| scholarly article | Q13442814 |
| P50 | author | William Riehl | Q59113749 |
| Alex Betts | Q63976455 | ||
| P2093 | author name string | Daniel Segrè | |
| Christopher J Marx | |||
| William R Harcombe | |||
| Pankaj Mehta | |||
| Nicholas Leiby | |||
| Alex H Lang | |||
| Brian R Granger | |||
| Gracia Bonilla | |||
| Amrita Kar | |||
| Ilija Dukovski | |||
| P2860 | cites work | Environments that induce synthetic microbial ecosystems | Q21563487 |
| Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection | Q22122301 | ||
| Estimating prokaryotic diversity and its limits | Q24533538 | ||
| Physics of chemoreception | Q24546294 | ||
| Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction | Q24649162 | ||
| Improvement of Escherichia coli production strains by modification of the phosphoenolpyruvate:sugar phosphotransferase system | Q24811419 | ||
| Metabolic and demographic feedbacks shape the emergent spatial structure and function of microbial communities | Q27323496 | ||
| Analysis of optimality in natural and perturbed metabolic networks | Q28213254 | ||
| Diversity, stability and resilience of the human gut microbiota | Q28274959 | ||
| What is flux balance analysis? | Q28275348 | ||
| High-throughput generation, optimization and analysis of genome-scale metabolic models | Q28291992 | ||
| Context-specific metabolic networks are consistent with experiments | Q28472711 | ||
| Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes | Q28474850 | ||
| A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks | Q28480577 | ||
| Community flux balance analysis for microbial consortia at balanced growth | Q28533513 | ||
| Flux imbalance analysis and the sensitivity of cellular growth to changes in metabolite pools | Q28536139 | ||
| Microdroplet-enabled highly parallel co-cultivation of microbial communities | Q28742380 | ||
| The human microbiome project | Q29547661 | ||
| An ecological and evolutionary perspective on human-microbe mutualism and disease | Q29614265 | ||
| Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors | Q31096211 | ||
| Development of a broad-host-range sacB-based vector for unmarked allelic exchange | Q33361018 | ||
| Population dynamics constrain the cooperative evolution of cross-feeding | Q33398050 | ||
| Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments | Q33585784 | ||
| An integrative approach to understanding microbial diversity: from intracellular mechanisms to community structure | Q33615178 | ||
| Rapid evolution of stability and productivity at the origin of a microbial mutualism | Q33719701 | ||
| A hybrid cellular automaton model of clonal evolution in cancer: the emergence of the glycolytic phenotype | Q33757776 | ||
| OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities | Q34154442 | ||
| Integrating flux balance analysis into kinetic models to decipher the dynamic metabolism of Shewanella oneidensis MR-1. | Q34154452 | ||
| Dynamic flux balance analysis of diauxic growth in Escherichia coli | Q34178626 | ||
| Ecosystems biology of microbial metabolism | Q34185936 | ||
| A programmable Escherichia coli consortium via tunable symbiosis | Q34221950 | ||
| Diversity of interaction types and ecological community stability | Q34289711 | ||
| An evolutionary scenario for the transition to undifferentiated multicellularity | Q34329059 | ||
| The evolution of cooperation. | Q34330940 | ||
| Temporal expression-based analysis of metabolism | Q34499316 | ||
| Resource competition and social conflict in experimental populations of yeast | Q34530526 | ||
| Development of an optimized medium, strain and high-throughput culturing methods for Methylobacterium extorquens | Q34706940 | ||
| Glucose Availability and the Growth Rate of Colonies of Pseudomonas fluorescens | Q69383279 | ||
| The influence of nutrition and temperature on the growth of colonies of Escherichia coli K12 | Q70187996 | ||
| Oxygen profiles in, and in the agar beneath, colonies of Bacillus cereus, Staphylococcus albus and Escherichia coli | Q70360126 | ||
| Penetration of oxygen into bacterial colonies | Q70445543 | ||
| Growth Measurements on Surface Colonies of Bacteria | Q71828147 | ||
| A kinetic study of the mode of growth of surface colonies of bacteria and fungi | Q72273562 | ||
| The microbial engines that drive Earth's biogeochemical cycles. | Q34780678 | ||
| The ability of flux balance analysis to predict evolution of central metabolism scales with the initial distance to the optimum | Q34789242 | ||
| Diffusion in biofilms | Q35068179 | ||
| Cooperation and conflict in microbial biofilms. | Q35612336 | ||
| Synthetic cooperation in engineered yeast populations | Q35629292 | ||
| Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem | Q35669722 | ||
| Metabolic modeling of a mutualistic microbial community. | Q35742362 | ||
| A quantitative test of population genetics using spatiogenetic patterns in bacterial colonies. | Q36063708 | ||
| A synthetic Escherichia coli predator-prey ecosystem | Q36663520 | ||
| Mass spectrometry imaging for in situ kinetic histochemistry | Q36764431 | ||
| Defined spatial structure stabilizes a synthetic multispecies bacterial community | Q36984976 | ||
| Imaging mass spectrometry in microbiology | Q37009407 | ||
| Spatial-temporal modelling of bacterial colony growth on solid media | Q37147803 | ||
| Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation. | Q37274785 | ||
| The expanding world of methylotrophic metabolism | Q37514133 | ||
| AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. | Q37694285 | ||
| Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli | Q38103147 | ||
| Competitive and cooperative metabolic interactions in bacterial communities. | Q39676882 | ||
| The Growth and Form of Bacterial Colonies | Q39714941 | ||
| The Three-Species Consortium of Genetically Improved Strains Cupriavidus necator RW112, Burkholderia xenovorans RW118, and Pseudomonas pseudoalcaligenes RW120 Grows with Technical Polychlorobiphenyl, Aroclor 1242 | Q40497732 | ||
| A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. | Q40519259 | ||
| Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources | Q41944754 | ||
| Emergent cooperation in microbial metabolism | Q42397954 | ||
| Stress and survival of aging Escherichia coli rpoS colonies | Q42922063 | ||
| Genome‐scale metabolic modeling of a clostridial co‐culture for consolidated bioprocessing | Q42954180 | ||
| Novel cooperation experimentally evolved between species | Q43184570 | ||
| Multidimensional optimality of microbial metabolism | Q43431493 | ||
| Cooperative organization of bacterial colonies: from genotype to morphotype | Q50127988 | ||
| A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks. | Q51523815 | ||
| Hybrid cellular automaton modeling of nutrient modulated cell growth in tissue engineering constructs. | Q51787084 | ||
| A framework for multidimensional modelling of activity and structure of multispecies biofilms. | Q51969475 | ||
| Individual-based modelling of biofilms. | Q52051890 | ||
| BacSim, a simulator for individual-based modelling of bacterial colony growth. | Q52227664 | ||
| Stability and complexity in model ecosystems. | Q52956176 | ||
| Factors affecting the growth of bacterial colonies on agar plates. | Q54692233 | ||
| Growth of yeast colonies on solid media | Q68085248 | ||
| P433 | issue | 4 | |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | ecosystem | Q37813 |
| spatial dynamics | Q123709600 | ||
| P6104 | maintained by WikiProject | WikiProject Ecology | Q10818384 |
| P304 | page(s) | 1104-1115 | |
| P577 | publication date | 2014-05-01 | |
| P1433 | published in | Cell Reports | Q5058165 |
| P1476 | title | Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics | |
| P478 | volume | 7 |
| Q38770026 | A Diverse Community To Study Communities: Integration of Experiments and Mathematical Models To Study Microbial Consortia |
| Q46258716 | A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites |
| Q89866016 | A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns |
| Q92672373 | A multidimensional perspective on microbial interactions |
| Q47888411 | A multiscale agent-based framework integrated with a constraint-based metabolic network model of cancer for simulating avascular tumor growth. |
| Q90207952 | A shared limiting resource leads to competitive exclusion in a cross-feeding system |
| Q46317858 | A systems-wide understanding of photosynthetic acclimation in algae and higher plants |
| Q95840488 | ACBM: An Integrated Agent and Constraint Based Modeling Framework for Simulation of Microbial Communities |
| Q42365828 | Adding biotic complexity alters the metabolic benefits of mutualism |
| Q36041733 | Advancing microbial sciences by individual-based modelling |
| Q35723074 | An Economic Framework of Microbial Trade |
| Q37036063 | An algorithm for designing minimal microbial communities with desired metabolic capacities |
| Q90442733 | An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment |
| Q64272355 | Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities |
| Q36377654 | BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities |
| Q92175325 | Behavioral heterogeneity in quorum sensing can stabilize social cooperation in microbial populations |
| Q46298707 | Biophysical processes supporting the diversity of microbial life in soil |
| Q35810400 | Calibration and analysis of genome-based models for microbial ecology |
| Q36124640 | Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods |
| Q38376483 | Challenges in microbial ecology: building predictive understanding of community function and dynamics |
| Q59830697 | Challenges in modeling the human gut microbiome |
| Q92663025 | Challenges of biofilm control and utilization: lessons from mathematical modelling |
| Q89980591 | Coexistence and cooperation in structured habitats |
| Q90242627 | Common principles and best practices for engineering microbiomes |
| Q39042756 | Community metabolic modeling approaches to understanding the gut microbiome: Bridging biochemistry and ecology |
| Q47164018 | Computational Approaches for Integrative Analysis of the Metabolome and Microbiome |
| Q36063811 | Constrained Allocation Flux Balance Analysis |
| Q39196318 | Constraint-based stoichiometric modelling from single organisms to microbial communities. |
| Q39266251 | Cooperation in microbial communities and their biotechnological applications. |
| Q64226353 | Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems |
| Q42379525 | Coupling between distant biofilms and emergence of nutrient time-sharing. |
| Q89508376 | Cross-feeding modulates antibiotic tolerance in bacterial communities |
| Q38897029 | Decoding molecular interactions in microbial communities |
| Q64064531 | Designing Metabolic Division of Labor in Microbial Communities |
| Q96577379 | Dissimilarity-Overlap analysis of replicate enrichment communities |
| Q58611287 | Early Changes in Nutritional Conditions Affect Formation of Synthetic Mutualism Between Chlorella sorokiniana and the Bacterium Azospirillum brasilense |
| Q35124389 | Ecological perspectives on synthetic biology: insights from microbial population biology. |
| Q60503746 | Effective models and the search for quantitative principles in microbial evolution |
| Q64930843 | Efficient assembly and long-term stability of defensive microbiomes via private resources and community bistability. |
| Q36373474 | Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism. |
| Q64295977 | Emergent Subpopulation Behavior Uncovered with a Community Dynamic Metabolic Model of Diauxic Growth |
| Q61797478 | Engineering microbial consortia by division of labor |
| Q98394817 | Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community |
| Q92982102 | Environmentally Mediated Social Dilemmas |
| Q62085670 | Evolution of bacterial trade in a two-species community |
| Q57805492 | Evolution of bidirectional costly mutualism from byproduct consumption |
| Q46250203 | Evolution on the bright side of life: microorganisms and the evolution of mutualism |
| Q58757809 | FLYCOP: metabolic modeling-based analysis and engineering microbial communities |
| Q26823314 | Fermented foods as experimentally tractable microbial ecosystems |
| Q91782230 | Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture |
| Q46217511 | From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality |
| Q52337391 | From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota. |
| Q97521221 | From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes |
| Q26800805 | From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems |
| Q46259934 | Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities. |
| Q38651067 | Genome-scale modelling of microbial metabolism with temporal and spatial resolution |
| Q98196772 | Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation |
| Q33786338 | Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis. |
| Q41889233 | Growth Trade-Offs Accompany the Emergence of Glycolytic Metabolism in Shewanella oneidensis MR-1. |
| Q30252921 | Growth-altering microbial interactions are responsive to chemical context |
| Q57012017 | Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe |
| Q57805738 | Human gut microbe co-cultures have greater potential than monocultures for food waste remediation to commodity chemicals |
| Q63383919 | Identification of bioactive metabolites using activity metabolomics |
| Q36368892 | Identification of the potentiating mutations and synergistic epistasis that enabled the evolution of inter-species cooperation |
| Q50868052 | In a quest for engineering acidophiles for biomining applications: challenges and opportunities. |
| Q36016966 | In silico substrate dependence increases community productivity but threatens biodiversity |
| Q57423229 | Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota |
| Q45984806 | Integrated Host-Pathogen Metabolic Reconstructions. |
| Q55204737 | Interactions mediated by a public good transiently increase cooperativity in growing Pseudomonas putida metapopulations. |
| Q57165376 | Interkingdom microbial consortia mechanisms to guide biotechnological applications |
| Q60213391 | Interrogating metabolism as an electron flow system |
| Q38763272 | Limitations of a metabolic network-based reverse ecology method for inferring host-pathogen interactions |
| Q90441826 | Lytic bacteriophage have diverse indirect effects in a synthetic cross-feeding community |
| Q35764339 | MICROBIOME. Microbial growth dynamics and human disease |
| Q37228280 | MMinte: an application for predicting metabolic interactions among the microbial species in a community. |
| Q58704192 | Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks |
| Q34616367 | Mapping the inner workings of the microbiome: genomic- and metagenomic-based study of metabolism and metabolic interactions in the human microbiome |
| Q92666481 | Massively parallel screening of synthetic microbial communities |
| Q61447420 | Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview |
| Q26744686 | Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems |
| Q55333463 | Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss. |
| Q36125643 | Metabolic modeling of a chronic wound biofilm consortium predicts spatial partitioning of bacterial species |
| Q38992090 | Metabolic modeling of synthesis gas fermentation in bubble column reactors |
| Q37192595 | Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment |
| Q98772179 | Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community |
| Q30279122 | Metabolic network modeling of microbial communities |
| Q83231503 | Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome |
| Q90571703 | Metabolically cohesive microbial consortia and ecosystem functioning |
| Q57165373 | Metabolism in dense microbial colonies: C metabolic flux analysis of E. coli grown on agar identifies two distinct cell populations with acetate cross-feeding |
| Q47686035 | Metabolite toxicity slows local diversity loss during expansion of a microbial cross-feeding community. |
| Q92509246 | Microbial carbon use efficiency predicted from genome-scale metabolic models |
| Q52340077 | Microbial interactions within the plant holobiont. |
| Q36277892 | Microstencils to generate defined, multi-species patterns of bacteria |
| Q40034903 | Model-based media selection to minimize the cost of metabolic cooperation in microbial ecosystems |
| Q92876693 | Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH) |
| Q57021885 | Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions |
| Q46254261 | Monitoring microbial communities using light sheet fluorescence microscopy |
| Q39433303 | More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes |
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