Related references
Note: Only part of the references are listed.Universality of human microbial dynamics
Amir Bashan et al.
NATURE (2016)
Quantification and Classification of E-coli Proteome Utilization and Unused Protein Costs across Environments
Edward J. O'Brien et al.
PLOS COMPUTATIONAL BIOLOGY (2016)
Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production
Gary D. Wu et al.
GUT (2016)
Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico
Almut Heinken et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2015)
Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome
Saeed Shoaie et al.
CELL METABOLISM (2015)
The Characterization of Feces and Urine: A Review of the Literature to Inform Advanced Treatment Technology
C. Rose et al.
CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY (2015)
Do genome-scale models need exact solvers or clearer standards?
Ali Ebrahim et al.
MOLECULAR SYSTEMS BIOLOGY (2015)
The gut microbiota modulates host amino acid and glutathione metabolism in mice
Adil Mardinoglu et al.
MOLECULAR SYSTEMS BIOLOGY (2015)
Short-chain fatty acids in control of body weight and insulin sensitivity
Emanuel E. Canfora et al.
NATURE REVIEWS ENDOCRINOLOGY (2015)
Marine microbial community dynamics and their ecological interpretation
Jed A. Fuhrman et al.
NATURE REVIEWS MICROBIOLOGY (2015)
The ecology of the microbiome: Networks, competition, and stability
Katharine Z. Coyte et al.
SCIENCE (2015)
Using a Genome-Scale Metabolic Model of Enterococcus faecalis V583 To Assess Amino Acid Uptake and Its Impact on Central Metabolism
Nadine Veith et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2015)
Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework
Almut Heinken et al.
GUT MICROBES (2015)
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction
Ibrahim E. El-Semman et al.
BMC SYSTEMS BIOLOGY (2014)
Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe
Almut Heinken et al.
JOURNAL OF BACTERIOLOGY (2014)
An integrated catalog of reference genes in the human gut microbiome
Junhua Li et al.
NATURE BIOTECHNOLOGY (2014)
optGpSampler: An Improved Tool for Uniformly Sampling the Solution-Space of Genome-Scale Metabolic Networks
Wout Megchelenbrink et al.
PLOS ONE (2014)
Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression
Charles K. Fisher et al.
PLOS ONE (2014)
Adaptive Evolution of Synthetic Cooperating Communities Improves Growth Performance
Xiaolin Zhang et al.
PLOS ONE (2014)
Genome -Scale Reconstruction of Metabolic Networks of Lactobacillus casei ATCC 334 and 12A
Elena Vinay-Lara et al.
PLOS ONE (2014)
d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities
All R. Zomorrodi et al.
ACS SYNTHETIC BIOLOGY (2014)
Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics
William R. Harcombe et al.
CELL REPORTS (2014)
Host lifestyle affects human microbiota on daily timescales
Lawrence A. David et al.
GENOME BIOLOGY (2014)
Lattice Microbes: High-Performance Stochastic Simulation Method for the Reaction-Diffusion Master Equation
Elijah Roberts et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)
Community Flux Balance Analysis for Microbial Consortia at Balanced Growth
Ruchir A. Khandelwal et al.
PLOS ONE (2013)
Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules
Roie Levy et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
The Long-Term Stability of the Human Gut Microbiota
Jeremiah J. Faith et al.
SCIENCE (2013)
Understanding the interactions between bacteria in the human gut through metabolic modeling
Saeed Shoaie et al.
SCIENTIFIC REPORTS (2013)
Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota
Richard R. Stein et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
Insights into the resistance and resilience of the soil microbial community
Bryan S. Griffiths et al.
FEMS MICROBIOLOGY REVIEWS (2013)
Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
Almut Heinken et al.
GUT MICROBES (2013)
Counting and Correcting Thermodynamically Infeasible Flux Cycles in Genome-Scale Metabolic Networks
Daniele De Martino et al.
METABOLITES (2013)
Redox balance is key to explaining full vs. partial switching to low-yield metabolism
Milan J. A. van Hoek et al.
