SteadyCom: Predicting microbial abundances while ensuring community stability

Universality of human microbial dynamics

(2016) Amir Bashan et al.   NATURE

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

(2016) Edward J. O’Brien et al.   PLoS Computational Biology

Anoxic Conditions Promote Species-Specific Mutualism between Gut MicrobesIn Silico

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

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

(2015) Saeed Shoaie et al.   Cell Metabolism

The Characterization of Feces and Urine: A Review of the Literature to Inform Advanced Treatment Technology

(2015) C. Rose et al.   CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY

Do genome-scale models need exact solvers or clearer standards?

(2015) A. Ebrahim et al.   Molecular Systems Biology

The gut microbiota modulates host amino acid and glutathione metabolism in mice

(2015) A. Mardinoglu et al.   Molecular Systems Biology

Short-chain fatty acids in control of body weight and insulin sensitivity

(2015) Emanuel E. Canfora et al.   Nature Reviews Endocrinology

Marine microbial community dynamics and their ecological interpretation

(2015) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

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

(2015) K. Z. Coyte et al.   SCIENCE

Using a Genome-Scale Metabolic Model of Enterococcus faecalis V583 To Assess Amino Acid Uptake and Its Impact on Central Metabolism

(2014) Nadine Veith et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production

(2014) Gary D Wu et al.   GUT

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

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

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

optGpSampler: An Improved Tool for Uniformly Sampling the Solution-Space of Genome-Scale Metabolic Networks

(2014) Wout Megchelenbrink et al.   PLoS One

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

(2014) Charles K. Fisher et al.   PLoS One

Adaptive Evolution of Synthetic Cooperating Communities Improves Growth Performance

(2014) Xiaolin Zhang et al.   PLoS One

Genome –Scale Reconstruction of Metabolic Networks of Lactobacillus casei ATCC 334 and 12A

(2014) Elena Vinay-Lara et al.   PLoS One

d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities

(2014) Ali R. Zomorrodi et al.   ACS Synthetic Biology

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

(2013) Ruchir A. Khandelwal et al.   PLoS One

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

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

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

(2013) Saeed Shoaie et al.   Scientific Reports

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

(2013) Richard R. Stein et al.   PLoS Computational Biology

Redox balance is key to explaining full vs. partial switching to low-yield metabolism

(2012) Milan JA van Hoek et al.   BMC Systems Biology

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

(2012) Jose C. Clemente et al.   CELL

Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation

(2012) Elijah Roberts et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

On flux coupling analysis of metabolic subsystems

(2012) Sayed-Amir Marashi et al.   JOURNAL OF THEORETICAL BIOLOGY

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

The role of the gut microbiota in nutrition and health

(2012) Harry J. Flint et al.   Nature Reviews Gastroenterology & Hepatology

Effects of Gut Microbes on Nutrient Absorption and Energy Regulation

(2012) Rosa Krajmalnik-Brown et al.   NUTRITION IN CLINICAL PRACTICE

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

(2012) Ali R. Zomorrodi et al.   PLoS Computational Biology

FFCA: a feasibility-based method for flux coupling analysis of metabolic networks

(2011) Laszlo David et al.   BMC BIOINFORMATICS

A vegan or vegetarian diet substantially alters the human colonic faecal microbiota

(2011) J Zimmer et al.   EUROPEAN JOURNAL OF CLINICAL NUTRITION

An Experimentally Validated Genome-Scale Metabolic Reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228

(2011) Y.-C. Liao et al.   JOURNAL OF BACTERIOLOGY

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

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

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts

(2011) Eric C. Martens et al.   PLOS BIOLOGY

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

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

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

(2010) Kai Zhuang et al.   ISME Journal

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

(2010) C. De Filippo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes

(2010) Sergio Bordel et al.   PLoS Computational Biology

Genome-Scale Model of Streptococcus thermophilus LMG18311 for Metabolic Comparison of Lactic Acid Bacteria

(2009) M. I. Pastink et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

Impact of the solvent capacity constraint on E. coli metabolism

(2008) Alexei Vazquez et al.   BMC Systems Biology

Metabolic Network Model of a Human Oral Pathogen

(2008) V. Mazumdar et al.   JOURNAL OF BACTERIOLOGY

Use of Randomized Sampling for Analysis of Metabolic Networks

(2008) Jan Schellenberger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE