Parallel Extreme Ray and Pathway Computation
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book
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January 2010 |
Microbial interactions: from networks to models
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journal
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July 2012 |
Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota
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journal
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December 2013 |
Prokaryotes: The unseen majority
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journal
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June 1998 |
Interactions in the microbiome: communities of organisms and communities of genes
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journal
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January 2014 |
Environments that Induce Synthetic Microbial Ecosystems
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journal
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November 2010 |
d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities
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journal
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November 2013 |
Error and attack tolerance of complex networks
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journal
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July 2000 |
Antimicrobial resistance in bacterial biofilms
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journal
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January 2006 |
Distilling Free-Form Natural Laws from Experimental Data
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journal
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April 2009 |
An improved algorithm for stoichiometric network analysis: theory and applications
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journal
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November 2004 |
Experimental methods and modeling techniques for description of cell population heterogeneity
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journal
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November 2011 |
You Are What You Host: Microbiome Modulation of the Aging Process
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journal
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January 2014 |
Phylogeny of Microorganisms Populating a Thick, Subaerial, Predominantly Lithotrophic Biofilm at an Extreme Acid Mine Drainage Site
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journal
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September 2000 |
Species Distribution Models: Ecological Explanation and Prediction Across Space and Time
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journal
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December 2009 |
Prediction of dynamic behavior of mutant strains from limited wild-type data
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journal
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March 2012 |
Metabolic modeling of a mutualistic microbial community
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journal
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January 2007 |
Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics
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journal
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May 2014 |
Computing the shortest elementary flux modes in genome-scale metabolic networks
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journal
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September 2009 |
Stochastic thermodynamics of chemical reaction networks
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journal
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January 2007 |
Relationship between Thermodynamic Driving Force and One-Way Fluxes in Reversible Processes
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journal
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January 2007 |
A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities
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journal
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January 2011 |
An improved cellular automaton method to model multispecies biofilms
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journal
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October 2013 |
Engineering ecosystems and synthetic ecologies
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journal
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January 2012 |
Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition
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journal
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January 2012 |
Modeling Microbial Dynamics in Heterogeneous Environments: Growth on Soil Carbon Sources
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journal
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December 2011 |
Challenges for Complex Microbial Ecosystems: Combination of Experimental Approaches with Mathematical Modeling
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journal
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January 2013 |
Time, Structure, and Fluctuations
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journal
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September 1978 |
Modeling product formation in anaerobic mixed culture fermentations
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journal
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January 2006 |
Quantifying the importance of local niche-based and stochastic processes to tropical tree community assembly
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journal
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April 2012 |
A Primer on Metagenomics
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journal
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February 2010 |
From Plant Traits to Plant Communities: A Statistical Mechanistic Approach to Biodiversity
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journal
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November 2006 |
Moving pictures of the human microbiome
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journal
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January 2011 |
A thermodynamically-based model for predicting microbial growth and community composition coupled to system geochemistry: Application to uranium bioreduction
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journal
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March 2010 |
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology
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journal
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January 2011 |
Identification of Functionally Relevant Populations in Enhanced Biological Phosphorus Removal Processes Based On Intracellular Polymers Profiles and Insights into the Metabolic Diversity and Heterogeneity
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journal
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April 2012 |
Soil biodiversity and soil community composition determine ecosystem multifunctionality
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journal
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March 2014 |
Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism
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journal
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February 2014 |
A predictive model of community assembly that incorporates intraspecific trait variation
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journal
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August 2012 |
Large-scale computation of elementary flux modes with bit pattern trees
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journal
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August 2008 |
Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures
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journal
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October 2010 |
Population balance modeling. Promise for the future
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journal
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February 2002 |
Evolutionary Dynamics of Biological Games
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journal
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February 2004 |
Evolutionary game theory: Theoretical concepts and applications to microbial communities
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journal
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October 2010 |
Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass
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journal
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August 2013 |
Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis
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journal
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October 2012 |
Competitive and cooperative metabolic interactions in bacterial communities
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journal
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September 2011 |
Enhanced Biofilm Formation and Increased Resistance to Antimicrobial Agents and Bacterial Invasion Are Caused by Synergistic Interactions in Multispecies Biofilms
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journal
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June 2006 |
Modeling microbial community structure and functional diversity across time and space
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journal
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May 2012 |
The role of physiological heterogeneity in microbial population behavior
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journal
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September 2010 |
Stochastic Simulation of Chemical Kinetics
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journal
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May 2007 |
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
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journal
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July 2010 |
Dynamic models of metabolism: Review of the cybernetic approach
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journal
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February 2012 |
Maximum entropy production and plant optimization theories
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journal
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May 2010 |
Bistability versus Bimodal Distributions in Gene Regulatory Processes from Population Balance
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journal
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August 2011 |
The microbiome: stress, health and disease
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journal
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November 2013 |
Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example
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journal
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March 2014 |
Emergent cooperation in microbial metabolism
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journal
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January 2010 |
Predicting bacterial community assemblages using an artificial neural network approach
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journal
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April 2012 |
Estimating the Dimension of a Model
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journal
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March 1978 |
Modeling metabolic systems: the need for dynamics
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journal
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November 2013 |
Snowdrift game dynamics and facultative cheating in yeast
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journal
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April 2009 |
Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation
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journal
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March 2009 |
Reduction of a set of elementary modes using yield analysis
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journal
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February 2009 |
A thermodynamic analysis of the anaerobic oxidation of methane in marine sediments
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journal
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December 2008 |
A hybrid model of anaerobic E. coli GJT001: Combination of elementary flux modes and cybernetic variables
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journal
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September 2008 |
Gut microbiome and metabolic diseases
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journal
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November 2013 |
Dynamic modeling of microbial cell populations
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journal
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October 2003 |
What is microbial community ecology?
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journal
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August 2009 |
Comparative Metagenomics of Microbial Communities
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journal
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April 2005 |
The functional design of the rotary enzyme ATP synthase is consistent with maximum entropy production
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journal
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October 2006 |
Scale-Free Networks
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journal
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May 2003 |
A bunch of tiny individuals—Individual-based modeling for microbes
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journal
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January 2009 |
Overview of Mathematical Approaches Used to Model Bacterial Chemotaxis II: Bacterial Populations
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journal
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July 2008 |
Super-individuals a simple solution for modelling large populations on an individual basis
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journal
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July 1995 |
In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study
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journal
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January 2009 |
Systematic development of hybrid cybernetic models: Application to recombinant yeast co-consuming glucose and xylose
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journal
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August 2009 |
Mathematical Description of Microbial Biofilms
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journal
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January 2010 |
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities
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journal
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February 2012 |
Stochastic and deterministic assembly processes in subsurface microbial communities
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journal
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March 2012 |
A road map for the development of community systems (CoSy) biology
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journal
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March 2012 |
Modeling microbial communities: Current, developing, and future technologies for predicting microbial community interaction
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journal
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July 2012 |
Individual-based Modelling: An Essential Tool for Microbiology
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journal
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April 2008 |
BacSim, a simulator for individual-based modelling of bacterial colony growth
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journal
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December 1998 |
Dynamic modeling of aerobic growth of Shewanella oneidensis. Predicting triauxic growth, flux distributions, and energy requirement for growth
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journal
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January 2013 |
Minimal cut sets in a metabolic network are elementary modes in a dual network
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journal
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December 2011 |
Microbial communities in industrial environment
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journal
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June 2009 |
The generation and maintenance of diversity in microbial communities
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journal
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March 2011 |
Large-scale in silico modeling of metabolic interactions between cell types in the human brain
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journal
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November 2010 |
A structured and dynamic framework to advance traits-based theory and prediction in ecology
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journal
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March 2010 |
Ecosystem functioning and maximum entropy production: a quantitative test of hypotheses
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journal
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May 2010 |
The design of long-term effective uranium bioremediation strategy using a community metabolic model
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journal
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April 2012 |
Towards novel approaches to modelling biotic interactions in multispecies assemblages at large spatial extents: Modelling multispecies interactions
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journal
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December 2011 |
Advances in modeling trait-based plant community assembly
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journal
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October 2013 |
Computational systems biology and in silico modeling of the human microbiome
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journal
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May 2012 |
Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
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journal
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December 2011 |
Community Flux Balance Analysis for Microbial Consortia at Balanced Growth
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journal
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May 2013 |
Microbial physiology-based model of ethanol metabolism in subsurface sediments
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journal
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July 2011 |
Attractants and repellents influence methylation and demethylation of methyl-accepting chemotaxis proteins in an extract of Escherichia coli.
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journal
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December 1979 |
Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks
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journal
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June 2011 |
Analysis of optimality in natural and perturbed metabolic networks
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journal
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November 2002 |
In Silico Geobacter sulfurreducens Metabolism and Its Representation in Reactive Transport Models
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journal
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November 2008 |
Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model
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journal
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March 2011 |
Scale-Free Networks: A Decade and Beyond
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journal
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July 2009 |
On enhancing productivity of bioethanol with multiple species
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journal
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January 2012 |
Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control
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journal
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June 2008 |
Deciphering microbial interactions and detecting keystone species with co-occurrence networks
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journal
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May 2014 |
Classification of metagenomic sequences: methods and challenges
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journal
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September 2012 |
Metabolic networks evolve towards states of maximum entropy production
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journal
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November 2011 |
Exacting predictions by cybernetic model confirmed experimentally: Steady state multiplicity in the chemostat
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journal
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July 2012 |
What is flux balance analysis?
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journal
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March 2010 |
Cybernetic models based on lumped elementary modes accurately predict strain-specific metabolic function
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journal
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October 2010 |
Gene-centric approach to integrating environmental genomics and biogeochemical models
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journal
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January 2014 |
Microbial community structure and its functional implications
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journal
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May 2009 |
Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism
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journal
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November 2008 |
Dynamic modelling of mixotrophic microalgal photobioreactor systems with time-varying yield coefficient for the lipid consumption
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journal
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June 2014 |
Dynamic metabolic modeling of a microaerobic yeast co-culture: predicting and optimizing ethanol production from glucose/xylose mixtures
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journal
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January 2013 |
iDynoMiCS: next-generation individual-based modelling of biofilms: iDynoMiCS for Biofilm Modelling
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journal
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March 2011 |