BMC SYSTEMS BIOLOGY (2012)
The Impact of the Gut Microbiota on Human Health: An Integrative View
Jose C. Clemente et al.
CELL (2012)
A vegan or vegetarian diet substantially alters the human colonic faecal microbiota
J. Zimmer et al.
EUROPEAN JOURNAL OF CLINICAL NUTRITION (2012)
On flux coupling analysis of metabolic subsystems
Sayed-Amir Marashi et al.
JOURNAL OF THEORETICAL BIOLOGY (2012)
Diversity, stability and resilience of the human gut microbiota
Catherine A. Lozupone et al.
NATURE (2012)
Structure, function and diversity of the healthy human microbiome
Curtis Huttenhower et al.
NATURE (2012)
The role of the gut microbiota in nutrition and health
Harry J. Flint et al.
NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY (2012)
Effects of Gut Microbes on Nutrient Absorption and Energy Regulation
Rosa Krajmalnik-Brown et al.
NUTRITION IN CLINICAL PRACTICE (2012)
Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
Sharon Greenblum et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities
Ali R. Zomorrodi et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
FFCA: a feasibility-based method for flux coupling analysis of metabolic networks
Laszlo David et al.
BMC BIOINFORMATICS (2011)
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
Kai Zhuang et al.
ISME JOURNAL (2011)
An Experimentally Validated Genome-Scale Metabolic Reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228
Yu-Chieh Liao et al.
JOURNAL OF BACTERIOLOGY (2011)
A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011
Jeffrey D. Orth et al.
MOLECULAR SYSTEMS BIOLOGY (2011)
Enterotypes of the human gut microbiome
Manimozhiyan Arumugam et al.
NATURE (2011)
Competitive and cooperative metabolic interactions in bacterial communities
Shiri Freilich et al.
NATURE COMMUNICATIONS (2011)
Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts
Eric C. Martens et al.
PLOS BIOLOGY (2011)
Moving pictures of the human microbiome
J. Gregory Caporaso et al.
GENOME BIOLOGY (2011)
Computationally efficient flux variability analysis
Steinn Gudmundsson et al.
BMC BIOINFORMATICS (2010)
The biomass objective function
Adam M. Feist et al.
CURRENT OPINION IN MICROBIOLOGY (2010)
Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
Carlotta De Filippo et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes
Sergio Bordel et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Genome-Scale Model of Streptococcus thermophilus LMG18311 for Metabolic Comparison of Lactic Acid Bacteria
Margreet I. Pastink et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)
Metabolic Network Model of a Human Oral Pathogen
Varun Mazumdar et al.
JOURNAL OF BACTERIOLOGY (2009)
Use of Randomized Sampling for Analysis of Metabolic Networks
Jan Schellenberger et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2009)
A core gut microbiome in obese and lean twins
Peter J. Turnbaugh et al.
NATURE (2009)
The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice
Peter J. Turnbaugh et al.
SCIENCE TRANSLATIONAL MEDICINE (2009)
Impact of the solvent capacity constraint on E. coli metabolism
Alexei Vazquez et al.
BMC SYSTEMS BIOLOGY (2008)
Evolution of mammals and their gut microbes
Ruth E. Ley et al.
SCIENCE (2008)
In vitro three-stage continuous fermentation of wheat arabinoxylan fractions and induction of hydrolase activity by the gut microflora
Maria Vardakou et al.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES (2007)
Diversity of the human intestinal microbial flora
PB Eckburg et al.
SCIENCE (2005)
Global organization of metabolic fluxes in the bacterium Escherichia coli
E Almaas et al.
NATURE (2004)
Flux coupling analysis of genome-scale metabolic network reconstructions
AP Burgard et al.
GENOME RESEARCH (2004)
Uniform sampling of steady-state flux spaces: Means to design experiments and to interpret enzymopathies
ND Price et al.
BIOPHYSICAL JOURNAL (2004)
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
R Mahadevan et al.
METABOLIC ENGINEERING (2003)