Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

Dynamic modelling of mixotrophic microalgal photobioreactor systems with time-varying yield coefficient for the lipid consumption

(2014) Sung Jin Yoo et al.   BIORESOURCE TECHNOLOGY

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

(2014) Caroline Heintz et al.   CELL

Gene-centric approach to integrating environmental genomics and biogeochemical models

(2014) Daniel C. Reed et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Soil biodiversity and soil community composition determine ecosystem multifunctionality

(2014) C. Wagg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

(2014) Elad Noor et al.   PLoS Computational Biology

Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example

(2014) Wilfred F. M. Röling et al.   Frontiers in Microbiology

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

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

The microbiome: stress, health and disease

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

Challenges for Complex Microbial Ecosystems: Combination of Experimental Approaches with Mathematical Modeling

(2013) Shin Haruta et al.   MICROBES AND ENVIRONMENTS

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

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

Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass

(2013) Jeremy J. Minty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gut microbiome and metabolic diseases

(2013) Shinji Fukuda et al.   Seminars in Immunopathology

Advances in modeling trait-based plant community assembly

(2013) Daniel C. Laughlin et al.   TRENDS IN PLANT SCIENCE

An improved cellular automaton method to model multispecies biofilms

(2013) Youneng Tang et al.   WATER RESEARCH

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

(2013) Richard R. Stein et al.   PLoS Computational Biology

Modeling metabolic systems: the need for dynamics

(2013) Hyun-Seob Song et al.   Current Opinion in Chemical Engineering

Dynamic models of metabolism: Review of the cybernetic approach

(2012) Doraiswami Ramkrishna et al.   AICHE JOURNAL

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

(2012) Yan Zhu et al.   BIOTECHNOLOGY AND BIOENGINEERING

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

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

Exacting predictions by cybernetic model confirmed experimentally: Steady state multiplicity in the chemostat

(2012) Jin Il Kim et al.   BIOTECHNOLOGY PROGRESS

Computational systems biology and in silico modeling of the human microbiome

(2012) E. Borenstein   BRIEFINGS IN BIOINFORMATICS

Classification of metagenomic sequences: methods and challenges

(2012) S. S. Mande et al.   BRIEFINGS IN BIOINFORMATICS

A predictive model of community assembly that incorporates intraspecific trait variation

(2012) Daniel C. Laughlin et al.   ECOLOGY LETTERS

Identification of Functionally Relevant Populations in Enhanced Biological Phosphorus Removal Processes Based On Intracellular Polymers Profiles and Insights into the Metabolic Diversity and Heterogeneity

(2012) Nehreen Majed et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Modeling microbial community structure and functional diversity across time and space

(2012) Peter E. Larsen et al.   FEMS MICROBIOLOGY LETTERS

Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen et al.   ISME Journal

Modeling microbial communities: Current, developing, and future technologies for predicting microbial community interaction

(2012) Peter Larsen et al.   JOURNAL OF BIOTECHNOLOGY

Prediction of dynamic behavior of mutant strains from limited wild-type data

(2012) Hyun-Seob Song et al.   METABOLIC ENGINEERING

Dynamic modeling of aerobic growth of Shewanella oneidensis. Predicting triauxic growth, flux distributions, and energy requirement for growth

(2012) Hyun-Seob Song et al.   METABOLIC ENGINEERING

Engineering ecosystems and synthetic ecologies

(2012) Michael T. Mee et al.   Molecular BioSystems

Predicting bacterial community assemblages using an artificial neural network approach

(2012) Peter E Larsen et al.   NATURE METHODS

A road map for the development of community systems (CoSy) biology

(2012) Karsten Zengler et al.   NATURE REVIEWS MICROBIOLOGY

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

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

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

Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition

(2012) Nicholas J. Bouskill et al.   Frontiers in Microbiology

The generation and maintenance of diversity in microbial communities

(2011) Noah Fierer et al.   AMERICAN JOURNAL OF BOTANY

Minimal cut sets in a metabolic network are elementary modes in a dual network

(2011) Kathrin Ballerstein et al.   BIOINFORMATICS

Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks

(2011) Siu Hung Joshua Chan et al.   BIOINFORMATICS

Experimental methods and modeling techniques for description of cell population heterogeneity

(2011) R. Lencastre Fernandes et al.   BIOTECHNOLOGY ADVANCES

On enhancing productivity of bioethanol with multiple species

(2011) Jun Geng et al.   BIOTECHNOLOGY AND BIOENGINEERING

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

(2011) Aarash Bordbar 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

Quantifying the importance of local niche-based and stochastic processes to tropical tree community assembly

(2011) Bill Shipley et al.   ECOLOGY

iDynoMiCS: next-generation individual-based modelling of biofilms

(2011) Laurent A. Lardon et al.   ENVIRONMENTAL MICROBIOLOGY

Towards novel approaches to modelling biotic interactions in multispecies assemblages at large spatial extents

