R3MG9M last accessed: 2022-11-04

BiGG_Models
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:07.345797

Other names: BIGG Database, Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions, BiGG_Models

BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. BiGG Models integrates more than 70 published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs.

Webpage:

http://bigg.ucsd.edu

Licence:

Name: BIGG Licence
URL: http://bigg.ucsd.edu/license#license

Publications:

Publications
More detailed information about this field from each metasource.

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
PMID: 26476456
metasource: Fairsharing.org
version: FAIRsharing.org: BiGG Models; BiGG Models; DOI: https://doi.org/10.25504/FAIRsharing.va62ke; Last edited: Feb. 7, 2021, 9:11 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
PMID: 20426874
metasource: Fairsharing.org
version: FAIRsharing.org: BiGG Models; BiGG Models; DOI: https://doi.org/10.25504/FAIRsharing.va62ke; Last edited: Feb. 7, 2021, 9:11 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
PMID: 31696234
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:07.345797

http://dx.doi.org/10.1093/nar/gkv1049
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models PubMed citations: 252.

252 articles citing: BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

A diagnostic model for overweight and obesity from untargeted urine metabolomics of soldiers. PMID:35898940
Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer. PMID:35875150
Genome-scale metabolic network models: from first-generation to next-generation. PMID:35829788
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis. PMID:35689204
Computational identification of protein complexes from network interactions: Present state, challenges, and the way forward. PMID:35685359
Dynamic proteome allocation regulates the profile of interaction of auxotrophic bacterial consortia. PMID:35592760
Horizontal gene transfer drives the evolution of dependencies in bacteria. PMID:35586069
ERMer: a serverless platform for navigating, analyzing, and visualizing Escherichia coli regulatory landscape through graph database. PMID:35489073
Network Reconstruction and Modelling Made Reproducible with moped. PMID:35448462
PyMiner: A method for metabolic pathway design based on the uniform similarity of substrate-product pairs and conditional search. PMID:35404943
Fluxomics - New Metabolomics Approaches to Monitor Metabolic Pathways. PMID:35387341
Contribution of genome-scale metabolic modelling to niche theory. PMID:35384214
Protein cost minimization promotes the emergence of coenzyme redundancy. PMID:35344442
COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. PMID:35320266
Reconstruction of a generic genome-scale metabolic network for chicken: Investigating network connectivity and finding potential biomarkers. PMID:35316277
Totoro: Identifying Active Reactions During the Transient State for Metabolic Perturbations. PMID:35281848
Can kidney parenchyma metabolites serve as prognostic biomarkers for long-term kidney function after nephrectomy for renal cell carcinoma? A preliminary study. PMID:35261758
DBHR: a collection of databases relevant to human research. PMID:35251694
Computational Models for Clinical Applications in Personalized Medicine-Guidelines and Recommendations for Data Integration and Model Validation. PMID:35207655
CobraMod: A pathway-centric curation tool for constraint-based metabolic models. PMID:35201291
Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models. PMID:35196325
Pathway Driven Target Selection in Klebsiella pneumoniae: Insights Into Carbapenem Exposure. PMID:35174104
Vivarium: an interface and engine for integrative multiscale modeling in computational biology. PMID:35134830
Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds. PMID:35108266
Project-based learning course on metabolic network modelling in computational systems biology. PMID:35085230
Genome-Scale Modeling Specifies the Metabolic Capabilities of Rhizophagus irregularis. PMID:35076269
Metagenome-Scale Metabolic Network Suggests Folate Produced by Bifidobacterium longum Might Contribute to High-Fiber-Diet-Induced Weight Loss in a Prader-Willi Syndrome Child. PMID:34946095
A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations. PMID:34907432
Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling. PMID:34887435
eQuilibrator 3.0: a database solution for thermodynamic constant estimation. PMID:34850162
Proteomic characterization of GSK3β knockout shows altered cell adhesion and metabolic pathway utilisation in colorectal cancer cells. PMID:34739494
A gap-filling algorithm for prediction of metabolic interactions in microbial communities. PMID:34723959
A Beginner's Guide to the COBRA Toolbox. PMID:34719002
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS). PMID:34635859
Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient. PMID:34630943
metaGEM: reconstruction of genome scale metabolic models directly from metagenomes. PMID:34614189
Genome Scale Modeling to Study the Metabolic Competition between Cells in the Tumor Microenvironment. PMID:34572839
Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models. PMID:34455914
Bayesian metamodeling of complex biological systems across varying representations. PMID:34453000
TCA Cycle and Its Relationship with Clavulanic Acid Production: A Further Interpretation by Using a Reduced Genome-Scale Metabolic Model of Streptomyces clavuligerus. PMID:34436106
PolyRound: Polytope rounding for random sampling in metabolic networks. PMID:34329395
Genome-scale metabolic modeling reveals key features of a minimal gene set. PMID:34288418
Nitrogenous Compound Utilization and Production of Volatile Organic Compounds among Commercial Wine Yeasts Highlight Strain-Specific Metabolic Diversity. PMID:34287034
Microbial production of advanced biofuels. PMID:34172951
Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. PMID:34161321
Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals. PMID:34129600
Mechanistic models of microbial community metabolism. PMID:34125127
Towards a Systems Biology Approach to Understanding the Lichen Symbiosis: Opportunities and Challenges of Implementing Network Modelling. PMID:34012428
From integrative structural biology to cell biology. PMID:33957123
In silico Design for Systems-Based Metabolic Engineering for the Bioconversion of Valuable Compounds From Industrial By-Products. PMID:33868371
A key role for the transporter OAT1 in systemic lipid metabolism. PMID:33785360
Genome-scale metabolic model of the diatom Thalassiosira pseudonana highlights the importance of nitrogen and sulfur metabolism in redox balance. PMID:33760840
A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives. PMID:33741955
Development of a Genome-Scale Metabolic Model and Phenome Analysis of the Probiotic Escherichia coli Strain Nissle 1917. PMID:33672760
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis. PMID:33602294
Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus. PMID:33594000
Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides. PMID:33585414
PhenoMapping: a protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models. PMID:33532729
Understanding the host-microbe interactions using metabolic modeling. PMID:33472685
Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations. PMID:33467644
Review on natural products databases: where to find data in 2020. PMID:33431011
Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools. PMID:33335687
From Glucose to Lactate and Transiting Intermediates Through Mitochondria, Bypassing Pyruvate Kinase: Considerations for Cells Exhibiting Dimeric PKM2 or Otherwise Inhibited Kinase Activity. PMID:33335484
A Multi-Scale Approach to Modeling E. coli Chemotaxis. PMID:33286869
Thermodynamic Limits and Optimality of Microbial Growth. PMID:33286054
High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies. PMID:33281796
Metabolic flux configuration determination using information entropy. PMID:33275628
Environmental flexibility does not explain metabolic robustness. PMID:33247119
GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level. PMID:33245091
Methanol-dependent Escherichia coli strains with a complete ribulose monophosphate cycle. PMID:33106470
Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media. PMID:33097709
Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence. PMID:33082337
Systematically gap-filling the genome-scale metabolic model of CHO cells. PMID:33040240
Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri. PMID:33004914
Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models. PMID:32994290
Minimizing the number of optimizations for efficient community dynamic flux balance analysis. PMID:32991583
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. PMID:32986834
Mapping the bacterial metabolic niche space. PMID:32985497
Metabolic reconstruction of Pseudomonas chlororaphis ATCC 9446 to understand its metabolic potential as a phenazine-1-carboxamide-producing strain. PMID:32984920
Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design. PMID:32974289
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production. PMID:32942174
Providing new insights on the biphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling. PMID:32925899
Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology. PMID:32850764
Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4. PMID:32804944
Defining the nutritional input for genome-scale metabolic models: A roadmap. PMID:32797084
Publishing reproducible dynamic kinetic models. PMID:32793969
Isolating structural errors in reaction networks in systems biology. PMID:32790862
Linking metabolic phenotypes to pathogenic traits among "Candidatus Liberibacter asiaticus" and its hosts. PMID:32753656
Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation. PMID:32747737
BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint. PMID:32703160
Continuous Cultivation as a Tool Toward the Rational Bioprocess Development With Pichia Pastoris Cell Factory. PMID:32671036
Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling. PMID:32663517
A comparison of Monte Carlo sampling methods for metabolic network models. PMID:32609776
Are synthetic biology standards applicable in everyday research practice? PMID:32567248
Modeling of nitrogen fixation and polymer production in the heterotrophic diazotroph Azotobacter vinelandii DJ. PMID:32551229
Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genus Sodalis. PMID:32543366
A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks. PMID:32542021
Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic modelling. PMID:32457330
Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks. PMID:32442279
Using Metabolomics to Identify Cell Line-Independent Indicators of Growth Inhibition for Chinese Hamster Ovary Cell-based Bioprocesses. PMID:32429145
Dynamic resource allocation drives growth under nitrogen starvation in eukaryotes. PMID:32415097
A reconciliation of genome-scale metabolic network model of Zymomonas mobilis ZM4. PMID:32385302
Towards the routine use of in silico screenings for drug discovery using metabolic modelling. PMID:32369553
libsbmljs-Enabling web-based SBML tools. PMID:32339626
Biological Filtering and Substrate Promiscuity Prediction for Annotating Untargeted Metabolomics. PMID:32326153
novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model. PMID:32313937
Flux-based hierarchical organization of Escherichia coli's metabolic network. PMID:32310959
Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments. PMID:32298268
Flux Balance Analysis for Media Optimization and Genetic Targets to Improve Heterologous Siderophore Production. PMID:32279062
Genome sequence of the potential probiotic eukaryote Saccharomyces cerevisiae KCCM 51299. PMID:32257741
Visualizing metabolic network dynamics through time-series metabolomic data. PMID:32245365
Genome-Scale Metabolic Model Reconstruction and in Silico Investigations of Methane Metabolism in Methylosinus trichosporium OB3b. PMID:32244934
Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth. PMID:32234775
Suggestions for Standardized Identifiers for Fatty Acyl Compounds in Genome Scale Metabolic Models and Their Application to the WormJam Caenorhabditis elegans Model. PMID:32231124
Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment. PMID:32221328
An atlas of human metabolism. PMID:32209698
Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen. PMID:32194617
Functional cooperation of the glycine synthase-reductase and Wood-Ljungdahl pathways for autotrophic growth of Clostridium drakei. PMID:32170009
Metabolic and genetic basis for auxotrophies in Gram-negative species. PMID:32132208
MEMOTE for standardized genome-scale metabolic model testing. PMID:32123384
The Future of Origin of Life Research: Bridging Decades-Old Divisions. PMID:32110893
Setup of a scientific computing environment for computational biology: Simulation of a genome-scale metabolic model of Escherichia coli as an example. PMID:32108317
Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling. PMID:32071157
MEMO: A Method for Computing Metabolic Modules for Cell-Free Production Systems. PMID:32069395
Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift. PMID:32058961
Reconstruction of a regulated two-cell metabolic model to study biohydrogen production in a diazotrophic cyanobacterium Anabaena variabilis ATCC 29413. PMID:31978122
Compartment and hub definitions tune metabolic networks for metabolomic interpretations. PMID:31972021
OptFill: A Tool for Infeasible Cycle-Free Gapfilling of Stoichiometric Metabolic Models. PMID:31954977
Automatic construction of metabolic models with enzyme constraints. PMID:31937255
A workflow for generating multi-strain genome-scale metabolic models of prokaryotes. PMID:31863076
FlySilico: Flux balance modeling of Drosophila larval growth and resource allocation. PMID:31748517
Genome-Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus. PMID:31744163
A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data. PMID:31720216
BioModels-15 years of sharing computational models in life science. PMID:31701150
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. PMID:31696234
Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models. PMID:31688932
Enzyme annotation in UniProtKB using Rhea. PMID:31688925
A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory. PMID:31665018
Metabolic Modeling of Streptococcus mutans Reveals Complex Nutrient Requirements of an Oral Pathogen. PMID:31662430
Bioengineering tools for the production of pharmaceuticals: current perspective and future outlook. PMID:31656120
Genome-Scale Metabolic Modeling from Yeast to Human Cell Models of Complex Diseases: Latest Advances and Challenges. PMID:31602620
MCS2: minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks. PMID:31510702
Challenges in the construction of knowledge bases for human microbiome-disease associations. PMID:31488215
Systems Biology and Pangenome of Salmonella O-Antigens. PMID:31455646
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. PMID:31395883
Microbial carbon use efficiency predicted from genome-scale metabolic models. PMID:31395870
A systematic assessment of current genome-scale metabolic reconstruction tools. PMID:31391098
Finding MEMo: minimum sets of elementary flux modes. PMID:31388689
In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by genome-scale metabolic modeling. PMID:31367232
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps. PMID:31296857
Genome-scale metabolic model of the rat liver predicts effects of diet restriction. PMID:31285465
Closing the gap between formats for storing layout information in systems biology. PMID:31273380
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. PMID:31244651
Genome-driven cell engineering review: in vivo and in silico metabolic and genome engineering. PMID:31243142
Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model of Danio rerio. PMID:31216234
Current status and applications of genome-scale metabolic models. PMID:31196170
Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data. PMID:31196115
Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks. PMID:31195955
Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome. PMID:31194675
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. PMID:31159881
Augmenting Biogas Process Modeling by Resolving Intracellular Metabolic Activity. PMID:31156601
A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber. PMID:31071110
Approaches to Computational Strain Design in the Multiomics Era. PMID:31024467
Impact framework: A python package for writing data analysis workflows to interpret microbial physiology. PMID:31011536
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. PMID:31009451
Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data. PMID:31002661
Designing Metabolic Division of Labor in Microbial Communities. PMID:30984871
Enzyme promiscuity shapes adaptation to novel growth substrates. PMID:30962359
Identification of bioactive metabolites using activity metabolomics. PMID:30814649
Gsmodutils: a python based framework for test-driven genome scale metabolic model development. PMID:30759197
Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling. PMID:30736318
Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview. PMID:30695998
Essential metabolism for a minimal cell. PMID:30657448
Characterizing and ranking computed metabolic engineering strategies. PMID:30649194
Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems. PMID:30626871
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. PMID:30625152
A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase. PMID:30564208
MoVE identifies metabolic valves to switch between phenotypic states. PMID:30552335
Metabolic Modeling of Microbial Community Interactions for Health, Environmental and Biotechnological Applications. PMID:30532650
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models. PMID:30531987
Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans. PMID:30488036
Harmonizing semantic annotations for computational models in biology. PMID:30462164
Metabolic adaptations underlying genome flexibility in prokaryotes. PMID:30372443
Identification of growth-coupled production strains considering protein costs and kinetic variability. PMID:30370222
ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling. PMID:30323767
Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice. PMID:30309961
Updates in Rhea: SPARQLing biochemical reaction data. PMID:30272209
Escher-FBA: a web application for interactive flux balance analysis. PMID:30257674
OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli. PMID:30248096
A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space. PMID:30241567
Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3). PMID:30240424
Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. PMID:30218022
BioModelKit - An Integrative Framework for Multi-Scale Biomodel-Engineering. PMID:30205646
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities. PMID:30192979
Reply to "Challenges in modeling the human gut microbiome". PMID:30080835
Challenges in modeling the human gut microbiome. PMID:30080831
Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism. PMID:29973148
A Constraint-Based Model Analysis of Enterocyte Mitochondrial Adaptation to Dietary Interventions of Lipid Type and Lipid Load. PMID:29962969
Genomic organization underlying deletional robustness in bacterial metabolic systems. PMID:29915048
Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models. PMID:29791443
Improved enzyme annotation with EC-specific cutoffs using DETECT v2. PMID:29722785
MetExplore: collaborative edition and exploration of metabolic networks. PMID:29718355
iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE. PMID:29692801
Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa. PMID:29688451
From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota. PMID:29600286
Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β Cell. PMID:29570991
A review of computational tools for design and reconstruction of metabolic pathways. PMID:29552648
From correlation to causation: analysis of metabolomics data using systems biology approaches. PMID:29503602
Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. PMID:29499714
Recon3D enables a three-dimensional view of gene variation in human metabolism. PMID:29457794
Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach. PMID:29410419
Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. PMID:29300748
In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host. PMID:29276507
ToxiM: A Toxicity Prediction Tool for Small Molecules Developed Using Machine Learning and Chemoinformatics Approaches. PMID:29249969
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes. PMID:29169408
TCSBN: a database of tissue and cancer specific biological networks. PMID:29069445
Towards dynamic genome-scale models. PMID:29040409
Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach. PMID:28990716
The Role of Soil Microorganisms in Plant Mineral Nutrition-Current Knowledge and Future Directions. PMID:28974956
Predicting Dynamic Metabolic Demands in the Photosynthetic Eukaryote Chlorella vulgaris. PMID:28951490
Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity. PMID:28903046
Population FBA predicts metabolic phenotypes in yeast. PMID:28886026
A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. PMID:28878200
Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection. PMID:28845460
Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects. PMID:28820904
Constraint and Contingency Pervade the Emergence of Novel Phenotypes in Complex Metabolic Systems. PMID:28793223
biochem4j: Integrated and extensible biochemical knowledge through graph databases. PMID:28708831
Constraint-based modeling identifies new putative targets to fight colistin-resistant A. baumannii infections. PMID:28623298
Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism. PMID:28596955
On the effects of alternative optima in context-specific metabolic model predictions. PMID:28557990
SSER: Species specific essential reactions database. PMID:28420402
IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models. PMID:28389638
Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics. PMID:28387366
An analytic approximation of the feasible space of metabolic networks. PMID:28382977
Constraint-based stoichiometric modelling from single organisms to microbial communities. PMID:28334697
Metabolic anchor reactions for robust biorefining. PMID:28232136
A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models. PMID:28215528
Exploring eukaryotic formate metabolisms to enhance microbial growth and lipid accumulation. PMID:28149324
Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G(B1). PMID:28119683
Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression. PMID:28098205
From 20th century metabolic wall charts to 21st century systems biology: database of mammalian metabolic enzymes. PMID:27974320
Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis. PMID:27911809
IDENTIFYING CANCER SPECIFIC METABOLIC SIGNATURES USING CONSTRAINT-BASED MODELS. PMID:27897000
A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. PMID:27883890
Harnessing Big Data for Systems Pharmacology. PMID:27814027
The RCSB protein data bank: integrative view of protein, gene and 3D structural information. PMID:27794042
Phenotypic innovation through recombination in genome-scale metabolic networks. PMID:27683361
Systems Medicine as an Emerging Tool for Cardiovascular Genetics. PMID:27626034
Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models. PMID:27559155
A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. PMID:27467583
OM-FBA: Integrate Transcriptomics Data with Flux Balance Analysis to Decipher the Cell Metabolism. PMID:27100883
ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis. PMID:26882475
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions PubMed citations: 206.

