4.6 Review

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Biochemistry & Molecular Biology

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

Caroline Heintz et al.

Review Biochemistry & Molecular Biology

The microbiome: stress, health and disease

Rachel D. Moloney et al.

MAMMALIAN GENOME (2014)

Article Multidisciplinary Sciences

Gene-centric approach to integrating environmental genomics and biogeochemical models

Daniel C. Reed et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

Soil biodiversity and soil community composition determine ecosystem multifunctionality

Cameron Wagg et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Review Immunology

Gut microbiome and metabolic diseases

Shinji Fukuda et al.

SEMINARS IN IMMUNOPATHOLOGY (2014)

Article Biochemical Research Methods

d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities

All R. Zomorrodi et al.

ACS SYNTHETIC BIOLOGY (2014)

Article Biochemical Research Methods

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

Elad Noor et al.

PLOS COMPUTATIONAL BIOLOGY (2014)

Review Microbiology

Interactions in the microbiome: communities of organisms and communities of genes

Eva Boon et al.

FEMS MICROBIOLOGY REVIEWS (2014)

Article Biotechnology & Applied Microbiology

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

Yan Zhu et al.

BIOTECHNOLOGY AND BIOENGINEERING (2013)

Article Biotechnology & Applied Microbiology

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

Timothy J. Hanly et al.

BIOTECHNOLOGY FOR BIOFUELS (2013)

Review Biotechnology & Applied Microbiology

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

Shin Haruta et al.

MICROBES AND ENVIRONMENTS (2013)

Article Multidisciplinary Sciences

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

Ruchir A. Khandelwal et al.

PLOS ONE (2013)

Article Multidisciplinary Sciences

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

Jeremy J. Minty et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Review Plant Sciences

Advances in modeling trait-based plant community assembly

Daniel C. Laughlin et al.

TRENDS IN PLANT SCIENCE (2013)

Article Engineering, Environmental

An improved cellular automaton method to model multispecies biofilms

Youneng Tang et al.

WATER RESEARCH (2013)

Article Biochemical Research Methods

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

Richard R. Stein et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Article Biotechnology & Applied Microbiology

Modeling metabolic systems: the need for dynamics

Hyun-Seob Song et al.

CURRENT OPINION IN CHEMICAL ENGINEERING (2013)

Review Engineering, Chemical

Dynamic models of metabolism: Review of the cybernetic approach

Doraiswami Ramkrishna et al.

AICHE JOURNAL (2012)

Article Biochemical Research Methods

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

Kathrin Ballerstein et al.

BIOINFORMATICS (2012)

Article Biotechnology & Applied Microbiology

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

K. Zhuang et al.

BIOTECHNOLOGY AND BIOENGINEERING (2012)

Article Biotechnology & Applied Microbiology

On enhancing productivity of bioethanol with multiple species

Jun Geng et al.

BIOTECHNOLOGY AND BIOENGINEERING (2012)

Article Biotechnology & Applied Microbiology

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

Jin Il Kim et al.

BIOTECHNOLOGY PROGRESS (2012)

Article Biochemical Research Methods

Computational systems biology and in silico modeling of the human microbiome

Elhanan Borenstein

BRIEFINGS IN BIOINFORMATICS (2012)

Article Biochemical Research Methods

Classification of metagenomic sequences: methods and challenges

Sharmila S. Mande et al.

BRIEFINGS IN BIOINFORMATICS (2012)

Review Microbiology

Modeling microbial community structure and functional diversity across time and space

Peter E. Larsen et al.

FEMS MICROBIOLOGY LETTERS (2012)

Article Biotechnology & Applied Microbiology

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

Peter Larsen et al.

JOURNAL OF BIOTECHNOLOGY (2012)

Review Biochemistry & Molecular Biology

Engineering ecosystems and synthetic ecologies

Michael T. Mee et al.

MOLECULAR BIOSYSTEMS (2012)

Article Biochemical Research Methods

Predicting bacterial community assemblages using an artificial neural network approach

Peter E. Larsen et al.

NATURE METHODS (2012)

Review Microbiology

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

Karsten Zengler et al.

NATURE REVIEWS MICROBIOLOGY (2012)

Review Microbiology

Microbial interactions: from networks to models

Karoline Faust et al.

NATURE REVIEWS MICROBIOLOGY (2012)

Article Biotechnology & Applied Microbiology

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

Hyun-Seob Song et al.

METABOLIC ENGINEERING (2012)

Article Multidisciplinary Sciences

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

Sharon Greenblum et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemical Research Methods

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

Ali R. Zomorrodi et al.

