A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia

Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities

(2022) Almut Heinken et al.   BIOINFORMATICS

Enzyme‐constrained models predict the dynamics of Saccharomyces cerevisiae growth in continuous, batch and fed‐batch bioreactors

(2022) Sara Moreno‐Paz et al.   Microbial Biotechnology

Introducing the FAIR Principles for research software

(2022) Michelle Barker et al.   Scientific Data

Modeling the metabolic dynamics at the genome-scale by optimized yield analysis

(2022) Hao Luo et al.   METABOLIC ENGINEERING

Model-driven approach for the production of butyrate from CO2/H2 by a novel co-culture of C. autoethanogenum and C. beijerinckii

(2022) Sara Benito-Vaquerizo et al.   Frontiers in Microbiology

Synthetic co-cultures: novel avenues for bio-based processes

(2021) Martijn Diender et al.   CURRENT OPINION IN BIOTECHNOLOGY

Complex yeast–bacteria interactions affect the yield of industrial ethanol fermentation

(2021) Felipe Senne de Oliveira Lino et al.   Nature Communications

Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals

(2021) Pavlos Stephanos Bekiaris et al.   PLoS Computational Biology

Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities

(2021) Liliana Angeles-Martinez et al.   PLoS Computational Biology

A General Model for Biofilm-Driven Microbial Electrosynthesis of Carboxylates From CO2

(2021) Oriol Cabau-Peinado et al.   Frontiers in Microbiology

Metabolic flux sampling predicts strain-dependent differences related to aroma production among commercial wine yeasts

(2021) William T. Scott et al.   Microbial Cell Factories

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

(2021) Ilija Dukovski et al.   Nature Protocols

A gap-filling algorithm for prediction of metabolic interactions in microbial communities

(2021) Dafni Giannari et al.   PLoS Computational Biology

Synthetic co‐culture of autotrophic Clostridium carboxidivorans and chain elongating Clostridium kluyveri monitored by flow cytometry

(2021) Miriam Bäumler et al.   Microbial Biotechnology

Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data

(2021) Anurag Passi et al.   Metabolites

MEMOTE for standardized genome-scale metabolic model testing

(2020) Christian Lieven et al.   NATURE BIOTECHNOLOGY

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

(2020) Christian Diener et al.   mSystems

ACBM: An Integrated Agent and Constraint Based Modeling Framework for Simulation of Microbial Communities

(2020) Emadoddin Karimian et al.   Scientific Reports

μBialSim: Constraint-Based Dynamic Simulation of Complex Microbiomes

(2020) Denny Popp et al.   Frontiers in Bioengineering and Biotechnology

SBML Level 3: an extensible format for the exchange and reuse of biological models

(2020) Sarah M Keating et al.   Molecular Systems Biology

Minimizing the number of optimizations for efficient community dynamic flux balance analysis

(2020) James D. Brunner et al.   PLoS Computational Biology

Predicting Nash equilibria for microbial metabolic interactions

(2020) Jingyi Cai et al.   BIOINFORMATICS

Emergent Subpopulation Behavior Uncovered with a Community Dynamic Metabolic Model of Escherichia coli Diauxic Growth

(2019) Antonella Succurro et al.   mSystems

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

Engineering microbial consortia by division of labor

(2019) Garrett W. Roell et al.   Microbial Cell Factories

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

(2019) Jean-Christophe Lachance et al.   PLoS Computational Biology

Designing Metabolic Division of Labor in Microbial Communities

(2019) Meghan Thommes et al.   mSystems

Toxicity drives facilitation between 4 bacterial species

(2019) Philippe Piccardi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)

(2019) Benedict Borer et al.   PLoS Computational Biology

Microbial community design: methods, applications, and opportunities

(2019) Alexander Eng et al.   CURRENT OPINION IN BIOTECHNOLOGY

Synthetic ecology of the human gut microbiota

(2019) Gino Vrancken et al.   NATURE REVIEWS MICROBIOLOGY

Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems

(2019) Joseph J. Gardner et al.   Scientific Reports

Metabolic shift induced by synthetic co-cultivation promotes high yield of chain elongated acids from syngas

(2019) Martijn Diender et al.   Scientific Reports

OUP accepted manuscript

(2018)   BIOINFORMATICS

Genome-scale metabolic reconstruction and analysis for Clostridium kluyveri

(2018) Wei Zou et al.   GENOME

Design of synthetic bacterial communities for predictable plant phenotypes

(2018) Sur Herrera Paredes et al.   PLOS BIOLOGY

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

(2018) Federico Baldini et al.   BIOINFORMATICS

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

(2018) Hao Wang et al.   PLoS Computational Biology

Direct cell-to-cell exchange of matter in a synthetic Clostridium syntrophy enables CO2 fixation, superior metabolite yields, and an expanded metabolic space

(2018) Kamil Charubin et al.   METABOLIC ENGINEERING

Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum

(2017) Kaspar Valgepea et al.   METABOLIC ENGINEERING

SteadyCom: Predicting microbial abundances while ensuring community stability

(2017) Siu Hung Joshua Chan et al.   PLoS Computational Biology

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

(2017) Eugen Bauer et al.   PLoS Computational Biology

Production of medium-chain fatty acids and higher alcohols by a synthetic co-culture grown on carbon monoxide or syngas

(2016) Martijn Diender et al.   Biotechnology for Biofuels

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

(2016) Stefanie Widder et al.   ISME Journal

Synthetic Ecology of Microbes: Mathematical Models and Applications

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

Constraint-based stoichiometric modelling from single organisms to microbial communities

(2016) Willi Gottstein et al.   Journal of the Royal Society Interface

Phosphorus mobilizing consortium Mammoth P™enhances plant growth

(2016) Peter Baas et al.   PeerJ

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

(2015) Saeed Shoaie et al.   Cell Metabolism

Better together: engineering and application of microbial symbioses

(2015) Stephanie G Hays et al.   CURRENT OPINION IN BIOTECHNOLOGY

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

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

Calibration and analysis of genome-based models for microbial ecology

(2015) Stilianos Louca et al.   eLife

Synergistic Effect of Yeast-Bacterial Co-Culture on Bioremediation of Oil-Contaminated Soil

(2014) Chengdong Zhang et al.   BIOREMEDIATION JOURNAL

Co-culture systems and technologies: taking synthetic biology to the next level

(2014) L. Goers et al.   Journal of the Royal Society Interface

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

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

Fast Reconstruction of Compact Context-Specific Metabolic Network Models

(2014) Nikos Vlassis et al.   PLoS Computational Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Multifactorial diversity sustains microbial community stability

(2013) Oylum Erkus et al.   ISME Journal

The influence of bioaugmentation and biosurfactant addition on bioremediation efficiency of diesel-oil contaminated soil: Feasibility during field studies

(2013) Alicja Szulc et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm Formation

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

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

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

Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures

(2010) Timothy J. Hanly et al.   BIOTECHNOLOGY AND BIOENGINEERING

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

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

(2009) Anu Raghunathan et al.   BMC Systems Biology

Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?

(2009) Hal Alper et al.   NATURE REVIEWS MICROBIOLOGY