206 articles citing: BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum. PMID:35710409
Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP. PMID:35688826
A Genome-Scale Metabolic Model of Methanoperedens nitroreducens: Assessing Bioenergetics and Thermodynamic Feasibility. PMID:35448501
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx. PMID:35322036
Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions. PMID:35130271
A Beginner's Guide to the COBRA Toolbox. PMID:34719002
WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization. PMID:34117752
Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster. PMID:33947801
Hunting for vital nodes in complex networks using local information. PMID:33911157
Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation Using Maximum Entropy-Based Simulations with Application to Central Metabolism of Neurospora crassa. PMID:33824861
A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives. PMID:33741955
WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization. PMID:33398287
Degree difference: a simple measure to characterize structural heterogeneity in complex networks. PMID:33288824
Flux Coupling and the Objective Functions' Length in EFMs. PMID:33260526
A permutation method for network assembly. PMID:33095802
Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli. PMID:32900868
Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level. PMID:32849823
Publishing reproducible dynamic kinetic models. PMID:32793969
A biochemical network modeling of a whole-cell. PMID:32764598
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. PMID:32670511
Impact of Facultative Bacteria on the Metabolic Function of an Obligate Insect-Bacterial Symbiosis. PMID:32665268
Genome-Scale Metabolic Model Driven Design of a Defined Medium for Campylobacter jejuni M1cam. PMID:32636809
Boosting the extraction of elementary flux modes in genome-scale metabolic networks using the linear programming approach. PMID:32348455
Biological Filtering and Substrate Promiscuity Prediction for Annotating Untargeted Metabolomics. PMID:32326153
Systems biology approach: Panacea for unravelling host-virus interactions and dynamics of vaccine induced immune response. PMID:32289096
An Integrated Multi-Disciplinary Perspectivefor Addressing Challenges of the Human Gut Microbiome. PMID:32155792
Metabolic and genetic basis for auxotrophies in Gram-negative species. PMID:32132208
Genome-scale metabolic reconstruction and in silico analysis of the rice leaf blight pathogen, Xanthomonas oryzae. PMID:32068953
An integrated computational and experimental study to investigate Staphylococcus aureus metabolism. PMID:32001720
Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions. PMID:31866953
The landscape of tiered regulation of breast cancer cell metabolism. PMID:31780802
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. PMID:31696234
Bayesian metabolic flux analysis reveals intracellular flux couplings. PMID:31510676
Flux balance analysis with or without molecular crowding fails to predict two thirds of experimentally observed epistasis in yeast. PMID:31413270
Integration of probabilistic regulatory networks into constraint-based models of metabolism with applications to Alzheimer's disease. PMID:31291905
iMet: A graphical user interface software tool to merge metabolic networks. PMID:31286073
Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development. PMID:31182013
Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models. PMID:31083653
Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model. PMID:31060515
Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data. PMID:31002661
Essential metabolism for a minimal cell. PMID:30657448
Leveraging Multilayered "Omics" Data for Atopic Dermatitis: A Road Map to Precision Medicine. PMID:30631320
Network spectra for drug-target identification in complex diseases: new guns against old foes. PMID:30596144
Computational prediction of changes in brain metabolic fluxes during Parkinson's disease from mRNA expression. PMID:30208076
Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling. PMID:30075203
A Genome-Scale Metabolic Reconstruction of Phytophthora infestans With the Integration of Transcriptional Data Reveals the Key Metabolic Patterns Involved in the Interaction of Its Host. PMID:30042788
An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment. PMID:30040834
KBase: The United States Department of Energy Systems Biology Knowledgebase. PMID:29979655
A portable structural analysis library for reaction networks. PMID:29857031
Genetic Optimization Algorithm for Metabolic Engineering Revisited. PMID:29772713
From correlation to causation: analysis of metabolomics data using systems biology approaches. PMID:29503602
Network Analyses in Plant Pathogens. PMID:29441045
Evolutionary adaptations to new environments generally reverse plastic phenotypic changes. PMID:29367589
Determinism and Contingency Shape Metabolic Complementation in an Endosymbiotic Consortium. PMID:29213256
Navigability of temporal networks in hyperbolic space. PMID:29118421
De novo MYC addiction as an adaptive response of cancer cells to CDK4/6 inhibition. PMID:28978620
An in-silico approach to predict and exploit synthetic lethality in cancer metabolism. PMID:28878380
Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils. PMID:28767679
Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal. PMID:28419089
Cooperative Metabolism in a Three-Partner Insect-Bacterial Symbiosis Revealed by Metabolic Modeling. PMID:28348026
Metabolic systems biology: a brief primer. PMID:28028815
Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes. PMID:27939572
In silico profiling of cell growth and succinate production in Escherichia coli NZN111. PMID:27909649
13C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids. PMID:27761435
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. PMID:27713404
Missing gene identification using functional coherence scores. PMID:27552989
Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding. PMID:27549116
Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets. PMID:27482704
Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti. PMID:27447951
Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions. PMID:27372244
Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. PMID:27286824
Reconstruction and applications of consensus yeast metabolic network based on RNA sequencing. PMID:27239440
A Caenorhabditis elegans Genome-Scale Metabolic Network Model. PMID:27211857
Metabolite concentrations, fluxes and free energies imply efficient enzyme usage. PMID:27159581
Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom. PMID:27152931
Photorespiratory Bypasses Lead to Increased Growth in Arabidopsis thaliana: Are Predictions Consistent with Experimental Evidence? PMID:27092301
Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis. PMID:27000948
Systems biology of the structural proteome. PMID:26969117
A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks. PMID:26909353
PSAMM: A Portable System for the Analysis of Metabolic Models. PMID:26828591
Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism. PMID:26812499
Adaptive Genetic Robustness of Escherichia coli Metabolic Fluxes. PMID:26733489
Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach. PMID:26629901
Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction. PMID:26566239
Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations. PMID:26531810
MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. PMID:26527720
Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli. PMID:26501058
Biconnectivity of the cellular metabolism: A cross-species study and its implication for human diseases. PMID:26490723
Transcriptomics profiling of human SGBS adipogenesis. PMID:26484102
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. PMID:26476456
An overview of bioinformatics methods for modeling biological pathways in yeast. PMID:26476430
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. PMID:26452770
A Method to Constrain Genome-Scale Models with 13C Labeling Data. PMID:26379153
An integrated network platform for contextual prioritization of drugs and pathways. PMID:26315485
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PMID:26313928
Obstructions to Sampling Qualitative Properties. PMID:26287384
Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition. PMID:26248853
Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization. PMID:26158726
Elementary Flux Mode Analysis Revealed Cyclization Pathway as a Powerful Way for NADPH Regeneration of Central Carbon Metabolism. PMID:26086807
Using Genome-scale Models to Predict Biological Capabilities. PMID:26000478
Mimoza: web-based semantic zooming and navigation in metabolic networks. PMID:25889977
Interplay between constraints, objectives, and optimality for genome-scale stoichiometric models. PMID:25849486
Using bioconductor package BiGGR for metabolic flux estimation based on gene expression changes in brain. PMID:25806817
