Research graph
References from A compact model of Escherichia coli core and biosynthetic metabolism. Local targets link to admitted publications; unresolved targets remain external evidence.
Engineering microbial chemical factories using metabolic models
10.1186/s42480-019-0021-9 · 2019 · External reference
Current status and applications of genome-scale metabolic models
10.1186/s13059-019-1730-3 · 2019 · External reference
In silico cell factory design driven by comprehensive genome-scale metabolic models: development and challenges
10.1007/s43393-022-00117-4 · 2022 · External reference
Reconstructing organisms in silico: genome-scale models and their emerging applications
10.1038/s41579-020-00440-4 · 2020 · External reference
Thirteen years of building constraint-based in silico models of Escherichia coli
10.1128/jb.185.9.2692-2699.2003 · 2003 · External reference
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
10.1038/msb4100155 · 2007 · External reference
A comprehensive genome-scale reconstruction of Escherichia coli metabolism–2011
10.1038/msb.2011.65 · 2011 · External reference
iML1515, a knowledgebase that computes Escherichia coli traits
10.1038/nbt.3956 · 2017 · External reference
Evaluating E. coli genome-scale metabolic model accuracy with high-throughput mutant fitness data
10.15252/msb.202311566 · 2023 · External reference
An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli
10.1016/j.ymben.2020.03.002 · 2020 · External reference
Awakening a latent carbon fixation cycle in Escherichia coli
10.1038/s41467-020-19564-5 · 2020 · External reference
Flux sampling and context-specific genome-scale metabolic models for biotechnological applications
2025 · External reference
Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield
10.1371/journal.pcbi.1006010 · 2018 · External reference
Thermodynamics-based metabolic flux analysis
10.1529/biophysj.106.093138 · 2007 · External reference
Reconstruction and use of microbial metabolic networks: the core Escherichia coli metabolic model as an educational guide
2010 · External reference
EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model
10.1038/srep39647 · 2017 · External reference
An algorithm for the reduction of genome-scale metabolic network models to meaningful core models
10.1186/s12918-015-0191-x · 2015 · External reference
COBRApy: COnstraints-Based Reconstruction and Analysis for Python
10.1186/1752-0509-7-74 · 2013 · External reference
Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways
2015 · External reference
Enabling anaerobic growth of Escherichia coli on glycerol in defined minimal medium using acetate as redox sink
10.1016/j.ymben.2022.05.006 · 2022 · External reference
The BioCyc collection of microbial genomes and metabolic pathways
10.1093/bib/bbx085 · 2019 · External reference
KEGG: new perspectives on genomes, pathways, diseases and drugs
10.1093/nar/gkw1092 · 2017 · External reference
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
10.1093/nar/gkaa992 · 2021 · External reference
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12
10.1093/nar/gkw1003 · 2017 · External reference
The EcoCyc Database 2023
2023 · External reference
Phosphofructokinases from Escherichia coli. Purification and characterization of the nonallosteric isozyme
10.1016/s0021-9258(17)34726-9 · 1978 · External reference
Mutant phenotypes for thousands of bacterial genes of unknown function
10.1038/s41586-018-0124-0 · 2018 · External reference
Automatic construction of metabolic models with enzyme constraints
10.1186/s12859-019-3329-9 · 2020 · External reference
Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints
10.15252/msb.20167411 · 2017 · External reference
Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers
10.1073/pnas.2001562117 · 2020 · External reference
The quantitative and condition-dependent Escherichia coli proteome
10.1038/nbt.3418 · 2016 · External reference
The protein cost of metabolic fluxes: prediction from enzymatic rate laws and cost minimization
10.1371/journal.pcbi.1005167 · 2016 · External reference
Resource allocation in metabolic networks: kinetic optimization and approximations by FBA
10.1042/bst20150156 · 2015 · External reference
Metabolic states with maximal specific rate carry flux through an elementary flux mode
10.1111/febs.12722 · 2014 · External reference
Consistent estimation of Gibbs energy using component contributions
10.1371/journal.pcbi.1003098 · 2013 · External reference
Pathway thermodynamics highlights kinetic obstacles in central metabolism
10.1371/journal.pcbi.1003483 · 2014 · External reference
Probabilistic thermodynamic analysis of metabolic networks
10.1093/bioinformatics/btab194 · 2021 · External reference
Thermodynamics shapes the in vivo enzyme burden of glycolytic pathways
2025 · External reference
Unlocking elementary conversion modes: ecmtool unveils all capabilities of metabolic networks
10.1016/j.patter.2020.100177 · 2020 · External reference
Deep learning allows genome-scale prediction of Michaelis constants from structural features
10.1371/journal.pbio.3001402 · 2021 · External reference
Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction
10.1038/s41929-022-00798-z · 2022 · External reference
Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning
10.1038/s41467-023-39840-4 · 2023 · External reference
ENKIE: a package for predicting enzyme kinetic parameter values and their uncertainties
10.1093/bioinformatics/btae652 · 2024 · External reference
Parameter balancing: consistent parameter sets for kinetic metabolic models
10.1093/bioinformatics/btz129 · 2019 · External reference
Pseudo-transition analysis identifies the key regulators of dynamic metabolic adaptations from steady-state data
10.1016/j.cels.2015.09.008 · 2015 · External reference
Metabolic flux responses to deletion of 20 core enzymes reveal flexibility and limits of E. coli metabolism
10.1016/j.ymben.2019.08.003 · 2019 · External reference
10.25080/tcwv9851
10.25080/tcwv9851 · External reference
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
10.1038/s41467-018-07652-6 · 2018 · External reference
PaxDb 5.0: curated protein quantification data suggests adaptive proteome changes in yeasts
10.1016/j.mcpro.2023.100640 · 2023 · External reference
Unresolved reference
External reference
CasADi: a software framework for nonlinear optimization and optimal control
10.1007/s12532-018-0139-4 · 2018 · External reference
BioNumbers–the database of key numbers in molecular and cell biology
10.1093/nar/gkp889 · 2010 · External reference
Large-scale computation of elementary flux modes with bit pattern trees
10.1093/bioinformatics/btn401 · 2008 · External reference
Inactivation of pyruvate formate-lyase by dioxygen: defining the mechanistic interplay of glycine 734 and cysteine 419 by rapid freeze-quench EPR
10.1021/bi002589k · 2001 · External reference
Succinate dehydrogenase and fumarate reductase from Escherichia coli
10.1016/s0005-2728(01)00238-9 · 2002 · External reference
The anaerobic oxidation of dihydroorotate by Escherichia coli K-12
10.1016/0005-2728(77)90197-9 · 1977 · External reference
eQuilibrator 3.0: a database solution for thermodynamic constant estimation
10.1093/nar/gkab1106 · 2022 · External reference
