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

Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction

(2014) Ibrahim E El-Semman et al.   BMC Systems Biology

Robust flux balance analysis of multiscale biochemical reaction networks

(2013) Yuekai Sun et al.   BMC BIOINFORMATICS

Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent

(2013) Laura Wrzosek et al.   BMC BIOLOGY

Faecalibacterium prausnitzii and human intestinal health

(2013) S Miquel et al.   CURRENT OPINION IN MICROBIOLOGY

Major phenylpropanoid-derived metabolites in the human gut can arise from microbial fermentation of protein

(2013) Wendy R. Russell et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling

(2013) J. A. H. Wodke et al.   Molecular Systems Biology

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

Semi-automated Curation of Metabolic Models via Flux Balance Analysis: A Case Study with Mycoplasma gallisepticum

(2013) Eddy J. Bautista et al.   PLoS Computational Biology

Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM

(2013) Jonathan M. Dreyfuss et al.   PLoS Computational Biology

How Can Faecalibacterium prausnitzii Employ Riboflavin for Extracellular Electron Transfer?

(2012) M. Tanweer Khan et al.   ANTIOXIDANTS & REDOX SIGNALING

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

A systems biology approach to studying the role of microbes in human health

(2012) Ines Thiele et al.   CURRENT OPINION IN BIOTECHNOLOGY

The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic–anoxic interphases

(2012) M Tanweer Khan et al.   ISME Journal

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

(2012) Junjie Qin et al.   NATURE

Functional interactions between the gut microbiota and host metabolism

(2012) Valentina Tremaroli et al.   NATURE

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

(2012) Ines Thiele et al.   PLoS One

Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole–time of flight mass spectrometry (UPLC–Q–ToF-MS)

(2011) Giuseppe Paglia et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Cultured Representatives of Two Major Phylogroups of Human Colonic Faecalibacterium prausnitzii Can Utilize Pectin, Uronic Acids, and Host-Derived Substrates for Growth

(2011) Mireia Lopez-Siles et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Recent advances in reconstruction and applications of genome-scale metabolic models

(2011) Tae Yong Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism

(2011) R. L. Chang et al.   Molecular Systems Biology

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

(2011) Jan Schellenberger et al.   Nature Protocols

IMG: the integrated microbial genomes database and comparative analysis system

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

Prospects for systems biology and modeling of the gut microbiome

(2011) Fredrik H. Karlsson et al.   TRENDS IN BIOTECHNOLOGY

Functional Characterization of Alternate Optimal Solutions of Escherichia coli's Transcriptional and Translational Machinery

(2010) Ines Thiele et al.   BIOPHYSICAL JOURNAL

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

Association between Faecalibacterium prausnitzii and dietary fibre in colonic fermentation in healthy human subjects

(2010) Robin F. J. Benus et al.   BRITISH JOURNAL OF NUTRITION

A Eubacterial Riboswitch Class That Senses the Coenzyme Tetrahydrofolate

(2010) Tyler D. Ames et al.   CHEMISTRY & BIOLOGY

Dominant and diet-responsive groups of bacteria within the human colonic microbiota

(2010) Alan W Walker et al.   ISME Journal

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

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

(2010) P. S. Novichkov et al.   NUCLEIC ACIDS RESEARCH

Insights into the evolution of sialic acid catabolism among bacteria

(2009) Salvador Almagro-Moreno et al.   BMC EVOLUTIONARY BIOLOGY

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

(2009) Monica L Mo et al.   BMC Systems Biology

The role of pH in determining the species composition of the human colonic microbiota

(2009) Sylvia H. Duncan et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2009) Petra Louis et al.   FEMS MICROBIOLOGY LETTERS

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

(2009) Pavel S. Novichkov et al.   NUCLEIC ACIDS RESEARCH

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

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

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii

(2008) Carlett Ramirez-Farias et al.   BRITISH JOURNAL OF NUTRITION

A Novel Class of Modular Transporters for Vitamins in Prokaryotes

(2008) D. A. Rodionov et al.   JOURNAL OF BACTERIOLOGY

Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major

(2008) Arvind K Chavali et al.   Molecular Systems Biology

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

(2008) H. Sokol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA