cellbauhaus · 692 papers with claims · 473 for outreach · 167 old · 52 reviews
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Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth
Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis
Properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis
Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism
Underground metabolism as a rich reservoir for pathway engineering
Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction
Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis
From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry
Systematic inference of functional phosphorylation events in yeast metabolism
Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or e
Model-based media selection to minimize the cost of metabolic cooperation in microbial ecosystems
BeReTa: a systematic method for identifying target transcriptional regulators to enhance microbial production of chemica
A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium <i>Rhodotherm
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and
In Silico Knockout Screening of<i> Plasmodium falciparum</i> Reactions and Prediction of Novel Essential Reactions by An
Towards applications of genome‐scale metabolic model‐based approaches in designing synthetic microbial communities
Novel Computational Tools for Linking Genotypes to Microbial Community Phenotypes
A multi-level approach to study the metabolic effects of chronic exposure to Aldrin in prostate cancer cells
Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
Ecology-guided prediction of cross-feeding interactions in the human gut microbiome
Computational biology predicts metabolic engineering targets for increased production of 102 valuable chemicals in yeast
Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-base
Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina
Investigation of two metabolic engineering approaches for (R,R)-2,3-butanediol production from glycerol in Bacillus subt
Genome-Scale Modelling of Chinese Hamster Ovary Cells by Hybrid Semi-Parametric Flux Balance Analysis
Metabolic modelling of microalgae for wastewater treatment
Gene Deletion Algorithms for Minimum Reaction Network Design by Mixed-integer Linear Programming for Metabolite Producti
Engineering Escherichia coli for the utilization of ethylene glycol
Systems-level approaches for understanding and engineering of the oleaginous cell factory Yarrowia lipolytica
Towards Rational Design of Biosynthesis Pathways
A multiscale modelling framework for the processes involved in consolidated bioprocessing
Genome-Scale Metabolic Model Based Engineering of Escherichia Coli Enhances Recombinant Single Chain Antibody Fragment P
Computationally evaluating high-yield metabolites for sustainable aviation fuel (SAF) using machine learning
Untitled
Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions
Algal Systems for Resource Recovery from Waste and Wastewater
In silico patient: systems medicine approach to inborn errors of metabolism
Desenvolvimento de métodos de análises e integração de dados de ômicas aplicados à construção de leveduras industriais p
Unraveling redox metabolism in Escherichia coli
A Novel Method for the Integration of Stochastic Petri Net Simulation and Transcriptomic Data Applied to a Metabolic Pat
Constrain and conquer
Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models
Systems Biology Methods to Model Cancer Metabolism and Epigenetics for Drug Discovery
A method for dynamic flux balance analysis with global constraints
Application of machine learning in systems biology
Decoding Complexity in Metabolic Networks using Integrated Mechanistic and Machine Learning Approaches
Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models
Developing strategies for systems metabolic engineering of Pichia pastoris
Constraint-based modeling of metabolism - interpreting predictions of growth and ATP synthesis in human and yeast
Computing abundance constraints in Saccharomyces cerevisiae’s metabolism
Investigating host-microbiota cooperation with gap-filling optimization problems
Dissecting the Regulatory Network of Sphingolipid Biosynthesis in Plants
Engineering Molecules, Mineralization and Magnetism in Biology by Directed Evolution and Computation
Optimization of microbial cell factories with systems biology
Investigation of Metabolic Modeling Strategies to Predict Phenotypes of Microbial Mutants Under Data Scarcity
Model-guided Analysis of Plant Metabolism and Design of Metabolic Engineering Strategies
Prioritisation of candidate disease genes via multi-omics data integration
Discovering Essential Multiple Gene Effects Through Large Scale Optimization: An Application to Human Cancer Metabolism
Improved production of 2,3‐butanediol and isobutanol by engineering electron transport chain in Escherichia coli
Cross‐compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom<i>Phaeodactylum tricornut
Competition for nutrients increases invasion resistance during assembly of microbial communities
Assessing Escherichia coli metabolism models and simulation approaches in phenotype predictions: Validation against expe
CHOmpact: A reduced metabolic model of Chinese hamster ovary cells with enhanced interpretability
Systems‐level approaches for understanding and engineering of the oleaginous cell factory <i>Yarrowia lipolytica</i>
Systems biology for crop improvement
Trade‐offs between the instantaneous growth rate and long‐term fitness: Consequences for microbial physiology and predic
Harnessing metabolic plasticity in CHO cells for enhanced perfusion cultivation
Synthesizing Systems Biology Knowledge from Omics Using Genome‐Scale Models
How reliable are Chinese hamster ovary (CHO) cell genome‐scale metabolic models?
