R3C33C last accessed: 2022-11-04

BioModels database
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:55.315427

biomodels
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:55.315427

Other names: BioModels database, biomodels

BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-linked to publicly available reference information.

Webpage:

https://www.ebi.ac.uk/biomodels/

Licence:

Name: Biomodels Terms of Use
URL: http://www.ebi.ac.uk/biomodels-main/termsofuse

Publications: (6)

Publications
More detailed information about this field from each metasource.

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
PMID: 16381960
metasource: Fairsharing.org
version: FAIRsharing.org: BioModels; BioModels; DOI: https://doi.org/10.25504/FAIRsharing.paz6mh; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
PMID: 20587024
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:55.315427

BioModels-15 years of sharing computational models in life science
PMID: 31701150
metasource: Fairsharing.org
version: FAIRsharing.org: BioModels; BioModels; DOI: https://doi.org/10.25504/FAIRsharing.paz6mh; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:55.315427

BioModels: Content, Features, Functionality, and Use
PMID: 26225232
metasource: Fairsharing.org
version: FAIRsharing.org: BioModels; BioModels; DOI: https://doi.org/10.25504/FAIRsharing.paz6mh; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

BioModels: expanding horizons to include more modelling approaches and formats
PMID: 29106614
metasource: Fairsharing.org
version: FAIRsharing.org: BioModels; BioModels; DOI: https://doi.org/10.25504/FAIRsharing.paz6mh; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: Fairsharing.org
version: FAIRsharing.org: BioModels; BioModels; DOI: https://doi.org/10.25504/FAIRsharing.paz6mh; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:55.315427

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

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems PubMed citations: 258.

258 articles citing: BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

Deciphering signal transduction networks in the liver by mechanistic mathematical modelling. PMID:35748700
A semantics, energy-based approach to automate biomodel composition. PMID:35657966
Structural Thermokinetic Modelling. PMID:35629936
BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts. PMID:35442944
Multi-omics-based label-free metabolic flux inference reveals obesity-associated dysregulatory mechanisms in liver glucose metabolism. PMID:35243212
Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. PMID:34900668
WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically. PMID:34888352
Computational Studies of the Intestinal Host-Microbiota Interactome. PMID:34765258
A protocol for dynamic model calibration. PMID:34619769
WinBEST-KIT: Biochemical Reaction Simulator for Analyzing Multi-Layered Metabolic Pathways. PMID:34436117
Mathematical Modeling of ceRNA-Based Interactions. PMID:34165711
History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications. PMID:33841175
Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases. PMID:33589928
Towards reproducible computational drug discovery. PMID:33430992
Biological network analysis with deep learning. PMID:33169146
Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media. PMID:33097709
The on-premise data sharing infrastructure e!DAL: Foster FAIR data for faster data acquisition. PMID:33090199
Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective. PMID:32993675
A compiler for biological networks on silicon chips. PMID:32966274
Executable biochemical space for specification and analysis of biochemical systems. PMID:32915842
Publishing reproducible dynamic kinetic models. PMID:32793969
Parameter Estimation and Uncertainty Quantification for Systems Biology Models. PMID:32719822
libsbmljs-Enabling web-based SBML tools. PMID:32339626
LK-DFBA: a linear programming-based modeling strategy for capturing dynamics and metabolite-dependent regulation in metabolism. PMID:32122331
A workflow for generating multi-strain genome-scale metabolic models of prokaryotes. PMID:31863076
BioModels-15 years of sharing computational models in life science. PMID:31701150
Membrane Tension Orchestrates Rear Retraction in Matrix-Directed Cell Migration. PMID:31607653
Systems Biology of Cancer Metastasis. PMID:31465728
Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. PMID:31201122
Recent advances in biomedical simulations: a manifesto for model engineering. PMID:30881691
PaperBot: open-source web-based search and metadata organization of scientific literature. PMID:30678631
Benchmark problems for dynamic modeling of intracellular processes. PMID:30624608
A Survey of Software Tool Utilization and Capabilities for Quantitative Systems Pharmacology: What We Have and What We Need. PMID:30417600
Using both qualitative and quantitative data in parameter identification for systems biology models. PMID:30254246
OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans. PMID:30201845
Reproducible Research Using Biomodels. PMID:30191472
A mechanism for bistability in glycosylation. PMID:30074989
FindSim: A Framework for Integrating Neuronal Data and Signaling Models. PMID:29997492
Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology. PMID:29906293
Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures. PMID:29765315
Evolution of computational models in BioModels Database and the Physiome Model Repository. PMID:29650016
Generalizing Gillespie's Direct Method to Enable Network-Free Simulations. PMID:29594824
Boolean network modeling in systems pharmacology. PMID:29307099
Evaluation of epidermal growth factor receptor signaling effects in gastric cancer cell lines by detailed motility-focused phenotypic characterization linked with molecular analysis. PMID:29237412
Competitive tuning: Competition's role in setting the frequency-dependence of Ca2+-dependent proteins. PMID:29107982
PTEN Regulates PI(3,4)P2 Signaling Downstream of Class I PI3K. PMID:29056325
The Role of Soil Microorganisms in Plant Mineral Nutrition-Current Knowledge and Future Directions. PMID:28974956
A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. PMID:28878200
Qualitative causal analyses of biosimulation models. PMID:28804276
Modeling and simulation of biological systems using SPICE language. PMID:28787027
COPASI and its applications in biotechnology. PMID:28655634
PharmML in Action: an Interoperable Language for Modeling and Simulation. PMID:28575551
SSER: Species specific essential reactions database. PMID:28420402
SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. PMID:28395655
Reproducibility and Comparability of Computational Models for Astrocyte Calcium Excitability. PMID:28270761
Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli. PMID:28187134
The promises of quantitative systems pharmacology modelling for drug development. PMID:27761201
Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience. PMID:27629590
Systems Level Analysis of the Yeast Osmo-Stat. PMID:27515486
Short relaxation times but long transient times in both simple and complex reaction networks. PMID:27411726
Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution. PMID:27380265
Coreference resolution improves extraction of Biological Expression Language statements from texts. PMID:27374122
Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli. PMID:27329289
Reproducibility in Computational Neuroscience Models and Simulations. PMID:27046845
The systems biology format converter. PMID:27044654
Challenges in horizontal model integration. PMID:26968798
libChEBI: an API for accessing the ChEBI database. PMID:26933452
Challenges of Inversely Estimating Jacobian from Metabolomics Data. PMID:26636075
Tracing regulatory routes in metabolism using generalised supply-demand analysis. PMID:26635009
NDEx, the Network Data Exchange. PMID:26594663
Kinetic modeling and the rise of systems pharmacology. PMID:26590172
Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction. PMID:26566239
Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability. PMID:26484978
Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure. PMID:26468131
Databases for multilevel biophysiology research available at Physiome.jp. PMID:26441671
Kinetics on Demand Is a Simple Mathematical Solution that Fits Recorded Caffeine-Induced Luminal SR Ca2+ Changes in Smooth Muscle Cells. PMID:26390403
Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases. PMID:26249223
Validation and selection of ODE based systems biology models: how to arrive at more reliable decisions. PMID:26152206
libRoadRunner: a high performance SBML simulation and analysis library. PMID:26085503
kpath: integration of metabolic pathway linked data. PMID:26055101
ModelView for ModelDB: Online Presentation of Model Structure. PMID:25896640
iPathCase(KEGG): An iPad interface for KEGG metabolic pathways. PMID:25825656
Computational modeling of drug response with applications to neuroscience. PMID:25733952
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. PMID:25632107
Ligand-dependent opening of the multiple AMPA receptor conductance states: a concerted model. PMID:25629405
Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity. PMID:25605374
A constraint solving approach to model reduction by tropical equilibration. PMID:25493095
BioModels: ten-year anniversary. PMID:25414348
Mechanistic modeling confronts the complexity of molecular cell biology. PMID:25368428
LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. PMID:25309419
Comparative Identification of Differential Interactions from Trajectories of Dynamic Biological Networks. PMID:25285064
A reappraisal of how to build modular, reusable models of biological systems. PMID:25275523
An online system for metabolic network analysis. PMID:25267793
KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. PMID:25115331
e!DAL--a framework to store, share and publish research data. PMID:24958009
The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. PMID:24911500
How informative is your kinetic model?: using resampling methods for model invalidation. PMID:24886662
Bridging the gaps in systems biology. PMID:24728588
Plant systems biology: insights, advances and challenges. PMID:24671625
A conceptual review on systems biology in health and diseases: from biological networks to modern therapeutics. PMID:24592295
Gene duplication and phenotypic changes in the evolution of mammalian metabolic networks. PMID:24489850
Reverse engineering and identification in systems biology: strategies, perspectives and challenges. PMID:24307566
Pathway Commons at virtual cell: use of pathway data for mathematical modeling. PMID:24273241
What can we learn from global sensitivity analysis of biochemical systems? PMID:24244458
A computational model of liver iron metabolism. PMID:24244122
SBML and CellML translation in antimony and JSim. PMID:24215024
Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. PMID:24123887
Investigating interventions in Alzheimer's disease with computer simulation models. PMID:24098635
Fuzzy optimization for detecting enzyme targets of human uric acid metabolism. PMID:24078686
Computational models of the JAK1/2-STAT1 signaling. PMID:24069559
The systems biology simulation core algorithm. PMID:23826941
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. PMID:23813008
Dynamical properties of Discrete Reaction Networks. PMID:23722628
Structure, function, and behaviour of computational models in systems biology. PMID:23721297
In silico modeling of shear-stress-induced nitric oxide production in endothelial cells through systems biology. PMID:23708369
Error Analysis and Propagation in Metabolomics Data Analysis. PMID:23667718
An improved swarm optimization for parameter estimation and biological model selection. PMID:23593445
Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs. PMID:23506153
Model composition through model reduction: a combined model of CD95 and NF-κB signaling pathways. PMID:23409788
A method for comparing multivariate time series with different dimensions. PMID:23393554
Random parameter sampling of a generic three-tier MAPK cascade model reveals major factors affecting its versatile dynamics. PMID:23365667
Accelerating cancer systems biology research through Semantic Web technology. PMID:23188758
Cycles and the qualitative evolution of chemical systems. PMID:23071525
An overview of computational life science databases & exchange formats of relevance to chemical biology research. PMID:22934944
The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models. PMID:22855577
State of the art in silico tools for the study of signaling pathways in cancer. PMID:22837650
Condor-COPASI: high-throughput computing for biochemical networks. PMID:22834945
Reduction of dynamical biochemical reactions networks in computational biology. PMID:22833754
PathCase-SB: integrating data sources and providing tools for systems biology research. PMID:22697505
Computational tools for metabolic engineering. PMID:22629572
A novel cost function to estimate parameters of oscillatory biochemical systems. PMID:22587221
A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development. PMID:22565629
A unifying hypothesis for familial and sporadic Alzheimer's disease. PMID:22482080
Tav4SB: integrating tools for analysis of kinetic models of biological systems. PMID:22480273
Proteus: a web-based, context-specific modelling tool for molecular networks. PMID:22426344
What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform. PMID:22419971
The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. PMID:22395476
Exploring the gap between dynamic and constraint-based models of metabolism. PMID:22306209
Propagating semantic information in biochemical network models. PMID:22289386
Genotype-Phenotype Map Characteristics of an In silico Heart Cell. PMID:22232604
Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. PMID:22172142
SABIO-RK--database for biochemical reaction kinetics. PMID:22102587
Understanding glycomechanics using mathematical modeling: a review of current approaches to simulate cellular glycosylation reaction networks. PMID:22090146
PathCase-SB architecture and database design. PMID:22070889
Controlled vocabularies and semantics in systems biology. PMID:22027554
Dupuytren's: a systems biology disease. PMID:21943049
Analyzing the functional properties of the creatine kinase system with multiscale 'sloppy' modeling. PMID:21912519
Robustness portraits of diverse biological networks conserved despite order-of-magnitude parameter uncertainty. PMID:21880701
Stochastic properties of the plant circadian clock. PMID:21880617
The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. PMID:21878109
Conserved and differential gene interactions in dynamical biological systems. PMID:21840874
A mechanistic modeling framework for predicting metabolic interactions in complex mixtures. PMID:21835728
Modelling the role of the Hsp70/Hsp90 system in the maintenance of protein homeostasis. PMID:21779370
Retrieval, alignment, and clustering of computational models based on semantic annotations. PMID:21772260
Modeling signal transduction leading to synaptic plasticity: evaluation and comparison of five models. PMID:21559300
Positive autoregulation delays the expression phase of mammalian clock gene Per2. PMID:21533189
A multiscale modeling approach to investigate molecular mechanisms of pseudokinase activation and drug resistance in the HER3/ErbB3 receptor tyrosine kinase signaling network. PMID:21509365
CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models. PMID:21423324
Systems biology: the next frontier for bioinformatics. PMID:21331364
Revision history aware repositories of computational models of biological systems. PMID:21235804
A unique transformation from ordinary differential equations to reaction networks. PMID:21203560
Postsynaptic signal transduction models for long-term potentiation and depression. PMID:21188161
Consistent robustness analysis (CRA) identifies biologically relevant properties of regulatory network models. PMID:21179566
Fan-out in gene regulatory networks. PMID:21167053
Systematic integration of experimental data and models in systems biology. PMID:21114840
MetNetAPI: A flexible method to access and manipulate biological network data from MetNet. PMID:21083943
Modelling the role of UCH-L1 on protein aggregation in age-related neurodegeneration. PMID:20949132
Systems analysis of salivary gland development and disease. PMID:20890964
Experimental and computational analysis of polyglutamine-mediated cytotoxicity. PMID:20885783
Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model. PMID:20865009
Kinetic Modeling using BioPAX ontology. PMID:20862270
In silico models of cancer. PMID:20836040
The BioPAX community standard for pathway data sharing. PMID:20829833
Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. PMID:20823846
A graphical method for reducing and relating models in systems biology. PMID:20823324
Using views of Systems Biology Cloud: application for model building. PMID:20730508
Simulation methods with extended stability for stiff biochemical Kinetics. PMID:20701766
Annotation of SBML models through rule-based semantic integration. PMID:20626923
Multiple ontologies in action: composite annotations for biosimulation models. PMID:20601121
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. PMID:20587024
NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PMID:20585541
Sloppy models, parameter uncertainty, and the role of experimental design. PMID:20556289
PINT: Pathways INtegration Tool. PMID:20538652
Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network. PMID:20498836
VISIBIOweb: visualization and layout services for BioPAX pathway models. PMID:20460470
Model composition for macromolecular regulatory networks. PMID:20431147
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. PMID:20426874
OptFlux: an open-source software platform for in silico metabolic engineering. PMID:20403172
An overview of the CellML API and its implementation. PMID:20377909
GSK3 and p53 - is there a link in Alzheimer's disease? PMID:20181016
Feedback between p21 and reactive oxygen production is necessary for cell senescence. PMID:20160708
Simulating plant metabolic pathways with enzyme-kinetic models. PMID:20118273
Towards a genome-scale kinetic model of cellular metabolism. PMID:20109182
Automated mass action model space generation and analysis methods for two-reactant combinatorially complex equilibriums: an analysis of ATP-induced ribonucleotide reductase R1 hexamerization data. PMID:20003203
BioModels.net Web Services, a free and integrated toolkit for computational modelling software. PMID:19939940
Computational systems biology in cancer: modeling methods and applications. PMID:19936081
The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. PMID:19906839
Chemical Entities of Biological Interest: an update. PMID:19854951
TIde: a software for the systematic scanning of drug targets in kinetic network models. PMID:19840374
Molecular machines or pleiomorphic ensembles: signaling complexes revisited. PMID:19835637
Trends in modeling Biomedical Complex Systems. PMID:19828068
Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway. PMID:19804630
From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways. PMID:19758470
Maximum entropy reconstructions of dynamic signaling networks from quantitative proteomics data. PMID:19707567
Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network. PMID:19698179
Towards reproducible descriptions of neuronal network models. PMID:19662159
Antimony: a modular model definition language. PMID:19578039
Consistent design schematics for biological systems: standardization of representation in biological engineering. PMID:19493898
The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. PMID:19480664
Towards the engineering of in vitro systems. PMID:19474076
Using chemical organization theory for model checking. PMID:19468053
Web services at the European Bioinformatics Institute-2009. PMID:19435877
Minimum criteria for DNA damage-induced phase advances in circadian rhythms. PMID:19424508
CycSim--an online tool for exploring and experimenting with genome-scale metabolic models. PMID:19420054
Cancer as a system failure. PMID:19390665
Designing and encoding models for synthetic biology. PMID:19364720
GetBonNie for building, analyzing and sharing rule-based models. PMID:19321734
SBML2L(A)T(E)X: conversion of SBML files into human-readable reports. PMID:19307240
Version control of pathway models using XML patches. PMID:19292901
Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. PMID:19133145
Genome-scale models of bacterial metabolism: reconstruction and applications. PMID:19067749
Microcirculation and the physiome projects. PMID:19051119
Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation. PMID:19045831
Dynamical modeling of the cholesterol regulatory pathway with Boolean networks. PMID:19025648
Asmparts: assembly of biological model parts. PMID:19003441
Update of KDBI: Kinetic Data of Bio-molecular Interaction database. PMID:18971255
The challenges for molecular nutrition research 4: the "nutritional systems biology level". PMID:18825427
Web-based applications for building, managing and analysing kinetic models of biological systems. PMID:18805901
Models from experiments: combinatorial drug perturbations of cancer cells. PMID:18766176
Explaining oscillations and variability in the p53-Mdm2 system. PMID:18706112
SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool. PMID:18706080
Programming with models: modularity and abstraction provide powerful capabilities for systems biology. PMID:18647734
Memory switches in chemical reaction space. PMID:18636099
A new strategy for assessing sensitivities in biochemical models. PMID:18632455
The model repository of the models of infectious disease agent study. PMID:18632331
Comparing simulation results of SBML capable simulators. PMID:18579569
Phenotype prediction in regulated metabolic networks. PMID:18439260
Integration of multi-scale biosimulation models via light-weight semantics. PMID:18229704
MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data. PMID:18171474
The cell cycle DB: a systems biology approach to cell cycle analysis. PMID:18160409
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. PMID:18078503
Dynamic simulation of regulatory networks using SQUAD. PMID:18039375
Universally sloppy parameter sensitivities in systems biology models. PMID:17922568
Interoperability of neuroscience modeling software: current status and future directions. PMID:17873374
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. PMID:17678529
RMBNToolbox: random models for biochemical networks. PMID:17524136
SenseLab: new developments in disseminating neuroscience information. PMID:17510162
An in silico model of the ubiquitin-proteasome system that incorporates normal homeostasis and age-related decline. PMID:17408507
Modeling biochemical transformation processes and information processing with Narrator. PMID:17389034
Reactome: a knowledge base of biologic pathways and processes. PMID:17367534
SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML). PMID:17341299
Refinement and expansion of signaling pathways: the osmotic response network in yeast. PMID:17267811
CellCircuits: a database of protein network models. PMID:17135207
Parameter estimate of signal transduction pathways. PMID:17118160
cPath: open source software for collecting, storing, and querying biological pathways. PMID:17101041
Modelling the checkpoint response to telomere uncapping in budding yeast. PMID:17015293
The ion channel inverse problem: neuroinformatics meets biophysics. PMID:16933979
Dry work in a wet world: computation in systems biology. PMID:16820781
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models PubMed citations: 200.

