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

Conditions for duality between fluxes and concentrations in biochemical networks

(2016) Ronan M.T. Fleming et al.   JOURNAL OF THEORETICAL BIOLOGY

Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis

(2016) Dmitry A. Ravcheev et al.   Frontiers in Microbiology

Anoxic Conditions Promote Species-Specific Mutualism between Gut MicrobesIn Silico

(2015) Almut Heinken et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The influence of diet on the gut microbiota and its consequences for health

(2015) Joël Doré et al.   CURRENT OPINION IN BIOTECHNOLOGY

Database resources of the National Center for Biotechnology Information

(2015)   NUCLEIC ACIDS RESEARCH

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Systems biology of host-microbe metabolomics

(2015) Almut Heinken et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires

(2015) Eugen Bauer et al.   Microbiome

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes

(2015) Stefanía Magnúsdóttir et al.   Frontiers in Genetics

Synthetic microbial communities

(2014) Tobias Großkopf et al.   CURRENT OPINION IN MICROBIOLOGY

Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe

(2014) A. Heinken et al.   JOURNAL OF BACTERIOLOGY

Recent trends in the metabolism and cell biology of vitamin K with special reference to vitamin K cycling and MK-4 biosynthesis

(2014) Martin J. Shearer et al.   JOURNAL OF LIPID RESEARCH

Towards a better understanding of Lactobacillus rhamnosus GG - host interactions

(2014) Marijke E Segers et al.   Microbial Cell Factories

Functional and phylogenetic assembly of microbial communities in the human microbiome

(2014) Afrah Shafquat et al.   TRENDS IN MICROBIOLOGY

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

(2014) M. Vital et al.   mBio

Prediction and quantification of bioactive microbiota metabolites in the mouse gut

(2014) Gautham V. Sridharan et al.   Nature Communications

Fast Reconstruction of Compact Context-Specific Metabolic Network Models

(2014) Nikos Vlassis et al.   PLoS Computational Biology

Emergent Biosynthetic Capacity in Simple Microbial Communities

(2014) Hsuan-Chao Chiu et al.   PLoS Computational Biology

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data

(2013) Brian J. Schmidt et al.   BIOINFORMATICS

Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs

(2013) Ahmad Barghash et al.   BMC BIOINFORMATICS

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

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

Software platforms to facilitate reconstructing genome-scale metabolic networks

(2013) Joshua J. Hamilton et al.   ENVIRONMENTAL MICROBIOLOGY

Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis

(2013) Lionel Rigottier-Gois   ISME Journal

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements: Table 1.

(2013) Hao Luo et al.   NUCLEIC ACIDS RESEARCH

Metabolic Proximity in the Order of Colonization of a Microbial Community

(2013) Varun Mazumdar et al.   PLoS One

Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome

(2013) Nathan P. McNulty et al.   PLOS BIOLOGY

Consistent Estimation of Gibbs Energy Using Component Contributions

(2013) Elad Noor et al.   PLoS Computational Biology

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

(2012) Jose C. Clemente et al.   CELL

Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota

(2012) Michael Graham Espey   FREE RADICAL BIOLOGY AND MEDICINE

Effect of extraction method on quality of orange juice: hand-squeezed, commercial-fresh squeezed and processed

(2012) Elizabeth A Baldwin et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

A framework for human microbiome research

(2012)   NATURE

Gut microbiota composition correlates with diet and health in the elderly

(2012) Marcus J. Claesson et al.   NATURE

The gut microbiota in IBD

(2012) Chaysavanh Manichanh et al.   Nature Reviews Gastroenterology & Hepatology

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

(2012) Ramy K. Aziz et al.   PLoS One

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks

(2011) S. G. Thorleifsson et al.   BIOINFORMATICS

The evolution of metabolic networks of E. coli

(2011) David J Baumler et al.   BMC Systems Biology

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

(2011) Ines Thiele et al.   BMC Systems Biology

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

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

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

MetaboliteDetector: Comprehensive Analysis Tool for Targeted and Nontargeted GC/MS Based Metabolome Analysis

(2009) Karsten Hiller et al.   ANALYTICAL CHEMISTRY

Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine

(2009) Petra Louis et al.   FEMS MICROBIOLOGY LETTERS

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Comparative genomics and functional annotation of bacterial transporters

(2007) Mikhail S. Gelfand et al.   Physics of Life Reviews