PLOS COMPUTATIONAL BIOLOGY (2012)

Article Plant Sciences

THE GENERATION AND MAINTENANCE OF DIVERSITY IN MICROBIAL COMMUNITIES

Noah Fierer et al.

AMERICAN JOURNAL OF BOTANY (2011)

Article Biochemical Research Methods

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

Siu Hung Joshua Chan et al.

BIOINFORMATICS (2011)

Review Biotechnology & Applied Microbiology

Experimental methods and modeling techniques for description of cell population heterogeneity

R. Lencastre Fernandes et al.

BIOTECHNOLOGY ADVANCES (2011)

Article Biotechnology & Applied Microbiology

Dynamic Flux Balance Modeling of Microbial Co-Cultures for Efficient Batch Fermentation of Glucose and Xylose Mixtures

Timothy J. Hanly et al.

BIOTECHNOLOGY AND BIOENGINEERING (2011)

Article Biotechnology & Applied Microbiology

Cybernetic Models Based on Lumped Elementary Modes Accurately Predict Strain-Specific Metabolic Function

Hyun-Seob Song et al.

BIOTECHNOLOGY AND BIOENGINEERING (2011)

Article Mathematical & Computational Biology

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

Aarash Bordbar et al.

BMC SYSTEMS BIOLOGY (2011)

Article Microbiology

iDynoMiCS: next-generation individual-based modelling of biofilms

Laurent A. Lardon et al.

ENVIRONMENTAL MICROBIOLOGY (2011)

Article Environmental Sciences

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

Yilin Fang et al.

JOURNAL OF CONTAMINANT HYDROLOGY (2011)

Article Environmental Sciences

Microbial physiology-based model of ethanol metabolism in subsurface sediments

Qusheng Jin et al.

JOURNAL OF CONTAMINANT HYDROLOGY (2011)

Editorial Material Microbiology

Microbiology by numbers

[Anonymous]

NATURE REVIEWS MICROBIOLOGY (2011)

Article Biotechnology & Applied Microbiology

Metabolic networks evolve towards states of maximum entropy production

Pornkamol Unrean et al.

METABOLIC ENGINEERING (2011)

Article Multidisciplinary Sciences

Competitive and cooperative metabolic interactions in bacterial communities

Shiri Freilich et al.

NATURE COMMUNICATIONS (2011)

Article Biochemical Research Methods

Bistability versus Bimodal Distributions in Gene Regulatory Processes from Population Balance

Che-Chi Shu et al.

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Biotechnology & Applied Microbiology

Moving pictures of the human microbiome

J. Gregory Caporaso et al.

GENOME BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Emergent cooperation in microbial metabolism

Edwin H. Wintermute et al.

MOLECULAR SYSTEMS BIOLOGY (2010)

Article Biotechnology & Applied Microbiology

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

Nathan E. Lewis et al.

NATURE BIOTECHNOLOGY (2010)

Article Biotechnology & Applied Microbiology

What is flux balance analysis?

Jeffrey D. Orth et al.

NATURE BIOTECHNOLOGY (2010)

Review Biochemistry & Molecular Biology

The role of physiological heterogeneity in microbial population behavior

Mary E. Lidstrom et al.

NATURE CHEMICAL BIOLOGY (2010)

Article Physics, Multidisciplinary

Evolutionary game theory: Theoretical concepts and applications to microbial communities

Erwin Frey

PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS (2010)

Article Biology

Maximum entropy production and plant optimization theories

Roderick C. Dewar

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2010)

Article Biology

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

Filip J. R. Meysman et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2010)

Review Mathematics, Applied

Mathematical Description of Microbial Biofilms

Isaac Klapper et al.

SIAM REVIEW (2010)

Article Biochemical Research Methods

Environments that Induce Synthetic Microbial Ecosystems

Niels Klitgord et al.

PLOS COMPUTATIONAL BIOLOGY (2010)

Review Biochemical Research Methods

A Primer on Metagenomics

John C. Wooley et al.

PLOS COMPUTATIONAL BIOLOGY (2010)

Review Ecology

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

Jane Elith et al.

ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS (2009)

Article Biotechnology & Applied Microbiology

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

E. L. King et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)

Review Biotechnology & Applied Microbiology

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

Cong T. Trinh et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2009)

Article Biochemical Research Methods

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

Luis F. de Figueiredo et al.

BIOINFORMATICS (2009)

Article Biotechnology & Applied Microbiology

Reduction of a Set of Elementary Modes Using Yield Analysis

Hyun-Seob Song et al.