MetaNET--a web-accessible interactive platform for biological metabolic network analysis. PMID:25779921
Integrative analysis of circadian transcriptome and metabolic network reveals the role of de novo purine synthesis in circadian control of cell cycle. PMID:25714999
Current state of genome-scale modeling in filamentous fungi. PMID:25700817
Double and multiple knockout simulations for genome-scale metabolic network reconstructions. PMID:25649004
Genome-scale modeling for metabolic engineering. PMID:25578304
Integration of a constraint-based metabolic model of Brassica napus developing seeds with (13)C-metabolic flux analysis. PMID:25566296
Improving collaboration by standardization efforts in systems biology. PMID:25538939
Network-based association of hypoxia-responsive genes with cardiovascular diseases. PMID:25530704
Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli. PMID:25502413
Computational strategies for a system-level understanding of metabolism. PMID:25427076
CONSTRICTOR: constraint modification provides insight into design of biochemical networks. PMID:25422896
Prediction of metabolic flux distribution from gene expression data based on the flux minimization principle. PMID:25397773
CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics. PMID:25392417
Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models. PMID:25329157
Computational approaches for microalgal biofuel optimization: a review. PMID:25309916
Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam. PMID:25293379
WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. PMID:25231498
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. PMID:25227965
Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca. PMID:25115351
MediaDB: a database of microbial growth conditions in defined media. PMID:25098325
Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice. PMID:25029527
Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. PMID:25002542
A computational approach to estimate interorgan metabolic transport in a mammal. PMID:24971892
Biochemical characterization of human gluconokinase and the proposed metabolic impact of gluconic acid as determined by constraint based metabolic network analysis. PMID:24896608
Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling. PMID:24886210
Computational tools for the secondary analysis of metabolomics experiments. PMID:24688685
optGpSampler: an improved tool for uniformly sampling the solution-space of genome-scale metabolic networks. PMID:24551039
Systems biology-based identification of Mycobacterium tuberculosis persistence genes in mouse lungs. PMID:24549847
MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data. PMID:24532766
Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches. PMID:24432138
A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803. PMID:24402049
Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways. PMID:24314206
A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis. PMID:24308365
Sybil--efficient constraint-based modelling in R. PMID:24224957
Metabolomics as a diagnostic tool in gastroenterology. PMID:24199025
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti. PMID:24176055
Contribution of serine, folate and glycine metabolism to the ATP, NADPH and purine requirements of cancer cells. PMID:24157871
Community structure and multi-modal oscillations in complex networks. PMID:24130720
Global insights into energetic and metabolic networks in Rhodobacter sphaeroides. PMID:24034347
Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks. PMID:23828783
Consensus and conflict cards for metabolic pathway databases. PMID:23803311
Identifying radiation exposure biomarkers from mouse blood transcriptome. PMID:23797995
Use of a global metabolic network to curate organismal metabolic networks. PMID:23603845
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. PMID:23530504
Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells. PMID:23492669
Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant. PMID:23432746
Linking genome-scale metabolic modeling and genome annotation. PMID:23417799
Application of Top-Down and Bottom-up Systems Approaches in Ruminant Physiology and Metabolism. PMID:23372424
Observability of complex systems. PMID:23359701
MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks. PMID:23357920
Reconstruction and in silico analysis of metabolic network for an oleaginous yeast, Yarrowia lipolytica. PMID:23236514
Identification of novel type 2 diabetes candidate genes involved in the crosstalk between the mitochondrial and the insulin signaling systems. PMID:23236286
Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. PMID:23234303
The chemical interactome space between the human host and the genetically defined gut metabotypes. PMID:23178670
WholeCellKB: model organism databases for comprehensive whole-cell models. PMID:23175606
Reconciliation of metabolites and biochemical reactions for metabolic networks. PMID:23172809
Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. PMID:23022739
METscout: a pathfinder exploring the landscape of metabolites, enzymes and transporters. PMID:23019219
Mechanistic systems modeling to guide drug discovery and development. PMID:22999913
Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling. PMID:22886542
NetWalker: a contextual network analysis tool for functional genomics. PMID:22732065
Identification of functional differences in metabolic networks using comparative genomics and constraint-based models. PMID:22666308
Computational tools for metabolic engineering. PMID:22629572
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. PMID:22591066
A network perspective on metabolic inconsistency. PMID:22583819
The central role of the host cell in symbiotic nitrogen metabolism. PMID:22513857
Redox balance is key to explaining full vs. partial switching to low-yield metabolism. PMID:22443685
Microbial metabolomics. PMID:22379393
Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis. PMID:22356827
Identifying neighborhoods of coordinated gene expression and metabolite profiles. PMID:22355360
In-silico studies in Chinese herbal medicines' research: evaluation of in-silico methodologies and phytochemical data sources, and a review of research to date. PMID:22326356
In silico insights into the symbiotic nitrogen fixation in Sinorhizobium meliloti via metabolic reconstruction. PMID:22319621
Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling. PMID:22289253
FAME, the Flux Analysis and Modeling Environment. PMID:22289213
Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A. PMID:22139506
Modeling metabolic adjustment in Mycobacterium tuberculosis upon treatment with isoniazid. PMID:22132057
Serine biosynthesis with one carbon catabolism and the glycine cleavage system represents a novel pathway for ATP generation. PMID:22073143
Parallelization of Nullspace Algorithm for the computation of metabolic pathways. PMID:22058581
Critical assessment of human metabolic pathway databases: a stepping stone for future integration. PMID:21999653
Systems biology of lactic acid bacteria: a critical review. PMID:21995498
Simulating the physiology of athletes during endurance sports events: modelling human energy conversion and metabolism. PMID:21969677
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. PMID:21962087
Systems biology and the future of medicine. PMID:21928407
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. PMID:21886097
Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. PMID:21846360
Structural diversity of biologically interesting datasets: a scaffold analysis approach. PMID:21824432
Technologies and approaches to elucidate and model the virulence program of salmonella. PMID:21687430
GLAMM: Genome-Linked Application for Metabolic Maps. PMID:21624891
Path finding methods accounting for stoichiometry in metabolic networks. PMID:21619601
Acorn: a grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface. PMID:21609434
Symbolic flux analysis for genome-scale metabolic networks. PMID:21605414
Network-based scoring system for genome-scale metabolic reconstructions. PMID:21595941
Molecular crowding defines a common origin for the Warburg effect in proliferating cells and the lactate threshold in muscle physiology. PMID:21559344
Unpredictability of metabolism--the key role of metabolomics science in combination with next-generation genome sequencing. PMID:21556754
A survey of metabolic databases emphasizing the MetaCyc family. PMID:21523460
Analog regulation of metabolic demand. PMID:21406074
Integrated metabolome and transcriptome analysis of the NCI60 dataset. PMID:21342567
Synthetic biology: a foundation for multi-scale molecular biology. PMID:21326830
Elimination of thermodynamically infeasible loops in steady-state metabolic models. PMID:21281568
MEMOSys: Bioinformatics platform for genome-scale metabolic models. PMID:21276275
Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043. PMID:21251315
Predicting functional associations from metabolism using bi-partite network algorithms. PMID:20630077
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree PubMed citations: 49.

