Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities

Cooperators trade off ecological resilience and evolutionary stability in public goods games

(2017) Joseph Rauch et al.   Journal of the Royal Society Interface

Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment

(2016) Tobias Großkopf et al.   BMC EVOLUTIONARY BIOLOGY

Challenges in microbial ecology: building predictive understanding of community function and dynamics

(2016) Stefanie Widder et al.   ISME Journal

The evolution of cooperation within the gut microbiota

(2016) Seth Rakoff-Nahoum et al.   NATURE

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

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities

(2016) Sebastian Germerodt et al.   PLoS Computational Biology

Private benefits and metabolic conflicts shape the emergence of microbial interdependencies

(2015) Sylvie Estrela et al.   ENVIRONMENTAL MICROBIOLOGY

Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes

(2015) Glen D'Souza et al.   EVOLUTION

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Black Queen evolution: the role of leakiness in structuring microbial communities

(2015) J. Jeffrey Morris   TRENDS IN GENETICS

Where Next for Microbiome Research?

(2015) Matthew K. Waldor et al.   PLOS BIOLOGY

Self-establishing communities enable cooperative metabolite exchange in a eukaryote

(2015) Kate Campbell et al.   eLife

An Economic Framework of Microbial Trade

(2015) Joshua Tasoff et al.   PLoS One

Evolutionary game theory: cells as players

(2014) Sabine Hummert et al.   Molecular BioSystems

Syntrophic exchange in synthetic microbial communities

(2014) M. T. Mee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary limits to cooperation in microbial communities

(2014) Nuno M. Oliveira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2013) Samay Pande et al.   ISME Journal

Feedback between Population and Evolutionary Dynamics Determines the Fate of Social Microbial Populations

(2013) Alvaro Sanchez et al.   PLOS BIOLOGY

Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms

(2012) Nicole Paczia et al.   Microbial Cell Factories

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

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

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

Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data

(2011) Ali R Zomorrodi et al.   BMC Systems Biology

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks

(2010) Eytan Ruppin et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2010) Kai Zhuang et al.   ISME Journal

Emergent cooperation in microbial metabolism

(2010) Edwin H Wintermute et al.   Molecular Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Evolutionary game theory: Theoretical concepts and applications to microbial communities

(2010) Erwin Frey   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Snowdrift game dynamics and facultative cheating in yeast

(2009) Jeff Gore et al.   NATURE

Eco-evolutionary feedbacks in community and ecosystem ecology: interactions between the ecological theatre and the evolutionary play

(2009) D. M. Post et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism

(2008) Cong T. Trinh et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY