cellbauhaus · 984 papers with claims · 602 for outreach · 328 old · 54 reviews
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Novel Computational Tools for Linking Genotypes to Microbial Community Phenotypes
Towards applications of genome‐scale metabolic model‐based approaches in designing synthetic microbial communities
Dynamic simulations of microbial communities under perturbations: opportunities for microbiome engineering
Genome‐scale metabolic models applied for human health and biopharmaceutical engineering
Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri
A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diver
Deep learning-driven automatic reconstruction of genome-scale metabolic networks
Elucidation of the metabolic mechanism for malate production in Myceliophthora thermophila via 13C metabolic flux analys
Genome Scale Constraint-Based Metabolic Reconstruction of Propionibacterium Freudenreichii DSM 20271
Genome-scale metabolic modelling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell facto
Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions
Genome-Scale Metabolic Model Based Engineering of Escherichia Coli Enhances Recombinant Single Chain Antibody Fragment P
Automation and machine learning drive rapid optimization of isoprenol production in Pseudomonas putida
A constraint-based modeling approach to reach an improved chemically defined minimal medium for recombinant antiEpEX-scF
Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus appro
Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-base
PARROT: Prediction of enzyme abundances using protein-constrained metabolic models
Systems-level approaches for understanding and engineering of the oleaginous cell factory Yarrowia lipolytica
Metabolic Engineering of Serratia marcescens
Constraint-based modeling and machine learning applications for analysis and optimization of fermentation parameters
Modelling Consolidated Bioprocessing of Cellulose via Population Balances Coupled with Cybernetic Models
Significant Differences in Media Components and Predicted Growth Rates of 58 Escherichia coli Genome-scale Models
Engineered yeast for efficient de novo synthesis of 7‐dehydrocholesterol
Systems‐level approaches for understanding and engineering of the oleaginous cell factory <i>Yarrowia lipolytica</i>
Microbial Methylotrophic Metabolism: Recent Metabolic Modeling Efforts and Their Applications In Industrial Biotechnolog
Yeast Systems Biology: Model Organism and Cell Factory
How reliable are Chinese hamster ovary (CHO) cell genome‐scale metabolic models?
Detecting the Significant Flux Backbone of Escherichia coli metabolism
<i>Clostridioides difficile</i> 630Δ<i>erm in silico</i> and <i>in vivo</i> – quantitative growth and extensive polysacc
Model validation and selection in metabolic flux analysis and flux balance analysis
Comparative genome‐scale analysis of <i>Pichia pastoris</i> variants informs selection of an optimal base strain
Assessing <i>Escherichia coli</i> metabolism models and simulation approaches in phenotype predictions: Validation again
Corynebacterium glutamicum , a natural overproducer of succinic acid?
Network reduction methods for genome-scale metabolic models.
Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism
In silico design of anaerobic growth-coupled product formation in Escherichia coli: experimental validation using a simp
Construction of advanced producers of first- and second-generation ethanol in Saccharomyces cerevisiae and selected spec
Metabolic pathway databases and model repositories
Development of a Framework for Metabolic Pathway Analysis-Driven Strain Optimization Methods
Kinetic ensemble model of gas fermenting Clostridium autoethanogenum for improved ethanol production
Systems biology's role in leveraging microalgal biomass potential: Current status and future perspectives
Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments
Enzyme-constrained metabolic model and in silico metabolic engineering of Clostridium ljungdahlii for the development of
Predicting metabolic fluxes from omics data via machine learning: Moving from knowledge-driven towards data-driven appro
Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the forei
Improving designer glycan production in Escherichia coli through model-guided metabolic engineering
CFSA: Comparative flux sampling analysis as a guide for strain design.
A Genome Scale Model of Geobacillus thermoglucosidasius (C56-YS93) reveals its biotechnological potential on rice straw
Model-driven evaluation of microbial physiology: insights from protein allocation
Exploring Biomass Precursor Synthesis as a Determinant in Microbial Adaptation to Unadapted Carbon Sources with AdaptUC
Constrain and conquer
Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models
Development of simple kinetic models and parameter estimation for simulation of recombinant human serum albumin producti
Inference of metabolic flux distributions from transcriptomic data
From In Silico Prediction To In Vivo Validation: Advancing Biohydrogen Production Through Metabolic Engineering Of E. Co
Current Status and Applications of Adaptive Laboratory Evolution in Industrial Microorganisms
Overflow metabolism originates from growth optimization and cell heterogeneity
Application of machine learning in systems biology
A method for dynamic flux balance analysis with global constraints
Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models
Investigating host-microbiota cooperation with gap-filling optimization problems
Genome-scale constraint-based metabolic modeling and analysis of Nannochloropsis Sp.