200 articles citing: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer. PMID:35875150
Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows. PMID:35792600
Alterations in Kynurenine and NAD+ Salvage Pathways during the Successful Treatment of Inflammatory Bowel Disease Suggest HCAR3 and NNMT as Potential Drug Targets. PMID:34948292
Synthetic Biology Advanced Natural Product Discovery. PMID:34822443
RDFizing the biosynthetic pathway of E.coli O-antigen to enable semantic sharing of microbiology data. PMID:34809564
Modular assembly of dynamic models in systems biology. PMID:34644304
WinBEST-KIT: Biochemical Reaction Simulator for Analyzing Multi-Layered Metabolic Pathways. PMID:34436117
Benchmarking of numerical integration methods for ODE models of biological systems. PMID:33514831
A cyanobacterial photorespiratory bypass model to enhance photosynthesis by rerouting photorespiratory pathway in C3 plants. PMID:33257792
Essential gene prediction using limited gene essentiality information-An integrative semi-supervised machine learning strategy. PMID:33253254
Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media. PMID:33097709
Best Practices for Making Reproducible Biochemical Models. PMID:32853539
Advances in Astrocyte Computational Models: From Metabolic Reconstructions to Multi-omic Approaches. PMID:32848690
libsbmljs-Enabling web-based SBML tools. PMID:32339626
Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines. PMID:32119655
Guidelines for benchmarking of optimization-based approaches for fitting mathematical models. PMID:31842943
Learning stable and predictive structures in kinetic systems. PMID:31776252
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
MCS2: minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks. PMID:31510702
Finding MEMo: minimum sets of elementary flux modes. PMID:31388689
Connecting signaling and metabolic pathways in EGF receptor-mediated oncogenesis of glioblastoma. PMID:31386654
An effective biomedical data migration tool from resource description framework to JSON. PMID:31343683
CRA toolbox: software package for conditional robustness analysis of cancer systems biology models in MATLAB. PMID:31288758
"Reproducible" Research in Mathematical Sciences Requires Changes in our Peer Review Culture and Modernization of our Current Publication Approach. PMID:30232583
BioModelKit - An Integrative Framework for Multi-Scale Biomodel-Engineering. PMID:30205646
Identifying frequent patterns in biochemical reaction networks: a workflow. PMID:29992320
Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology. PMID:29906293
Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation. PMID:29688381
Evolution of computational models in BioModels Database and the Physiome Model Repository. PMID:29650016
Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. PMID:29447151
Biotea: semantics for Pubmed Central. PMID:29312824
pSSAlib: The partial-propensity stochastic chemical network simulator. PMID:29206229
Competitive tuning: Competition's role in setting the frequency-dependence of Ca2+-dependent proteins. PMID:29107982
Disease Progression Modeling: Key Concepts and Recent Developments. PMID:28936389
A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. PMID:28878200
Methods of Model Reduction for Large-Scale Biological Systems: A Survey of Current Methods and Trends. PMID:28656491
A Bayesian approach to estimating hidden variables as well as missing and wrong molecular interactions in ordinary differential equation-based mathematical models. PMID:28615495
PharmML in Action: an Interoperable Language for Modeling and Simulation. PMID:28575551
A combined model reduction algorithm for controlled biochemical systems. PMID:28193218
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PMID:28114351
Toward Multiscale Models of Cyanobacterial Growth: A Modular Approach. PMID:28083530
DTNI: a novel toxicogenomics data analysis tool for identifying the molecular mechanisms underlying the adverse effects of toxic compounds. PMID:28032149
Modeling the Role of Lanthionine Synthetase C-Like 2 (LANCL2) in the Modulation of Immune Responses to Helicobacter pylori Infection. PMID:27936058
FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. PMID:27899646
Inferring catalysis in biological systems. PMID:27879475
Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks. PMID:27870845
A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. PMID:27830063
Power-Law Modeling of Cancer Cell Fates Driven by Signaling Data to Reveal Drug Effects. PMID:27764199
Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis. PMID:27736793
Modelling the Structure and Dynamics of Biological Pathways. PMID:27509052
SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena. PMID:27412095
BioNetGen 2.2: advances in rule-based modeling. PMID:27402907
COMODI: an ontology to characterise differences in versions of computational models in biology. PMID:27401413
Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable. PMID:27393343
Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution. PMID:27380265
A physiome interoperability roadmap for personalized drug development. PMID:27051513
Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models. PMID:26958881
ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis. PMID:26882475
Learning (from) the errors of a systems biology model. PMID:26865316
To senesce or not to senesce: how primary human fibroblasts decide their cell fate after DNA damage. PMID:26830321
Polyphasic analysis of an Azoarcus-Leptothrix-dominated bacterial biofilm developed on stainless steel surface in a gasoline-contaminated hypoxic groundwater. PMID:26825521
Modeling the ascorbate-glutathione cycle in chloroplasts under light/dark conditions. PMID:26797294
Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases. PMID:26716837
JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. PMID:26704692
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. PMID:26559508
Dynamic Metabolic Disruption in Rats Perinatally Exposed to Low Doses of Bisphenol-A. PMID:26517871
An algorithm to detect and communicate the differences in computational models describing biological systems. PMID:26490504
Development of a robust DNA damage model including persistent telomere-associated damage with application to secondary cancer risk assessment. PMID:26359627
Examining and elucidation of human weight cycle model adopting e-cell simulation system. PMID:26339149
Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks. PMID:26317784
Quantitative analysis reveals how EGFR activation and downregulation are coupled in normal but not in cancer cells. PMID:26264748
Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development. PMID:26225259
Regulation of ERK-MAPK signaling in human epidermis. PMID:26209520
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. PMID:26202570
Tensor methods for parameter estimation and bifurcation analysis of stochastic reaction networks. PMID:26063822
The role of markup for enabling interoperability in health informatics. PMID:26042043
Finding the positive feedback loops underlying multi-stationarity. PMID:26013004
A computational approach to persistence, permanence, and endotacticity of biochemical reaction systems. PMID:25986743
Quantification of Interactions between Dynamic Cellular Network Functionalities by Cascaded Layering. PMID:25933116
Mathematical modelling of metabolic regulation in aging. PMID:25923415
Annotation-based feature extraction from sets of SBML models. PMID:25904997
Mimoza: web-based semantic zooming and navigation in metabolic networks. PMID:25889977
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. PMID:25880925
Causal drift, robust signaling, and complex disease. PMID:25774510
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. PMID:25759811
Combining computational models, semantic annotations and simulation experiments in a graph database. PMID:25754863
Computationally Modeling Lipid Metabolism and Aging: A Mini-review. PMID:25750699
Thermodynamics of random reaction networks. PMID:25723751
Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions. PMID:25611683
Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity. PMID:25605374
Causal inference in biology networks with integrated belief propagation. PMID:25592596
Transparency in metabolic network reconstruction enables scalable biological discovery. PMID:25562137
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. PMID:25494900
Oxidative changes and signalling pathways are pivotal in initiating age-related changes in articular cartilage. PMID:25475114
Synergy-COPD: a systems approach for understanding and managing chronic diseases. PMID:25472826
Computational strategies for a system-level understanding of metabolism. PMID:25427076
BioModels: ten-year anniversary. PMID:25414348
The zigzag model of plant-microbe interactions: is it time to move on? PMID:25382065
MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae. PMID:25378328
Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering. PMID:25344492
A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors. PMID:25315994
Anti-inflammatory effects of reactive oxygen species - a multi-valued logical model validated by formal concept analysis. PMID:25315877
Bioremediation in marine ecosystems: a computational study combining ecological modeling and flux balance analysis. PMID:25309577
MOSBIE: a tool for comparison and analysis of rule-based biochemical models. PMID:25253680
BioModels linked dataset. PMID:25182954
esyN: network building, sharing and publishing. PMID:25181461
Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942. PMID:25141288
Personalized medicine approaches for colon cancer driven by genomics and systems biology: OncoTrack. PMID:25074435
Prediction uncertainty assessment of a systems biology model requires a sample of the full probability distribution of its parameters. PMID:25024907
On functional module detection in metabolic networks. PMID:24958145
What mRNA Abundances Can Tell us about Metabolism. PMID:24957650
Optimality principles in the regulation of metabolic networks. PMID:24957646
Cooperative gene regulation by microRNA pairs and their identification using a computational workflow. PMID:24875477
XTMS: pathway design in an eXTended metabolic space. PMID:24792156
A computer simulation approach to assessing therapeutic intervention points for the prevention of cytokine-induced cartilage breakdown. PMID:24757149
A rule-based ontological framework for the classification of molecules. PMID:24735706
Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. PMID:24708852
cuTauLeaping: a GPU-powered tau-leaping stochastic simulator for massive parallel analyses of biological systems. PMID:24663957
Identification of key regulators in glycogen utilization in E. coli based on the simulations from a hybrid functional Petri net model. PMID:24565082
Modeling intracellular signaling underlying striatal function in health and disease. PMID:24560149
MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data. PMID:24532766
Convergence in parameters and predictions using computational experimental design. PMID:24511374
The EBI RDF platform: linked open data for the life sciences. PMID:24413672
Cutting the wires: modularization of cellular networks for experimental design. PMID:24411264
Sparsity as cellular objective to infer directed metabolic networks from steady-state metabolome data: a theoretical analysis. PMID:24391961
A mathematical model of the colon crypt capturing compositional dynamic interactions between cell types. PMID:24354351
Analytical solution of steady-state equations for chemical reaction networks with bilinear rate laws. PMID:24334389
Systematic construction of kinetic models from genome-scale metabolic networks. PMID:24324546
Ontology of physics for biology: representing physical dependencies as a basis for biological processes. PMID:24295137
Kinetic modelling of phospholipid synthesis in Plasmodium knowlesi unravels crucial steps and relative importance of multiple pathways. PMID:24209716
Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein. PMID:24195591
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
Root systems biology: integrative modeling across scales, from gene regulatory networks to the rhizosphere. PMID:24143806
Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. PMID:24123887
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. PMID:24093723
A C library for retrieving specific reactions from the BioModels database. PMID:24078714
Fuzzy optimization for detecting enzyme targets of human uric acid metabolism. PMID:24078686
Computational models of the JAK1/2-STAT1 signaling. PMID:24069559
Using biological pathway data with paxtools. PMID:24068901
Conversion of KEGG metabolic pathways to SBGN maps including automatic layout. PMID:23953132
Extracting reaction networks from databases-opening Pandora's box. PMID:23946492
Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PMID:23935467
COBRApy: COnstraints-Based Reconstruction and Analysis for Python. PMID:23927696
A physiologically required G protein-coupled receptor (GPCR)-regulator of G protein signaling (RGS) interaction that compartmentalizes RGS activity. PMID:23900842
FieldML, a proposed open standard for the Physiome project for mathematical model representation. PMID:23900627
The impact of mathematical modeling on the understanding of diabetes and related complications. PMID:23842097
CPT: Pharmacometrics and Systems Pharmacology. PMID:23835888
A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. PMID:23831062
The systems biology simulation core algorithm. PMID:23826941
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. PMID:23813008
An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data. PMID:23805196
Towards the collaborative curation of the registry underlying Identifiers.org. PMID:23584831
In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae. PMID:23514624
A mathematical model of the unfolded protein stress response reveals the decision mechanism for recovery, adaptation and apoptosis. PMID:23433609
Transfer functions for protein signal transduction: application to a model of striatal neural plasticity. PMID:23405211
ADEMA: an algorithm to determine expected metabolite level alterations using mutual information. PMID:23341761
CySBGN: a Cytoscape plug-in to integrate SBGN maps. PMID:23324051
Boolean model of yeast apoptosis as a tool to study yeast and human apoptotic regulations. PMID:23233838
Computational modeling of the metabolic States regulated by the kinase akt. PMID:23181020
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. PMID:23180789
Modeling regulatory networks to understand plant development: small is beautiful. PMID:23110896
Data management strategies for multinational large-scale systems biology projects. PMID:23047157
A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. PMID:23046614
Multiscale models of breast cancer progression. PMID:23008097
A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient-Derived Dermal Fibroblasts and iPS Cells. PMID:22969728
Trajectory-oriented Bayesian experiment design versus Fisher A-optimal design: an in depth comparison study. PMID:22962478
Evaluation of research in biomedical ontologies. PMID:22962340
Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. PMID:22913808
Understanding regulation of metabolism through feasibility analysis. PMID:22808034
Combinatorial drug therapy for cancer in the post-genomic era. PMID:22781697
Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion. PMID:22723865
PathCase-SB: integrating data sources and providing tools for systems biology research. PMID:22697505
A tool for multi-scale modelling of the renal nephron. PMID:22670210
A specialized ODE integrator for the efficient computation of parameter sensitivities. PMID:22607742
STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies. PMID:22574658
DIPSBC--data integration platform for systems biology collaborations. PMID:22568834
A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development. PMID:22565629
OREMPdb: a semantic dictionary of computational pathway models. PMID:22536973
Structure-based classification and ontology in chemistry. PMID:22480202
BioNetSim: a Petri net-based modeling tool for simulations of biochemical processes. PMID:22410784
Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics. PMID:22390191
Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). PMID:22180826
An open-ended plea for the development of a global database of HIV vaccine responses. PMID:22156846
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. PMID:22140103
PathCase-SB architecture and database design. PMID:22070889
Controlled vocabularies and semantics in systems biology. PMID:22027554
Kinase inhibitors can produce off-target effects and activate linked pathways by retroactivity. PMID:21970676
3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. PMID:21959866
Integrating systems biology models and biomedical ontologies. PMID:21835028
iRsp1095: a genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network. PMID:21777427
A framework for the study of multiple realizations: the importance of levels of analysis. PMID:21772823
An integrated mathematical model of thrombin-, histamine-and VEGF-mediated signalling in endothelial permeability. PMID:21756365
JSBML: a flexible Java library for working with SBML. PMID:21697129
Quantitative analysis of transient and sustained transforming growth factor-β signaling dynamics. PMID:21613981
Thermodynamically consistent model calibration in chemical kinetics. PMID:21548948
A multiscale modeling approach to investigate molecular mechanisms of pseudokinase activation and drug resistance in the HER3/ErbB3 receptor tyrosine kinase signaling network. PMID:21509365
MEMOSys: Bioinformatics platform for genome-scale metabolic models. PMID:21276275
Software that goes with the flow in systems biology. PMID:21114874
Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems. PMID:21054868
Ranked retrieval of Computational Biology models. PMID:20701772
BioModels-15 years of sharing computational models in life science PubMed citations: 67.

67 articles citing: BioModels-15 years of sharing computational models in life science

HistoML, a markup language for representation and exchange of histopathological features in pathology images. PMID:35803960
Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows. PMID:35792600
Boolean modelling as a logic-based dynamic approach in systems medicine. PMID:35782730
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. PMID:35671510
Modeling Calcium Signaling in S. cerevisiae Highlights the Role and Regulation of the Calmodulin-Calcineurin Pathway in Response to Hypotonic Shock. PMID:35664674
A semantics, energy-based approach to automate biomodel composition. PMID:35657966
Disentangling ERBB Signaling in Breast Cancer Subtypes-A Model-Based Analysis. PMID:35625984
Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges. PMID:35625648
Building digital twins of the human immune system: toward a roadmap. PMID:35595830
Combination of Genome-Scale Models and Bioreactor Dynamics to Optimize the Production of Commodity Chemicals. PMID:35573743
Innovations in Genomics and Big Data Analytics for Personalized Medicine and Health Care: A Review. PMID:35563034
BioSimulators: a central registry of simulation engines and services for recommending specific tools. PMID:35524558
From Qualitative to Quantitative AOP: A Case Study of Neurodegeneration. PMID:35434701
Exploring the evolution of biochemical models at the network level. PMID:35312734
Systems Biology of Gut Microbiota-Human Receptor Interactions: Toward Anti-inflammatory Probiotics. PMID:35308387
All Driven by Energy Demand? Integrative Comparison of Metabolism of Enterococcus faecalis Wildtype and a Glutamine Synthase Mutant. PMID:35234500
Computational models in systems biology: standards, dissemination, and best practices. PMID:35217296
Computational Models for Clinical Applications in Personalized Medicine-Guidelines and Recommendations for Data Integration and Model Validation. PMID:35207655
A Computational Model of Bacterial Population Dynamics in Gastrointestinal Yersinia enterocolitica Infections in Mice. PMID:35205164
Kinetic and Stoichiometric Modeling-Based Analysis of Docosahexaenoic Acid (DHA) Production Potential by Crypthecodinium cohnii from Glycerol, Glucose and Ethanol. PMID:35200644
Patient-specific Boolean models of signalling networks guide personalised treatments. PMID:35164900
Capturing Biomarkers and Molecular Targets in Cellular Landscapes From Dynamic Reaction Network Models and Machine Learning. PMID:35127516
Dynamic optimization reveals alveolar epithelial cells as key mediators of host defense in invasive aspergillosis. PMID:34898608
Logical and experimental modeling of cytokine and eicosanoid signaling in psoriatic keratinocytes. PMID:34877506
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032. PMID:34867870
The European Bioinformatics Institute (EMBL-EBI) in 2021. PMID:34850134
Recent applications of quantitative systems pharmacology and machine learning models across diseases. PMID:34671863
Model comparison via simplicial complexes and persistent homology. PMID:34659787
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism. PMID:34625561
Modelling microbial communities: Harnessing consortia for biotechnological applications. PMID:34584635
The Systems Biology Simulation Core Library. PMID:34554191
Bayesian metamodeling of complex biological systems across varying representations. PMID:34453000
WinBEST-KIT: Biochemical Reaction Simulator for Analyzing Multi-Layered Metabolic Pathways. PMID:34436117
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19. PMID:34353886
Relating simulation studies by provenance-Developing a family of Wnt signaling models. PMID:34351901
Metformin Transport Rates Between Plasma and Red Blood Cells in Humans. PMID:34309806
Assembling Disease Networks From Causal Interaction Resources. PMID:34178043
Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective. PMID:34083542
Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target. PMID:34073716
In Silico Logical Modelling to Uncover Cooperative Interactions in Cancer. PMID:34063110
A comprehensive survey of developmental programs reveals a dearth of tree-like lineage graphs and ubiquitous regeneration. PMID:34020630
RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats. PMID:34019658
From integrative structural biology to cell biology. PMID:33957123
First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. PMID:33918864
Constructing and analysing dynamic models with modelbase v1.2.3: a software update. PMID:33879053
Physiologically based metformin pharmacokinetics model of mice and scale-up to humans for the estimation of concentrations in various tissues. PMID:33826656
Reproducibility in systems biology modelling. PMID:33620773
Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer's disease. PMID:33590873
A Mechanistic Model of NMDA and AMPA Receptor-Mediated Synaptic Transmission in Individual Hippocampal CA3-CA1 Synapses: A Computational Multiscale Approach. PMID:33546429
Emergence and propagation of epistasis in metabolic networks. PMID:33527897
Benchmarking of numerical integration methods for ODE models of biological systems. PMID:33514831
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. PMID:33378765
The Need for Research-Grade Systems Modeling Technologies for Life Science Education. PMID:33334676
ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species. PMID:33324679
Evaluation of Single Sample Network Inference Methods for Metabolomics-Based Systems Medicine. PMID:33267585
Computational Model Informs Effective Control Interventions against Y. enterocolitica Co-Infection. PMID:33266094
Environmental flexibility does not explain metabolic robustness. PMID:33247119
Inhibiting the reproduction of SARS-CoV-2 through perturbations in human lung cell metabolic network. PMID:33234678
Systems Biology Approaches to Understanding the Human Immune System. PMID:32849587
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
Isolating structural errors in reaction networks in systems biology. PMID:32790862
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). PMID:32598315
BioModels Parameters: a treasure trove of parameter values from published systems biology models. PMID:32573648
On the Use of Correlation and MI as a Measure of Metabolite-Metabolite Association for Network Differential Connectivity Analysis. PMID:32344593
Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. PMID:32313939
The 27th annual Nucleic Acids Research database issue and molecular biology database collection. PMID:31906604
BioModels: Content, Features, Functionality, and Use PubMed citations: 32.

32 articles citing: BioModels: Content, Features, Functionality, and Use

Potential inhibitors of the main protease of SARS-CoV-2 and modulators of arachidonic acid pathway: Non-steroidal anti-inflammatory drugs against COVID-19. PMID:34340125
Mathematical Modelling in Biomedicine: A Primer for the Curious and the Skeptic. PMID:33430432
A systems approach to infectious disease. PMID:32060427
Multi-domain semantic similarity in biomedical research. PMID:31138117
System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris. PMID:31072303
Identifying frequent patterns in biochemical reaction networks: a workflow. PMID:29992320
Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z. PMID:29843739
A Digitally Programmable Cytomorphic Chip for Simulation of Arbitrary Biochemical Reaction Networks. PMID:29570063
Responses to auxin signals: an operating principle for dynamical sensitivity yet high resilience. PMID:29410878
MAGPIE: Simplifying access and execution of computational models in the life sciences. PMID:29244826
From word models to executable models of signaling networks using automated assembly. PMID:29175850
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes. PMID:29169408
SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. PMID:29057095
Recent Advances in the Systems Biology of Aging. PMID:29020802
A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. PMID:28878200
Cooperative binding mitigates the high-dose hook effect. PMID:28807050
OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets. PMID:28792687
Reciprocal regulation of ARPP-16 by PKA and MAST3 kinases provides a cAMP-regulated switch in protein phosphatase 2A inhibition. PMID:28613156
Metabolic modeling of energy balances in Mycoplasma hyopneumoniae shows that pyruvate addition increases growth rate. PMID:28600895
PharmML in Action: an Interoperable Language for Modeling and Simulation. PMID:28575551
Genome-Scale Reconstruction of the Human Astrocyte Metabolic Network. PMID:28243200
The Impact of Mathematical Modeling in Understanding the Mechanisms Underlying Neurodegeneration: Evolving Dimensions and Future Directions. PMID:28063254
Metabolic systems biology: a brief primer. PMID:28028815
Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction. PMID:27895706
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PMID:27336457
Challenges in structural approaches to cell modeling. PMID:27255863
Systems medicine in colorectal cancer: from a mathematical model toward a new type of clinical trial. PMID:27240214
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. PMID:27051515
Reproducibility in Computational Neuroscience Models and Simulations. PMID:27046845
KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins. PMID:26989151
Comparing Alzheimer's and Parkinson's diseases networks using graph communities structure. PMID:26935435
Data integration in biological research: an overview. PMID:26336651
BioModels: expanding horizons to include more modelling approaches and formats PubMed citations: 26.

26 articles citing: BioModels: expanding horizons to include more modelling approaches and formats

Computational Models for Clinical Applications in Personalized Medicine-Guidelines and Recommendations for Data Integration and Model Validation. PMID:35207655
A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations. PMID:34907432
Generation of multicellular spatiotemporal models of population dynamics from ordinary differential equations, with applications in viral infection. PMID:34496857
Relating simulation studies by provenance-Developing a family of Wnt signaling models. PMID:34351901
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus. PMID:34188046
Maximization of information transmission influences selection of native phosphorelay architectures. PMID:34178454
libOmexMeta: Enabling semantic annotation of models to support FAIR principles. PMID:34132740
Reconstructing organisms in silico: genome-scale models and their emerging applications. PMID:32958892
Isolating structural errors in reaction networks in systems biology. PMID:32790862
Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. PMID:32313939
Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth. PMID:32234775
Modelling the effect of subcellular mutations on the migration of cells in the colorectal crypt. PMID:32126976
Genome-scale metabolic reconstruction and in silico analysis of the rice leaf blight pathogen, Xanthomonas oryzae. PMID:32068953
Organizing genome engineering for the gigabase scale. PMID:32019919
BioModels-15 years of sharing computational models in life science. PMID:31701150
Enzyme annotation in UniProtKB using Rhea. PMID:31688925
Quantifying the impact of public omics data. PMID:31383865
FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria. PMID:31333719
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. PMID:31225582
Current status and applications of genome-scale metabolic models. PMID:31196170
Quantitative Analyses of the Yeast Oxidative Protein Folding Pathway In Vitro and In Vivo. PMID:30880408
Reproducibility of Quantitative Systems Pharmacology Models: Current Challenges and Future Opportunities. PMID:30697975
Harmonizing semantic annotations for computational models in biology. PMID:30462164
SemGen: a tool for semantics-based annotation and composition of biosimulation models. PMID:30256901
MetExplore: collaborative edition and exploration of metabolic networks. PMID:29718355
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510

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biological process
metasource: Fairsharing.org
version: FAIRsharing.org: BioModels; BioModels; DOI: https://doi.org/10.25504/FAIRsharing.paz6mh; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

mathematical model
metasource: Fairsharing.org
version: FAIRsharing.org: BioModels; BioModels; DOI: https://doi.org/10.25504/FAIRsharing.paz6mh; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: BioModels; BioModels; DOI: https://doi.org/10.25504/FAIRsharing.paz6mh; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

network model
metasource: Fairsharing.org
version: FAIRsharing.org: BioModels; BioModels; DOI: https://doi.org/10.25504/FAIRsharing.paz6mh; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

other molecular biology databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

biological models
metasource: re3data.org
version: re3data.org: BioModels; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3C33C last accessed: 2022-11-04

biology
metasource: re3data.org
version: re3data.org: BioModels; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3C33C last accessed: 2022-11-04

biology - mathematical models
metasource: re3data.org
version: re3data.org: BioModels; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3C33C last accessed: 2022-11-04

dna
metasource: re3data.org
version: re3data.org: BioModels; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3C33C last accessed: 2022-11-04

gene expression
metasource: re3data.org
version: re3data.org: BioModels; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3C33C last accessed: 2022-11-04

genes
metasource: re3data.org
version: re3data.org: BioModels; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3C33C last accessed: 2022-11-04

genetics
metasource: re3data.org
version: re3data.org: BioModels; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3C33C last accessed: 2022-11-04

molecular biology
metasource: re3data.org
version: re3data.org: BioModels; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3C33C last accessed: 2022-11-04

nucleotide sequence
metasource: re3data.org
version: re3data.org: BioModels; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3C33C last accessed: 2022-11-04

proteins
metasource: re3data.org
version: re3data.org: BioModels; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3C33C last accessed: 2022-11-04

rna
metasource: re3data.org
version: re3data.org: BioModels; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3C33C last accessed: 2022-11-04

simulations
metasource: re3data.org
version: re3data.org: BioModels; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3C33C last accessed: 2022-11-04

systems biology
metasource: re3data.org
version: re3data.org: BioModels; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3C33C last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:55.315427

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:55.315427

biological process mathematical model molecular interaction network model molecular biology biological models biology - mathematical models dna gene expression gene genetics molecular biology nucleotide sequence proteins rna simulations systems biology molecular interactions, pathways and networks

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BioModels Parameter

BioModels Ontology

Path2Models

Experimental data repository for KInetic MOdels of biological SYStems

Minimal Information Required In the Annotation of Models

Systems Biology Ontology

The European Bioinformatics Institute Tools

BioStudies

Integrated resource of protein families, domains and functional sites

ModBase database of comparative protein structure models

Mathematical Modelling Ontology

ModelDB

Protein Model Database

MGnify

ChEMBL

Systems Biology Markup Language

HydroShare

European Nucleotide Archive

Gene Ontology Annotation Database

Manually Curated Database of Rice Proteins