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

Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of Prochlorococcus

(2021) Shany Ofaim et al.   Frontiers in Genetics

Non-additive microbial community responses to environmental complexity

(2021) Alan R. Pacheco et al.   Nature Communications

MEMOTE for standardized genome-scale metabolic model testing

(2020) Christian Lieven et al.   NATURE BIOTECHNOLOGY

Bridging substrate intake kinetics and bacterial growth phenotypes with flux balance analysis incorporating proteome allocation

(2020) Hong Zeng et al.   Scientific Reports

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

(2019) Alan R. Pacheco et al.   Nature Communications

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

(2019) Laurent Heirendt et al.   Nature Protocols

The Integrative Human Microbiome Project

(2019)   NATURE

Massively parallel screening of synthetic microbial communities

(2019) Jared Kehe 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

On the growth of non-motile bacteria colonies: an agent-based model for pattern formation

(2019) Lautaro Vassallo et al.   EUROPEAN PHYSICAL JOURNAL B

Global Trends in Marine Plankton Diversity across Kingdoms of Life

(2019) Federico M. Ibarbalz et al.   CELL

Microbial carbon use efficiency predicted from genome-scale metabolic models

(2019) Mustafa Saifuddin et al.   Nature Communications

OUP accepted manuscript

(2018)   BIOINFORMATICS

Modeling metabolism of the human gut microbiome

(2018) Stefanía Magnúsdóttir et al.   CURRENT OPINION IN BIOTECHNOLOGY

The spatial and metabolic basis of colony size variation

(2018) Jeremy M. Chacón et al.   ISME Journal

Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

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

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Diffusion-Limited Growth of Microbial Colonies

(2018) Hayden Tronnolone et al.   Scientific Reports

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

A shared limiting resource leads to competitive exclusion in a cross-feeding system

(2018) Sarah P. Hammarlund et al.   ENVIRONMENTAL MICROBIOLOGY

Evolution of bidirectional costly mutualism from byproduct consumption

(2018) William R. Harcombe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the deformability of an empirical fitness landscape by microbial evolution

(2018) Djordje Bajić et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks

(2018) Demetrius DiMucci et al.   mSystems

The microbial habitat in soil: Scale, heterogeneity and functional consequences

(2017) Naoise Nunan   JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE

The evolution of the host microbiome as an ecosystem on a leash

(2017) Kevin R. Foster et al.   NATURE

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Investment in secreted enzymes during nutrient-limited growth is utility dependent

(2017) Brent Cezairliyan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A New Improved and Extended Version of the Multicell Bacterial Simulator gro

(2017) Martín Gutiérrez et al.   ACS Synthetic Biology

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

(2017) Eugen Bauer et al.   PLoS Computational Biology

Spatiotemporal modeling of microbial metabolism

(2016) Jin Chen et al.   BMC Systems Biology

Principles for designing synthetic microbial communities

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

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

(2016) Stefanie Widder et al.   ISME Journal

Constraint-based stoichiometric modelling from single organisms to microbial communities

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

The evolution of cooperation within the gut microbiota

(2016) Seth Rakoff-Nahoum et al.   NATURE

Spatial structure, cooperation and competition in biofilms

(2016) Carey D. Nadell et al.   NATURE REVIEWS MICROBIOLOGY

Constrained Allocation Flux Balance Analysis

(2016) Matteo Mori et al.   PLoS Computational Biology

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities

(2016) Sebastian Germerodt et al.   PLoS Computational Biology

Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus

(2016) John R. Casey et al.   mSystems

A Model of Extracellular Enzymes in Free-Living Microbes: Which Strategy Pays Off?

(2015) Sachia J. Traving et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Spatially-resolved metabolic cooperativity within dense bacterial colonies

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

Using Genome-scale Models to Predict Biological Capabilities

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

Branching instability in expanding bacterial colonies

(2015) C. Giverso et al.   Journal of the Royal Society Interface

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

The global ocean microbiome

(2015) M. A. Moran   SCIENCE

Rhizosphere interactions: root exudates, microbes, and microbial communities

(2014) Xing-Feng Huang et al.   Botany

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

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

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

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

An objective function exploiting suboptimal solutions in metabolic networks

(2013) Edwin H Wintermute et al.   BMC Systems Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

An Ecological Network of Polysaccharide Utilization among Human Intestinal Symbionts

(2013) Seth Rakoff-Nahoum et al.   CURRENT BIOLOGY

Mechanically Driven Growth of Quasi-Two-Dimensional Microbial Colonies

(2013) F. D. C. Farrell et al.   PHYSICAL REVIEW LETTERS

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

A reliable simulator for dynamic flux balance analysis

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

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

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

Fundamentals of Microbial Community Resistance and Resilience

(2012) Ashley Shade et al.   Frontiers in Microbiology

Cell design in bacteria as a convex optimization problem

(2011) Anne Goelzer et al.   AUTOMATICA

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

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

A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities

(2011) Eleftheria Tzamali et al.   BMC 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

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

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

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

Genetic demixing and evolution in linear stepping stone models

(2010) K. S. Korolev et al.   REVIEWS OF MODERN PHYSICS

Manufacturing Molecules Through Metabolic Engineering

(2010) J. D. Keasling   SCIENCE

Metabolomics of recombinant yeast: Gene expression, flux analysis and a mathematical model for gene regulation of metabolism

(2008) J.A. Asenjo et al.   JOURNAL OF BIOTECHNOLOGY

Resistance, resilience, and redundancy in microbial communities

(2008) S. D. Allison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology