Mathematical Modeling of Microbial Community Dynamics: A Methodological Review
- Authors:
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1418704
- Grant/Contract Number:
- Biological and Environmental Research (FWP 56820); Biological and Environmental Research (FWP 56812); Laboratory Directed Research and Development
- Resource Type:
- Published Article
- Journal Name:
- Processes
- Additional Journal Information:
- Journal Name: Processes Journal Volume: 2 Journal Issue: 4; Journal ID: ISSN 2227-9717
- Publisher:
- MDPI AG
- Country of Publication:
- Switzerland
- Language:
- English
Citation Formats
Song, Hyun-Seob, Cannon, William, Beliaev, Alexander, and Konopka, Allan. Mathematical Modeling of Microbial Community Dynamics: A Methodological Review. Switzerland: N. p., 2014.
Web. doi:10.3390/pr2040711.
Song, Hyun-Seob, Cannon, William, Beliaev, Alexander, & Konopka, Allan. Mathematical Modeling of Microbial Community Dynamics: A Methodological Review. Switzerland. https://doi.org/10.3390/pr2040711
Song, Hyun-Seob, Cannon, William, Beliaev, Alexander, and Konopka, Allan. Fri .
"Mathematical Modeling of Microbial Community Dynamics: A Methodological Review". Switzerland. https://doi.org/10.3390/pr2040711.
@article{osti_1418704,
title = {Mathematical Modeling of Microbial Community Dynamics: A Methodological Review},
author = {Song, Hyun-Seob and Cannon, William and Beliaev, Alexander and Konopka, Allan},
abstractNote = {},
doi = {10.3390/pr2040711},
journal = {Processes},
number = 4,
volume = 2,
place = {Switzerland},
year = {Fri Oct 17 00:00:00 EDT 2014},
month = {Fri Oct 17 00:00:00 EDT 2014}
}
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Works referenced in this record:
Parallel Extreme Ray and Pathway Computation
book, January 2010
- Terzer, Marco; Stelling, Jörg
- Parallel Processing and Applied Mathematics
Microbial interactions: from networks to models
journal, July 2012
- Faust, Karoline; Raes, Jeroen
- Nature Reviews Microbiology, Vol. 10, Issue 8
Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota
journal, December 2013
- Stein, Richard R.; Bucci, Vanni; Toussaint, Nora C.
- PLoS Computational Biology, Vol. 9, Issue 12
Prokaryotes: The unseen majority
journal, June 1998
- Whitman, W. B.; Coleman, D. C.; Wiebe, W. J.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 12
Interactions in the microbiome: communities of organisms and communities of genes
journal, January 2014
- Boon, Eva; Meehan, Conor J.; Whidden, Chris
- FEMS Microbiology Reviews, Vol. 38, Issue 1
Environments that Induce Synthetic Microbial Ecosystems
journal, November 2010
- Klitgord, Niels; Segrè, Daniel
- PLoS Computational Biology, Vol. 6, Issue 11
d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities
journal, November 2013
- Zomorrodi, Ali R.; Islam, Mohammad Mazharul; Maranas, Costas D.
- ACS Synthetic Biology, Vol. 3, Issue 4
Error and attack tolerance of complex networks
journal, July 2000
- Albert, Réka; Jeong, Hawoong; Barabási, Albert-László
- Nature, Vol. 406, Issue 6794
Antimicrobial resistance in bacterial biofilms
journal, January 2006
- Rodríguez-Martínez, Jose M.; Pascual, Alvaro
- Reviews in Medical Microbiology, Vol. 17, Issue 3
Distilling Free-Form Natural Laws from Experimental Data
journal, April 2009
- Schmidt, Michael; Lipson, Hod
- Science, Vol. 324, Issue 5923
An improved algorithm for stoichiometric network analysis: theory and applications
journal, November 2004
- Urbanczik, R.; Wagner, C.
- Bioinformatics, Vol. 21, Issue 7
Experimental methods and modeling techniques for description of cell population heterogeneity
journal, November 2011
- Lencastre Fernandes, R.; Nierychlo, M.; Lundin, L.
- Biotechnology Advances, Vol. 29, Issue 6
You Are What You Host: Microbiome Modulation of the Aging Process
journal, January 2014
- Heintz, Caroline; Mair, William
- Cell, Vol. 156, Issue 3
Phylogeny of Microorganisms Populating a Thick, Subaerial, Predominantly Lithotrophic Biofilm at an Extreme Acid Mine Drainage Site
journal, September 2000
- Bond, P. L.; Smriga, S. P.; Banfield, J. F.
- Applied and Environmental Microbiology, Vol. 66, Issue 9
Species Distribution Models: Ecological Explanation and Prediction Across Space and Time
journal, December 2009
- Elith, Jane; Leathwick, John R.
- Annual Review of Ecology, Evolution, and Systematics, Vol. 40, Issue 1
Prediction of dynamic behavior of mutant strains from limited wild-type data
journal, March 2012
- Song, Hyun-Seob; Ramkrishna, Doraiswami
- Metabolic Engineering, Vol. 14, Issue 2
Metabolic modeling of a mutualistic microbial community
journal, January 2007
- Stolyar, Sergey; Van Dien, Steve; Hillesland, Kristina Linnea
- Molecular Systems Biology, Vol. 3, Issue 1
Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics
journal, May 2014
- Harcombe, William R.; Riehl, William J.; Dukovski, Ilija
- Cell Reports, Vol. 7, Issue 4
Computing the shortest elementary flux modes in genome-scale metabolic networks
journal, September 2009
- de Figueiredo, Luis F.; Podhorski, Adam; Rubio, Angel
- Bioinformatics, Vol. 25, Issue 23
Stochastic thermodynamics of chemical reaction networks
journal, January 2007
- Schmiedl, Tim; Seifert, Udo
- The Journal of Chemical Physics, Vol. 126, Issue 4
Relationship between Thermodynamic Driving Force and One-Way Fluxes in Reversible Processes
journal, January 2007
- Beard, Daniel A.; Qian, Hong
- PLoS ONE, Vol. 2, Issue 1
A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities
journal, January 2011
- Tzamali, Eleftheria; Poirazi, Panayiota; Tollis, Ioannis G.
- BMC Systems Biology, Vol. 5, Issue 1
An improved cellular automaton method to model multispecies biofilms
journal, October 2013
- Tang, Youneng; Valocchi, Albert J.
- Water Research, Vol. 47, Issue 15
Engineering ecosystems and synthetic ecologies
journal, January 2012
- Mee, Michael T.; Wang, Harris H.
- Molecular BioSystems, Vol. 8, Issue 10
Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition
journal, January 2012
- Bouskill, Nicholas J.; Tang, Jinyun; Riley, William J.
- Frontiers in Microbiology, Vol. 3
Modeling Microbial Dynamics in Heterogeneous Environments: Growth on Soil Carbon Sources
journal, December 2011
- Resat, Haluk; Bailey, Vanessa; McCue, Lee Ann
- Microbial Ecology, Vol. 63, Issue 4
Challenges for Complex Microbial Ecosystems: Combination of Experimental Approaches with Mathematical Modeling
journal, January 2013
- Haruta, Shin; Yoshida, Takehito; Aoi, Yoshiteru
- Microbes and Environments, Vol. 28, Issue 3
Time, Structure, and Fluctuations
journal, September 1978
- Prigogine, I.
- Science, Vol. 201, Issue 4358
Modeling product formation in anaerobic mixed culture fermentations
journal, January 2006
- Rodríguez, Jorge; Kleerebezem, Robbert; Lema, Juan M.
- Biotechnology and Bioengineering, Vol. 93, Issue 3
Quantifying the importance of local niche-based and stochastic processes to tropical tree community assembly
journal, April 2012
- Shipley, Bill; Paine, C. E. Timothy; Baraloto, Christopher
- Ecology, Vol. 93, Issue 4
A Primer on Metagenomics
journal, February 2010
- Wooley, John C.; Godzik, Adam; Friedberg, Iddo
- PLoS Computational Biology, Vol. 6, Issue 2
From Plant Traits to Plant Communities: A Statistical Mechanistic Approach to Biodiversity
journal, November 2006
- Shipley, B.; Vile, D.; Garnier, E.
- Science, Vol. 314, Issue 5800
Moving pictures of the human microbiome
journal, January 2011
- Caporaso, J. Gregory; Lauber, Christian L.; Costello, Elizabeth K.
- Genome Biology, Vol. 12, Issue 5
A thermodynamically-based model for predicting microbial growth and community composition coupled to system geochemistry: Application to uranium bioreduction
journal, March 2010
- Istok, J. D.; Park, M.; Michalsen, M.
- Journal of Contaminant Hydrology, Vol. 112, Issue 1-4
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology
journal, January 2011
- Bordbar, Aarash; Feist, Adam M.; Usaite-Black, Renata
- BMC Systems Biology, Vol. 5, Issue 1
Identification of Functionally Relevant Populations in Enhanced Biological Phosphorus Removal Processes Based On Intracellular Polymers Profiles and Insights into the Metabolic Diversity and Heterogeneity
journal, April 2012
- Majed, Nehreen; Chernenko, Tatyana; Diem, Max
- Environmental Science & Technology, Vol. 46, Issue 9
Soil biodiversity and soil community composition determine ecosystem multifunctionality
journal, March 2014
- Wagg, C.; Bender, S. F.; Widmer, F.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 14
Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism
journal, February 2014
- Noor, Elad; Bar-Even, Arren; Flamholz, Avi
- PLoS Computational Biology, Vol. 10, Issue 2
A predictive model of community assembly that incorporates intraspecific trait variation
journal, August 2012
- Laughlin, Daniel C.; Joshi, Chaitanya; van Bodegom, Peter M.
- Ecology Letters, Vol. 15, Issue 11
Large-scale computation of elementary flux modes with bit pattern trees
journal, August 2008
- Terzer, Marco; Stelling, Jörg
- Bioinformatics, Vol. 24, Issue 19
Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures
journal, October 2010
- Hanly, Timothy J.; Henson, Michael A.
- Biotechnology and Bioengineering, Vol. 108, Issue 2
Population balance modeling. Promise for the future
journal, February 2002
- Ramkrishna, Doraiswami; Mahoney, Alan W.
- Chemical Engineering Science, Vol. 57, Issue 4
Evolutionary Dynamics of Biological Games
journal, February 2004
- Nowak, M. A.
- Science, Vol. 303, Issue 5659
Evolutionary game theory: Theoretical concepts and applications to microbial communities
journal, October 2010
- Frey, Erwin
- Physica A: Statistical Mechanics and its Applications, Vol. 389, Issue 20
Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass
journal, August 2013
- Minty, Jeremy J.; Singer, Marc E.; Scholz, Scott A.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 36
Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis
journal, October 2012
- Zhu, Yan; Song, Jiangning; Xu, Zixiang
- Biotechnology and Bioengineering, Vol. 110, Issue 3
Competitive and cooperative metabolic interactions in bacterial communities
journal, September 2011
- Freilich, Shiri; Zarecki, Raphy; Eilam, Omer
- Nature Communications, Vol. 2, Issue 1
Enhanced Biofilm Formation and Increased Resistance to Antimicrobial Agents and Bacterial Invasion Are Caused by Synergistic Interactions in Multispecies Biofilms
journal, June 2006
- Burmolle, M.; Webb, J. S.; Rao, D.
- Applied and Environmental Microbiology, Vol. 72, Issue 6
Modeling microbial community structure and functional diversity across time and space
journal, May 2012
- Larsen, Peter E.; Gibbons, Sean M.; Gilbert, Jack A.
- FEMS Microbiology Letters, Vol. 332, Issue 2
The role of physiological heterogeneity in microbial population behavior
journal, September 2010
- Lidstrom, Mary E.; Konopka, Michael C.
- Nature Chemical Biology, Vol. 6, Issue 10
Stochastic Simulation of Chemical Kinetics
journal, May 2007
- Gillespie, Daniel T.
- Annual Review of Physical Chemistry, Vol. 58, Issue 1
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
journal, July 2010
- Zhuang, Kai; Izallalen, Mounir; Mouser, Paula
- The ISME Journal, Vol. 5, Issue 2
Dynamic models of metabolism: Review of the cybernetic approach
journal, February 2012
- Ramkrishna, Doraiswami; Song, Hyun-Seob
- AIChE Journal, Vol. 58, Issue 4
Maximum entropy production and plant optimization theories
journal, May 2010
- Dewar, Roderick C.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 365, Issue 1545
Bistability versus Bimodal Distributions in Gene Regulatory Processes from Population Balance
journal, August 2011
- Shu, Che-Chi; Chatterjee, Anushree; Dunny, Gary
- PLoS Computational Biology, Vol. 7, Issue 8
The microbiome: stress, health and disease
journal, November 2013
- Moloney, Rachel D.; Desbonnet, Lieve; Clarke, Gerard
- Mammalian Genome, Vol. 25, Issue 1-2
Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example
journal, March 2014
- Röling, Wilfred F. M.; van Bodegom, Peter M.
- Frontiers in Microbiology, Vol. 5
Emergent cooperation in microbial metabolism
journal, January 2010
- Wintermute, Edwin H.; Silver, Pamela A.
- Molecular Systems Biology, Vol. 6, Issue 1
Predicting bacterial community assemblages using an artificial neural network approach
journal, April 2012
- Larsen, Peter E.; Field, Dawn; Gilbert, Jack A.
- Nature Methods, Vol. 9, Issue 6
Estimating the Dimension of a Model
journal, March 1978
- Schwarz, Gideon
- The Annals of Statistics, Vol. 6, Issue 2
Modeling metabolic systems: the need for dynamics
journal, November 2013
- Song, Hyun-Seob; DeVilbiss, Frank; Ramkrishna, Doraiswami
- Current Opinion in Chemical Engineering, Vol. 2, Issue 4
Snowdrift game dynamics and facultative cheating in yeast
journal, April 2009
- Gore, Jeff; Youk, Hyun; van Oudenaarden, Alexander
- Nature, Vol. 459, Issue 7244
Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation
journal, March 2009
- Scheibe, Timothy D.; Mahadevan, Radhakrishnan; Fang, Yilin
- Microbial Biotechnology, Vol. 2, Issue 2
Reduction of a set of elementary modes using yield analysis
journal, February 2009
- Song, Hyun-Seob; Ramkrishna, Doraiswami
- Biotechnology and Bioengineering, Vol. 102, Issue 2
A thermodynamic analysis of the anaerobic oxidation of methane in marine sediments
journal, December 2008
- Larowe, D. E.; Dale, A. W.; Regnier, P.
- Geobiology, Vol. 6, Issue 5
A hybrid model of anaerobic E. coli GJT001: Combination of elementary flux modes and cybernetic variables
journal, September 2008
- Kim, Jin Il; Varner, Jeffery D.; Ramkrishna, Doraiswami
- Biotechnology Progress, Vol. 24, Issue 5
Gut microbiome and metabolic diseases
journal, November 2013
- Fukuda, Shinji; Ohno, Hiroshi
- Seminars in Immunopathology, Vol. 36, Issue 1
Dynamic modeling of microbial cell populations
journal, October 2003
- Henson, Michael A.
- Current Opinion in Biotechnology, Vol. 14, Issue 5
What is microbial community ecology?
journal, August 2009
- Konopka, Allan
- The ISME Journal, Vol. 3, Issue 11
Comparative Metagenomics of Microbial Communities
journal, April 2005
- Tringe, S. G.
- Science, Vol. 308, Issue 5721
The functional design of the rotary enzyme ATP synthase is consistent with maximum entropy production
journal, October 2006
- Dewar, R. C.; Juretić, D.; Županović, P.
- Chemical Physics Letters, Vol. 430, Issue 1-3
Scale-Free Networks
journal, May 2003
- Barabási, Albert-László; Bonabeau, Eric
- Scientific American, Vol. 288, Issue 5
A bunch of tiny individuals—Individual-based modeling for microbes
journal, January 2009
- Hellweger, Ferdi L.; Bucci, Vanni
- Ecological Modelling, Vol. 220, Issue 1
Overview of Mathematical Approaches Used to Model Bacterial Chemotaxis II: Bacterial Populations
journal, July 2008
- Tindall, M. J.; Maini, P. K.; Porter, S. L.
- Bulletin of Mathematical Biology, Vol. 70, Issue 6
Super-individuals a simple solution for modelling large populations on an individual basis
journal, July 1995
- Scheffer, M.; Baveco, J. M.; DeAngelis, D. L.
- Ecological Modelling, Vol. 80, Issue 2-3
In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study
journal, January 2009
- Taffs, Reed; Aston, John E.; Brileya, Kristen
- BMC Systems Biology, Vol. 3, Issue 1
Systematic development of hybrid cybernetic models: Application to recombinant yeast co-consuming glucose and xylose
journal, August 2009
- Song, Hyun-Seob; Morgan, John A.; Ramkrishna, Doraiswami
- Biotechnology and Bioengineering, Vol. 103, Issue 5
Mathematical Description of Microbial Biofilms
journal, January 2010
- Klapper, Isaac; Dockery, Jack
- SIAM Review, Vol. 52, Issue 2
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities
journal, February 2012
- Zomorrodi, Ali R.; Maranas, Costas D.