Network reduction methods for genome-scale metabolic models.
Model validation and selection in metabolic flux analysis and flux balance analysis
Multi‐omic data integration and exploiting metabolic models using systems biology approach increase precision in subtypi
<i>Clostridioides difficile</i> 630Δ<i>erm in silico</i> and <i>in vivo</i> – quantitative growth and extensive polysacc
Genome‐scale metabolic models applied for human health and biopharmaceutical engineering
Optimized elemental sulfur recovery from sulfide-containing streams applying systems biology and genome-scale metabolic
Mitigating biomass composition uncertainties in flux balance analysis using ensemble representations
Synthetic biology tools for environmental protection
Retrosynthetic design of metabolic pathways to chemicals not found in nature
Systems biology's role in leveraging microalgal biomass potential: Current status and future perspectives
A model-driven approach to upcycling recalcitrant feedstocks in Pseudomonas putida by decoupling PHA production from nut
Predicting metabolic fluxes from omics data via machine learning: Moving from knowledge-driven towards data-driven appro
Improving designer glycan production in Escherichia coli through model-guided metabolic engineering
Enzyme-constrained metabolic model and in silico metabolic engineering of Clostridium ljungdahlii for the development of
Unstructured kinetic models to simulate an arabinose switch that decouples cell growth from metabolite production
Automated generation of bacterial resource allocation models
A genome-scale dynamic constraint-based modelling (gDCBM) framework predicts growth dynamics, medium composition and int
Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae
Synthetic Microbial Cocultivation for Targeted Production of Odd-Chain Carboxylates and Alcohols from Carbon Monoxide
Computational Framework for Machine-Learning-Enabled 13C Fluxomics.
Systems analysis of minimal metabolic networks In prokaryotes
Genomic and metabolic plasticity drive alternative scenarios for adapting <i>Pseudomonas putida</i> to non-native substr
A method to identify high consensus predictions of single-cell metabolic flux
Simulation of biochemical systems using constraint-based methods and complex networks
Metabolic characterization and viable delivery of Akkermansia muciniphila for its future application
Transcriptional landscapes of lipid producing microalgae
Microbiome.config : Deciphering microbial lifestyles for rational design of plant growth promoting communities
Enzyme promiscuity approaches to predict metabolic pathways in the human gut microbiota.
Model-Based Hypothesis Testing in Biomedicine : How Systems Biology Can Drive the Growth of Scientific Knowledge
Metabolic flux analysis in Euglena gracilis
Computational approaches for understanding one-carbon metabolism in cancer
Model-driven evaluation of microbial physiology: insights from protein allocation
Integrating a dynamic central metabolism model of cancer cells with a hybrid 3D multiscale model for vascular hepatocell
Bridging substrate intake kinetics and bacterial growth phenotypes with flux balance analysis incorporating proteome all
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shi
Predicting the decision making chemicals used for bacterial growth
Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections
Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediati
Fine-tuning mitochondrial activity in Yarrowia lipolytica for citrate overproduction
Pichia pastoris growth—coupled heme biosynthesis analysis using metabolic modelling
Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic mod
Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression
Diverse classes of constraints enable broader applicability of a linear programming-based dynamic metabolic modeling fra
High Production of 3-Hydroxypropionic Acid in Klebsiella pneumoniae by Systematic Optimization of Glycerol Metabolism
Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states
Sequence Specific Modeling of E. coli Cell-Free Protein Synthesis
Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach
Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis
Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion
Improving Designer Glycan Production in <i>Escherichia coli</i> through Model-Guided Metabolic Engineering
Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth cond
Combining multiple functional annotation tools increases coverage of metabolic annotation
The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of
Bayesian genome scale modelling identifies thermal determinants of yeast metabolism
Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence
Systematically gap-filling the genome-scale metabolic model of CHO cells
Development of a genome-scale metabolic model of <i>Clostridium thermocellum</i> and its applications for integration of
Enzyme capacity-based genome scale modelling of CHO cells
Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resi
Ecology-guided prediction of cross-feeding interactions in the human gut microbiome
Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm
Systematic evaluation of parameters for genome-scale metabolic models of cultured mammalian cells
Modeling a co-culture of <i>Clostridium autoethanogenum</i> and <i>Clostridium kluyveri</i> to increase syngas conversio
Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multiomics integration
ΔFBA: Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data
Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism
A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the i
<i>In silico</i> analysis of the fast-growing thermophile <i>Geobacillus</i> sp. LC300 using a novel genome-scale metabo
Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
Elucidating Tumor-stromal Metabolic Crosstalk in Colorectal Cancer through Integration of Constraint-Based Models and LC
A genome-scale metabolic model of <i>Saccharomyces cerevisiae</i> that integrates expression constraints and reaction th
Genome-scale modeling of <i>Pseudomonas aeruginosa</i> PA14 unveils its broad metabolic capabilities and role of metabol
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
Diverse classes of constraints enable broader applicability of a linear programming-based dynamic metabolic modeling fra
Melhoria experimental por auditoria e alisamento de dados: aplicação em produção de biopolímero..
ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualizati
The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism
Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism
Predicting microbial interactions with approaches based on flux balance analysis: an evaluation
RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in ch
ICON-GEMs: integration of co-expression network in genome-scale metabolic models, shedding light through systems biology
Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina
Combining multiple functional annotation tools increases coverage of metabolic annotation
High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
Automatic construction of metabolic models with enzyme constraints
Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica
Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enabl
Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z
OptPipe - a pipeline for optimizing metabolic engineering targets
Improved production of Taxol® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering
Metabolic engineering of Synechococcus elongatus PCC 7942 for improvement of 1,3-propanediol and glycerol production bas
A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory
Modelling overflow metabolism in Escherichia coli with flux balance analysis incorporating differential proteomic effici
Systems biology of the structural proteome
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework
Fast exchange fluxes around the pyruvate node: a leaky cell model to explain the gain and loss of unlabelled and labelle
On the optimality of the enzyme–substrate relationship in bacteria
Elucidating genomic gaps using phenotypic profiles
Elucidating genomic gaps using phenotypic profiles
Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of pr
lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target m
An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment
OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for ana
OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling
Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model
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
In silico co-factor balance estimation using constraint-based modelling informs metabolic engineering in Escherichia col
From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline
BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale
E-Flux2 and SPOT: Validated Methods for Inferring Intracellular Metabolic Flux Distributions from Transcriptomic Data
Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom
Type and capacity of glucose transport influences succinate yield in two-stage cultivations
Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Develop
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
Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis
Ethanol production improvement driven by genome-scale metabolic modeling and sensitivity analysis in Scheffersomyces sti
Distributed flux balance analysis simulations of serial biomass fermentation by two organisms
Metabolic flux configuration determination using information entropy
Flux prediction using artificial neural network (ANN) for the upper part of glycolysis
Osmoregulation in the Halophilic Bacterium Halomonas elongata: A Case Study for Integrative Systems Biology
Constraints-based analysis identifies NAD+ recycling through metabolic reprogramming in antibiotic resistant Chromobacte
<i>Vibrio natriegens</i> genome‐scale modeling reveals insights into halophilic adaptations and resource allocation
A study of a diauxic growth experiment using an expanded dynamic flux balance framework
Microbiome distribution modeling using gradient descent strategies for mock, in vitro and clinical community distributio
Evaluating <i>E. coli</i> genome‐scale metabolic model accuracy with high‐throughput mutant fitness data
Genome‐scale metabolic modeling reveals key features of a minimal gene set
The Evolution of Cell Free Biomanufacturing
ecBSU1: A Genome-scale Enzyme-constrained Model of <em>Bacillus subtilis</em> based on the ECMpy Workflow
A new metabolic model of<i>Drosophila melanogaster</i>and the integrative analysis of Parkinson’s disease
Comprehensive genome-scale metabolic model of the human pathogen Cryptococcus neoformans: A platform for understanding p
Multi-scale models of whole cells: progress and challenges
A Computational Framework to Identify Metabolic Engineering Strategies for the Co-Production of Metabolites
Mapping the Physiological Response of Oenococcus oeni to Ethanol Stress Using an Extended Genome-Scale Metabolic Model
Combination of Genome-Scale Models and Bioreactor Dynamics to Optimize the Production of Commodity Chemicals
From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model
Model-driven approach for the production of butyrate from CO2/H2 by a novel co-culture of C. autoethanogenum and C. beij
A Systematic Strategy to Find Potential Therapeutic Targets for Pseudomonas aeruginosa Using Integrated Computational Mo
DataSheet1_Understanding Metabolic Flux Behaviour in Whole-Cell Model Output.pdf
Reconstructed Metabolic Network Models Predict Flux-Level Metabolic Reprogramming in Glioblastoma
Understanding Antimicrobial Resistance Using Genome-Scale Metabolic Modeling
Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology
Questions, data and models underpinning metabolic engineering
Control Theory and Systems Biology: Potential Applications in Neurodegeneration and Search for Therapeutic Targets
A Two-Compartment Fermentation System to Quantify Strain-Specific Interactions in Microbial Co-Cultures
From Shallow to Deep Bioprocess Hybrid Modeling: Advances and Future Perspectives
Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine
Reconstruction of a Genome-Scale Metabolic Model of Streptomyces albus J1074: Improved Engineering Strategies in Natural
Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic Signatures
Machine Learning Methods for Analysis of Metabolic Data and Metabolic Pathway Modeling
Dynamic Sequence Specific Constraint-Based Modeling of Cell-Free Protein Synthesis
ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow
Arduino Soft Sensor for Monitoring Schizochytrium sp. Fermentation, a Proof of Concept for the Industrial Application of
A Genome-Scale Metabolic Model of Thalassiosira pseudonana CCMP 1335 for a Systems-Level Understanding of Its Metabolism
Uncovering Novel Pathways for Enhancing Hyaluronan Synthesis in Recombinant Lactococcus lactis: Genome-Scale Metabolic M
The Evolution of Cell Free Biomanufacturing
Biosynthesis of fatty acids and biosurfactants by the yeast Yarrowia lipolytica with emphasis on metabolic networks and
Dissecting the Metabolic Reprogramming of Maize Root under Nitrogen Limiting Stress Condition
Data integration across conditions improves turnover number estimates and metabolic predictions
A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium <i>Rhodotherm
Quantifying the propagation of parametric uncertainty on flux balance analysis
A universal dynamical metabolic model representing mixotrophic growth of Chlorella sp
A study of a diauxic growth experiment using an expanded dynamic flux balance framework
Phenotype-Centric Modeling for Rational Metabolic Engineering
Data-Driven Flow-Map Models for Data-Efficient Discovery of Dynamics and Fast Uncertainty Quantification of Biological a
Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism
Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model
MAMBA: a model-driven, constraint-based multiomic integration method
mergem : merging and comparing genome-scale metabolic models using universal identifiers
A Novel Algorithm to Calculate Elementary Modes: Analysis of Campylobacter jejuni Metabolism
Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling
Novel Context-Specific Genome-Scale Modelling Explores the Potential of <i>Chlamydomonas reinhardtii</i> for Synthetic B
Model-driven approach for the production of butyrate from CO <sub>2</sub> /H <sub>2</sub> by a novel co-culture of <i>C.
Analysis of the genome-scale metabolic model of <i>Bacillus subtilis</i> to design novel in-silico strategies for native
Debottlenecking and reformulating feed media for improved CHO cell growth and titer by data-driven and model-guided anal
Sulfate limitation increases specific plasmid DNA yield and productivity in <i>E. coli</i> fed-batch processes
Proteomics and constraint-based modelling reveal enzyme kinetic properties of <i>Chlamydomonas reinhardtii</i> on a geno
Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states
Integrated Constraint-Based Modeling of E. coli Cell-Free Protein Synthesis
CFSA: Comparative Flux Sampling Analysis as a Guide for Strain Design
BayFlux: A <i>Bay</i> esian method to quantify metabolic <i>Flux</i> es and their uncertainty at the genome scale
Genome-scale metabolic models consistently predict <i>in vitro</i> characteristics of <i>Corynebacterium striatum</i>
lista -GEM: the genome-scale metabolic reconstruction of Lipomyces starkeyi
Machine learning predicts system-wide metabolic flux control in cyanobacteria
A new genome-scale metabolic model of oleaginous microalgae with refined lipid metabolism elucidates Microchloropsis gad
Multi-omic characterization of antibody-producing CHO cell lines elucidates metabolic reprogramming and nutrient uptake
COSMIC-dFBA: A novel multi-scale hybrid framework for bioprocess modeling
Understanding systems level metabolic adaptation resulting from osmotic stress
Quantitative differences in anaerobic growth and metabolism of three different <i>E. coli</i> strains using <sup>13</sup
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
A constraint-based framework to reconstruct interaction networks in microbial communities
BayesianSSA: a Bayesian statistical model based on structural sensitivity analysis for predicting responses to enzyme pe
Entangled stoichiometric objectives shape microbial catabolism
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework
Uncovering novel pathways for enhancing hyaluronan synthesis in recombinant <i>Lactococcus lactis</i> : Genome-scale met
A metabolic reconstruction of <i>Lactobacillus reuteri</i> JCM 1112 and analysis of its potential as a cell factory
MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering
Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism
Modeling genome-wide evolution of catalytic turnover rates: Strong epistasis shaped modern enzyme kinetics
A comprehensive genome-scale model for <i>Rhodosporidium toruloides</i> IFO0880 accounting for functional genomics and p
Predictive engineering and optimization of tryptophan metabolism in yeast through a combination of mechanistic and machi
Flux-based hierarchical organization of Escherichia coli ’s metabolic network
Charting the metabolic landscape of the facultative methylotroph Bacillus methanolicus
A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks
Pangenome Flux Balance Analysis Toward Panphenomes
Modeling population heterogeneity from microbial communities to immune response in cells
Substrate type and CO2 addition significantly influence succinic acid production of Basfia succiniciproducens
Multi-omic data integration enables discovery of hidden biological regularities
A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
Enzyme I facilitates reverse flux from pyruvate to phosphoenolpyruvate in Escherichia coli
Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale
Artificial neural networks enable genome-scale simulations of intracellular signaling
Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism
Spatial-fluxomics provides a subcellular-compartmentalized view of reductive glutamine metabolism in cancer cells
The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models
A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodyn
Characterizing cancer metabolism from bulk and single-cell RNA-seq data using METAFlux
The protein translation machinery is expressed for maximal efficiency in Escherichia coli
Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resi
Data integration across conditions improves turnover number estimates and metabolic predictions
Proteome allocations change linearly with the specific growth rate of Saccharomyces cerevisiae under glucose limitation
An unconventional uptake rate objective function approach enhances applicability of genome-scale models for mammalian ce
Teasing out missing reactions in genome-scale metabolic networks through hypergraph learning
Bayesian genome scale modelling identifies thermal determinants of yeast metabolism
Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source
A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models
Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scal
Rational strain design with minimal phenotype perturbation
13C-metabolic flux analysis of respiratory chain disrupted strain ΔndhF1 of Synechocystis sp. PCC 6803
AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities
Metabolic network model guided engineering ethylmalonyl-CoA pathway to improve ascomycin production in Streptomyces hygr
H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum
Christoph; Waschina, Silvio
s.waschina@nutrinf.uni-kiel.de
gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
ViewPanikov, Nicolai
n.panikov@northeastern.edu
Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes and Challenges
ViewHenk; Chu, Ju
juchu@ecust.edu.cn
Multi-omics integrative analysis with genome-scale metabolic model simulation reveals global cellular adaptation of Aspe
ViewPayam; Zare, Habil
zare@uthscsa.edu
Rapid-SL identifies synthetic lethal sets with an arbitrary cardinality
ViewEvangelos; Baliga, Nitin S.; Aitchison
nbaliga@systemsbiology.org
Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast
ViewAlter, Tobias B.; Blank
tobias.alter@rwth-aachen.de
Michael; Zanghellini, Jürgen
juergen.zanghellini@univie.ac.at
David; Lercher, Martin J.
martin.lercher@hhu.de
Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning
ViewJingyi; Ma, Hongwu
ma_hw@tib.cas.cn
Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models
ViewGlobal connectivity in genome-scale metabolic networks revealed by comprehensive FBA-based pathway analysis
ViewChiara; Pescini, Dario
dario.pescini@unimib.it
GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction
ViewEliza J. R.; Baliga, Nitin S.
nitin.baliga@isbscience.org
Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks of <i>Mycobacterium tubercul
ViewPaulo; Rocha, Miguel; Rocha
mrocha@di.uminho.pt
Comparison of pathway analysis and constraint-based methods for cell factory design
ViewA pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale
ViewA pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale
ViewDaniel; Yoon, Sung Ho
syoon@konkuk.ac.kr
Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks
ViewShuhei; Shirai, Tomokazu; Kondo
tomokazu.shirai@riken.jp
Investigation of two metabolic engineering approaches for (R,R)-2,3-butanediol production from glycerol in Bacillus subt
ViewTerence; Martin, Olivier; Martino
andrea.demartino@roma1.infn.it
Pieter C.; Zengler, Karsten
kzengler@ucsd.edu
Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
ViewA genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollut
ViewSynthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth
ViewNoushin; Hatzimanikatis, Vassily
vassily.hatzimanikatis@epfl.ch
Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically con
ViewNathan; Palsson, Bernhard Ø.
palsson@ucsd.edu
Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types
ViewKeith E. J.; Bomble, Yannick J.