49 articles citing: BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0. PMID:35773252
SALARECON connects the Atlantic salmon genome to growth and feed efficiency. PMID:35687595
Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges. PMID:35625648
Systems biology approach to functionally assess the Clostridioides difficile pangenome reveals genetic diversity with discriminatory power. PMID:35476524
KEMET - A python tool for KEGG Module evaluation and microbial genome annotation expansion. PMID:35422973
Mathematical models to study the biology of pathogens and the infectious diseases they cause. PMID:35359802
Systems Biology of Gut Microbiota-Human Receptor Interactions: Toward Anti-inflammatory Probiotics. PMID:35308387
Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions. PMID:35130271
A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations. PMID:34907432
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032. PMID:34867870
Synthetic Biology Advanced Natural Product Discovery. PMID:34822443
Toward modeling metabolic state from single-cell transcriptomics. PMID:34785394
Global connectivity in genome-scale metabolic networks revealed by comprehensive FBA-based pathway analysis. PMID:34696732
Deep learning allows genome-scale prediction of Michaelis constants from structural features. PMID:34665809
Protocol for hybrid flux balance, statistical, and machine learning analysis of multi-omic data from the cyanobacterium Synechococcus sp. PCC 7002. PMID:34632416
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism. PMID:34625561
Novel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis. PMID:34609164
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. PMID:34597405
Modelling microbial communities: Harnessing consortia for biotechnological applications. PMID:34584635
Path to improving the life cycle and quality of genome-scale models of metabolism. PMID:34555324
The Systems Biology Simulation Core Library. PMID:34554191
TCA Cycle and Its Relationship with Clavulanic Acid Production: A Further Interpretation by Using a Reduced Genome-Scale Metabolic Model of Streptomyces clavuligerus. PMID:34436106
Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19. PMID:34353886
Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms. PMID:34342537
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus. PMID:34188046
Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target. PMID:34073716
Towards a Systems Biology Approach to Understanding the Lichen Symbiosis: Opportunities and Challenges of Implementing Network Modelling. PMID:34012428
Strategies for Enhancing in vitro Degradation of Linuron by Variovorax sp. Strain SRS 16 Under the Guidance of Metabolic Modeling. PMID:33937210
First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. PMID:33918864
Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes. PMID:33781078
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis. PMID:33602294
Integrative characterization of the near-minimal bacterium Mesoplasma florum. PMID:33331123
High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies. PMID:33281796
Environmental flexibility does not explain metabolic robustness. PMID:33247119
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. PMID:33156326
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. PMID:33134082
Using optimal control to understand complex metabolic pathways. PMID:33087041
Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence. PMID:33082337
Reconstructing organisms in silico: genome-scale models and their emerging applications. PMID:32958892
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
Community standards to facilitate development and address challenges in metabolic modeling. PMID:32845080
Publishing reproducible dynamic kinetic models. PMID:32793969
Isolating structural errors in reaction networks in systems biology. PMID:32790862
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. PMID:32670511
Escher-Trace: a web application for pathway-based visualization of stable isotope tracing data. PMID:32650717
A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus. PMID:32635563
Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks. PMID:32442279
Current Status and Future Prospects of Genome-Scale Metabolic Modeling to Optimize the Use of Mesenchymal Stem Cells in Regenerative Medicine. PMID:32296688
The 27th annual Nucleic Acids Research database issue and molecular biology database collection. PMID:31906604
http://dx.doi.org/10.1093/nar/gkv1049

