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References from Genome-scale metabolic models enable predictive strain and process design for sustainable biomanufacturing. Local targets link to admitted publications; unresolved targets remain external evidence.
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum
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Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger
10.1038/msb.2008.12 · 2008 · External reference
Metabolic modeling of microbial community interactions for health, environmental and biotechnological applications
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A snapshot of biomanufacturing and the need for enabling research infrastructure
10.1016/j.tibtech.2024.10.014 · 2025 · External reference
Interpretable domain adaptation enables robust lactic acid fermentation monitoring from waste
10.1016/j.rineng.2025.108477 · 2025 · External reference
Advances and applications of machine learning and intelligent optimization algorithms in genome-scale metabolic network models
10.1007/s43393-022-00115-6 · 2023 · External reference
Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale
10.1038/s41467-020-19171-4 · 2020 · External reference
Integration of genome-scale metabolic model with biorefinery process model reveals market-competitive carbon-negative sustainable aviation fuel utilizing microbial cell mass lipids and biogenic CO 2
10.15376/biores.19.3.4056-4086 · 2024 · External reference
eQuilibrator 3.0: a database solution for thermodynamic constant estimation
10.1093/nar/gkab1106 · 2022 · External reference
Construction of multiscale genome-scale metabolic models: frameworks and challenges
10.3390/biom12050721 · 2022 · External reference
Improving genome-scale metabolic models of incomplete genomes with deep learning
10.1016/j.isci.2024.111349 · 2024 · External reference
How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies
2024 · External reference
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
10.1038/nbt.3893 · 2017 · External reference
A community-driven reconstruction of the Aspergillus niger metabolic network
10.1186/s40694-018-0060-7 · 2018 · External reference
Recon3D enables a three-dimensional view of gene variation in human metabolism
10.1038/nbt.4072 · 2018 · External reference
Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
10.1002/bit.10803 · 2003 · External reference
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
10.1093/nar/gkv1164 · 2016 · External reference
The MetaCyc database of metabolic pathways and enzymes-a 2019 update
10.1093/nar/gkz862 · 2020 · External reference
Reconstruction of compartmentalized genome-scale metabolic models using deep learning for over 800 fungi
2023 · External reference
Recent advances in systems metabolic engineering tools and strategies
10.1016/j.copbio.2017.06.007 · 2017 · External reference
Yeast optimizes metal utilization based on metabolic network and enzyme kinetics
10.1073/pnas.2020154118 · 2021 · External reference
Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO toolbox 3.0
10.1038/s41596-023-00931-7 · 2024 · External reference
Systems metabolic engineering of microorganisms for food and cosmetics production
10.1038/s44222-023-00076-y · 2023 · External reference
Systems metabolic engineering strategies: integrating systems and synthetic biology with metabolic engineering
10.1016/j.tibtech.2019.01.003 · 2019 · External reference
Unresolved reference
2023 · External reference
ChatGEM: an agentic architecture enabling interactive simulation of genome-scale metabolic models
2026 · External reference
Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters
10.1016/j.cell.2014.06.034 · 2014 · External reference
UniProt: a worldwide hub of protein knowledge
10.1093/nar/gky1049 · 2019 · External reference
Applications of genome-scale metabolic models to the study of human diseases: A systematic review
10.1016/j.cmpb.2024.108397 · 2024 · External reference
Integrated knowledge mining, genome-scale modeling, and machine learning for predicting Yarrowia lipolytica bioproduction
10.1016/j.ymben.2021.07.003 · 2021 · External reference
Using resource constraints derived from genomic and proteomic data in metabolic network models
2022 · External reference
CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions
10.1093/bioinformatics/btv096 · 2015 · External reference
Reconstructing genome-scale metabolic models with merlin
10.1093/nar/gkv294 · 2015 · External reference
More is different: metabolic modeling of diverse microbial communities
10.1128/msystems.01270-22 · 2023 · External reference
Novopathfinder: a webserver of designing novel-pathway with integrating GEM-model
10.1093/nar/gkaa230 · 2020 · External reference
Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
10.1038/s41467-022-31421-1 · 2022 · External reference
Systems properties of the Haemophilus influenzaeRd metabolic genotype
10.1074/jbc.274.25.17410 · 1999 · External reference
TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life
10.1093/nar/gkw1068 · 2017 · External reference
Advances in genome-scale metabolic modeling toward microbial community analysis of the human microbiome
10.1021/acssynbio.1c00140 · 2021 · External reference
Unraveling principles of thermodynamics for genome-scale metabolic networks using graph neural networks
2025 · External reference
Methods for automated genome-scale metabolic model reconstruction
10.1042/bst20170246 · 2018 · External reference
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
10.1038/nbt1401 · 2008 · External reference
Protein constraints in genome-scale metabolic models: data integration, parameter estimation, and prediction of metabolic phenotypes
10.1002/bit.28650 · 2024 · External reference
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
10.1126/science.7542800 · 1995 · External reference
In silico analysis of Clostridium acetobutylicum ATCC 824 metabolic response to an external electron supply
10.1007/s00449-015-1513-5 · 2016 · External reference
A natural in situ fabrication method of functional bacterial cellulose using a microorganism
10.1038/s41467-018-07879-3 · 2019 · External reference
The role of computational cellular models in industrial bioprocesses: from genetic engineering to plant design
10.1016/j.biotechadv.2026.108962 · 2026 · External reference
Genome-scale metabolic network models of Bacillus species suggest that model improvement is necessary for biotechnological applications
10.21859/ijb.1684 · 2018 · External reference
Dynamic flux balance analysis using DFBAlab
2017 · External reference
Genome-scale metabolic network models for industrial microorganisms metabolic engineering: current advances and future prospects
10.1016/j.biotechadv.2024.108319 · 2024 · External reference
Current status and applications of genome-scale metabolic models
10.1186/s13059-019-1730-3 · 2019 · External reference
Computationally efficient flux variability analysis
10.1186/1471-2105-11-489 · 2010 · External reference
Unresolved reference
2022 · External reference
Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models
10.1016/j.bpj.2013.06.011 · 2013 · External reference
Advances in genome-scale metabolic models of industrially important fungi
10.1016/j.copbio.2023.103005 · 2023 · External reference
Alphagem enables precise genome-scale metabolic modelling by integrating protein structure alignment with deep-learning-based dark metabolism mining
10.1038/s41467-026-75549-w · 2026 · External reference
Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality
10.1038/s41540-024-00348-2 · 2024 · External reference
Metabolic engineering of Bacillus subtilis based on genome-scale metabolic model to promote fengycin production
10.1007/s13205-021-02990-7 · 2021 · 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
Thermodynamics-based metabolic flux analysis
10.1529/biophysj.106.093138 · 2007 · External reference
High-throughput generation, optimization and analysis of genome-scale metabolic models
10.1038/nbt.1672 · 2010 · External reference
Elucidating redox balance shift in Scheffersomyces stipitis’ fermentative metabolism using a modified genome-scale metabolic model
10.1186/s12934-018-0983-y · 2018 · External reference
A reliable simulator for dynamic flux balance analysis
10.1002/bit.24748 · 2013 · External reference
Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches
10.1038/s41540-024-00384-y · 2024 · External reference
Integration of metatranscriptomics data improves the predictive capacity of microbial community metabolic models
10.1093/ismejo/wraf109 · 2025 · External reference
The systems biology markup language (SBML): language specification for level 3 version 1 core
2018 · External reference
Integrated production of levan and hyaluronic acid in Bacillus subtilis: metabolic bottleneck analysis using enzyme constraint genome-scale modeling and process economics
10.1016/j.biteb.2026.102656 · 2026 · External reference
Resource sharing of an infant gut microbiota synthetic community in combinations of human milk oligosaccharides
10.1093/ismejo/wrae209 · 2024 · External reference
Nanopore sequencing and assembly of a human genome with ultra-long reads
10.1038/nbt.4060 · 2018 · External reference
Recent advances in the design-build-test-learn (DBTL) cycle for systems metabolic engineering of Corynebacterium glutamicum
10.71150/jm.2501021 · 2025 · External reference
Advances in functional analysis of the microbiome: integrating metabolic modeling, metabolite prediction, and pathway inference with Next-Generation Sequencing data
10.71150/jm.2411006 · 2025 · External reference
KEGG: Kyoto encyclopedia of genes and genomes
10.1093/nar/28.1.27 · 2000 · External reference
KEGG: integrating viruses and cellular organisms
10.1093/nar/gkaa970 · 2021 · External reference
The BioCyc collection of microbial genomes and metabolic pathways
10.1093/bib/bbx085 · 2019 · External reference
Optimization of lipid production with a genome-scale model of Yarrowia lipolytica
10.1186/s12918-015-0217-4 · 2015 · External reference
Current state and applications of microbial genome-scale metabolic models
10.1016/j.coisb.2017.03.001 · 2017 · External reference
In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by genome-scale metabolic modeling
10.1186/s13068-019-1518-4 · 2019 · External reference
Machine learning applications in systems metabolic engineering
10.1016/j.copbio.2019.08.010 · 2020 · External reference
Comprehensive evaluation of the capacities of microbial cell factories
10.1038/s41467-025-58227-1 · 2025 · External reference
Causal AI digital twin for bioprocess bottleneck diagnosis via metabolic flexibility and rigidification maps
10.1016/j.isci.2026.116820 · 2026 · External reference
Assembly: a resource for assembled genomes at NCBI
10.1093/nar/gkv1226 · 2016 · External reference
Analyses of extracellular protein production in Bacillus subtilis–I: genome-scale metabolic model reconstruction based on updated gene-enzyme-reaction data
10.1016/j.bej.2017.07.005 · 2017 · External reference
Reducing assembly complexity of microbial genomes with single-molecule sequencing
10.1186/gb-2013-14-9-r101 · 2013 · External reference
Machine learning for the advancement of genome-scale metabolic modeling
10.1016/j.biotechadv.2024.108400 · 2024 · External reference
Pan-reactome analysis of Streptomyces strains reveals association and disconnection between primary and secondary metabolism
10.1016/j.ymben.2025.08.005 · 2025 · External reference
Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity
10.1038/s41540-019-0110-7 · 2019 · External reference
Deep learning-based k cat prediction enables improved enzyme-constrained model reconstruction
10.1038/s41929-022-00798-z · 2022 · External reference
Improving gibberellin GA3 production with the construction of a genome-scale metabolic model of fusarium fujikuroi
10.1021/acs.jafc.3c05309 · 2023 · External reference
Coarse-grained modeling elucidates differential metabolism of Saccharomyces cerevisiae under varied nutrient limitations
10.1021/acssynbio.4c00803 · 2025 · External reference
MEMOTE for standardized genome-scale metabolic model testing
10.1038/s41587-020-0446-y · 2020 · External reference
Impact of iron reduction on the metabolism of Clostridium acetobutylicum
10.1111/1462-2920.14640 · 2019 · External reference
Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
10.1371/journal.pcbi.1006848 · 2019 · External reference
Microbial physiological engineering increases the efficiency of microbial cell factories
10.1080/07388551.2020.1856770 · 2021 · External reference
Bacterial conversion routes for lignin valorization
10.1016/j.biotechadv.2022.108000 · 2022 · External reference
Shaping Aspergillus niger into a next-generation cell factory for L-malic acid
10.1016/j.copbio.2026.103452 · 2026 · External reference
Inspecting the solution space of genome-scale metabolic models
10.3390/metabo12010043 · 2022 · External reference
A consensus S. Cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
10.1038/s41467-019-11581-3 · 2019 · External reference
In silico cell factory design driven by comprehensive genome-scale metabolic models: development and challenges
10.1007/s43393-022-00117-4 · 2023 · External reference
Reconstruction of human metabolic models with large language models
10.1073/pnas.2516511123 · 2026 · External reference
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
10.1093/nar/gky537 · 2018 · External reference
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
10.1016/j.ymben.2003.09.002 · 2003 · External reference
Dynamic flux balance analysis of diauxic growth in Escherichia coli
10.1016/s0006-3495(02)73903-9 · 2002 · External reference
Advances in machine learning models for predicting enzyme kinetic parameters
10.1021/acs.jcim.5c02428 · 2026 · External reference
ECMpy, a simplified workflow for constructing enzymatic constrained metabolic network model
10.3390/biom12010065 · 2022 · External reference
In silico identification of gene targets to enhance C12 fatty acid production in Escherichia coli
10.1007/s00253-025-13501-6 · 2025 · External reference
Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico
10.1186/1752-0509-6-42 · 2012 · External reference
A systematic assessment of current genome-scale metabolic reconstruction tools
10.1186/s13059-019-1769-1 · 2019 · External reference
Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica
10.1186/s12918-018-0542-5 · 2018 · External reference
Genome-scale metabolic modelling of P. Thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism
2021 · External reference
I ML1515, a knowledgebase that computes Escherichia coli traits
10.1038/nbt.3956 · 2017 · External reference
MetaNetX/MNXref–reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks
10.1093/nar/gkv1117 · 2016 · External reference
KAAS: an automatic genome annotation and pathway reconstruction server
10.1093/nar/gkm321 · 2007 · External reference
Unresolved reference
2024 · External reference
Flux sampling and context-specific genome-scale metabolic models for biotechnological applications
2025 · External reference
Fast thermodynamically constrained flux variability analysis
10.1093/bioinformatics/btt059 · 2013 · External reference
Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri
10.1038/s41598-020-73253-3 · 2020 · External reference
A required sensitivity analysis for predictive reliability of genome–scale metabolic networks: probing biomass, nutrient conditions, and specialised metabolism with Penicillium rubens as a case study
10.1002/bit.70181 · 2026 · External reference
Curating a comprehensive set of enzymatic reaction rules for efficient novel biosynthetic pathway design
10.1016/j.ymben.2021.02.006 · 2021 · External reference
Innovation trends in industrial biotechnology
10.1016/j.tibtech.2022.03.007 · 2022 · External reference
METEOR: joint genome-scale reconstruction and enzyme prediction
2026 · External reference
A workflow for generating multi-strain genome-scale metabolic models of prokaryotes
10.1038/s41596-019-0254-3 · 2020 · External reference
BiGG models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
2020 · External reference
A reconciliation of genome-scale metabolic network model of Zymomonas mobilis ZM4
10.1038/s41598-020-64721-x · 2020 · External reference
Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
2013 · External reference
Using genome-scale models to predict biological capabilities
10.1016/j.cell.2015.05.019 · 2015 · External reference
What is flux balance analysis?
10.1038/nbt.1614 · 2010 · External reference
A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011
10.1038/msb.2011.65 · 2011 · External reference
Dynamic co-culture metabolic models reveal the fermentation dynamics, metabolic capacities and interplays of cheese starter cultures
10.1002/bit.27565 · 2021 · External reference
Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production
10.1186/1752-0509-5-101 · 2011 · External reference
Effect of pH on the metabolic flux of Klebsiella oxytoca producing 2, 3-butanediol in continuous cultures at different dilution rates
10.1007/s00449-013-0932-4 · 2013 · External reference
Clarifying the regulation of NO/N2O production in Nitrosomonas europaea during anoxic–oxic transition via flux balance analysis of a metabolic network model
10.1016/j.watres.2014.04.049 · 2014 · External reference
XomicsToModel: omics data integration and generation of thermodynamically consistent metabolic models
2025 · External reference
Improving acetoin production through construction of a genome-scale metabolic model
10.1016/j.compbiomed.2023.106833 · 2023 · External reference
Design of the biosensor-dependent coupling system stabilizes the high-synthesis phenotype of cell factory
10.1038/s41467-026-71801-5 · 2026 · External reference
Moving from genome-scale to community-scale metabolic models for the human gut microbiome
2025 · External reference
Moving from genome-scale to community-scale metabolic models for the human gut microbiome
10.1038/s41564-025-01972-2 · 2025 · External reference
Genome-scale architecture of small molecule regulatory networks and the fundamental trade-off between regulation and enzymatic activity
10.1016/j.celrep.2017.08.066 · 2017 · External reference
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis
10.1093/bioinformatics/bty499 · 2019 · External reference
Systematizing microbial bioplastic production for developing sustainable bioeconomy: metabolic nexus modeling, economic and environmental technologies assessment
10.1007/s10924-023-02787-0 · 2023 · External reference
Current state, challenges, and opportunities in genome-scale resource allocation models: a mathematical perspective
10.3390/metabo14070365 · 2024 · External reference
Curation and analysis of a Saccharomyces cerevisiae genome-scale metabolic model for predicting production of sensory impact molecules under enological conditions
10.3390/pr8091195 · 2020 · External reference
Metabolic modeling unveils potential probiotic roles of Flavonifractor plautii in reshaping the Western gut microbiota landscape
10.1093/ismeco/ycag077 · 2026 · External reference
Dynamic genome-scale modeling of Saccharomyces cerevisiae unravels mechanisms for ester formation during alcoholic fermentation
10.1002/bit.28421 · 2023 · External reference
Unresolved reference
2025 · External reference
The ModelSEED biochemistry database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
10.1093/nar/gkaa746 · 2021 · External reference
Analysis of optimality in natural and perturbed metabolic networks
10.1073/pnas.232349399 · 2002 · External reference
Flux sampling and graph neural networks for improved gene essentiality prediction in mammalian genome-scale metabolic models
10.1038/s41540-026-00738-8 · 2026 · External reference
Using metabolic networks to predict cross-feeding and competition interactions between microorganisms
10.1128/spectrum.02287-23 · 2024 · External reference
Network reduction methods for genome-scale metabolic models
10.1007/s00018-019-03383-z · 2020 · External reference
Evaluation of enzyme-constrained genome-scale model through metabolic engineering of anaerobic co-production of 2, 3-butanediol and glycerol by Saccharomyces cerevisiae
10.1016/j.ymben.2024.01.007 · 2024 · External reference
A low-complexity metabolic network model for the respiratory and fermentative metabolism of Escherichia coli
10.1371/journal.pone.0202565 · 2018 · External reference
Unresolved reference
2025 · External reference
Benchmarking biochemical networks generated by large language models
10.7554/elife.109709.3 · 2026 · External reference
A protocol for generating a high-quality genome-scale metabolic reconstruction
10.1038/nprot.2009.203 · 2010 · External reference
Model of metabolism and gene expression predicts proteome allocation in pseudomonas putida
10.1038/s41540-025-00521-1 · 2025 · External reference
The dawn of high-throughput and genome-scale kinetic modeling: recent advances and future directions
10.1021/acssynbio.4c00868 · 2025 · External reference
Advances in the integration of transcriptional regulatory information into genome-scale metabolic models
10.1016/j.biosystems.2016.06.001 · 2016 · External reference
Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis
10.1093/bioinformatics/btad600 · 2023 · External reference
Combining metabolomics and network analysis to improve tacrolimus production in Streptomyces tsukubaensis using different exogenous feedings
10.1007/s10295-017-1974-4 · 2017 · External reference
EnzymeTuning improves enzyme-constrained metabolic modeling and proteome abundance prediction through deep learning
10.1038/s41467-026-73744-3 · 2026 · External reference
Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing
10.1371/journal.pcbi.1010905 · 2023 · External reference
Genome sequencing and metabolic network reconstruction of a novel sulfur-oxidizing bacterium Acidithiobacillus Ameehan
10.3389/fmicb.2023.1277847 · 2023 · External reference
Deciphering and designing microbial communities by genome-scale metabolic modelling
10.1016/j.csbj.2024.04.055 · 2024 · External reference
Applications of machine learning in the reconstruction and curation of genome-scale metabolic models
2025 · External reference
Paradigm of engineering recalcitrant non-model microorganism with dominant metabolic pathway as a biorefinery chassis
10.1038/s41467-024-54897-5 · 2024 · External reference
Characterization of the enzyme kinetics of EMP and HMP pathway in Corynebacterium glutamicum: reference for modeling metabolic networks
10.3389/fbioe.2023.1296880 · 2023 · External reference
IMGMD: a platform for the integration and standardisation of in silico microbial genome-scale metabolic models
10.1038/s41598-017-00820-6 · 2017 · External reference
Genome-scale metabolic network models: from first-generation to next-generation
10.1007/s00253-022-12066-y · 2022 · External reference
Metabolic engineering of Escherichia coli for direct production of 1, 4-butanediol
10.1038/nchembio.580 · 2011 · External reference
Strategies for improving fengycin production: a review
10.1186/s12934-024-02425-x · 2024 · External reference
A new genome-scale metabolic model of Corynebacterium glutamicum and its application
10.1186/s13068-017-0856-3 · 2017 · External reference
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community
10.1038/s44320-024-00060-7 · 2024 · External reference
Discover the maze-like network for glabridin biosynthesis
2026 · External reference
Engineering Corynebacterium glutamicum for the production of 5-aminolevulinic acid under microaerobic conditions guided by a genome-scale metabolic network
10.1021/acs.jafc.4c10853 · 2025 · External reference
Simultaneous design of fermentation and microbe
10.1002/aic.18501 · 2024 · External reference
metaGEM: reconstruction of genome scale metabolic models directly from metagenomes
10.1093/nar/gkab815 · 2021 · External reference
