Published in PLoS One on May 31, 2013
Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell Rep (2014) 1.39
Synthetic microbial communities. Curr Opin Microbiol (2014) 1.19
Towards predictive models of the human gut microbiome. J Mol Biol (2014) 1.09
Emergent biosynthetic capacity in simple microbial communities. PLoS Comput Biol (2014) 0.99
Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example. Front Microbiol (2014) 0.95
Synthetic Ecology of Microbes: Mathematical Models and Applications. J Mol Biol (2015) 0.88
Metabolic network modeling of microbial communities. Wiley Interdiscip Rev Syst Biol Med (2015) 0.83
Systems biology of host-microbe metabolomics. Wiley Interdiscip Rev Syst Biol Med (2015) 0.83
Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems. Front Microbiol (2016) 0.82
Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure. Front Microbiol (2015) 0.82
An Economic Framework of Microbial Trade. PLoS One (2015) 0.79
Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process. Biotechnol Biofuels (2016) 0.78
A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods. Microb Cell Fact (2015) 0.78
Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism. BMC Syst Biol (2017) 0.78
MMinte: an application for predicting metabolic interactions among the microbial species in a community. BMC Bioinformatics (2016) 0.77
Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis. Front Microbiol (2016) 0.77
Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment. BMC Evol Biol (2016) 0.77
From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems. Cell Mol Life Sci (2015) 0.76
Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community. PLoS Comput Biol (2015) 0.76
A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs. Biol Direct (2014) 0.76
From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the "terroir" Concept. Front Microbiol (2017) 0.76
A diverse community to study communities: integration of experiments and mathematical models to study microbial consortia. J Bacteriol (2017) 0.75
Model-based quantification of metabolic interactions from dynamic microbial-community data. PLoS One (2017) 0.75
Multiscale Model of Mycobacterium tuberculosis Infection Maps Metabolite and Gene Perturbations to Granuloma Sterilization Predictions. Infect Immun (2016) 0.75
Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function. Archaea (2017) 0.75
Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves. PLoS One (2016) 0.75
Constraint-based stoichiometric modelling from single organisms to microbial communities. J R Soc Interface (2016) 0.75
SteadyCom: Predicting microbial abundances while ensuring community stability. PLoS Comput Biol (2017) 0.75
A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems. PLoS One (2017) 0.75
Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine. Microbiome (2017) 0.75
Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects. PLoS One (2017) 0.75
Microbial ecology: human gut microbes associated with obesity. Nature (2006) 36.98
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol (2003) 10.46
Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol (2004) 9.61
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol (1994) 6.26
Applications of genome-scale metabolic reconstructions. Mol Syst Biol (2009) 5.54
Microbial community structure and its functional implications. Nature (2009) 4.23
Emergent biogeography of microbial communities in a model ocean. Science (2007) 4.03
Bug juice: harvesting electricity with microorganisms. Nat Rev Microbiol (2006) 3.57
Evolution of Escherichia coli during growth in a constant environment. Genetics (1987) 3.44
Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli. Genetics (1994) 3.19
Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys J (2002) 3.10
Metabolic modeling of a mutualistic microbial community. Mol Syst Biol (2007) 2.40
Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnol Bioeng (2002) 2.14
Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proc Natl Acad Sci U S A (2011) 2.05
Environments that induce synthetic microbial ecosystems. PLoS Comput Biol (2010) 2.04
Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol (2005) 2.03
Emergent cooperation in microbial metabolism. Mol Syst Biol (2010) 1.87
Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nat Biotechnol (2010) 1.85
Modelling cellular systems with PySCeS. Bioinformatics (2004) 1.74
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. ISME J (2010) 1.63
Diversity and dynamics of microbial communities in engineered environments and their implications for process stability. Curr Opin Biotechnol (2003) 1.63
OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comput Biol (2012) 1.48
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. BMC Syst Biol (2011) 1.37
Systems approaches to microbial communities and their functioning. Curr Opin Biotechnol (2010) 1.26
Computational systems biology and in silico modeling of the human microbiome. Brief Bioinform (2012) 1.15
Application of macroscopic principles to microbial metabolism. Biotechnol Bioeng (2009) 1.08
Stability of the bacterial communities supported by a seven-stage biological process treating pharmaceutical wastewater as revealed by PCR-DGGE. Water Res (2002) 1.01
Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing. Biotechnol J (2010) 1.01
Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks. Sci Rep (2012) 1.01
Metabolic modelling of syntrophic-like growth of a 1,3-propanediol producer, Clostridium butyricum, and a methanogenic archeon, Methanosarcina mazei, under anaerobic conditions. Bioprocess Biosyst Eng (2009) 0.93
Comparative life cycle assessment and financial analysis of mixed culture polyhydroxyalkanoate production. Bioresour Technol (2007) 0.90
A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities. BMC Syst Biol (2011) 0.90
A practical guide to genome-scale metabolic models and their analysis. Methods Enzymol (2011) 0.86
Towards metagenome-scale models for industrial applications--the case of Lactic Acid Bacteria. Curr Opin Biotechnol (2012) 0.85
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J Integr Bioinform (2015) 3.61
Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. Proc Natl Acad Sci U S A (2002) 3.18
Marine microorganisms make a meal of oil. Nat Rev Microbiol (2006) 3.15
Cancer: a Systems Biology disease. Biosystems (2006) 2.29
Shifts in growth strategies reflect tradeoffs in cellular economics. Mol Syst Biol (2009) 2.26
Retracted Population-level transcription cycles derive from stochastic timing of single-cell transcription. Cell (2009) 2.09
Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol (2005) 2.03
Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics (2006) 1.97
Lost in transition: start-up of glycolysis yields subpopulations of nongrowing cells. Science (2014) 1.96
Effects of sequestration on signal transduction cascades. FEBS J (2006) 1.84
Control of MAPK signalling: from complexity to what really matters. Oncogene (2005) 1.82
Principles behind the multifarious control of signal transduction. ERK phosphorylation and kinase/phosphatase control. FEBS J (2005) 1.71
CD36 deficiency increases insulin sensitivity in muscle, but induces insulin resistance in the liver in mice. J Lipid Res (2003) 1.54
Correlation between sequence conservation and the genomic context after gene duplication. Nucleic Acids Res (2005) 1.54
Increased hepatic insulin sensitivity together with decreased hepatic triglyceride stores in hormone-sensitive lipase-deficient mice. Endocrinology (2003) 1.47
Co-regulation of metabolic genes is better explained by flux coupling than by network distance. PLoS Comput Biol (2008) 1.46
Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features. PLoS One (2011) 1.25
StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes. PLoS One (2013) 1.25
Towards building the silicon cell: a modular approach. Biosystems (2005) 1.22
Microbial community structure and functioning along metal pollution gradients. Environ Toxicol Chem (2013) 1.20
Genome data mining of lactic acid bacteria: the impact of bioinformatics. Curr Opin Biotechnol (2004) 1.19
Community assembly, species richness and nestedness of arbuscular mycorrhizal fungi in agricultural soils. Mol Ecol (2012) 1.19
Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1. Microb Cell Fact (2007) 1.17
Systems biology: the elements and principles of life. FEBS Lett (2009) 1.17
