Systems Biology Graphical Notation
Names
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Systems Biology Graphical Notation
metasource: Fairsharing.org
version: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
SBGN
metasource: Fairsharing.org
version: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
Names
More detailed information about this field from each metasource.
Systems Biology Graphical Notation
metasource: Fairsharing.orgversion: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
SBGN
metasource: Fairsharing.orgversion: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
Names
More detailed information about this field from each metasource.
Systems Biology Graphical Notation
metasource: Fairsharing.orgversion: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
SBGN
metasource: Fairsharing.orgversion: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
The Systems Biology Graphical Notation (SBGN) project is an effort to standardize the graphical notation used in maps of biological processes. The mission of SBGN project is to develop high quality, standard graphical languages for representing biological processes and interactions. Each SBGN language is based on the consensus of the broad international SBGN community of biologists, curators and software developers.
Description
More detailed information about this field from each metasource.
The Systems Biology Graphical Notation (SBGN) project is an effort to standardize the graphical notation used in maps of biological processes. The mission of SBGN project is to develop high quality, standard graphical languages for representing biological processes and interactions. Each SBGN language is based on the consensus of the broad international SBGN community of biologists, curators and software developers.
metasource: Fairsharing.orgversion: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
Webpage:
https://sbgn.github.io/Webpage
More detailed information about this field from each metasource.
https://sbgn.github.io/
metasource: Fairsharing.orgversion: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
The Systems Biology Graphical Notation
PMID: 19668183
metasource: Fairsharing.org
version: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
γCaMKII shuttles Ca²⁺/CaM to the nucleus to trigger CREB phosphorylation and gene expression
PMID: 25303525
metasource: Fairsharing.org
version: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2
PMID: 26528562
metasource: Fairsharing.org
version: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2
PMID: 26528563
metasource: Fairsharing.org
version: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
Publications
More detailed information about this field from each metasource.
The Systems Biology Graphical Notation
PMID: 19668183
metasource: Fairsharing.org
version: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
γCaMKII shuttles Ca²⁺/CaM to the nucleus to trigger CREB phosphorylation and gene expression
PMID: 25303525
metasource: Fairsharing.org
version: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2
PMID: 26528562
metasource: Fairsharing.org
version: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2
PMID: 26528563
metasource: Fairsharing.org
version: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
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The Systems Biology Graphical Notation
PubMed citations: 348.
348 articles citing: The Systems Biology Graphical Notation
Exploring the evolution of biochemical models at the network level. PMID:35312734
Computational Models for Clinical Applications in Personalized Medicine-Guidelines and Recommendations for Data Integration and Model Validation. PMID:35207655
Periodic synchronization of isolated network elements facilitates simulating and inferring gene regulatory networks including stochastic molecular kinetics. PMID:34986805
A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws. PMID:34983366
WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically. PMID:34888352
Thoroughly Calibrated Modular Agent-Based Model of the Human Cardiovascular and Renal Systems for Blood Pressure Regulation in Health and Disease. PMID:34867451
SBGNview: towards data analysis, integration and visualization on all pathways. PMID:34864890
Author-sourced capture of pathway knowledge in computable form using Biofactoid. PMID:34860157
CyFi-MAP: an interactive pathway-based resource for cystic fibrosis. PMID:34782688
PANTHER: Making genome-scale phylogenetics accessible to all. PMID:34717010
paraSBOLv: a foundation for standard-compliant genetic design visualization tools. PMID:34712845
Specifications of standards in systems and synthetic biology: status and developments in 2021. PMID:34674411
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. PMID:34664389
A Modular Mathematical Model of Exercise-Induced Changes in Metabolism, Signaling, and Gene Expression in Human Skeletal Muscle. PMID:34638694