- PLoS Computational Biology, Vol. 8, Issue 2
Stochastic and deterministic assembly processes in subsurface microbial communities
journal, March 2012
- Stegen, James C.; Lin, Xueju; Konopka, Allan E.
- The ISME Journal, Vol. 6, Issue 9
A road map for the development of community systems (CoSy) biology
journal, March 2012
- Zengler, Karsten; Palsson, Bernhard O.
- Nature Reviews Microbiology, Vol. 10, Issue 5
Modeling microbial communities: Current, developing, and future technologies for predicting microbial community interaction
journal, July 2012
- Larsen, Peter; Hamada, Yuki; Gilbert, Jack
- Journal of Biotechnology, Vol. 160, Issue 1-2
Individual-based Modelling: An Essential Tool for Microbiology
journal, April 2008
- Ferrer, Jordi; Prats, Clara; López, Daniel
- Journal of Biological Physics, Vol. 34, Issue 1-2
BacSim, a simulator for individual-based modelling of bacterial colony growth
journal, December 1998
- Kreft, J. -U.; Booth, G.; Wimpenny, J. W. T.
- Microbiology, Vol. 144, Issue 12
Dynamic modeling of aerobic growth of Shewanella oneidensis. Predicting triauxic growth, flux distributions, and energy requirement for growth
journal, January 2013
- Song, Hyun-Seob; Ramkrishna, Doraiswami; Pinchuk, Grigoriy E.
- Metabolic Engineering, Vol. 15
Minimal cut sets in a metabolic network are elementary modes in a dual network
journal, December 2011
- Ballerstein, Kathrin; von Kamp, Axel; Klamt, Steffen
- Bioinformatics, Vol. 28, Issue 3
Microbial communities in industrial environment
journal, June 2009
- Maukonen, Johanna; Saarela, Maria
- Current Opinion in Microbiology, Vol. 12, Issue 3
The generation and maintenance of diversity in microbial communities
journal, March 2011
- Fierer, Noah; Lennon, Jay T.
- American Journal of Botany, Vol. 98, Issue 3
Large-scale in silico modeling of metabolic interactions between cell types in the human brain
journal, November 2010
- Lewis, Nathan E.; Schramm, Gunnar; Bordbar, Aarash
- Nature Biotechnology, Vol. 28, Issue 12
A structured and dynamic framework to advance traits-based theory and prediction in ecology
journal, March 2010
- Webb, Colleen T.; Hoeting, Jennifer A.; Ames, Gregory M.
- Ecology Letters, Vol. 13, Issue 3
Ecosystem functioning and maximum entropy production: a quantitative test of hypotheses
journal, May 2010
- Meysman, Filip J. R.; Bruers, Stijn
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 365, Issue 1545
The design of long-term effective uranium bioremediation strategy using a community metabolic model
journal, April 2012
- Zhuang, K.; Ma, E.; Lovley, Derek R.
- Biotechnology and Bioengineering, Vol. 109, Issue 10
Towards novel approaches to modelling biotic interactions in multispecies assemblages at large spatial extents: Modelling multispecies interactions
journal, December 2011
- Kissling, W. D.; Dormann, Carsten F.; Groeneveld, Jürgen
- Journal of Biogeography, Vol. 39, Issue 12
Advances in modeling trait-based plant community assembly
journal, October 2013
- Laughlin, Daniel C.; Laughlin, David E.
- Trends in Plant Science, Vol. 18, Issue 10
Computational systems biology and in silico modeling of the human microbiome
journal, May 2012
- Borenstein, E.
- Briefings in Bioinformatics, Vol. 13, Issue 6
Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
journal, December 2011
- Greenblum, S.; Turnbaugh, P. J.; Borenstein, E.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 2
Community Flux Balance Analysis for Microbial Consortia at Balanced Growth
journal, May 2013
- Khandelwal, Ruchir A.; Olivier, Brett G.; Röling, Wilfred F. M.
- PLoS ONE, Vol. 8, Issue 5
Microbial physiology-based model of ethanol metabolism in subsurface sediments
journal, July 2011
- Jin, Qusheng; Roden, Eric E.