Yannick.Bomble@nrel.gov
Bayesian inference of metabolic kinetics from genome-scale multiomics data
ViewZahra; Nikoloski, Zoran
nikoloski@mpimp-golm.mpg.de
Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the p
ViewAlvar A.; Poyatos, Juan F.
jpoyatos@cnb.csic.es
Zhitao; Mao, Yufeng; Wu
mao_zt@tib.cas.cn
Construction and Analysis of an Enzyme‐constrained Metabolic Model of <em>Corynebacterium glutamicum</em>
ViewECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model
ViewYara; Almaas, Eivind
eivind.almaas@ntnu.no
Phenotypic response of yeast metabolic network to availability of proteinogenic amino acids
ViewAdil; Saha, Rajib
rsaha2@unl.edu
Characterizing the interplay of rubisco and nitrogenase enzymes in anaerobic-photoheterotrophically grown <i>Rhodopseudo
Viewm.heinemann@rug.nl
Unbiased metabolic flux inference through combined thermodynamic and 13 C flux analysis
mfishel@iu.edu
A graph neural network model to estimate cell-wise metabolic flux using single cell RNA-seq data
msampaio@ceb.uminho.pt
A diel multi-tissue genome-scale metabolic model of Vitis vinifera
j.nogales@csic.es
Metabolic modelling approaches for describing and engineering microbial communities
xuqin523@sjtu.edu.cn
Theoretical Studies of Intracellular Concentration of Micro-organisms’ Metabolites
s.a.wahl@tudelft.nl
Alpha-ketoglutarate utilization in Saccharomyces cerevisiae: transport, compartmentation and catabolism
alok.kumar.patel@ltu.se
Data-driven synthetic microbes for sustainable future
pauloepburke@gmail.com
A biochemical network modeling of a whole-cell
salis@psu.edu
Automated Parameterization of Predictive Kinetic Metabolic Models from Sparse Datasets for Efficient Optimization of Man
melissa.kemp@bme.gatech.edu
Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors
sahar.elaidy@rug.nl
Understanding the host-microbe interactions using metabolic modeling
wendel.silveira@ufv.br
Protein Abundance Prediction Through Machine Learning Methods
trevor.nicks@tufts.edu
Analysis of Metabolic Network Disruption in Engineered Microbial Hosts due to Enzyme Promiscuity
petri.lahtvee@ut.ee
Xylose Metabolism and the Effect of Oxidative Stress on Lipid and Carotenoid Production in <i>Rhodotorula toruloides</i>
david.ruckerbauer@univie.ac.at
Inclusion of maintenance energy improves the intracellular flux predictions of CHO
xqian@ece.tamu.edu
TRIMER: Transcription Regulation Integrated with MEtabolic Regulation
peter.gawthrop@unimelb.edu.au
Modular Dynamic Biomolecular Modelling with Bond Graphs: The Unification of Stoichiometry, Thermodynamics, Kinetics and
pierre.millard@insa-toulouse.fr
Control and regulation of acetate overflow in Escherichia coli
e.yaneske@tees.ac.uk
The poly-omics of ageing through individual-based metabolic modelling
nuno.mira@ist.utl.pt
MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering
mmoll@rice.edu
Improving the organization and interactivity of metabolic pathfinding with precomputed pathways
dominique.schneider@ujf-grenoble.fr
Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evo
yanq2@vcu.edu
Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model
dmontoyac@unal.edu.co
Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of
alara@correo.cua.uam.mx
Heterogeneous oxygen availability affects the titer and topology but not the fidelity of plasmid DNA produced by Escheri
krishna.mahadevan@utoronto.ca
Engineering Escherichia coli for the utilization of ethylene glycol
nunthaphan.vikromvarasiri@riken.jp
Metabolic engineering design to enhance (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis based on flux
nidelet@supagro.inra.fr
Diversity of flux distribution in central carbon metabolism of S. cerevisiae strains from diverse environments
jyxia@ecust.edu.cn
Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions
lyang@eng.ucsd.edu
DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression
sun_jb@tib.cas.cn
Systems metabolic engineering for citric acid production by Aspergillus niger in the post-genomic era
irocha@itqb.unl.pt
Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate
f.brancodossantos@uva.nl
Alignment of microbial fitness with engineered product formation: obligatory coupling between acetate production and pho
