Networks of energetic and metabolic interactions define dynamics in microbial communities
|
journal
|
November 2015 |
Ecosystems biology of microbial metabolism
|
journal
|
August 2011 |
The phenomenon of microbial uncultivability
|
journal
|
October 2013 |
From Cell Differentiation to Cell Collectives: Bacillus subtilis Uses Division of Labor to Migrate
|
journal
|
April 2015 |
Environments that Induce Synthetic Microbial Ecosystems
|
journal
|
November 2010 |
Distributing a metabolic pathway among a microbial consortium enhances production of natural products
|
journal
|
January 2015 |
Extreme genome reduction in symbiotic bacteria
|
journal
|
November 2011 |
Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism
|
journal
|
August 2016 |
Analysis of fluorescent reporters indicates heterogeneity in glucose uptake and utilization in clonal bacterial populations
|
journal
|
January 2013 |
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
|
journal
|
August 2003 |
Metabolic modeling of a mutualistic microbial community
|
journal
|
January 2007 |
Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics
|
journal
|
May 2014 |
Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe
|
journal
|
July 2014 |
Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide
|
journal
|
September 2010 |
Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules
|
journal
|
July 2013 |
The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss
|
journal
|
March 2012 |
Division of Labor in Biofilms: the Ecology of Cell Differentiation
|
journal
|
April 2015 |
Precise manipulation of bacterial chromosomes by conjugative assembly genome engineering
|
journal
|
September 2014 |
Engineering microbial consortia for controllable outputs
|
journal
|
March 2016 |
Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss
|
journal
|
June 2018 |
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
|
journal
|
August 2011 |
NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species
|
journal
|
July 2012 |
Modeling central metabolism and energy biosynthesis across microbial life
|
journal
|
August 2016 |
A functional perspective on phenotypic heterogeneity in microorganisms
|
journal
|
July 2015 |
Escherichia coli alpha-ketoglutarate permease is a constitutively expressed proton symporter.
|
journal
|
March 1992 |
Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies
|
journal
|
April 2017 |
Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring
|
journal
|
November 2017 |
Close Interspecies Interactions between Prokaryotes from Sulfureous Environments
|
journal
|
January 2011 |
Repeated evolution of an acetate-crossfeeding polymorphism in long-term populations of Escherichia coli
|
journal
|
July 1998 |
Unusual cyanobacterial TCA cycles: not broken just different
|
journal
|
September 2012 |
Less is More: Selective Advantages can Explain the Prevalent loss of Biosynthetic Genes in Bacteria: Adaptive loss of Biosynthetic Genes in Bacteria
|
journal
|
July 2014 |
The dynamics of molecular evolution over 60,000 generations
|
journal
|
October 2017 |
The E. coli molecular phenotype under different growth conditions
|
journal
|
April 2017 |
Syntrophic exchange in synthetic microbial communities
|
journal
|
April 2014 |
Using Genome-scale Models to Predict Biological Capabilities
|
journal
|
May 2015 |
Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction: COMMUNITY DATA-DRIVEN METABOLIC NETWORK MODELING
|
journal
|
June 2016 |
Sampling for Metabolome Analysis of Microorganisms
|
journal
|
May 2007 |
Metabolic interactions in microbial communities: untangling the Gordian knot
|
journal
|
October 2015 |
Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia
|
journal
|
February 2018 |
Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity
|
journal
|
January 2012 |
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
|
journal
|
November 2016 |
Competitive and cooperative metabolic interactions in bacterial communities
|
journal
|
September 2011 |
Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities
|
journal
|
November 2017 |
Optimal allocation of metabolic functions among organisms in a microbial ecosystem
|
conference
|
December 2016 |
A Programmable Escherichia coli Consortium via Tunable Symbiosis
|
journal
|
March 2012 |
Quantitative flux coupling analysis
|
journal
|
December 2018 |
Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA
|
journal
|
March 2017 |
Variation and evolution of the citric-acid cycle: a genomic perspective
|
journal
|
July 1999 |
Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli
|
journal
|
December 2017 |
Long-Term Experimental Evolution in Escherichia coli. XIII. Phylogenetic History of a Balanced Polymorphism
|
journal
|
June 2005 |
Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota
|
journal
|
September 2018 |
Novel Cooperation Experimentally Evolved Between Species
|
journal
|
February 2010 |
Tricarboxylic Acid Cycle and Glyoxylate Bypass
|
journal
|
July 2005 |
Design and analysis of synthetic carbon fixation pathways
|
journal
|
April 2010 |
Sequence homologies between proteins of bacterial phosphoenolpyruvate-dependent sugar phosphotransferase systems: identification of possible phosphate-carrying histidine residues.
|
journal
|
July 1987 |
Bacterial Unculturability and the Formation of Intercellular Metabolic Networks
|
journal
|
May 2017 |
Emergent cooperation in microbial metabolism
|
journal
|
January 2010 |
Metabolic Changes Associated With Adaptive Diversification in Escherichia coli
|
journal
|
February 2008 |
Metabolic dependencies drive species co-occurrence in diverse microbial communities
|
journal
|
May 2015 |
Oxygen-regulated gene expression in Escherichia coli: (Delivered at the 122nd Ordinary Meeting of the Society for General Microbiology, 25 March 1992)
|
journal
|
November 1992 |
Experimental Evidence for Sympatric Ecological Diversification due to Frequency-Dependent Competition in Escherichia coli
|
journal
|
January 2004 |
Snowdrift game dynamics and facultative cheating in yeast
|
journal
|
April 2009 |
Stochastic Gene Expression in a Single Cell
|
journal
|
August 2002 |
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
|
journal
|
October 2015 |
The Incomplete Tricarboxylic Acid Cycle in the Blue-green Alga Anabaena Variabilis
|
journal
|
March 1969 |
Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms
|
journal
|
January 2012 |
From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints
|
journal
|
April 2017 |
Programming cells by multiplex genome engineering and accelerated evolution
|
journal
|
July 2009 |
Metabolic division of labor in microbial systems
|
journal
|
February 2018 |
Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species
|
journal
|
October 2016 |
Emergent Biosynthetic Capacity in Simple Microbial Communities
|
journal
|
July 2014 |
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities
|
journal
|
February 2012 |
Bayesian metabolic flux analysis reveals intracellular flux couplings
|
journal
|
July 2019 |
Metabolic interactions between dynamic bacterial subpopulations
|
journal
|
May 2018 |
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
|
journal
|
October 2003 |
Adaptive Diversification in Genes That Regulate Resource Use in Escherichia coli
|
journal
|
January 2007 |
The PEP—pyruvate—oxaloacetate node as the switch point for carbon flux distribution in bacteria: We dedicate this paper to Rudolf K. Thauer, Director of the Max-Planck-Institute for Terrestrial Microbiology in Marburg, Germany, on the occasion of his 65th birthday
|
journal
|
September 2005 |
New approach for understanding genome variations in KEGG
|
journal
|
October 2018 |
Systematic changes in gene expression patterns following adaptive evolution in yeast
|
journal
|
August 1999 |
The Importance of Compartmentalization in Metabolic flux Models: Yeast as an Ecosystem of Organelles
|
conference
|
January 2012 |
Adaptation increases the likelihood of diversification in an experimental bacterial lineage
|
journal
|
January 2008 |
Flux Coupling Analysis of Genome-Scale Metabolic Network Reconstructions
|
journal
|
February 2004 |
Development and application of a differential method for reliable metabolome analysis in Escherichia coli
|
journal
|
March 2009 |
Synthetic cooperation in engineered yeast populations
|
journal
|
January 2007 |
Metabolic network modeling of microbial communities: Metabolic network modeling
- Biggs, Matthew B.; Medlock, Gregory L.; Kolling, Glynis L.
-
Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Vol. 7, Issue 5
https://doi.org/10.1002/wsbm.1308
|
journal
|
June 2015 |
Community Flux Balance Analysis for Microbial Consortia at Balanced Growth
|
journal
|
May 2013 |
Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow
|
journal
|
October 2017 |
Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli.
|
journal
|
August 1994 |
Synthetic Ecology of Microbes: Mathematical Models and Applications
|
journal
|
February 2016 |
Genomics and Evolution of Heritable Bacterial Symbionts
|
journal
|
December 2008 |
Long‐Term Experimental Evolution in Escherichia coli . VIII. Dynamics of a Balanced Polymorphism
|
journal
|
January 2000 |
From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota
|
journal
|
March 2018 |
Overflow metabolism in Escherichia coli results from efficient proteome allocation
|
journal
|
December 2015 |
Biogeography, Evolution, and Diversity of Epibionts in Phototrophic Consortia
|
journal
|
August 2004 |
F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks
|
journal
|
April 2012 |
Sugar Synthesis from CO2 in Escherichia coli
|
journal
|
June 2016 |
NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation
|
journal
|
May 2015 |
Multiplex Genome Engineering Using CRISPR/Cas Systems
|
journal
|
January 2013 |
Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation
|
journal
|
June 2003 |
A challenge for 21st century molecular biology and biochemistry: what are the causes of obligate autotrophy and methanotrophy?
|
journal
|
June 2004 |
Building a morbidostat: an automated continuous-culture device for studying bacterial drug resistance under dynamically sustained drug inhibition
|
journal
|
February 2013 |
Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria
|
journal
|
November 2013 |