Elongation dynamics shape bursty transcription and translation. Proc Natl Acad Sci U S A (2009) 1.16
Apolipoprotein C3 deficiency results in diet-induced obesity and aggravated insulin resistance in mice. Diabetes (2005) 1.11
Genome-scale model of Streptococcus thermophilus LMG18311 for metabolic comparison of lactic acid bacteria. Appl Environ Microbiol (2009) 1.10
Intestinal lipid absorption is not affected in CD36 deficient mice. Mol Cell Biochem (2002) 1.07
Systems biology towards life in silico: mathematics of the control of living cells. J Math Biol (2008) 1.06
Positive effects of organic farming on below-ground mutualists: large-scale comparison of mycorrhizal fungal communities in agricultural soils. New Phytol (2010) 1.06
FAME, the Flux Analysis and Modeling Environment. BMC Syst Biol (2012) 1.04
Predicting metabolic fluxes using gene expression differences as constraints. IEEE/ACM Trans Comput Biol Bioinform (2010) 1.03
The VLDL receptor plays a major role in chylomicron metabolism by enhancing LPL-mediated triglyceride hydrolysis. J Lipid Res (2004) 1.03
Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks. Sci Rep (2012) 1.01
Availability of public goods shapes the evolution of competing metabolic strategies. Proc Natl Acad Sci U S A (2013) 0.99
AmtB-mediated NH3 transport in prokaryotes must be active and as a consequence regulation of transport by GlnK is mandatory to limit futile cycling of NH4(+)/NH3. FEBS Lett (2010) 0.98
A critical view of metabolic network adaptations. HFSP J (2008) 0.98
Testing potential effects of maize expressing the Bacillus thuringiensis Cry1Ab endotoxin (Bt maize) on mycorrhizal fungal communities via DNA- and RNA-based pyrosequencing and molecular fingerprinting. Appl Environ Microbiol (2012) 0.97
Stratification and seasonal stability of diverse bacterial communities in a Pinus merkusii (pine) forest soil in central Java, Indonesia. Environ Microbiol (2002) 0.96
Bioinformatics and systems biology: bridging the gap between heterogeneous student backgrounds. Brief Bioinform (2013) 0.96
Standardized assay medium to measure Lactococcus lactis enzyme activities while mimicking intracellular conditions. Appl Environ Microbiol (2011) 0.95
The transport of triglycerides through the secretory pathway of hepatocytes is impaired in apolipoprotein E deficient mice. J Hepatol (2004) 0.94
Role of phosphate in the central metabolism of two lactic acid bacteria--a comparative systems biology approach. FEBS J (2012) 0.93
Understanding the physiology of Lactobacillus plantarum at zero growth. Mol Syst Biol (2010) 0.93
Restriction point control of the mammalian cell cycle via the cyclin E/Cdk2:p27 complex. FEBS J (2009) 0.93
Comparative systems biology: from bacteria to man. Wiley Interdiscip Rev Syst Biol Med (2010) 0.93
Effects of probiotic Lactobacillus salivarius W24 on the compositional stability of oral microbial communities. Arch Oral Biol (2008) 0.92
Effect of amino acid availability on vitamin B12 production in Lactobacillus reuteri. Appl Environ Microbiol (2009) 0.92
Molecular diversity and distribution of aromatic hydrocarbon-degrading anaerobes across a landfill leachate plume. Environ Microbiol (2011) 0.92
A strictly anaerobic betaproteobacterium Georgfuchsia toluolica gen. nov., sp. nov. degrades aromatic compounds with Fe(III), Mn(IV) or nitrate as an electron acceptor. FEMS Microbiol Ecol (2009) 0.92
Dominance of Geobacteraceae in BTX-degrading enrichments from an iron-reducing aquifer. FEMS Microbiol Ecol (2007) 0.91
A multivariate statistical approach to spatial representation of groundwater contamination using hydrochemistry and microbial community profiles. Environ Sci Technol (2005) 0.90
Microbial aspects of anaerobic BTEX degradation. Biomed Environ Sci (2002) 0.89
Stability and resilience of oral microcosms toward acidification and Candida outgrowth by arginine supplementation. Microb Ecol (2014) 0.89
A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803. Plant Physiol (2014) 0.89
How molecular competition influences fluxes in gene expression networks. PLoS One (2011) 0.88
Design principles of nuclear receptor signaling: how complex networking improves signal transduction. Mol Syst Biol (2010) 0.88
A specific mutation in the promoter region of the silent cel cluster accounts for the appearance of lactose-utilizing Lactococcus lactis MG1363. Appl Environ Microbiol (2012) 0.87
Phylogenetic and physiological diversity of dissimilatory ferric iron reducers in sediments of the polluted Scheldt estuary, Northwest Europe. Environ Microbiol (2007) 0.87
The influence of long-term copper contaminated agricultural soil at different pH levels on microbial communities and springtail transcriptional regulation. Environ Sci Technol (2011) 0.86
Functional identification in Lactobacillus reuteri of a PocR-like transcription factor regulating glycerol utilization and vitamin B12 synthesis. Microb Cell Fact (2011) 0.86
How Geobacteraceae may dominate subsurface biodegradation: physiology of Geobacter metallireducens in slow-growth habitat-simulating retentostats. Environ Microbiol (2009) 0.86
Functional ingredient production: application of global metabolic models. Curr Opin Biotechnol (2005) 0.86
A practical guide to genome-scale metabolic models and their analysis. Methods Enzymol (2011) 0.86
Eukaryotic diversity in an anaerobic aquifer polluted with landfill leachate. Appl Environ Microbiol (2008) 0.86
Geobacteraceae community composition is related to hydrochemistry and biodegradation in an iron-reducing aquifer polluted by a neighboring landfill. Appl Environ Microbiol (2005) 0.85
Systematic evaluation of bias in microbial community profiles induced by whole genome amplification. Environ Microbiol (2014) 0.85
Towards metagenome-scale models for industrial applications--the case of Lactic Acid Bacteria. Curr Opin Biotechnol (2012) 0.85
Metabolic control analysis to identify optimal drug targets. Prog Drug Res (2007) 0.85
JWS online cellular systems modelling and microbiology. Microbiology (2003) 0.84
Towards understanding inter-strain attachment variations of Escherichia coli during transport in saturated quartz sand. Water Res (2009) 0.84
MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis. Mol Biosyst (2014) 0.84
Sensitive life detection strategies for low-biomass environments: optimizing extraction of nucleic acids adsorbing to terrestrial and Mars analogue minerals. FEMS Microbiol Ecol (2012) 0.84
Reactive transport modelling of biogeochemical processes and carbon isotope geochemistry inside a landfill leachate plume. J Contam Hydrol (2004) 0.83
Metabolic shifts: a fitness perspective for microbial cell factories. Biotechnol Lett (2012) 0.83
Metabolic states with maximal specific rate carry flux through an elementary flux mode. FEBS J (2014) 0.83
Response of apolipoprotein E*3-Leiden transgenic mice to dietary fatty acids: combining liver proteomics with physiological data. FASEB J (2005) 0.82
Multi-tasking of biosynthetic and energetic functions of glycolysis explained by supply and demand logic. Bioessays (2014) 0.82
Spatial heterogeneity in sediment-associated bacterial and eukaryotic communities in a landfill leachate-contaminated aquifer. FEMS Microbiol Ecol (2008) 0.82
The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints. J Integr Bioinform (2015) 0.82
How biochemical constraints of cellular growth shape evolutionary adaptations in metabolism. Genetics (2013) 0.82
Optimization of stress response through the nuclear receptor-mediated cortisol signalling network. Nat Commun (2013) 0.82
Enzymes or redox couples? The kinetics of thioredoxin and glutaredoxin reactions in a systems biology context. Biochem J (2009) 0.82
Transcription stochasticity of complex gene regulation models. Biophys J (2012) 0.81
Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico. FEBS J (2012) 0.81
Acute inhibition of hepatic beta-oxidation in APOE*3Leiden mice does not affect hepatic VLDL secretion or insulin sensitivity. J Lipid Res (2005) 0.80
Basic concepts and principles of stoichiometric modeling of metabolic networks. Biotechnol J (2013) 0.80
Biogeochemistry and isotope geochemistry of a landfill leachate plume. J Contam Hydrol (2003) 0.80
Systems biology from micro-organisms to human metabolic diseases: the role of detailed kinetic models. Biochem Soc Trans (2010) 0.80
Microbial communities in the world's largest acidic volcanic lake, Kawah Ijen in Indonesia, and in the Banyupahit river originating from it. Microb Ecol (2006) 0.80