- Journal of Contaminant Hydrology, Vol. 125, Issue 1-4
Attractants and repellents influence methylation and demethylation of methyl-accepting chemotaxis proteins in an extract of Escherichia coli.
journal, December 1979
- Kleene, S. J.; Hobson, A. C.; Adler, J.
- Proceedings of the National Academy of Sciences, Vol. 76, Issue 12
Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks
journal, June 2011
- Chan, Siu Hung Joshua; Ji, Ping
- Bioinformatics, Vol. 27, Issue 16
Analysis of optimality in natural and perturbed metabolic networks
journal, November 2002
- Segre, D.; Vitkup, D.; Church, G. M.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 23
In Silico Geobacter sulfurreducens Metabolism and Its Representation in Reactive Transport Models
journal, November 2008
- King, E. L.; Tuncay, K.; Ortoleva, P.
- Applied and Environmental Microbiology, Vol. 75, Issue 1
Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model
journal, March 2011
- Fang, Yilin; Scheibe, Timothy D.; Mahadevan, Radhakrishnan
- Journal of Contaminant Hydrology, Vol. 122, Issue 1-4
Scale-Free Networks: A Decade and Beyond
journal, July 2009
- Barabási, Albert-László
- Science, Vol. 325, Issue 5939
On enhancing productivity of bioethanol with multiple species
journal, January 2012
- Geng, Jun; Song, Hyun-Seob; Yuan, Jingqi
- Biotechnology and Bioengineering, Vol. 109, Issue 6
Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control
journal, June 2008
- Young, Jamey D.; Henne, Kristene L.; Morgan, John A.
- Biotechnology and Bioengineering, Vol. 100, Issue 3
Deciphering microbial interactions and detecting keystone species with co-occurrence networks
journal, May 2014
- Berry, David; Widder, Stefanie
- Frontiers in Microbiology, Vol. 5
Classification of metagenomic sequences: methods and challenges
journal, September 2012
- Mande, S. S.; Mohammed, M. H.; Ghosh, T. S.
- Briefings in Bioinformatics, Vol. 13, Issue 6
Metabolic networks evolve towards states of maximum entropy production
journal, November 2011
- Unrean, Pornkamol; Srienc, Friedrich
- Metabolic Engineering, Vol. 13, Issue 6
Exacting predictions by cybernetic model confirmed experimentally: Steady state multiplicity in the chemostat
journal, July 2012
- Kim, Jin Il; Song, Hyun-Seob; Sunkara, Sunil R.
- Biotechnology Progress, Vol. 28, Issue 5
What is flux balance analysis?
journal, March 2010
- Orth, Jeffrey D.; Thiele, Ines; Palsson, Bernhard Ø
- Nature Biotechnology, Vol. 28, Issue 3
Cybernetic models based on lumped elementary modes accurately predict strain-specific metabolic function
journal, October 2010
- Song, Hyun-Seob; Ramkrishna, Doraiswami
- Biotechnology and Bioengineering, Vol. 108, Issue 1
Gene-centric approach to integrating environmental genomics and biogeochemical models
journal, January 2014
- Reed, Daniel C.; Algar, Christopher K.; Huber, Julie A.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 5
Microbial community structure and its functional implications
journal, May 2009
- Fuhrman, Jed A.
- Nature, Vol. 459, Issue 7244
Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism
journal, November 2008
- Trinh, Cong T.; Wlaschin, Aaron; Srienc, Friedrich
- Applied Microbiology and Biotechnology, Vol. 81, Issue 5
Dynamic modelling of mixotrophic microalgal photobioreactor systems with time-varying yield coefficient for the lipid consumption
journal, June 2014
- Yoo, Sung Jin; Kim, Jung Hun; Lee, Jong Min
- Bioresource Technology, Vol. 162
Dynamic metabolic modeling of a microaerobic yeast co-culture: predicting and optimizing ethanol production from glucose/xylose mixtures
journal, January 2013
- Hanly, Timothy J.; Henson, Michael A.
- Biotechnology for Biofuels, Vol. 6, Issue 1
iDynoMiCS: next-generation individual-based modelling of biofilms: iDynoMiCS for Biofilm Modelling
journal, March 2011
- Lardon, Laurent A.; Merkey, Brian V.; Martins, Sónia
- Environmental Microbiology, Vol. 13, Issue 9