WikiNetworks: translating manually created biological pathways for topological analysis. PMID:34636843
An Interactive View of Glycosylation. PMID:34611864
Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms' representation. PMID:34600580
QSDB-a graphical Quorum Sensing Database. PMID:34559210
The role of metadata in reproducible computational research. PMID:34553169
Experiment Selection in Meta-Analytic Piecemeal Causal Discovery. PMID:34532201
Inference of an Integrative, Executable Network for Rheumatoid Arthritis Combining Data-Driven Machine Learning Approaches and a State-of-the-Art Mechanistic Disease Map. PMID:34442429
The Interdependency and Co-Regulation of the Vitamin D and Cholesterol Metabolism. PMID:34440777
WinBEST-KIT: Biochemical Reaction Simulator for Analyzing Multi-Layered Metabolic Pathways. PMID:34436117
Relating simulation studies by provenance-Developing a family of Wnt signaling models. PMID:34351901
CFTR Lifecycle Map-A Systems Medicine Model of CFTR Maturation to Predict Possible Active Compound Combinations. PMID:34299207
Design and Implementation of a Tool to Assess Students' Understanding of Metabolic Pathways Dynamics and Regulation. PMID:34100646
Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective. PMID:34083542
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
A detailed map of coupled circadian clock and cell cycle with qualitative dynamics validation. PMID:33975535
Reactome and the Gene Ontology: Digital convergence of data resources. PMID:33964129
Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling. PMID:33834185
VaximmutorDB: A Web-Based Vaccine Immune Factor Database and Its Application for Understanding Vaccine-Induced Immune Mechanisms. PMID:33777032
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. PMID:33758926
Control and regulation of acetate overflow in Escherichia coli. PMID:33720011
Thyroid hormone: sex-dependent role in nervous system regulation and disease. PMID:33685490
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. PMID:33378765
Metabolic Reprogramming of Fibroblasts as Therapeutic Target in Rheumatoid Arthritis and Cancer: Deciphering Key Mechanisms Using Computational Systems Biology Approaches. PMID:33374292
Modelling of Immune Checkpoint Network Explains Synergistic Effects of Combined Immune Checkpoint Inhibitor Therapy and the Impact of Cytokines in Patient Response. PMID:33276543
Cholesterol Homeostasis: An In Silico Investigation into How Aging Disrupts Its Key Hepatic Regulatory Mechanisms. PMID:33007859
Network and Systems Medicine: Position Paper of the European Collaboration on Science and Technology Action on Open Multiscale Systems Medicine. PMID:32954378
Best Practices for Making Reproducible Biochemical Models. PMID:32853539
Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology. PMID:32850764
Publishing reproducible dynamic kinetic models. PMID:32793969
Disentangling molecular mechanisms regulating sensitization of interferon alpha signal transduction. PMID:32696599
Effects of repetitive Iodine thyroid blocking on the foetal brain and thyroid in rats: a systems biology approach. PMID:32616734
Specifications of standards in systems and synthetic biology: status and developments in 2020. PMID:32598316
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). PMID:32598315
ccNetViz: a WebGL-based JavaScript library for visualization of large networks. PMID:32516383
COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. PMID:32371892
Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases. PMID:32316560
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. PMID:32311035
ScalaFlux: A scalable approach to quantify fluxes in metabolic subnetworks. PMID:32287281
Visualizing metabolic network dynamics through time-series metabolomic data. PMID:32245365
EFMviz: A COBRA Toolbox extension to visualize Elementary Flux Modes in Genome-Scale Metabolic Models. PMID:32059585
Role of the Dihydrodipicolinate Synthase DapA1 on Iron Homeostasis During Cyanide Assimilation by the Alkaliphilic Bacterium Pseudomonas pseudoalcaligenes CECT5344. PMID:32038602
Repository of proposed pathways and protein-protein interaction networks in age-related macular degeneration. PMID:31934346
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
A multiscale signalling network map of innate immune response in cancer reveals cell heterogeneity signatures. PMID:31641119
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
PathBank: a comprehensive pathway database for model organisms. PMID:31602464
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
Application of Modeling Approaches to Explore Vaccine Adjuvant Mode-of-Action. PMID:31572370
Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. PMID:31548717
Multisite rate control analysis identifies ribosomal scanning as the sole high-capacity/low-flux-control step in mRNA translation. PMID:31520451
Communicating Structure and Function in Synthetic Biology Diagrams. PMID:31348656
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. PMID:31301675
An NFκB Activity Calculator to Delineate Signaling Crosstalk: Type I and II Interferons Enhance NFκB via Distinct Mechanisms. PMID:31293585
Closing the gap between formats for storing layout information in systems biology. PMID:31273380
Mental-Map Preserving Visualisation of Partitioned Networks in Vanted. PMID:31199771
BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. PMID:31131402
Modeling the Dynamics of Human Liver Failure Post Liver Resection. PMID:31131255
PathMe: merging and exploring mechanistic pathway knowledge. PMID:31092193
Metabopolis: scalable network layout for biological pathway diagrams in urban map style. PMID:30991966
Computational Modeling to Quantify the Contributions of VEGFR1, VEGFR2, and Lateral Inhibition in Sprouting Angiogenesis. PMID:30971939
High-Performance Biocomputing in Synthetic Biology-Integrated Transcriptional and Metabolic Circuits. PMID:30915329
A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae. PMID:30899000
Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli. PMID:30677026
Best Practices to Maximize the Use and Reuse of Quantitative and Systems Pharmacology Models: Recommendations From the United Kingdom Quantitative and Systems Pharmacology Network. PMID:30667172
A computational model to understand mouse iron physiology and disease. PMID:30608934
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. PMID:30576488
Harmonizing semantic annotations for computational models in biology. PMID:30462164
Chronic platelet-derived growth factor receptor signaling exerts control over initiation of protein translation in glioma. PMID:30456354
Subunit exchange enhances information retention by CaMKII in dendritic spines. PMID:30418153
Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse. PMID:30401736
Using Systems Biology and Mathematical Modeling Approaches in the Discovery of Therapeutic Targets for Spinal Muscular Atrophy. PMID:30334226
Systems Oncology: Bridging Pancreatic and Castrate Resistant Prostate Cancer. PMID:30220022
Reproducible Research Using Biomodels. PMID:30191472
In Vitro Tracking of Intracellular Metabolism-Derived Cancer Volatiles via Isotope Labeling. PMID:30159401
Clustering approaches for visual knowledge exploration in molecular interaction networks. PMID:30157777
Estimating the protein burden limit of yeast cells by measuring the expression limits of glycolytic proteins. PMID:30095406
Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0. PMID:29971008
Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms. PMID:29872544
Efficient methods and readily customizable libraries for managing complexity of large networks. PMID:29813080
A logic-based method to build signaling networks and propose experimental plans. PMID:29777117
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
Signalling maps in cancer research: construction and data analysis. PMID:29688383
Community-driven roadmap for integrated disease maps. PMID:29688273
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. PMID:29684165
Evolution of computational models in BioModels Database and the Physiome Model Repository. PMID:29650016
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. PMID:29596055
No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases. PMID:29575574
A graphical and computational modeling platform for biological pathways. PMID:29543794
The Genome-Scale Integrated Networks in Microorganisms. PMID:29527198
Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. PMID:29447151
Interleukins and their signaling pathways in the Reactome biological pathway database. PMID:29378288
Reactome diagram viewer: data structures and strategies to boost performance. PMID:29186351
From word models to executable models of signaling networks using automated assembly. PMID:29175850
The Reactome Pathway Knowledgebase. PMID:29145629
Automated visualization of rule-based models. PMID:29131816
Computer simulation models as a tool to investigate the role of microRNAs in osteoarthritis. PMID:29095952
Reactome enhanced pathway visualization. PMID:29077811
PTEN Regulates PI(3,4)P2 Signaling Downstream of Class I PI3K. PMID:29056325
Using computer simulation models to investigate the most promising microRNAs to improve muscle regeneration during ageing. PMID:28951568
Is systems pharmacology ready to impact upon therapy development? A study on the cholesterol biosynthesis pathway. PMID:28910500
A scalable moment-closure approximation for large-scale biochemical reaction networks. PMID:28881983
Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures. PMID:28775339
MUFINS: multi-formalism interaction network simulator. PMID:28725480
MINERVA-a platform for visualization and curation of molecular interaction networks. PMID:28725475
Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways. PMID:28725465
Network reconstruction and validation of the Snf1/AMPK pathway in baker's yeast based on a comprehensive literature review. PMID:28725459