(2011) W. D. Kissling et al.   JOURNAL OF BIOGEOGRAPHY

Microbial physiology-based model of ethanol metabolism in subsurface sediments

(2011) Qusheng Jin et al.   JOURNAL OF CONTAMINANT HYDROLOGY

Metabolic networks evolve towards states of maximum entropy production

(2011) Pornkamol Unrean et al.   METABOLIC ENGINEERING

Modeling Microbial Dynamics in Heterogeneous Environments: Growth on Soil Carbon Sources

(2011) Haluk Resat et al.   MICROBIAL ECOLOGY

Microbiology by numbers

(2011)   NATURE REVIEWS MICROBIOLOGY

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

(2011) S. Greenblum 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

Bistability versus Bimodal Distributions in Gene Regulatory Processes from Population Balance

(2011) Che-Chi Shu et al.   PLoS Computational Biology

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME 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

Cybernetic models based on lumped elementary modes accurately predict strain-specific metabolic function

(2010) Hyun-Seob Song et al.   BIOTECHNOLOGY AND BIOENGINEERING

A structured and dynamic framework to advance traits-based theory and prediction in ecology

(2010) Colleen T. Webb et al.   ECOLOGY LETTERS

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

(2010) Kai Zhuang et al.   ISME Journal

Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model

(2010) Yilin Fang et al.   JOURNAL OF CONTAMINANT HYDROLOGY

Emergent cooperation in microbial metabolism

(2010) Edwin H Wintermute 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

The role of physiological heterogeneity in microbial population behavior

(2010) Mary E Lidstrom et al.   Nature Chemical Biology

Maximum entropy production and plant optimization theories

(2010) R. C. Dewar   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ecosystem functioning and maximum entropy production: a quantitative test of hypotheses

(2010) F. J. R. Meysman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolutionary game theory: Theoretical concepts and applications to microbial communities

(2010) Erwin Frey   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Mathematical Description of Microbial Biofilms

(2010) Isaac Klapper et al.   SIAM REVIEW

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

A Primer on Metagenomics

(2010) John C. Wooley et al.   PLoS Computational Biology

Species Distribution Models: Ecological Explanation and Prediction Across Space and Time

(2009) Jane Elith et al.   Annual Review of Ecology Evolution and Systematics

Computing the shortest elementary flux modes in genome-scale metabolic networks

(2009) Luis F. de Figueiredo et al.   BIOINFORMATICS

Systematic development of hybrid cybernetic models: Application to recombinant yeast co-consuming glucose and xylose

(2009) Hyun-Seob Song et al.   BIOTECHNOLOGY AND BIOENGINEERING

In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study

(2009) Reed Taffs et al.   BMC Systems Biology

Microbial communities in industrial environment

(2009) Johanna Maukonen et al.   CURRENT OPINION IN MICROBIOLOGY

What is microbial community ecology?

(2009) Allan Konopka   ISME Journal

A thermodynamically-based model for predicting microbial growth and community composition coupled to system geochemistry: Application to uranium bioreduction

(2009) J.D. Istok et al.   JOURNAL OF CONTAMINANT HYDROLOGY

Snowdrift game dynamics and facultative cheating in yeast

(2009) Jeff Gore et al.   NATURE

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

Scale-Free Networks: A Decade and Beyond

(2009) Albert-László Barabási   SCIENCE

Distilling Free-Form Natural Laws from Experimental Data

(2009) Michael Schmidt et al.   SCIENCE

Coupling a genome-scale metabolic model with a reactive transport model to describein situuranium bioremediation

(2009) Timothy D. Scheibe et al.   Microbial Biotechnology

In Silico Geobacter sulfurreducens Metabolism and Its Representation in Reactive Transport Models

(2008) E. L. King et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism

(2008) Cong T. Trinh et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Large-scale computation of elementary flux modes with bit pattern trees

(2008) Marco Terzer et al.   BIOINFORMATICS

Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control

(2008) Jamey D. Young et al.   BIOTECHNOLOGY AND BIOENGINEERING

Reduction of a set of elementary modes using yield analysis

(2008) Hyun-Seob Song et al.   BIOTECHNOLOGY AND BIOENGINEERING

A hybrid model of anaerobicE. coliGJT001: Combination of elementary flux modes and cybernetic variables

(2008) Jin Il Kim et al.   BIOTECHNOLOGY PROGRESS

Overview of Mathematical Approaches Used to Model Bacterial Chemotaxis II: Bacterial Populations

(2008) M. J. Tindall et al.   BULLETIN OF MATHEMATICAL BIOLOGY

A bunch of tiny individuals—Individual-based modeling for microbes

(2008) Ferdi L. Hellweger et al.   ECOLOGICAL MODELLING

A thermodynamic analysis of the anaerobic oxidation of methane in marine sediments

(2008) D. E. LAROWE et al.   Geobiology

Individual-based Modelling: An Essential Tool for Microbiology

(2008) Jordi Ferrer et al.   JOURNAL OF BIOLOGICAL PHYSICS