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computational predictions
metasource: Fairsharing.org
version: FAIRsharing.org: BiGG Models; BiGG Models; DOI: https://doi.org/10.25504/FAIRsharing.va62ke; Last edited: Feb. 7, 2021, 9:11 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

network model
metasource: Fairsharing.org
version: FAIRsharing.org: BiGG Models; BiGG Models; DOI: https://doi.org/10.25504/FAIRsharing.va62ke; Last edited: Feb. 7, 2021, 9:11 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metabolic pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

biochemistry
metasource: re3data.org
version: re3data.org: BIGG Database; editing status 2018-12-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MG9M last accessed: 2022-11-04

bioinformatics
metasource: re3data.org
version: re3data.org: BIGG Database; editing status 2018-12-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MG9M last accessed: 2022-11-04

genetics
metasource: re3data.org
version: re3data.org: BIGG Database; editing status 2018-12-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MG9M last accessed: 2022-11-04

genomics
metasource: re3data.org
version: re3data.org: BIGG Database; editing status 2018-12-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MG9M last accessed: 2022-11-04

metabolic network
metasource: re3data.org
version: re3data.org: BIGG Database; editing status 2018-12-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MG9M last accessed: 2022-11-04

metabolic pathway
metasource: re3data.org
version: re3data.org: BIGG Database; editing status 2018-12-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MG9M last accessed: 2022-11-04

metabolism
metasource: re3data.org
version: re3data.org: BIGG Database; editing status 2018-12-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MG9M last accessed: 2022-11-04

metabolomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:07.345797

small molecules
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:07.345797

endocrinology and metabolism
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:07.345797

phylogenetics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:07.345797

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:07.345797

computational predictions network model metabolic and signaling pathways metabolic and signaling pathways biochemistry bioinformatics genetics genomics metabolic network metabolic pathway metabolism metabolomics small molecule endocrinology and metabolism phylogenetics molecular interactions, pathways and networks

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