Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community

Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions

(2014) Adrian Jinich et al.   Scientific Reports

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

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

Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models

(2013) Joshua J. Hamilton et al.   BIOPHYSICAL JOURNAL

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

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

Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association

(2013) Harish Nagarajan et al.   Nature Communications

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

(2013) Saeed Shoaie et al.   Scientific Reports

Consistent Estimation of Gibbs Energy Using Component Contributions

(2013) Elad Noor et al.   PLoS Computational Biology

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Beyond the genome: community-level analysis of the microbial world

(2012) Iratxe Zarraonaindia et al.   BIOLOGY & PHILOSOPHY

Mathematical optimization applications in metabolic networks

(2012) Ali R. Zomorrodi et al.   METABOLIC ENGINEERING

Complete genome sequence of Syntrophobacter fumaroxidans strain (MPOBT)

(2012) Caroline M. Plugge et al.   Standards in Genomic Sciences

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

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

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

(2011) Jan Schellenberger et al.   BIOPHYSICAL JOURNAL

Fifteen years of large scale metabolic modeling of yeast: Developments and impacts

(2011) Tobias Österlund et al.   BIOTECHNOLOGY ADVANCES

Genome-Scale Metabolic Reconstruction and Hypothesis Testing in the Methanogenic Archaeon Methanosarcina acetivorans C2A

(2011) M. N. Benedict et al.   JOURNAL OF BACTERIOLOGY

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

(2011) Jan Schellenberger et al.   Nature Protocols

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation

(2010) Jessica R. Sieber et al.   Annual Review of Microbiology

Growth- and substrate-dependent transcription of formate dehydrogenase and hydrogenase coding genes in Syntrophobacter fumaroxidans and Methanospirillum hungatei

(2010) P. Worm et al.   MICROBIOLOGY-SGM

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

(2010) Aarash Bordbar et al.   Molecular Systems Biology

Emergent cooperation in microbial metabolism

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

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

(2010) Nathan E Lewis et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

(2010) Radhakrishnan Mahadevan et al.   NATURE REVIEWS MICROBIOLOGY

Syntrophic butyrate and propionate oxidation processes: from genomes to reaction mechanisms

(2010) Nicolai Müller et al.   Environmental Microbiology Reports

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Syntrophy in anaerobic global carbon cycles

(2009) Michael J McInerney et al.   CURRENT OPINION IN BIOTECHNOLOGY

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Electron transfer in syntrophic communities of anaerobic bacteria and archaea

(2009) Alfons J. M. Stams et al.   NATURE REVIEWS MICROBIOLOGY

Physiology, Ecology, Phylogeny, and Genomics of Microorganisms Capable of Syntrophic Metabolism

(2008) Michael J. McInerney et al.   Annals of the New York Academy of Sciences

Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea

(2008) Yuchen Liu et al.   Annals of the New York Academy of Sciences

Methanogenic archaea: ecologically relevant differences in energy conservation

(2008) Rudolf K. Thauer et al.   NATURE REVIEWS MICROBIOLOGY