Logic Modeling in Quantitative Systems Pharmacology. PMID:28681552
Reciprocal regulation of ARPP-16 by PKA and MAST3 kinases provides a cAMP-regulated switch in protein phosphatase 2A inhibition. PMID:28613156
Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient. PMID:28521769
Graphical Modeling Meets Systems Pharmacology. PMID:28469411
ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network. PMID:28442501
BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences. PMID:28365720
A Web Tool for Generating High Quality Machine-readable Biological Pathways. PMID:28287524
Mathematical analysis of the influence of brain metabolism on the BOLD signal in Alzheimer's disease. PMID:28271954
A taxonomy of visualization tasks for the analysis of biological pathway data. PMID:28251869
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. PMID:28187405
Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli. PMID:28187134
Acetate fluxes in Escherichia coli are determined by the thermodynamic control of the Pta-AckA pathway. PMID:28186174
Bioactive Nutrients and Nutrigenomics in Age-Related Diseases. PMID:28075340
A Machine Learning Approach to Predict Gene Regulatory Networks in Seed Development in Arabidopsis. PMID:28066488
STON: exploring biological pathways using the SBGN standard and graph databases. PMID:27919219
A systems study reveals concurrent activation of AMPK and mTOR by amino acids. PMID:27869123
A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. PMID:27830063
Notions of similarity for systems biology models. PMID:27742665
Statistical Techniques Complement UML When Developing Domain Models of Complex Dynamical Biosystems. PMID:27571414
Ion Channel ElectroPhysiology Ontology (ICEPO) - a case study of text mining assisted ontology development. PMID:27570648
Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL). PMID:27554092
Modelling the Structure and Dynamics of Biological Pathways. PMID:27509052
Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases. PMID:27441714
Guidelines for Reproducibly Building and Simulating Systems Biology Models. PMID:27429432
Simulated Interventions to Ameliorate Age-Related Bone Loss Indicate the Importance of Timing. PMID:27379013
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PMID:27336457
BioASF: a framework for automatically generating executable pathway models specified in BioPAX. PMID:27307645
Qualitative dynamics semantics for SBGN process description. PMID:27306057
Toward Community Standards and Software for Whole-Cell Modeling. PMID:27305665
A Six-Stage Workflow for Robust Application of Systems Pharmacology. PMID:27299936
OFFl Models: Novel Schema for Dynamical Modeling of Biological Systems. PMID:27270918
A rule-based model of insulin signalling pathway. PMID:27245161
Modeling and gene knockdown to assess the contribution of nonsense-mediated decay, premature termination, and selenocysteine insertion to the selenoprotein hierarchy. PMID:27208313
Reactome from a WikiPathways Perspective. PMID:27203685
SBtab: a flexible table format for data exchange in systems biology. PMID:27153616
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. PMID:27051515
A physiome interoperability roadmap for personalized drug development. PMID:27051513
Data- and knowledge-based modeling of gene regulatory networks: an update. PMID:27047314
The systems biology format converter. PMID:27044654
Differentiation resistance through altered retinoblastoma protein function in acute lymphoblastic leukemia: in silico modeling of the deregulations in the G1/S restriction point pathway. PMID:26932523
Comprehensive Map of Molecules Implicated in Obesity. PMID:26886906
Pathway Analysis: State of the Art. PMID:26733877
Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks. PMID:26729218
Spatially transformed fluorescence image data for ERK-MAPK and selected proteins within human epidermis. PMID:26675891
SBOL Visual: A Graphical Language for Genetic Designs. PMID:26633141
Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos. PMID:26572793
Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants. PMID:26557642
Specifications of Standards in Systems and Synthetic Biology. PMID:26528556
Modeling and Simulation of Optimal Resource Management during the Diurnal Cycle in Emiliania huxleyi by Genome-Scale Reconstruction and an Extended Flux Balance Analysis Approach. PMID:26516924
WikiPathways: capturing the full diversity of pathway knowledge. PMID:26481357
Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure. PMID:26468131
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. PMID:26452770
Impact of kinetic isotope effects in isotopic studies of metabolic systems. PMID:26410690
An algorithm for automated layout of process description maps drawn in SBGN. PMID:26363029
Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells. PMID:26284497
Regulation of ERK-MAPK signaling in human epidermis. PMID:26209520
The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms. PMID:26205660
Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps. PMID:26192618
Modeling for (physical) biologists: an introduction to the rule-based approach. PMID:26178138
SEEK: a systems biology data and model management platform. PMID:26160520
Tools for visualization and analysis of molecular networks, pathways, and -omics data. PMID:26082651
Potential unsatisfiability of cyclic constraints on stochastic biological networks biases selection towards hierarchical architectures. PMID:26040595
SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps. PMID:26030594
Integrated Stochastic Model of DNA Damage Repair by Non-homologous End Joining and p53/p21-Mediated Early Senescence Signalling. PMID:26020242
NaviCell Web Service for network-based data visualization. PMID:25958393
Pathways with PathWhiz. PMID:25934797
Mathematical modelling of metabolic regulation in aging. PMID:25923415
Mimoza: web-based semantic zooming and navigation in metabolic networks. PMID:25889977
A generalised enzyme kinetic model for predicting the behaviour of complex biochemical systems. PMID:25859426
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. PMID:25759811
Rapid proteasomal elimination of 3-hydroxy-3-methylglutaryl-CoA reductase by interferon-γ in primary macrophages requires endogenous 25-hydroxycholesterol synthesis. PMID:25759117
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
PathVisio 3: an extendable pathway analysis toolbox. PMID:25706687
A novel mathematical model describing adaptive cellular drug metabolism and toxicity in the chemoimmune system. PMID:25699998
Dynamics of elongation factor 2 kinase regulation in cortical neurons in response to synaptic activity. PMID:25698741
Dendritic geometry shapes neuronal cAMP signalling to the nucleus. PMID:25692798
Integrative analysis of metabolic models - from structure to dynamics. PMID:25674560
Quantitative and logic modelling of molecular and gene networks. PMID:25645874
An integrated network visualization framework towards metabolic engineering applications. PMID:25547011
Improving collaboration by standardization efforts in systems biology. PMID:25538939
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. PMID:25503938
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. PMID:25494900
Mechanistic modeling confronts the complexity of molecular cell biology. PMID:25368428
Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering. PMID:25344492
Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut. PMID:25295490
Modelling biological behaviours with the unified modelling language: an immunological case study and critique. PMID:25142524
Integrating biological pathways and genomic profiles with ChiBE 2. PMID:25086704
NetworkViewer: visualizing biochemical reaction networks with embedded rendering of molecular interaction rules. PMID:24934175
The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. PMID:24911500
In silico modeling of the effects of alpha-synuclein oligomerization on dopaminergic neuronal homeostasis. PMID:24885905
An Interaction Library for the FcεRI Signaling Network. PMID:24782869
A computer simulation approach to assessing therapeutic intervention points for the prevention of cytokine-induced cartilage breakdown. PMID:24757149
Bridging the gaps in systems biology. PMID:24728588
BiNA: a visual analytics tool for biological network data. PMID:24551056
Viral enhancer mimicry of host innate-immune promoters. PMID:24516378
Combinatorial regulation of lipoprotein lipase by microRNAs during mouse adipogenesis. PMID:24457907
ModeLang: a new approach for experts-friendly viral infections modeling. PMID:24454531
A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803. PMID:24402049
A systems' biology approach to study microRNA-mediated gene regulatory networks. PMID:24350286
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. PMID:24321545
A computational model of liver iron metabolism. PMID:24244122
Annotating cancer variants and anti-cancer therapeutics in reactome. PMID:24213504
Elementary flux modes analysis of functional domain networks allows a better metabolic pathway interpretation. PMID:24204596
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
Translation of SBGN maps: Process Description to Activity Flow. PMID:24176088
Neural Schematics as a unified formal graphical representation of large-scale Neural Network Structures. PMID:24167490
Toward an integrated software platform for systems pharmacology. PMID:24150748
Pathways of Toxicity. PMID:24127042
Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. PMID:24123887
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. PMID:24099179
A comprehensive map of the influenza A virus replication cycle. PMID:24088197
QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells. PMID:24064420
Conversion of KEGG metabolic pathways to SBGN maps including automatic layout. PMID:23953132
Extracting reaction networks from databases-opening Pandora's box. PMID:23946492