Developing strategies for systems metabolic engineering of Pichia pastoris
Development and application of computer-aided design methods for cell factory optimization
Optimization of microbial cell factories with systems biology
METABOLIC MODELING AND OMICS-INTEGRATIVE ANALYSIS OF SINGLE AND MULTI-ORGANISM SYSTEMS: DISCOVERY AND REDESIGN
Quantitative prediction of Basfia succiniciproducens metabolic potential, for succinic acid and 1,4-butanediol productio
Ontwikkeling van hybride modellen in (Bio)Chemische Heterogene Populatiesystemen
TRFBA: an algorithm to integrate genome-scale metabolic and transcriptional regulatory networks with incorporation of ex
Underground metabolism as a rich reservoir for pathway engineering
Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis
Predicting Nash equilibria for microbial metabolic interactions
Multimodal regularized linear models with flux balance analysis for mechanistic integration of omics data
BeReTa: a systematic method for identifying target transcriptional regulators to enhance microbial production of chemica
From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry
Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm
A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium <i>Rhodotherm
Gsmodutils: a python based framework for test-driven genome scale metabolic model development
Elevated energy costs of biomass production in mitochondrial respiration-deficient<i>Saccharomyces cerevisiae</i>
Metabolic reconstruction of the human pathogen <i>Candida auris</i>: using a cross-species approach for drug target pred
Co-feeding enhances the yield of methyl ketones
Lifestyle, metabolism and environmental adaptation in Lactococcus lactis
<i>merlin</i> , an improved framework for the reconstruction of high-quality genome-scale metabolic models
Genome-scale modeling of yeast: chronology, applications and critical perspectives.
A flux-based machine learning model to simulate the impact of pathogen metabolic heterogeneity on drug interactions
Phenotypic innovation through recombination in genome-scale metabolic networks
Discovering Essential Multiple Gene Effects Through Large Scale Optimization: An Application to Human Cancer Metabolism
Genome‐Scale Model of <i>Rhizopus microsporus</i> : Metabolic integration of a fungal holobiont with its bacterial and v
Fine‐tuning the P. pastoris iMT1026 genome‐scale metabolic model for improved prediction of growth on methanol or glycer
Competition for nutrients increases invasion resistance during assembly of microbial communities
High‐quality genome‐scale metabolic modelling of <i>Pseudomonas putida</i> highlights its broad metabolic capabilities
Unveiling the Potential of Lentilactobacillus hilgardii in Malolactic Fermentation: Comparative Genomics and Fermentatio
Enzyme‐constrained models predict the dynamics of <i>Saccharomyces cerevisiae</i> growth in continuous, batch and fed‐ba
Development of a genome-scale metabolic model for the lager hybrid yeast S. pastorianus to understand the evolution of m
Zymomonas mobilis as a model system for production of biofuels and biochemicals
Quantifying Methane and Methanol Metabolism of “ <i>Methylotuvimicrobium buryatense</i> ” 5GB1C under Substrate Limitati
Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function
Glycerol as a key reactant in the production of 3-hydroxypropanoic acid using engineered microbes
Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers
Energy metabolism controls phenotypes by protein efficiency and allocation
Multiscale plant modeling: from genome to phenome and beyond
Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or e
PYF: a multi-functional algorithm for predicting production and optimizing metabolic engineering strategy in <i>Escheric
Towards dynamic genome-scale models
CO2 to succinic acid – Estimating the potential of biocatalytic routes
Functional genomics for the oleaginous yeast Yarrowia lipolytica
Metabolic engineering of human gut microbiome: Recent developments and future perspectives
A genome-scale dynamic constraint-based modelling (gDCBM) framework predicts growth dynamics, medium composition and int
A dynamic kinetic model captures cell-free metabolism for improved butanol production
Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bior
Self-controlled in silico gene knockdown strategies to enhance the sustainable production of heterologous terpenoid by S
Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models.
Reconstruction of the Fatty Acid Biosynthetic Pathway of<i>Exiguobacterium antarcticum</i>B7 Based on Genomic and Biblio
Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes
OM-FBA: Integrate Transcriptomics Data with Flux Balance Analysis to Decipher the Cell Metabolism
Ethanol production improvement driven by genome-scale metabolic modeling and sensitivity analysis in Scheffersomyces sti
Constraints-based analysis identifies NAD+ recycling through metabolic reprogramming in antibiotic resistant Chromobacte
Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Develop
E-Flux2 and SPOT: Validated Methods for Inferring Intracellular Metabolic Flux Distributions from Transcriptomic Data.
Flux prediction using artificial neural network (ANN) for the upper part of glycolysis
Metabolic flux configuration determination using information entropy
Distributed flux balance analysis simulations of serial biomass fermentation by two organisms
Predictive evolution of metabolic phenotypes using model-designed environments.
Comparison of Optimization-Modelling Methods for Metabolites Production in Escherichia coli
Genome‐scale metabolic modeling reveals key features of a minimal gene set
Evaluating <i>E. coli</i> genome‐scale metabolic model accuracy with high‐throughput mutant fitness data
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation
Development of a Stoichiometric Model for Estimation of Metabolic Fluxes in <em>Saccharomyces cerevisiae</em> during Teq
Bridging the gap between mechanistic biological models and machine learning surrogates
ecBSU1: A Genome-scale Enzyme-constrained Model of <em>Bacillus subtilis</em> based on the ECMpy Workflow
Genome-Scale Metabolic Network Models of Bacillus Species Suggest that Model Improvement is Necessary for Biotechnologic
Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis
NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome
Estimation of biomass composition from genomic and transcriptomic information
Conceptos básicos de análisis de fluxes metabólicos
A Computational Framework to Identify Metabolic Engineering Strategies for the Co-Production of Metabolites
LGEM+: A First-Order Logic Framework for Automated Improvement of Metabolic Network Models Through Abduction
Modeling population heterogeneity from microbial communities to immune response in cells
Metabolic control analysis enabled the improvement of the L-cysteine production process with Escherichia coli
Genome-scale modeling of Chinese hamster ovary cells by hybrid semi-parametric flux balance analysis
Strategies to increase the robustness of microbial cell factories
A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium <i>Rhodotherm
Investigating the chemolithoautotrophic and formate metabolism of <i>Nitrospira moscoviensis</i> by constraint-based met
Enzyme-constrained models predict the dynamics of <i>Saccharomyces cerevisiae</i> growth in continuous, batch and fed-ba
Genome-scale modeling of <i>Pseudomonas aeruginosa</i> PA14 unveils its broad metabolic capabilities and role of metabol
Genome-Scale Metabolic Model Accurately Predicts Fermentation of Glucose by <i>Chromochloris zofingiensis</i>
Optimality of extracellular enzyme production and activity in dynamic flux balance modeling
Deep learning based k cat prediction enables improved enzyme constrained model reconstruction
Rhythm of The Night (and Day): Predictive metabolic modeling of circadian growth in <i>Chlamydomonas</i>
A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models
Data integration across conditions improves turnover number estimates and metabolic predictions
Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-produ
A Genome-Scale Metabolic Model of Marine Heterotroph Vibrio splendidus sp. 1A01
Evaluating proteome allocation of <i>Saccharomyces cerevisiae</i> phenotypes with resource balance analysis
Glycolysis revisited: from steady state growth to glucose pulses
Metabolic modeling of <i>Hermetia illucens</i> larvae resource allocation for high-value fatty acid production
Teasing out Missing Reactions in Genome-scale Metabolic Networks through Graph Convolutional Networks
Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium <i>Fibrobacter succinogenes</i>
Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states
Transcriptome guided metabolic network analysis reveals rearrangements of carbon flux distribution in <i>Neisseria gonor
Guidelines for extracting biologically relevant context-specific metabolic models using gene expression data
Analysis of the genome-scale metabolic model of <i>Bacillus subtilis</i> to design novel in-silico strategies for native
Critical assessment of <i>E. coli</i> genome-scale metabolic model with high-throughput mutant fitness data
Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling
A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia
Overall biomass yield on multiple nutrient sources
BayFlux: A <i>Bay</i> esian method to quantify metabolic <i>Flux</i> es and their uncertainty at the genome scale
Pichia pastoris growth - coupled heme biosynthesis analysis using metabolic modelling
METABOLIC MODELLING AS A POWERFUL TOOL TO IDENTIFY CRITICAL COMPONENTS OF <i>PNEUMOCYSTIS</i> GROWTH MEDIUM
Machine learning predicts system-wide metabolic flux control in cyanobacteria
Improved Production of Taxol® Precursors in <i>S. cerevisiae</i> using Combinatorial <i>in silico</i> Design and Metabol
Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning
Dynamic Flux Balance Analysis Models in SBML
Modelling dynamic host-pathway interactions at the genome scale with machine learning
Yeast9: A Consensus Yeast Metabolic Model Enables Quantitative Analysis of Cellular Metabolism By Incorporating Big Data
Machine Learning and Metabolic Model Guided CRISPRi Reveals a Central Role for Phosphoglycerate Mutase in <i>Chlamydia t
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
A genome-scale metabolic model for <i>Methylococcus capsulatus</i> predicts reduced efficiency uphill electron transfer
Metabolic modeling of <i>Pectobacterium parmentieri</i> SCC3193 provides insights into metabolic pathways of plant patho
Metabolic modeling of <i>Streptococcus mutans</i> reveals complex nutrient requirements of an oral pathogen
Modeling genome-wide evolution of catalytic turnover rates: Strong epistasis shaped modern enzyme kinetics
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework
Elementary Growth Modes provide a molecular description of cellular self-fabrication
Reconstruction of a Genome-Scale Metabolic Model of Streptomyces albus J1074: Improved Engineering Strategies in Natural
Machine Learning Methods for Analysis of Metabolic Data and Metabolic Pathway Modeling
Quantification of Microbial Phenotypes
An Improved Genome-Scale Metabolic Model of Arthrospira platensis C1 (iAK888) and Its Application in Glycogen Overproduc
A Genome-Scale Metabolic Model of Thalassiosira pseudonana CCMP 1335 for a Systems-Level Understanding of Its Metabolism
ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow.
The Use of Interdisciplinary Approaches to Understand the Biology of Campylobacter jejuni
Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic B
Uncovering Novel Pathways for Enhancing Hyaluronan Synthesis in Recombinant Lactococcus lactis: Genome-Scale Metabolic M
Effect of Delays on the Response of Microalgae When Exposed to Dynamic Environmental Conditions
Arduino Soft Sensor for Monitoring Schizochytrium sp. Fermentation, a Proof of Concept for the Industrial Application of
Biosynthesis of fatty acids and biosurfactants by the yeast Yarrowia lipolytica with emphasis on metabolic networks and
Pangenome-Scale Mathematical Modelling of ANAMMOX Bacteria Metabolism
Dynamic in silico assessment of potential gene targets for enhancing clavulanic acid production in Streptomyces clavulig
A yield-cost tradeoff governs Escherichia coli’s decision between fermentation and respiration in carbon-limited growth
DeepMetabolism: A Deep Learning System to Predict Phenotype from Genome Sequencing
Sequence Specific Modeling of E. coli Cell-Free Protein Synthesis
Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism
Gene-centric constraint of metabolic models
Benchmarking kinetic models of Escherichia coli metabolism
Proteome overabundance enables respiration but limitation onsets carbon overflow
Improving Designer Glycan Production in <i>Escherichia coli</i> through Model-Guided Metabolic Engineering
Genome-scale metabolic rewiring to achieve predictable titers rates and yield of a non-native product at scale
Development of a genome-scale metabolic model of <i>Clostridium thermocellum</i> and its applications for integration of
Bayesian genome scale modelling identifies thermal determinants of yeast metabolism
A genome-scale study of metabolic complementation in endosymbiotic consortia: the case of the cedar aphid
A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the i
Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm
Modeling a co-culture of <i>Clostridium autoethanogenum</i> and <i>Clostridium kluyveri</i> to increase syngas conversio
ΔFBA: Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data
Active and machine learning-based approaches to rapidly enhance microbial chemical production
A genome-scale metabolic model of <i>Saccharomyces cerevisiae</i> that integrates expression constraints and reaction th
Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments
Genome-scale metabolic modelling of <i>P. thermoglucosidasius</i> NCIMB 11955 reveals metabolic bottlenecks in anaerobic
Genome-scale metabolic modelling when changes in environmental conditions affect biomass composition
Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments
Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments
Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models
Predictive engineering and optimization of tryptophan metabolism in yeast through a combination of mechanistic and machi
Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models
A metabolic reconstruction of <i>Lactobacillus reuteri</i> JCM 1112 and analysis of its potential as a cell factory
ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualizati
Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pres
An unconventional uptake rate objective function approach enhances applicability of genome-scale models for mammalian ce
Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacteriu
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using ge
Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source
Dynamic resource allocation drives growth under nitrogen starvation in eukaryotes
Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models.
Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic state
Constraint-based modeling identifies new putative targets to fight colistin-resistant A. baumannii infections
Predicting the murine enterocyte metabolic response to diets that differ in lipid and carbohydrate composition
Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach
Bridging substrate intake kinetics and bacterial growth phenotypes with flux balance analysis incorporating proteome all
Find_tfSBP: find thermodynamics-feasible and smallest balanced pathways with high yield from large-scale metabolic netwo
Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri
Improved production of the non-native cofactor F420 in Escherichia coli
Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models
Characterization and engineering of Streptomyces griseofuscus DSM 40191 as a potential host for heterologous expression
Integrating glycolysis, citric acid cycle, pentose phosphate pathway, and fatty acid beta-oxidation into a single comput
Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction
Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediati
Pichia pastoris growth—coupled heme biosynthesis analysis using metabolic modelling
Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation
Thermochemical hydrolysis of macroalgae Ulva for biorefinery: Taguchi robust design method
Principles of proteome allocation are revealed using proteomic data and genome-scale models
EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scal
Yeast metabolic chassis designs for diverse biotechnological products
Discovering missing reactions of metabolic networks by using gene co-expression data
A multiscale spatiotemporal model including a switch from aerobic to anaerobic metabolism reproduces succession in the e
Statistical prediction of microbial metabolic traits from genomes
Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta
Metabolic characterization and viable delivery of Akkermansia muciniphila for its future application
Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production
Improved functional annotations are key to realize the potential of algal biotechnology
Fungal Alcohol Dehydrogenases: Physiological Function, Molecular Properties, Regulation of Their Production, and Biotech
Metabolic fluxes-oriented control of bioreactors: a novel approach to tune micro-aeration and substrate feeding in ferme
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0
lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target m
Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA
Population FBA predicts metabolic phenotypes in yeast
OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling.
redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core m
Characterizing steady states of genome-scale metabolic networks in continuous cell cultures
From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline
Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants
BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale
Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth cond
Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4
Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic act
Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enabl
Engineering microbial consortia by division of labor
Improved production of Taxol® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering
Resource-aware whole-cell model of division of labour in a microbial consortium for complex-substrate degradation
Automation assisted anaerobic phenotyping for metabolic engineering
High throughput 13C-metabolic flux analysis of 3-hydroxypropionic acid producing Pichia pastoris reveals limited availab
FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization
A novel engineered strain of Methylorubrum extorquens for methylotrophic production of glycolic acid
Engineering the synthetic β-alanine pathway in Komagataella phaffii for conversion of methanol into 3-hydroxypropionic a
Mapping the landscape of metabolic goals of a cell
A systematic assessment of current genome-scale metabolic reconstruction tools
Enumeration of minimal stoichiometric precursor sets in metabolic networks
In silico-guided metabolic engineering of Bacillus subtilis for efficient biosynthesis of purine nucleosides by blocking
Single mutation at a highly conserved region of chloramphenicol acetyltransferase enables isobutyl acetate production di
Dynamic flux balance modeling to increase the production of high-value compounds in green microalgae
In silico profiling of cell growth and succinate production in Escherichia coli NZN111
Pyrophosphate-free glycolysis in Clostridium thermocellum increases both thermodynamic driving force and ethanol titers
Comprehensive reconstruction and evaluation of Pichia pastoris genome-scale metabolic model that accounts for 1243 ORFs
Elucidating genomic gaps using phenotypic profiles
Elucidating genomic gaps using phenotypic profiles
Automatic construction of metabolic models with enzyme constraints
RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in ch
Understanding and mathematical modelling of cellular resource allocation in microorganisms: a comparative synthesis
Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina
High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis
ICON-GEMs: integration of co-expression network in genome-scale metabolic models, shedding light through systems biology
In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria
Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Predicting microbial interactions with approaches based on flux balance analysis: an evaluation
Metabolic flux analysis for metabolome data validation of naturally xylose-fermenting yeasts
Genome-scale insights into the metabolic versatility of Limosilactobacillus reuteri
Dynamic genome-scale metabolic modeling of the yeast Pichia pastoris
Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism
Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica
The use of genome-scale metabolic network reconstruction to predict fluxes and equilibrium composition of N-fixing versu
Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora
Modelling overflow metabolism in Escherichia coli with flux balance analysis incorporating differential proteomic effici
DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems
Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework
A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced b
Genomic sequencing, genome-scale metabolic network reconstruction, and in silico flux analysis of the grape endophytic f
OptPipe - a pipeline for optimizing metabolic engineering targets
Metabolic engineering of Synechococcus elongatus PCC 7942 for improvement of 1,3-propanediol and glycerol production bas
Role of phosphate limitation and pyruvate decarboxylase in rewiring of the metabolic network for increasing flux towards
Metabolic network model guided engineering ethylmalonyl-CoA pathway to improve ascomycin production in Streptomyces hygr
Metabolic engineering of Corynebacterium glutamicum for anthocyanin production
Combining metabolite doping and metabolic engineering to improve 2-phenylethanol production by engineered cyanobacteria
Engineering Saccharomyces cerevisiae for the Overproduction of β-Ionone and Its Precursor β-Carotene
Production of biopolymer precursors beta-alanine and L-lactic acid from CO2 with metabolically versatile Rhodococcus opa
Perspectives and Challenges in Microbial Communities Metabolic Modeling
Multi-scale models of whole cells: progress and challenges
Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation
Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing
Physiological Response of Corynebacterium glutamicum to Increasingly Nutrient-Rich Growth Conditions
Determinism and Contingency Shape Metabolic Complementation in an Endosymbiotic Consortium
Does It Pay Off to Explicitly Link Functional Gene Expression to Denitrification Rates in Reaction Models?
Rewiring of Metabolic Network in Mycobacterium tuberculosis During Adaptation to Different Stresses
Uncovering the Role of Metabolism in Oomycete–Host Interactions Using Genome-Scale Metabolic Models
Reconstructed Metabolic Network Models Predict Flux-Level Metabolic Reprogramming in Glioblastoma
Combination of Genome-Scale Models and Bioreactor Dynamics to Optimize the Production of Commodity Chemicals
Flux Balance Analysis of Plant Metabolism: The Effect of Biomass Composition and Model Structure on Model Predictions
Questions, data and models underpinning metabolic engineering
Probing Genome-Scale Model Reveals Metabolic Capability and Essential Nutrients for Growth of Probiotic Limosilactobacil
From Shallow to Deep Bioprocess Hybrid Modeling: Advances and Future Perspectives
Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions
A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains
Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human patho
Microbial carbon use efficiency predicted from genome-scale metabolic models
Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities
Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast
Rewiring carbon metabolism in yeast for high level production of aromatic chemicals
Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale
Bayesian genome scale modelling identifies thermal determinants of yeast metabolism
Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism
Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints
Teasing out missing reactions in genome-scale metabolic networks through hypergraph learning
Functional comparison of metabolic networks across species
Data integration across conditions improves turnover number estimates and metabolic predictions
A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models
Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity
Engineering a synthetic energy-efficient formaldehyde assimilation cycle in Escherichia coli
Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes
From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s disease
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shi
Fine-tuning mitochondrial activity in Yarrowia lipolytica for citrate overproduction
Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic mod
Genome scale modeling of the protein secretory pathway reveals novel targets for improved recombinant protein production
A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory.
Benjamín J. Sánchez; Cheng Zhang; Avlant Nilsson; Petri-Jaan Lahtvee; E. Kerkhoven; J. Nielsen
nielsenj@chalmers.se
Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints
ViewJens; Teusink, Bas
b.teusink@vu.nl
Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments
ViewWhole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies
ViewThe number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates
ViewThe number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates
ViewPeter; Rocha, Isabel; Patil
irocha@itqb.unl.pt
Model‐guided development of an evolutionarily stable yeast chassis
ViewAlter, Tobias B.; Blank
tobias.alter@rwth-aachen.de
Zhitao; Mao, Yufeng; Wu
mao_zt@tib.cas.cn
Construction and Analysis of an Enzyme‐constrained Metabolic Model of <em>Corynebacterium glutamicum</em>
ViewZhitao Mao; Xin Zhao; Xue Yang; Peiji Zhang; Jiawei Du; Qianqian Yuan; Hongwu Ma
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krishna.mahadevan@utoronto.ca
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gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
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Miguel; Dias, Óscar
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Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R
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Microbial Biosynthesis of L-Malic Acid and Related Metabolic Engineering Strategies: Advances and Prospects
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Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)
dbaumler@umn.edu
Using genome-scale metabolic models to compare serovars of the foodborne pathogen Listeria monocytogenes
eunylee@khu.ac.kr
Comparative genomic analysis of Methylocystis sp. MJC1 as a platform strain for polyhydroxybutyrate biosynthesis
s.gharaghani@ut.ac.ir
Structural systems pharmacology: A framework for integrating metabolic network and structure-based virtual screening for
eivind.almaas@ntnu.no
A study of a diauxic growth experiment using an expanded dynamic flux balance framework
ola.oyelade@covenantuniversity.edu.ng
Machine learning methods for predicting essential metabolic genes from Plasmodium falciparum genome-scale metabolic netw
Paul.Race@bristol.ac.uk
Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology
monika.heiner@b-tu.de
Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models
pnsaa@uc.cl
Metabolic modeling of Halomonas campaniensis improves polyhydroxybutyrate production under nitrogen limitation
lahtvee@ut.ee
C/N ratio and carbon source-dependent lipid production profiling in Rhodotorula toruloides
martina.cappelletti2@unibo.it
Systems biology and metabolic engineering of Rhodococcus for bioconversion and biosynthesis processes
xqian@ece.tamu.edu
TRIMER: Transcription Regulation Integrated with MEtabolic Regulation
lbry@bwh.harvard.edu
Real-time HRMAS <sup>13</sup> C NMR of obligately anaerobic cells identifies new metabolic targets in the pathogen <i>Cl
