microbial communities and their functioning

(2010) Wilfred FM Röling et al.   CURRENT OPINION IN BIOTECHNOLOGY

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

Bacterial diversity in the oral cavity of 10 healthy individuals

(2010) Elisabeth M Bik et al.   ISME Journal

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Oral multispecies biofilm development and the key role of cell–cell distance

(2010) Paul E. Kolenbrander et al.   NATURE REVIEWS MICROBIOLOGY

The large-scale organization of the bacterial network of ecological co-occurrence interactions

(2010) Shiri Freilich et al.   NUCLEIC ACIDS RESEARCH

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives

(2010) Jesse R. Zaneveld et al.   NUCLEIC ACIDS RESEARCH

Succession of microbial consortia in the developing infant gut microbiome

(2010) J. E. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri, with Their Insect Host, Homalodisca coagulata

(2010) Ludovic Cottret et al.   PLoS Computational Biology

Obesity and the human microbiome

(2009) Ruth E Ley   CURRENT OPINION IN GASTROENTEROLOGY

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

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

Topological Signatures of Species Interactions in Metabolic Networks

(2009) Elhanan Borenstein et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Bacterial Community Variation in Human Body Habitats Across Space and Time

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

Metabolic-network-driven analysis of bacterial ecological strategies

(2009) Shiri Freilich et al.   GENOME BIOLOGY

An Invitation to the Marriage of Metagenomics and Metabolomics

(2008) Peter J. Turnbaugh et al.   CELL

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

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

Phylogenetic analysis of community assembly and structure over space and time

(2008) Brent C. Emerson et al.   TRENDS IN ECOLOGY & EVOLUTION