Integration of biochemical and electrical signaling-multiscale model of the medium spiny neuron of the striatum. PMID:23843966
Reaction-contingency based bipartite Boolean modelling. PMID:23835289
Integrating pathways of Parkinson's disease in a molecular interaction map. PMID:23832570
Neural systems language: a formal modeling language for the systematic description, unambiguous communication, and automated digital curation of neural connectivity. PMID:23787962
Pathway databases: making chemical and biological sense of the genomic data flood. PMID:23706629
Evidence for extensive heterotrophic metabolism, antioxidant action, and associated regulatory events during winter hardening in Sitka spruce. PMID:23631437
A comprehensive machine-readable view of the mammalian cholesterol biosynthesis pathway. PMID:23583456
Biographer: web-based editing and rendering of SBGN compliant biochemical networks. PMID:23574737
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. PMID:23550210
PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways. PMID:23547033
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. PMID:23453054
Model composition through model reduction: a combined model of CD95 and NF-κB signaling pathways. PMID:23409788
CySBGN: a Cytoscape plug-in to integrate SBGN maps. PMID:23324051
Conceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle. PMID:23308089
Mathematical modeling of sustainable synaptogenesis by repetitive stimuli suggests signaling mechanisms in vivo. PMID:23284653
OPTIMAS-DW: a comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize. PMID:23272737
Signalling network construction for modelling plant defence response. PMID:23272172
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. PMID:23193289
Computational modeling of the metabolic States regulated by the kinase akt. PMID:23181020
Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. PMID:23175748
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564
VANTED v2: a framework for systems biology applications. PMID:23140568
A UML profile for the OBO relation ontology. PMID:23095840
A semi-mechanistic integrated toxicokinetic-toxicodynamic (TK/TD) model for arsenic(III) in hepatocytes. PMID:23069314
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
Elucidating the sources of β-catenin dynamics in human neural progenitor cells. PMID:22952611
Reduction of dynamical biochemical reactions networks in computational biology. PMID:22833754
Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs. PMID:22798498
A model of flux regulation in the cholesterol biosynthesis pathway: Immune mediated graduated flux reduction versus statin-like led stepped flux reduction. PMID:22664637
AlzPathway: a comprehensive map of signaling pathways of Alzheimer's disease. PMID:22647208
Computational tools for metabolic engineering. PMID:22629572
RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry. PMID:22607382
Software support for SBGN maps: SBGN-ML and LibSBGN. PMID:22581176
DIPSBC--data integration platform for systems biology collaborations. PMID:22568834
FluxMap: a VANTED add-on for the visual exploration of flux distributions in biological networks. PMID:22548786
A framework for mapping, visualisation and automatic model creation of signal-transduction networks. PMID:22531118
Short-term information processing, long-term responses: Insights by mathematical modeling of signal transduction. Early activation dynamics of key signaling mediators can be predictive for cell fate decisions. PMID:22528856
Large-scale sequestration of atmospheric carbon via plant roots in natural and agricultural ecosystems: why and how. PMID:22527402
Systems biology of fungal infection. PMID:22485108
An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells. PMID:22416242
Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation. PMID:22383037
Towards a quantitative understanding of the MITF-PIAS3-STAT3 connection. PMID:22316093
Structural analysis and stochastic modelling suggest a mechanism for calmodulin trapping by CaMKII. PMID:22279535
Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach. PMID:22260221
Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). PMID:22180826
Leveraging modeling approaches: reaction networks and rules. PMID:22161349
Modeling formalisms in Systems Biology. PMID:22141422
IPAVS: Integrated Pathway Resources, Analysis and Visualization System. PMID:22140115
MetaCrop 2.0: managing and exploring information about crop plant metabolism. PMID:22086948
Model-based global sensitivity analysis as applied to identification of anti-cancer drug targets and biomarkers of drug resistance in the ErbB2/3 network. PMID:22085636
Software for systems biology: from tools to integrated platforms. PMID:22048662
Controlled vocabularies and semantics in systems biology. PMID:22027554
BioPAX support in CellDesigner. PMID:22021903
Critical assessment of human metabolic pathway databases: a stepping stone for future integration. PMID:21999653
A comprehensive curated resource for follicle stimulating hormone signaling. PMID:21996254