karsten.hiller@uni.lu
Bridging the gap between non-targeted stable isotope labeling and metabolic flux analysis
byungkim@snu.ac.kr
In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by gen
david.heckmann@hhu.de
Deep learning allows genome-scale prediction of Michaelis constants from structural features
forrest.bao@gmail.com
Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming
vitor.martinsdossantos@wur.nl
Efficient Reconstruction of Predictive Consensus Metabolic Network Models
anne.siegel@irisa.fr
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks
pde_atauri@ub.edu
p13CMFA: Parsimonious 13C metabolic flux analysis
mesbah@berkeley.edu
Fast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansions
d.beste@surrey.ac.uk
A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks
alejandro.zepeda@correo.uady.mx
The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predi
jane.hawkey@monash.edu
Impact of insertion sequences on convergent evolution of Shigella species
lium@tsinghua.edu.cn
PyMiner: A method for metabolic pathway design based on the uniform similarity of substrate-product pairs and conditiona
mauriceling@colossus-tech.com
Of (Biological) Models and Simulations
joaquin.dopazo@juntadeandalucia.es
A Mechanistic Model for Genome-Scale Estimations of Metabolic Activity
k.borah@surrey.ac.uk
Dissecting Host-Pathogen Interactions in TB Using Systems-Based Omic Approaches
clelia.peano@itb.cnr.it
Time-Resolved Transcriptomics and Constraint-Based Modeling Identify System-Level Metabolic Features and Overexpression
jheath@isbscience.org
Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer
ines.thiele@uni.lu
MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models
abeck@carroll.edu
Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities
peter.neubauer@tu-berlin.de
TCA Cycle and Its Relationship with Clavulanic Acid Production: A Further Interpretation by Using a Reduced Genome-Scale
ypzhuang@ecust.edu.cn
From Spatial-Temporal Multiscale Modeling to Application: Bridging the Valley of Death in Industrial Biotechnology
dlagoa@ceb.uminho.pt
Genome-Scale Metabolic Model of the Human Pathogen Candida albicans: A Promising Platform for Drug Target Prediction
m.yamamoto@nibiohn.go.jp
Prediction of Metabolic Flux Distribution by Flux Sampling: As a Case Study, Acetate Production from Glucose in Escheric
bixinyu@stu.jiangnan.edu.cn
Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges
Carrie.Eckert@nrel.gov
The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels
chechung@umich.edu
Next-Generation Genome-Scale Metabolic Modeling through Integration of Regulatory Mechanisms
z.iqbal@my.westminster.ac.uk
State-of-the-Art Genetic Modalities to Engineer Cyanobacteria for Sustainable Biosynthesis of Biofuel and Fine-Chemicals
dipali.singh@quadram.ac.uk
Genome-Scale Metabolic Modelling Approach to Understand the Metabolism of the Opportunistic Human Pathogen Staphylococcu
steffen.waldherr@kuleuven.be
A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models
kzengler@eng.ucsd.edu
Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data
ruimiguel.x.correiaportela@gsk.com
Time Integrated Flux Analysis: Exploiting the Concentration Measurements Directly for Cost-Effective Metabolic Network F
zhuangrong_huang@student.uml.edu
Integration of Time-Series Transcriptomic Data with Genome-Scale CHO Metabolic Models for mAb Engineering
kornecki@itv.tu-clausthal.de
Accelerating Biologics Manufacturing by Upstream Process Modelling
bartoshunor@uni.sapientia.ro
Production of High Added-Value Chemicals in Basfia succiniciproducens: Role of Medium Composition
pasquale.palumbo@unimib.it
Parameter Identification in Metabolic Reaction Networks by Means of Multiple Steady-State Measurements
lavandosque@usp.br
Polyamine-Mediated Growth Regulation in Microalgae: Integrating Redox Balance and Amino Acids Pathway into Metabolic Eng
5robert.hall@wur.nl
Parameter estimation in tree graph metabolic networks
ssdatta@princeton.edu
Microbial mutualism generates multistable and oscillatory growth dynamics
ioscani.jimenezdelval@ucd.ie
