Constraint-based stoichiometric modelling from single organisms to microbial communities

Spatiotemporal modeling of microbial metabolism

(2016) Jin Chen et al.   BMC Systems Biology

Public goods and metabolic strategies

(2016) Herwig Bachmann et al.   CURRENT OPINION IN MICROBIOLOGY

Synergistic growth in bacteria depends on substrate complexity

(2016) Yi-Jie Deng et al.   JOURNAL OF MICROBIOLOGY

Biological trade and markets

(2016) Peter Hammerstein et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Efficient Reconstruction of Predictive Consensus Metabolic Network Models

(2016) Ruben G. A. van Heck et al.   PLoS Computational Biology

Constrained Allocation Flux Balance Analysis

(2016) Matteo Mori et al.   PLoS Computational Biology

Recovering complete and draft population genomes from metagenome datasets

(2016) Naseer Sangwan et al.   Microbiome

Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase

(2016) Avlant Nilsson et al.   Scientific Reports

Anoxic Conditions Promote Species-Specific Mutualism between Gut MicrobesIn Silico

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

Spatially-resolved metabolic cooperativity within dense bacterial colonies

(2015) John A Cole et al.   BMC Systems Biology

Fermented Foods as Experimentally Tractable Microbial Ecosystems

(2015) Benjamin E. Wolfe et al.   CELL

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Metabolic interactions in microbial communities: untangling the Gordian knot

(2015) Olga Ponomarova et al.   CURRENT OPINION IN MICROBIOLOGY

Metabolic co-dependence gives rise to collective oscillations within biofilms

(2015) Jintao Liu et al.   NATURE

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

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

Metabolic network modeling of microbial communities

(2015) Matthew B. Biggs et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Relatedness, Conflict, and the Evolution of Eusociality

(2015) Xiaoyun Liao et al.   PLOS BIOLOGY

Interplay between Constraints, Objectives, and Optimality for Genome-Scale Stoichiometric Models

(2015) Timo R. Maarleveld et al.   PLoS Computational Biology

Self-establishing communities enable cooperative metabolite exchange in a eukaryote

(2015) Kate Campbell et al.   eLife

Elucidating the adaptation and temporal coordination of metabolic pathways using in-silico evolution

(2014) Willi Gottstein et al.   BIOSYSTEMS

Stoichiometric model and flux balance analysis for a mixed culture ofLeptospirillum ferriphilumandFerroplasma acidiphilum

(2014) M. P. Merino et al.   BIOTECHNOLOGY PROGRESS

Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction

(2014) Ibrahim E El-Semman et al.   BMC Systems Biology

You Are What You Host: Microbiome Modulation of the Aging Process

(2014) Caroline Heintz et al.   CELL

Synthetic microbial communities

(2014) Tobias Großkopf et al.   CURRENT OPINION IN MICROBIOLOGY

Dynamic flux balance analysis for synthetic microbial communities

(2014) Michael A. Henson et al.   IET Systems Biology

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

(2014) A. K. Hawley 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

Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities

(2014) Y. Verastegui et al.   mBio

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

A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities

(2014) Amit Ghosh et al.   PLoS Computational Biology

Emergent Biosynthetic Capacity in Simple Microbial Communities

(2014) Hsuan-Chao Chiu et al.   PLoS Computational Biology

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

(2014) Hyun-Seob Song et al.   Processes

Dynamic metabolic modeling of a microaerobic yeast co-culture: predicting and optimizing ethanol production from glucose/xylose mixtures

(2013) Timothy J Hanly et al.   Biotechnology for Biofuels

Dynamic strain scanning optimization: an efficient strain design strategy for balanced yield, titer, and productivity. DySScO strategy for strain design

(2013) Kai Zhuang et al.   BMC BIOTECHNOLOGY

Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology

(2013) Martin von Bergen et al.   ISME Journal

The microbiome: stress, health and disease

(2013) Rachel D. Moloney et al.   MAMMALIAN GENOME

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

(2013) E. J. O{middle dot}Brien et al.   Molecular Systems Biology

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

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

Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm Formation

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

Gut microbiome and metabolic diseases

(2013) Shinji Fukuda et al.   Seminars in Immunopathology

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

(2013) Saeed Shoaie et al.   Scientific Reports

The design of long-term effective uranium bioremediation strategy using a community metabolic model

(2012) K. Zhuang et al.   BIOTECHNOLOGY AND BIOENGINEERING

Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species

(2012) Kevin R. Foster et al.   CURRENT BIOLOGY

Multidimensional Optimality of Microbial Metabolism

(2012) R. Schuetz et al.   SCIENCE

In silico method for modelling metabolism and gene product expression at genome scale

(2012) Joshua A. Lerman et al.   Nature Communications

Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks

(2012) Steven M. Kelk et al.   Scientific Reports

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

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

GENOME-BASED MODELING AND DESIGN OF METABOLIC INTERACTIONS IN MICROBIAL COMMUNITIES

(2012) Radhakrishnan Mahadevan et al.   Computational and Structural Biotechnology Journal

Dynamic flux balance modeling of S. cerevisiae and E. coli co-cultures for efficient consumption of glucose/xylose mixtures

(2011) Timothy J. Hanly et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

(2011) Tobias Österlund et al.   BIOTECHNOLOGY ADVANCES

Economics of membrane occupancy and respiro-fermentation

(2011) K. Zhuang et al.   Molecular Systems Biology

In the light of evolution V: Cooperation and conflict

(2011) J. E. Strassmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

(2011) Tomer Shlomi et al.   PLoS Computational Biology

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains

(2010) Joonhoon Kim et al.   BMC Systems Biology

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2010) Kai Zhuang et al.   ISME Journal

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

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

Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways

(2009) N. Tepper et al.   BIOINFORMATICS

Flux balance analysis of biological systems: applications and challenges

(2009) K. Raman et al.   BRIEFINGS IN BIOINFORMATICS

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology

Genome-scale gene/reaction essentiality and synthetic lethality analysis

(2009) Patrick F Suthers et al.   Molecular Systems Biology

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

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

(2009) Hal Alper et al.   NATURE REVIEWS MICROBIOLOGY

Bacterial competition: surviving and thriving in the microbial jungle

(2009) Michael E. Hibbing et al.   NATURE REVIEWS MICROBIOLOGY

Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico Optimisation

(2009) Bas Teusink et al.   PLoS Computational Biology

Impact of the solvent capacity constraint on E. coli metabolism

(2008) Alexei Vazquez et al.   BMC Systems Biology

Linking phylogenetic identities of bacteria to starch fermentation in anin vitromodel of the large intestine by RNA-based stable isotope probing

(2008) Petia Kovatcheva-Datchary et al.   ENVIRONMENTAL MICROBIOLOGY

A Bioinformatician's Guide to Metagenomics

(2008) V. Kunin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Engineering microbial consortia: a new frontier in synthetic biology

(2008) Katie Brenner et al.   TRENDS IN BIOTECHNOLOGY

Is maximization of molar yield in metabolic networks favoured by evolution?

(2007) Stefan Schuster et al.   JOURNAL OF THEORETICAL BIOLOGY