NetSlim: high-confidence curated signaling maps. PMID:21959865
Dupuytren's: a systems biology disease. PMID:21943049
Logical network of genotoxic stress-induced NF-κB signal transduction predicts putative target structures for therapeutic intervention strategies. PMID:21918620
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Intuitive visualization and analysis of multi-omics data and application to Escherichia coli carbon metabolism. PMID:21731702
The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways. PMID:21653523
Guidelines for visualizing and annotating rule-based models. PMID:21647530
The Dynamical Systems Properties of the HOG Signaling Cascade. PMID:21637384
PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs). PMID:21636591
Social engineering for virtual 'big science' in systems biology. PMID:21587248
A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. PMID:21586134
Ontologies and standards in bioscience research: for machine or for human. PMID:21519400
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
Automated ensemble modeling with modelMaGe: analyzing feedback mechanisms in the Sho1 branch of the HOG pathway. PMID:21483474
Systems glycobiology: biochemical reaction networks regulating glycan structure and function. PMID:21436236
Current trends and new challenges of databases and web applications for systems driven biological research. PMID:21423387
Grand challenges in systems physiology. PMID:21423346
Systems biology: the next frontier for bioinformatics. PMID:21331364
Synthetic biology: a foundation for multi-scale molecular biology. PMID:21326830
The PluriNetWork: an electronic representation of the network underlying pluripotency in mouse, and its applications. PMID:21179244
A comprehensive map of the mTOR signaling network. PMID:21179025
ExprEssence--revealing the essence of differential experimental data in the context of an interaction/regulation net-work. PMID:21118483
DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells. PMID:21092113
Pathway Commons, a web resource for biological pathway data. PMID:21071392
Reactome: a database of reactions, pathways and biological processes. PMID:21067998
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. PMID:21045058
Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson's, Huntington's, Alzheimer's, prions, bactericides, chemical toxicology and others as examples. PMID:20967426
A comprehensive molecular interaction map of the budding yeast cell cycle. PMID:20865008
The BioPAX community standard for pathway data sharing. PMID:20829833
SBML2TikZ: supporting the SBML render extension in LaTeX. PMID:20829443
Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PMID:20824171
A graphical method for reducing and relating models in systems biology. PMID:20823324
The caspase-8 dimerization/dissociation balance is a highly potent regulator of caspase-8, -3, -6 signaling. PMID:20702410
Editing, validating and translating of SBGN maps. PMID:20628075
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. PMID:20587024
PINT: Pathways INtegration Tool. PMID:20538652
PathText: a text mining integrator for biological pathway visualizations. PMID:20529930
Perspectives for computer modeling in the study of T cell activation. PMID:20516137
The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways. PMID:20478018
Construction of a large scale integrated map of macrophage pathogen recognition and effector systems. PMID:20470404
VISIBIOweb: visualization and layout services for BioPAX pathway models. PMID:20460470
Arcadia: a visualization tool for metabolic pathways. PMID:20453003
Payao: a community platform for SBML pathway model curation. PMID:20371497
Visualizing biological data-now and in the future. PMID:20195254
Signal transduction networks in cancer: quantitative parameters influence network topology. PMID:20179207
Simulating plant metabolic pathways with enzyme-kinetic models. PMID:20118273
Hematopoiesis and its disorders: a systems biology approach. PMID:20103779
Biocharts: a visual formalism for complex biological systems. PMID:20022895
Metabolic networks: how to identify key components in the regulation of metabolism and growth. PMID:20018593
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. PMID:20015972
ChiBE: interactive visualization and manipulation of BioPAX pathway models. PMID:20007251
The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. PMID:19906839
An empirical Bayesian approach for model-based inference of cellular signaling networks. PMID:19900289
TinkerCell: modular CAD tool for synthetic biology. PMID:19874625
Molecular machines or pleiomorphic ensembles: signaling complexes revisited. PMID:19835637
How to visually interpret biological data using networks. PMID:19816451
A switchable light-input, light-output system modelled and constructed in yeast. PMID:19761615 -
γCaMKII shuttles Ca²⁺/CaM to the nucleus to trigger CREB phosphorylation and gene expression
PubMed citations: 112.