wilkenst@hhu.de
Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models
mamori@ucsd.edu
Functional Decomposition of Metabolism allows a system-level quantification of fluxes and protein allocation towards spe
yang_x@tib.cas.cn
The necessity of considering enzymes as compartments in constraint-based genome-scale metabolic models
tim.scheibe@pnnl.gov
Coupling Flux Balance Analysis with Reactive Transport Modeling through Machine Learning for Rapid and Stable Simulation
sgibbons@isbscience.org
Microbial community-scale metabolic modeling predicts personalized short chain fatty acid production profiles in the hum
joshua.chan@colostate.edu
Microbial Interactions from a New Perspective: Reinforcement Learning Reveals New Insights into Microbiome Evolution
joonhoonkim@lbl.gov
Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in <i>Pseudomonas
y.chen3@siat.ac.cn
Minimization of proteome reallocation explains metabolic transition in hierarchical utilization of carbon sources
aidong.yang@eng.ox.ac.uk
DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates
marta.tortajadaserra@uchceu.es
Flux modelling analysis reveals the metabolic impact of cryptic plasmids and environmental conditions in probiotic Esche
tazza@inf.u-szeged.hu
MINN: A METABOLIC-INFORMED NEURAL NETWORK FOR INTEGRATING OMICS DATA INTO GENOME-SCALE METABOLIC MODELING
georgecolin.dicenzo@unifi.it
Robustness encoded across essential and accessory replicons in an ecologically versatile bacterium
cailean.carter@quadram.ac.uk
Genome-scale metabolic modelling of trimethoprim’s mode of action reveals free ATP salvaged to restore purine pool
jean-christophe.lachance@usherbrooke.ca
BOFdat: generating biomass objective function stoichiometric coefficients from experimental data
damien.eveillard@univ-nantes.fr
MIMEco: Multi-objective metabolic modeling to predict and explain pairwise interactions
tim.nies@hhu.de
Microbial Pathway Thermodynamics: Stoichiometric Models Unveil Anabolic and Catabolic Processes
kzengler@eng.ucsd.edu
Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data
eforsberg@sdsu.edu
Towards Predicting Gut Microbial Metabolism: Integration of Flux Balance Analysis and Untargeted Metabolomics
kyano@meiji.ac.jp
Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana
amnah.alzahmi@nyu.edu
Algal Cell Factories: Approaches, Applications, and Potentials
z.iqbal@my.westminster.ac.uk
State-of-the-Art Genetic Modalities to Engineer Cyanobacteria for Sustainable Biosynthesis of Biofuel and Fine-Chemicals
oaltay@kth.se
Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabol
n.lameyer@dil-ev.de
Metabolic Modeling of Hermetia illucens Larvae Resource Allocation for High-Value Fatty Acid Production
dipali.singh@quadram.ac.uk
Genome-Scale Metabolic Modelling Approach to Understand the Metabolism of the Opportunistic Human Pathogen Staphylococcu
julia.koblitz@dsmz.de
The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases
lea.adolf@student.uni-tuebingen.de
Nutritional Interactions between Bacterial Species Colonising the Human Nasal Cavity: Current Knowledge and Future Prosp
aclyne@umd.edu
Isotope-Assisted Metabolic Flux Analysis: A Powerful Technique to Gain New Insights into the Human Metabolome in Health
gabmonteiro@tecnico.ulisboa.pt
The Effect of Recombinant Protein Production in Lactococcus lactis Transcriptome and Proteome
mgpoolman@brookes.ac.uk
Substrate Utilisation and Energy Metabolism in Non-Growing Campylobacter jejuni M1cam
isma.belouah@tftak.eu
The Quantitative Measurement of Peptidoglycan Components Obtained from Acidic Hydrolysis in Gram-Positive and Gram-Negat
chlee123@konkuk.ac.kr
Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing Megasphaera elsdenii
m-iman@alumni.tums.ac.ir
Systems Biology Approach to Bioremediation of Nitroaromatics: Constraint-Based Analysis of 2,4,6-Trinitrotoluene Biotran
schowdhury2@mymail.vcu.edu
Computational Modeling of the Human Microbiome
dmuench@ucalgary.ca
Understanding Plant Nitrogen Metabolism through Metabolomics and Computational Approaches
m.kulyashov@mail.ru
A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus
david.ruckerbauer@boku.ac.at
Key Challenges in Designing CHO Chassis Platforms
chenhao.sun@manchester.ac.uk
Dynamic Metabolic Analysis of Cupriavidus necator DSM545 Producing Poly(3-hydroxybutyric acid) from Glycerol
jnogales@cib.csic.es
Expanding the computable reactome in <i>Pseudomonas putida</i> reveals metabolic cycles providing robustness
j.nogales@csic.es
Providing new insights on the byphasic lifestyle of the predatory bacterium <i>Bdellovibrio bacteriovorus</i> through ge
wendel.silveira@ufv.br
Protein Abundance Prediction Through Machine Learning Methods
nlewisres@ucsd.edu
A genome-scale metabolic network model and machine learning predict amino acid concentrations in Chinese Hamster Ovary c
david.ruckerbauer@univie.ac.at
Inclusion of maintenance energy improves the intracellular flux predictions of CHO
eddy.smid@wur.nl
Nitrogenous Compound Utilization and Production of Volatile Organic Compounds among Commercial Wine Yeasts Highlight Str
papin@virginia.edu
Functional Anabolic Network Analysis of Human-associated Lactobacillus Strains
utrilla@ccg.unam.mx
A quantitative method for proteome reallocation using minimal regulatory interventions
porob@post.bgu.ac.il
Genome-Scale reconstruction of <i>Paenarthrobacter aurescens</i> TC1 metabolic model towards the study of atrazine biore
