BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

Synthetic Ecology of Microbes: Mathematical Models and Applications

(2016) Ali R. Zomorrodi et al.   JOURNAL OF MOLECULAR BIOLOGY

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities

(2016) Sebastian Germerodt et al.   PLoS Computational Biology

Agent Based Modeling of Human Gut Microbiome Interactions and Perturbations

(2016) Tatiana Shashkova et al.   PLoS One

Anoxic Conditions Promote Species-Specific Mutualism between Gut MicrobesIn Silico

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

Quantitative Imaging of Gut Microbiota Spatial Organization

(2015) Kristen A. Earle et al.   Cell Host & Microbe

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

(2015) Saeed Shoaie et al.   Cell Metabolism

Metabolic co-dependence gives rise to collective oscillations within biofilms

(2015) Jintao Liu et al.   NATURE

Calibration and analysis of genome-based models for microbial ecology

(2015) Stilianos Louca et al.   eLife

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

(2015) Eugen Bauer et al.   Microbiome

Solving Differential Equations inR: PackagedeSolve

(2015) Karline Soetaert et al.   Journal of Statistical Software

Rcpp: SeamlessRandC++Integration

(2015) Dirk Eddelbuettel et al.   Journal of Statistical Software

Gut Microbiota-Produced Succinate Promotes C. difficile Infection after Antibiotic Treatment or Motility Disturbance

(2014) Jessica A. Ferreyra et al.   Cell Host & Microbe

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

Genomically and biochemically accurate metabolic reconstruction ofMethanosarcina barkeriFusaro, iMG746

(2013) Matthew C. Gonnerman et al.   Biotechnology Journal

sybil – Efficient constraint-based modelling in R

(2013) Gabriel Gelius-Dietrich et al.   BMC Systems Biology

Investigating biocomplexity through the agent-based paradigm

(2013) H. Kaul et al.   BRIEFINGS IN BIOINFORMATICS

Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria

(2013) Samay Pande et al.   ISME Journal

Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm Formation

(2013) Matthew B. Biggs et al.   PLoS One

BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology

(2012) Thomas E. Gorochowski et al.   PLoS One

The Evolution of Mutualism in Gut Microbiota Via Host Epithelial Selection

(2012) Jonas Schluter et al.   PLOS BIOLOGY

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

(2011) Caroline B Milne et al.   BMC Systems Biology

Human nutrition, the gut microbiome and the immune system

(2011) Andrew L. Kau et al.   NATURE

Mucin dynamics and enteric pathogens

(2011) Michael A. McGuckin et al.   NATURE REVIEWS MICROBIOLOGY

Anaerobic physiology of Pseudomonas aeruginosa in the cystic fibrosis lung

(2010) Max Schobert et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

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

(2010) Kai Zhuang et al.   ISME Journal

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

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network

(2008) Joungmin Lee et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1

(2008) M. A. Oberhardt et al.   JOURNAL OF BACTERIOLOGY

Physiological heterogeneity in biofilms

(2008) Philip S. Stewart et al.   NATURE REVIEWS MICROBIOLOGY