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References from In silico identification of switching nodes in metabolic networks. Local targets link to admitted publications; unresolved targets remain external evidence.
The paradoxes hidden behind the Droop model highlighted by a metabolic approach
10.3389/fpls.2022.941230 · 2022 · External reference
DRUM: A New Framework for Metabolic Modeling under Non-Balanced Growth. Application to the Carbon Metabolism of Unicellular Microalgae
10.1371/journal.pone.0104499 · 2014 · External reference
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis
10.1186/s13059-021-02289-z · 2021 · External reference
Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
10.1073/pnas.1811971115 · 2018 · External reference
Flux coupling analysis of genome-scale metabolic network reconstructions
10.1101/gr.1926504 · 2004 · External reference
A computational method to identify key players in metabolic rewiring
10.24072/pci.mcb.100193 · 2024 · External reference
Coordination of microbial metabolism
10.1038/nrmicro3238 · 2014 · External reference
Reconstructing organisms in silico: genome-scale models and their emerging applications
10.1038/s41579-020-00440-4 · 2020 · External reference
A genome-scale metabolic reconstruction for it Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
10.1038/msb4100155 · 2007 · External reference
Resource allocation in living organisms
10.1042/bst20160436 · 2017 · External reference
Current status and applications of genome-scale metabolic models
10.1186/s13059-019-1730-3 · 2019 · External reference
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
10.1038/s41596-018-0098-2 · 2019 · External reference
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
10.1038/nbt1492 · 2008 · External reference
Flux balance analysis of primary metabolism in the diatom it Phaeodactylum tricornutum
10.1111/tpj.13081 · 2016 · External reference
Metabolite essentiality elucidates robustness of Escherichia coli metabolism
10.1073/pnas.0703262104 · 2007 · External reference
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
10.1371/journal.pcbi.1004321 · 2015 · External reference
An Introduction to Metabolic Networks and Their Structural Analysis
10.1109/tcbb.2008.79 · 2008 · External reference
Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks
10.7717/peerj.3860 · 2017 · External reference
Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models
10.1038/msb.2010.47 · 2010 · External reference
The connectivity structure, giant strong component and centrality of metabolic networks
10.1093/bioinformatics/btg177 · 2003 · External reference
fmairet/ISIS: In silico identification of switching nodes. Version v1.0
10.5281/zenodo.13951432 · 2024 · External reference
optGpSampler: an improved tool for uniformly sampling the solution-space of genome-scale metabolic networks
10.1371/journal.pone.0086587 · 2014 · External reference
Using genome-scale models to predict biological capabilities
10.1016/j.cell.2015.05.019 · 2015 · External reference
Reconstruction and use of microbial metabolic networks: the core it Escherichia coli metabolic model as an educational guide
10.1128/ecosalplus.10.2.1 · 2010 · External reference
What is flux balance analysis?
10.1038/nbt.1614 · 2010 · External reference
Uncovering transcriptional regulation of metabolism by using metabolic network topology
10.1073/pnas.0406811102 · 2005 · External reference
Integrating –omics data into genome-scale metabolic network models: principles and challenges
10.1042/ebc20180011 · 2018 · External reference
Comparison of different approaches for identifying subnetworks in metabolic networks
10.1142/s0219720017500251 · 2017 · External reference
A metabolite-centric view on flux distributions in genome-scale metabolic models
10.1186/1752-0509-7-33 · 2013 · External reference
The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria
10.1016/j.femsre.2004.11.002 · 2005 · External reference
Global transcriptional and physiological responses of it Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation
10.1128/aem.00548-06 · 2006 · External reference
Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling
10.1093/bib/bbx053 · 2017 · External reference
The small world inside large metabolic networks
10.1098/rspb.2001.1711 · 2001 · External reference
Experimental methods for dissecting the it terraincognita of protein-metabolite interactomes
10.1016/j.coisb.2021.100403 · 2021 · External reference
Understanding and mathematical modelling of cellular resource allocation in microorganisms: a comparative synthesis
10.1186/s12859-021-04382-3 · 2021 · External reference