andrea.demartino@roma1.infn.it
A yield-cost tradeoff governs Escherichia coli’s decision between fermentation and respiration in carbon-limited growth
alok.kumar.patel@ltu.se
Data-driven synthetic microbes for sustainable future
nikoloski@mpimp-golm.mpg.de
Resolving the central metabolism of Arabidopsis guard cells
zhangyxzsh@163.com
Reconstruction and analysis of carbon metabolic pathway of Ketogulonicigenium vulgare SPU B805 by genome and transcripto
sundpe301@163.com
Reconstruction of a Genome-scale Metabolic Network of Komagataeibacter nataicola RZS01 for Cellulose Production
magbubah.essack@kaust.edu.sa
Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factor
geiger@tauex.tau.ac.il
The landscape of tiered regulation of breast cancer cell metabolism
nboyle@mnies.edu
Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems
Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319
rmoore305@gatech.edu
Unveiling metabolic pathways involved in the extreme desiccation tolerance of an Atacama cyanobacterium
sun_jb@tib.cas.cn
Adaptive laboratory evolution enhances methanol tolerance and conversion in engineered Corynebacterium glutamicum
giuseppe.facchetti@jic.ac.uk
A simple strategy guides the complex metabolic regulation in Escherichia coli
almut-katrin.heinken@univ-lorraine.fr
Personalized modeling of gut microbiome metabolism throughout the first year of life
joanarodrigues@deb.uminho.pt
Optimization of chondroitin production in E. coli using genome scale models
leesy@kaist.ac.kr
Systems approach to characterize the metabolism of liver cancer stem cells expressing CD133
meadows@amyris.com
An Automated Scientist to Design and Optimize Microbial Strains for the Industrial Production of Small Molecules
simon.labarthe@inrae.fr
A digital twin of bacterial metabolism during cheese production
seppe.kuehn@uchicago.edu
Statistical prediction of microbial metabolic traits from genomes
liudehu@caas.cn
Metabolic Engineering of Model Microorganisms for the Production of Xanthophyll
dmachado@deb.uminho.pt
Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to
pierre.millard@insa-toulouse.fr
Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production a
hatakeyama@complex.c.u-tokyo.ac.jp
Metabolic dynamics restricted by conserved carriers: Jamming and feedback
c.kaleta@iem.uni-kiel.de
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
pierre-etienne.jacques@usherbrooke.ca
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
palsson@eng.ucsd.edu
Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments
jrcasey@mit.edu
A steady-state model of microbial acclimation to substrate limitation
Yannick.Bomble@nrel.gov
Bayesian inference of metabolic kinetics from genome-scale multiomics data
jpoyatos@cnb.csic.es
Genetic buffering and potentiation in metabolism
alejandro.zepeda@correo.uady.mx
The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predi
dkim@unist.ac.kr
Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum
khekim@korea.ac.kr
Strain engineering and metabolic flux analysis of a probiotic yeast Saccharomyces boulardii for metabolizing l-fucose, a
nunthaphan.vikromvarasiri@riken.jp
Metabolic engineering design to enhance (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis based on flux
Per.Bruheim@ntnu.no
Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisi
tian_cg@tib.cas.cn
Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-base
peter.lindblad@kemi.uu.se
Enhancement of photosynthetic isobutanol production in engineered cells of Synechocystis PCC 6803
ctrinh@utk.edu
Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostr
zhangyun@im.ac.cn
A new genome-scale metabolic model of Corynebacterium glutamicum and its application
jufwang@scut.edu.cn
Model-based driving mechanism analysis for butyric acid production in Clostridium tyrobutyricum
sandra.castillo@vtt.fi
Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction
jamie.wood@york.ac.uk
An accurate description of Aspergillus niger organic acid batch fermentation through dynamic metabolic modelling
f.brancodossantos@uva.nl
Alignment of microbial fitness with engineered product formation: obligatory coupling between acetate production and pho
gongzhiwei@wust.edu.cn
A metabolic model of Lipomyces starkeyi for predicting lipogenesis potential from diverse low-cost substrates
wuxin@tib.cas.cn
Deciphering cell wall sensors enabling the construction of robust P. pastoris for single-cell protein production
peter.schaap@wur.nl
Genome-scale metabolic modeling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factor
byungkim@snu.ac.kr
In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by gen
mervi.toivari@vtt.fi
Evaluation of synthetic formaldehyde and methanol assimilation pathways in Yarrowia lipolytica
juchu@ecust.edu.cn
In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342
qhua@ecust.edu.cn
Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylgl
david.heckmann@hhu.de
Deep learning allows genome-scale prediction of Michaelis constants from structural features
sandra.pucciarelli@unicam.it
CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design
mrocha@di.uminho.pt
Comparison of pathway analysis and constraint-based methods for cell factory design
c.angione@tees.ac.uk
Multiplex methods provide effective integration of multi-omic data in genome-scale models
nuno.mira@ist.utl.pt
MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering
yanq2@vcu.edu
Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model
axel.theorell@bsse.ethz.ch
Assumptions on decision making and environment can yield multiple steady states in microbial community models
gustavo.tamasco@usp.br
ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualizati
kmaeda@bio.kyutech.ac.jp
MLAGO: machine learning-aided global optimization for Michaelis constant estimation of kinetic modeling
rainer.breitling@manchester.ac.uk
Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism
fbguo@uestc.edu.cn
SSER: Species specific essential reactions database
yeimy.morales@udg.edu
PFA toolbox: a MATLAB tool for Metabolic Flux Analysis
dmontoyac@unal.edu.co
Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of
dongyuplee@skku.edu
In silico model-guided identification of transcriptional regulator targets for efficient strain design
jyxia@ecust.edu.cn
Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions
Kyle.Pomraning@pnnl.gov
Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid
fgzhao@scut.edu.cn
Characterization of the enzyme kinetics of EMP and HMP pathway in Corynebacterium glutamicum: reference for modeling met
schleiff@bio.uni-frankfurt.de
Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Conte
nathan.tintle@dordt.edu
A Bayesian Framework for the Classification of Microbial Gene Activity States
jan.vanimpe@kuleuven.be
Simulation of Escherichia coli Dynamics in Biofilms and Submerged Colonies with an Individual-Based Model Including Meta
acelis@uniandes.edu.co
Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling
clelia.peano@itb.cnr.it
Time-Resolved Transcriptomics and Constraint-Based Modeling Identify System-Level Metabolic Features and Overexpression
arabolaza@ibr-conicet.gov.ar
Identification of FadAB Complexes Involved in Fatty Acid β-Oxidation in Streptomyces coelicolor and Construction of a Tr
w.bryant@imperial.ac.uk
In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Ind
bioding@163.com
Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccha
stephane.delaunay@univ-lorraine.fr
Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio
acontreras@ucm.cl
Metabolic behavior for a mutant Oenococcus oeni strain with high resistance to ethanol to survive under oenological mult
gsantamaria@fc.ul.pt
Bioinformatic Analysis of Metabolomic Data: From Raw Spectra to Biological Insight
ypzhuang@ecust.edu.cn
From Spatial-Temporal Multiscale Modeling to Application: Bridging the Valley of Death in Industrial Biotechnology
m.yamamoto@nibiohn.go.jp
Prediction of Metabolic Flux Distribution by Flux Sampling: As a Case Study, Acetate Production from Glucose in Escheric
jan.strauss@cssb-hamburg.de
Genome-Scale Metabolic Reconstruction and in Silico Perturbation Analysis of the Polar Diatom Fragilariopsis cylindrus P
d.g.e.piebes@uva.nl
Simultaneous Integration of Gene Expression and Nutrient Availability for Studying the Metabolism of Hepatocellular Carc
guodongs@njnu.edu.cn
Optimization and Scale-Up of Fermentation Processes Driven by Models
peter.neubauer@tu-berlin.de
TCA Cycle and Its Relationship with Clavulanic Acid Production: A Further Interpretation by Using a Reduced Genome-Scale
tomokazu.shirai@riken.jp
In Silico Design Strategies for the Production of Target Chemical Compounds Using Iterative Single-Level Linear Programm
tix@fh-aachen.de
Substrate Gas Utilization and C3/C4 Metabolic Analysis of Actinobacillus succinogenes: Integration into a Model for Ferm
bixinyu@stu.jiangnan.edu.cn
Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges
anna.stikane@lu.lv
Impact of Waste as a Substrate on Biomass Formation, and Optimization of Spent Microbial Biomass Re-Use by Sustainable M
irocha@unl.pt
A Genome-Scale Metabolic Model for the Human Pathogen Candida Parapsilosis and Early Identification of Putative Novel An
jnogales@cnb.csic.es
Optimized De Novo Eriodictyol Biosynthesis in Streptomyces albidoflavus Using an Expansion of the Golden Standard Toolki
zhuowang@sjtu.edu.cn
Genome-Scale Metabolic Model of Actinosynnema pretiosum ATCC 31280 and Its Application for Ansamitocin P-3 Production Im
n.plant@surrey.ac.uk
MUFINS: multi-formalism interaction network simulator
dheckmann@ucsd.edu
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
kkim@knu.ac.kr
Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase
venturelli@wisc.edu
Design of synthetic human gut microbiome assembly and butyrate production
zampieri@imsb.biol.ethz.ch
Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli
longliu@jiangnan.edu.cn
De novo biosynthesis of rubusoside and rebaudiosides in engineered yeasts
Gianni.Panagiotou@leibniz-hki.de
Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome
weidu@jlu.edu.cn
Local flux coordination and global gene expression regulation in metabolic modeling
linlu2019@sdu.edu.cn
Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium
i.s.roberts@manchester.ac.uk
A genome-scale metabolic model of parasitic whipworm
toerb@mpi-marburg.mpg.de
Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo
conggao@jiangnan.edu.cn
RETRACTED ARTICLE: Systems engineering of Escherichia coli for high-level glutarate production from glucose
Nouhin.hadadi@unige.ch
Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models
zhang_dw@tib.cas.cn
Protein engineering and iterative multimodule optimization for vitamin B6 production in Escherichia coli