In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host

More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes

(2017) Kees C. H. van der Ark et al.   Microbiome

Outer membrane vesicles secreted by pathogenic and nonpathogenic Bacteroides fragilis represent different metabolic activities

(2017) Natalya B. Zakharzhevskaya et al.   Scientific Reports

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

A novel mechanism for the biogenesis of outer membrane vesicles in Gram-negative bacteria

(2016) Sandro Roier et al.   Nature Communications

Activation of Immune and Defense Responses in the Intestinal Mucosa by Outer Membrane Vesicles of Commensal and Probiotic Escherichia coli Strains

(2016) María José Fábrega et al.   Frontiers in Microbiology

Colitogenic Bacteroides thetaiotaomicron Antigens Access Host Immune Cells in a Sulfatase-Dependent Manner via Outer Membrane Vesicles

(2015) Christina A. Hickey et al.   Cell Host & Microbe

Outer-membrane vesicles from Gram-negative bacteria: biogenesis and functions

(2015) Carmen Schwechheimer et al.   NATURE REVIEWS MICROBIOLOGY

MetaboAnalyst 3.0—making metabolomics more meaningful

(2015) Jianguo Xia et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2015)   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

fastGapFill: efficient gap filling in metabolic networks

(2014) Ines Thiele et al.   BIOINFORMATICS

Cephalosporinases associated with outer membrane vesicles released by Bacteroides spp. protect gut pathogens and commensals against β-lactam antibiotics

(2014) Régis Stentz et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Bacterial Vesicles in Marine Ecosystems

(2014) S. J. Biller et al.   SCIENCE

A Bacterial Homolog of a Eukaryotic Inositol Phosphate Signaling Enzyme Mediates Cross-kingdom Dialog in the Mammalian Gut

(2014) Régis Stentz et al.   Cell Reports

Fast Reconstruction of Compact Context-Specific Metabolic Network Models

(2014) Nikos Vlassis et al.   PLoS Computational Biology

Elucidating the interactions between the human gut microbiota and its host through metabolic modeling

(2014) Saeed Shoaie et al.   Frontiers in Genetics

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks

(2013) M. Ganter et al.   BIOINFORMATICS

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

An Ecological Network of Polysaccharide Utilization among Human Intestinal Symbionts

(2013) Seth Rakoff-Nahoum et al.   CURRENT BIOLOGY

Metabolic modeling for multi-objective optimization of ethanol production in a Synechocystis mutant

(2013) Tirthankar Sengupta et al.   PHOTOSYNTHESIS RESEARCH

Understanding the interactions between bacteria in the human gut through metabolic modeling

(2013) Saeed Shoaie et al.   Scientific Reports

An integrated open framework for thermodynamics of reactions that combines accuracy and coverage

(2012) Elad Noor et al.   BIOINFORMATICS

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

Outer Membrane Vesicles of a Human Commensal Mediate Immune Regulation and Disease Protection

(2012) Yue Shen et al.   Cell Host & Microbe

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

(2012) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Biological Functions and Biogenesis of Secreted Bacterial Outer Membrane Vesicles

(2010) Adam Kulp et al.   Annual Review of Microbiology

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

(2010) Aarash Bordbar et al.   Molecular Systems Biology

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

MouseCyc: a curated biochemical pathways database for the laboratory mouse

(2009) Alexei V Evsikov et al.   GENOME BIOLOGY

Mucosal Glycan Foraging Enhances Fitness and Transmission of a Saccharolytic Human Gut Bacterial Symbiont

(2008) Eric C. Martens et al.   Cell Host & Microbe

Intracellular Organic Osmolytes: Function and Regulation

(2008) Maurice B. Burg et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes

(2008) Sandrine P Claus et al.   Molecular Systems Biology

The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria

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