BIOTECHNOLOGY AND BIOENGINEERING (2009)

Article Biotechnology & Applied Microbiology

Systematic Development of Hybrid Cybernetic Models: Application to Recombinant Yeast Co-Consuming Glucose and Xylose

Hyun-Seob Song et al.

BIOTECHNOLOGY AND BIOENGINEERING (2009)

Article Mathematical & Computational Biology

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

Reed Taffs et al.

BMC SYSTEMS BIOLOGY (2009)

Review Microbiology

Microbial communities in industrial environment

Johanna Maukonen et al.

CURRENT OPINION IN MICROBIOLOGY (2009)

Review Ecology

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

Ferdi L. Hellweger et al.

ECOLOGICAL MODELLING (2009)

Article Ecology

What is microbial community ecology?

Allan Konopka

ISME JOURNAL (2009)

Article Multidisciplinary Sciences

Snowdrift game dynamics and facultative cheating in yeast

Jeff Gore et al.

NATURE (2009)

Review Multidisciplinary Sciences

Microbial community structure and its functional implications

Jed A. Fuhrman

NATURE (2009)

Editorial Material Multidisciplinary Sciences

Scale-Free Networks: A Decade and Beyond

Albert-Laszlo Barabasi

SCIENCE (2009)

Article Multidisciplinary Sciences

Distilling Free-Form Natural Laws from Experimental Data

Michael Schmidt et al.

SCIENCE (2009)

Article Biotechnology & Applied Microbiology

Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation

Timothy D. Scheibe et al.

MICROBIAL BIOTECHNOLOGY (2009)

Article Biochemical Research Methods

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

Marco Terzer et al.

BIOINFORMATICS (2008)

Article Biotechnology & Applied Microbiology

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

Jamey D. Young et al.

BIOTECHNOLOGY AND BIOENGINEERING (2008)

Article Biotechnology & Applied Microbiology

A Hybrid Model of Anaerobic E. coli GJT001: Combination of Elementary Flux Modes and Cybernetic Variables

Jin Il Kim et al.

BIOTECHNOLOGY PROGRESS (2008)

Review Biophysics

Individual-based Modelling: An Essential Tool for Microbiology

Jordi Ferrer et al.

JOURNAL OF BIOLOGICAL PHYSICS (2008)

Article Biotechnology & Applied Microbiology

Microbial interactions within a cheese microbial community

Jerome Mounier et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2008)

Article Biochemistry & Molecular Biology

Metabolic modeling of a mutualistic microbial community

Sergey Stolyar et al.

MOLECULAR SYSTEMS BIOLOGY (2007)

Article Chemistry, Physical

Stochastic thermodynamics of chemical reaction networks

Tim Schmiedl et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Multidisciplinary Sciences

Relationship between Thermodynamic Driving Force and One-Way Fluxes in Reversible Processes

Daniel A. Beard et al.

PLOS ONE (2007)

Review Chemistry, Physical

Stochastic simulation of chemical kinetics

Daniel T. Gillespie

ANNUAL REVIEW OF PHYSICAL CHEMISTRY (2007)

Article Biotechnology & Applied Microbiology

Modeling product formation in anaerobic mixed culture fermentations

J Rodríguez et al.

BIOTECHNOLOGY AND BIOENGINEERING (2006)

Article Multidisciplinary Sciences

Comparative metagenomics of microbial communities

SG Tringe et al.

SCIENCE (2005)

Article Biochemical Research Methods

An improved algorithm for stoichiometric network analysis: theory and applications

R Urbanczik et al.

BIOINFORMATICS (2005)

Review Multidisciplinary Sciences

Evolutionary dynamics of biological games

MA Nowak et al.

SCIENCE (2004)

Review Biochemical Research Methods

Dynamic modeling of microbial cell populations

MA Henson

CURRENT OPINION IN BIOTECHNOLOGY (2003)

Article Multidisciplinary Sciences

Scale-free networks

AL Barabási et al.

SCIENTIFIC AMERICAN (2003)

Article Multidisciplinary Sciences

Analysis of optimality in natural and perturbed metabolic networks

D Segrè et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Biophysics

Dynamic flux balance analysis of diauxic growth in Escherichia coli

R Mahadevan et al.

BIOPHYSICAL JOURNAL (2002)

Article Engineering, Chemical

Population balance modeling. Promise for the future

D Ramkrishna et al.

CHEMICAL ENGINEERING SCIENCE (2002)

Article Biotechnology & Applied Microbiology

Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site

PL Bond et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2000)

Article Multidisciplinary Sciences

Error and attack tolerance of complex networks

R Albert et al.

NATURE (2000)