CHOmpact: A reduced metabolic model of Chinese hamster ovary cells with enhanced interpretability
wilkenst@hhu.de
Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models
william.scott@wur.nl
Dynamic genome-scale modeling of <i>Saccharomyces cerevisiae</i> unravels mechanisms for ester formation during alcoholi
mamori@ucsd.edu
Functional Decomposition of Metabolism allows a system-level quantification of fluxes and protein allocation towards spe
nielsenj@chalmers.se
Computational biology predicts metabolic engineering targets for increased production of 102 valuable chemicals in yeast
kelly.wyres@monash.edu
Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models
onogiakio@gmail.com
A Bayesian model for genomic prediction using metabolic networks
yang_x@tib.cas.cn
The necessity of considering enzymes as compartments in constraint-based genome-scale metabolic models
riccardo.milanesi@unimib.it
Time-resolved, deuterium-based fluxomics uncovers the hierarchy and dynamics of sugar processing by <i>Pseudomonas putid
sgibbons@isbscience.org
Microbial community-scale metabolic modeling predicts personalized short chain fatty acid production profiles in the hum
ina.koch@bioinformatik.uni-frankfurt.de
Stochastic modeling of the dynamics of Salmonella infection of epithelial cells
meineboer@gmail.com
Improving genome-scale metabolic models of incomplete genomes with deep learning
samrat.chatterjee@thsti.res.in
Targeting metabolic fluxes reverts metastatic transitions in ovarian cancer
jplfaria@anl.gov
ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway pred
daizw@sustech.edu.cn
Unraveling principles of thermodynamics for genome-scale metabolic networks using graph neural networks
tiagoaomendes@ufv.br
First Genome-Scale Metabolic Modeling of <i>Brucella abortus</i> Predicts Pathogen Gene Essentiality and New Drug Target
aidong.yang@eng.ox.ac.uk
DLTKcat: deep learning based prediction of temperature dependent enzyme turnover rates
thorsen@ll.mit.edu
Experiments and simulations on short chain fatty acid production in a colonic bacterial community
a.succurro@uni-koeln.de
Emergent sub-population behavior uncovered with a community dynamic metabolic model of <i>Escherichia coli</i> diauxic g
b.m.bakker01@umcg.nl
Cofactors revisited – Predicting the impact of flavoprotein-related diseases on a genome scale
LeonorGuedesdaSilva@gmail.com
Revealing metabolic flexibility of <i>Candidatus</i> Accumulibacter phosphatis through redox cofactor analysis and metab
porob@post.bgu.ac.il
Genome-Scale reconstruction of <i>Paenarthrobacter aurescens</i> TC1 metabolic model towards the study of atrazine biore
jegallagher@mail.wvu.edu
Effects of MCHM on yeast metabolism
mhenson@umass.edu.
Metabolic Modeling of Cystic Fibrosis Airway Communities Predicts Mechanisms of Pathogen Dominance
suvi.santala@tuni.fi
Wax ester production in nitrogen-rich conditions by metabolically engineered <i>Acinetobacter baylyi</i> ADP1
paul.hudson@scilifelab.se
Pooled CRISPRi screening of the cyanobacterium <i>Synechocystis</i> sp. PCC 6803 for enhanced growth, tolerance, and che
pnsaa@uc.cl
Metabolic modeling of Halomonas campaniensis improves polyhydroxybutyrate production under nitrogen limitation
baojun.wang@ed.ac.uk
Scaling up genetic circuit design for cellular computing: advances and prospects
Olivier.hamant@ens-lyon.fr
What is quantitative plant biology?
dheckmann@ucsd.edu
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
jvorholt@ethz.ch
Methanol-dependent Escherichia coli strains with a complete ribulose monophosphate cycle
zhang_dw@tib.cas.cn
Protein engineering and iterative multimodule optimization for vitamin B6 production in Escherichia coli
leesy@kaist.ac.kr
Targeted and high-throughput gene knockdown in diverse bacteria using synthetic sRNAs
tania.dottorini@nottingham.ac.uk
Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken f
niall.mangan@northwestern.edu
Modelling the pyrenoid-based CO2-concentrating mechanism provides insights into its operating principles and a roadmap f
moritz.x.von-stosch@gsk.com
Towards a widespread adoption of metabolic modeling tools in biopharmaceutical industry: a process systems biology engin