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

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

(2020) Christian Diener et al.   mSystems

Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs

(2020) Marco Mauri et al.   PLoS Computational Biology

An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets

(2020) Philipp Schneider et al.   PLoS Computational Biology

Dynamic control in metabolic engineering: Theories, tools, and applications

(2020) Christopher J. Hartline et al.   METABOLIC ENGINEERING

RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion

(2019) Sabine Koch et al.   PLoS Computational Biology

Engineering microbial consortia by division of labor

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

Designing Metabolic Division of Labor in Microbial Communities

(2019) Meghan Thommes et al.   mSystems

Enhanced Population Control in a Synthetic Bacterial Consortium by Interconnected Carbon Cross-Feeding

(2019) Pauli S. Losoi et al.   ACS Synthetic Biology

Evolutionary causes and consequences of metabolic division of labour: why anaerobes do and aerobes don’t

(2019) Jan-Ulrich Kreft et al.   CURRENT OPINION IN BIOTECHNOLOGY

Review and perspective on mathematical modeling of microbial ecosystems

(2018) Antonella Succurro et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Co-culture-based biological carbon monoxide conversion by Citrobacter amalonaticus Y19 and Sporomusa ovata via a reducing-equivalent transfer mediator

(2018) Cho Rong Lee et al.   BIORESOURCE TECHNOLOGY

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Metabolic division of labor in microbial systems

(2018) Ryan Tsoi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli

(2018) Oliver Hädicke et al.   PLoS Computational Biology

MoVE identifies metabolic valves to switch between phenotypic states

(2018) Naveen Venayak et al.   Nature Communications

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Complete Biosynthesis of Anthocyanins Using E. coli Polycultures

(2017) J. Andrew Jones et al.   mBio

EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model

(2017) Oliver Hädicke et al.   Scientific Reports

SteadyCom: Predicting microbial abundances while ensuring community stability

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

Principles for designing synthetic microbial communities

(2016) Nathan I Johns et al.   CURRENT OPINION IN MICROBIOLOGY

Engineering microbial consortia for controllable outputs

(2016) Stephen R Lindemann et al.   ISME Journal

Experimental and computational optimization of an Escherichia coli co-culture for the efficient production of flavonoids

(2016) J. Andrew Jones et al.   METABOLIC ENGINEERING

Modular co-culture engineering, a new approach for metabolic engineering

(2016) Haoran Zhang et al.   METABOLIC ENGINEERING

Metabolic Burden: Cornerstones in Synthetic Biology and Metabolic Engineering Applications

(2016) Gang Wu et al.   TRENDS IN BIOTECHNOLOGY

The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization

(2016) Elad Noor et al.   PLoS Computational Biology

Distributing a metabolic pathway among a microbial consortium enhances production of natural products

(2015) Kang Zhou et al.   NATURE BIOTECHNOLOGY

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

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

Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community

(2015) Joshua J. Hamilton et al.   PLoS Computational Biology

Quantifying the effects of the division of labor in metabolic pathways

(2014) Emily Harvey et al.   JOURNAL OF THEORETICAL BIOLOGY

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

(2014) Elad Noor et al.   PLoS Computational Biology

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

(2014) Hyun-Seob Song et al.   Processes

Fast thermodynamically constrained flux variability analysis

(2013) Arne C. Müller et al.   BIOINFORMATICS

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

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

(2013) Samay Pande et al.   ISME Journal

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

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

Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis

(2012) Yan Zhu et al.   BIOTECHNOLOGY AND BIOENGINEERING

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

(2011) Jan Schellenberger et al.   BIOPHYSICAL JOURNAL

Flux balance analysis of mixed anaerobic microbial communities: Effects of linoleic acid (LA) and pH on biohydrogen production

(2011) Subba Rao Chaganti et al.   INTERNATIONAL JOURNAL OF HYDROGEN ENERGY

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

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

eQuilibrator--the biochemical thermodynamics calculator

(2011) A. Flamholz et al.   NUCLEIC ACIDS RESEARCH

Escherichia coli Binary Culture Engineered for Direct Fermentation of Hemicellulose to a Biofuel

(2010) H.-D. Shin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY