A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)
出版年份 2021 全文链接
标题
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)
作者
关键词
-
出版物
Nature Protocols
Volume 16, Issue 11, Pages 5030-5082
出版商
Springer Science and Business Media LLC
发表日期
2021-10-12
DOI
10.1038/s41596-021-00593-3
参考文献
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。- Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of Prochlorococcus
- (2021) Shany Ofaim et al. Frontiers in Genetics
- Non-additive microbial community responses to environmental complexity
- (2021) Alan R. Pacheco et al. Nature Communications
- MEMOTE for standardized genome-scale metabolic model testing
- (2020) Christian Lieven et al. NATURE BIOTECHNOLOGY
- Bridging substrate intake kinetics and bacterial growth phenotypes with flux balance analysis incorporating proteome allocation
- (2020) Hong Zeng et al. Scientific Reports
- Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems
- (2019) Alan R. Pacheco et al. Nature Communications
- Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
- (2019) Laurent Heirendt et al. Nature Protocols
- The Integrative Human Microbiome Project
- (2019) NATURE
- Massively parallel screening of synthetic microbial communities
- (2019) Jared Kehe et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)
- (2019) Benedict Borer et al. PLoS Computational Biology
- On the growth of non-motile bacteria colonies: an agent-based model for pattern formation
- (2019) Lautaro Vassallo et al. EUROPEAN PHYSICAL JOURNAL B
- Global Trends in Marine Plankton Diversity across Kingdoms of Life
- (2019) Federico M. Ibarbalz et al. CELL
- Microbial carbon use efficiency predicted from genome-scale metabolic models
- (2019) Mustafa Saifuddin et al. Nature Communications
- OUP accepted manuscript
- (2018) BIOINFORMATICS
- Modeling metabolism of the human gut microbiome
- (2018) Stefanía Magnúsdóttir et al. CURRENT OPINION IN BIOTECHNOLOGY
- The spatial and metabolic basis of colony size variation
- (2018) Jeremy M. Chacón et al. ISME Journal
- Deciphering microbial interactions in synthetic human gut microbiome communities
- (2018) Ophelia S Venturelli et al. Molecular Systems Biology
- KBase: The United States Department of Energy Systems Biology Knowledgebase
- (2018) Adam P Arkin et al. NATURE BIOTECHNOLOGY
- Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
- (2018) Daniel Machado et al. NUCLEIC ACIDS RESEARCH
- Diffusion-Limited Growth of Microbial Colonies
- (2018) Hayden Tronnolone et al. Scientific Reports
- Emergent simplicity in microbial community assembly
- (2018) Joshua E. Goldford et al. SCIENCE
- A shared limiting resource leads to competitive exclusion in a cross-feeding system
- (2018) Sarah P. Hammarlund et al. ENVIRONMENTAL MICROBIOLOGY
- Evolution of bidirectional costly mutualism from byproduct consumption
- (2018) William R. Harcombe et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- On the deformability of an empirical fitness landscape by microbial evolution
- (2018) Djordje Bajić et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks
- (2018) Demetrius DiMucci et al. mSystems
- The microbial habitat in soil: Scale, heterogeneity and functional consequences
- (2017) Naoise Nunan JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE
- The evolution of the host microbiome as an ecosystem on a leash
- (2017) Kevin R. Foster et al. NATURE
- A communal catalogue reveals Earth’s multiscale microbial diversity
- (2017) Luke R. Thompson et al. NATURE
- Investment in secreted enzymes during nutrient-limited growth is utility dependent
- (2017) Brent Cezairliyan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A New Improved and Extended Version of the Multicell Bacterial Simulator gro
- (2017) Martín Gutiérrez et al. ACS Synthetic Biology
- BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
- (2017) Eugen Bauer et al. PLoS Computational Biology
- Spatiotemporal modeling of microbial metabolism
- (2016) Jin Chen et al. BMC Systems Biology
- Principles for designing synthetic microbial communities
- (2016) Nathan I Johns et al. CURRENT OPINION IN MICROBIOLOGY
- Challenges in microbial ecology: building predictive understanding of community function and dynamics
- (2016) Stefanie Widder et al. ISME Journal
- Constraint-based stoichiometric modelling from single organisms to microbial communities
- (2016) Willi Gottstein et al. Journal of the Royal Society Interface
- The evolution of cooperation within the gut microbiota
- (2016) Seth Rakoff-Nahoum et al. NATURE
- Spatial structure, cooperation and competition in biofilms
- (2016) Carey D. Nadell et al. NATURE REVIEWS MICROBIOLOGY
- Constrained Allocation Flux Balance Analysis
- (2016) Matteo Mori et al. PLoS Computational Biology
- Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities
- (2016) Sebastian Germerodt et al. PLoS Computational Biology
- Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus
- (2016) John R. Casey et al. mSystems
- A Model of Extracellular Enzymes in Free-Living Microbes: Which Strategy Pays Off?
- (2015) Sachia J. Traving et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Spatially-resolved metabolic cooperativity within dense bacterial colonies
- (2015) John A Cole et al. BMC Systems Biology
- Using Genome-scale Models to Predict Biological Capabilities
- (2015) Edward J. O’Brien et al. CELL
- Branching instability in expanding bacterial colonies
- (2015) C. Giverso et al. Journal of the Royal Society Interface
- BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
- (2015) Zachary A. King et al. NUCLEIC ACIDS RESEARCH
- Metabolic dependencies drive species co-occurrence in diverse microbial communities
- (2015) Aleksej Zelezniak et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The global ocean microbiome
- (2015) M. A. Moran SCIENCE
- Rhizosphere interactions: root exudates, microbes, and microbial communities
- (2014) Xing-Feng Huang et al. Botany
- Synthetic microbial communities
- (2014) Tobias Großkopf et al. CURRENT OPINION IN MICROBIOLOGY
- Dynamic flux balance analysis for synthetic microbial communities
- (2014) Michael A. Henson et al. IET Systems Biology
- Constraint-based models predict metabolic and associated cellular functions
- (2014) Aarash Bordbar et al. NATURE REVIEWS GENETICS
- Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics
- (2014) William R. Harcombe et al. Cell Reports
- An objective function exploiting suboptimal solutions in metabolic networks
- (2013) Edwin H Wintermute et al. BMC Systems Biology
- COBRApy: COnstraints-Based Reconstruction and Analysis for Python
- (2013) Ali Ebrahim et al. BMC Systems Biology
- An Ecological Network of Polysaccharide Utilization among Human Intestinal Symbionts
- (2013) Seth Rakoff-Nahoum et al. CURRENT BIOLOGY
- Mechanically Driven Growth of Quasi-Two-Dimensional Microbial Colonies
- (2013) F. D. C. Farrell et al. PHYSICAL REVIEW LETTERS
- Community Flux Balance Analysis for Microbial Consortia at Balanced Growth
- (2013) Ruchir A. Khandelwal et al. PLoS One
- Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm Formation
- (2013) Matthew B. Biggs et al. PLoS One
- A reliable simulator for dynamic flux balance analysis
- (2012) K. Höffner et al. BIOTECHNOLOGY AND BIOENGINEERING
- Diversity, stability and resilience of the human gut microbiota
- (2012) Catherine A. Lozupone et al. NATURE
- OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities
- (2012) Ali R. Zomorrodi et al. PLoS Computational Biology
- Fundamentals of Microbial Community Resistance and Resilience
- (2012) Ashley Shade et al. Frontiers in Microbiology
- Cell design in bacteria as a convex optimization problem
- (2011) Anne Goelzer et al. AUTOMATICA
- Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data
- (2011) Ali R Zomorrodi et al. BMC Systems Biology
- A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities
- (2011) Eleftheria Tzamali et al. BMC Systems Biology
- Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures
- (2010) Timothy J. Hanly et al. BIOTECHNOLOGY AND BIOENGINEERING
- The biomass objective function
- (2010) Adam M Feist et al. CURRENT OPINION IN MICROBIOLOGY
- Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
- (2010) Kai Zhuang et al. ISME Journal
- Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models
- (2010) Nathan E Lewis et al. Molecular Systems Biology
- What is flux balance analysis?
- (2010) Jeffrey D Orth et al. NATURE BIOTECHNOLOGY
- A protocol for generating a high-quality genome-scale metabolic reconstruction
- (2010) Ines Thiele et al. Nature Protocols
- Genetic demixing and evolution in linear stepping stone models
- (2010) K. S. Korolev et al. REVIEWS OF MODERN PHYSICS
- Manufacturing Molecules Through Metabolic Engineering
- (2010) J. D. Keasling SCIENCE
- Metabolomics of recombinant yeast: Gene expression, flux analysis and a mathematical model for gene regulation of metabolism
- (2008) J.A. Asenjo et al. JOURNAL OF BIOTECHNOLOGY
- Resistance, resilience, and redundancy in microbial communities
- (2008) S. D. Allison et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Context-Specific Metabolic Networks Are Consistent with Experiments
- (2008) Scott A. Becker et al. PLoS Computational Biology
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now