112 articles citing: γCaMKII shuttles Ca²⁺/CaM to the nucleus to trigger CREB phosphorylation and gene expression
A Critical Role for γCaMKII in Decoding NMDA Signaling to Regulate AMPA Receptors in Putative Inhibitory Interneurons. PMID:35290589
Calcium and calcium-related proteins in endometrial cancer: opportunities for pharmacological intervention. PMID:35173539
Inhibitory Effects of 6,8-Diprenylorobol on Endometriosis Progression in Humans by Disrupting Calcium Homeostasis and Mitochondrial Function. PMID:35052675
Golgi Phosphoprotein 73: The Driver of Epithelial-Mesenchymal Transition in Cancer. PMID:34950590
Shuttling of cellular proteins between the plasma membrane and nucleus (Review). PMID:34779504
Regulation of neuronal excitation-transcription coupling by Kv2.1-induced clustering of somatic L-type Ca2+ channels at ER-PM junctions. PMID:34750263
Neuronal activity regulates the nuclear proteome to promote activity-dependent transcription. PMID:34617965
Phosphorylation of CREB at Serine 142 and 143 Is Essential for Visual Cortex Plasticity. PMID:34607805
CAMK2G is identified as a novel therapeutic target for myelofibrosis. PMID:34521112
Depolarization induces nociceptor sensitization by CaV1.2-mediated PKA-II activation. PMID:34431981
Spatiotemporal Regulation of Transcript Isoform Expression in the Hippocampus. PMID:34305526
Preservation of vision after CaMKII-mediated protection of retinal ganglion cells. PMID:34297923
Ischemic heart injury leads to HIF1-dependent differential splicing of CaMK2γ. PMID:34162925
CaMKIV Signaling Is Not Essential for the Maintenance of Intrinsic or Synaptic Properties in Mouse Visual Cortex. PMID:34001638
Enhanced excitability of cortical neurons in low-divalent solutions is primarily mediated by altered voltage-dependence of voltage-gated sodium channels. PMID:33973519
Biochemical Activity Architectures Visualized-Using Genetically Encoded Fluorescent Biosensors to Map the Spatial Boundaries of Signaling Compartments. PMID:33949851
Store-Operated Calcium Entry: Shaping the Transcriptional and Epigenetic Landscape in Pancreatic Cancer. PMID:33919156
The role of nuclear Ca2+ in maintaining neuronal homeostasis and brain health. PMID:33912918
Calcium/Calmodulin-Dependent Protein Kinase II in Cerebrovascular Diseases. PMID:33713030
Dihydropyridine Calcium Channel Blockers Suppress the Transcription of PD-L1 by Inhibiting the Activation of STAT1. PMID:33519429
Totally Rad? The Long and Winding Road to Understanding CaV1.2 Regulation. PMID:33411632
High neural activity accelerates the decline of cognitive plasticity with age in Caenorhabditis elegans. PMID:33228848
Adaptor protein APPL1 links neuronal activity to chromatin remodeling in cultured hippocampal neurons. PMID:33104190
CaV channels reject signaling from a second CaM in eliciting Ca2+-dependent feedback regulation. PMID:32820053
CaMKII controls neuromodulation via neuropeptide gene expression and axonal targeting of neuropeptide vesicles. PMID:32776935
Activity-Dependent Gene Expression in Neurons. PMID:32727285
Heterogeneity in human hippocampal CaMKII transcripts reveals allosteric hub-dependent regulation. PMID:32694170
Retracted: Allopregnanolone restores the tyrosine hydroxylase-positive neurons and motor performance in a 6-OHDA-injected mouse model. PMID:32602622
CaMKII/calpain interaction mediates ischemia/reperfusion injury in isolated rat hearts. PMID:32439852
Calcium and cell function. PMID:32350889
Functional implications of CaMKII alternative splicing. PMID:32343011
Obesity-induced overexpression of miR-802 impairs insulin transcription and secretion. PMID:32286278
Synaptic GluN2A-Containing NMDA Receptors: From Physiology to Pathological Synaptic Plasticity. PMID:32102377
Neuronal L-Type Calcium Channel Signaling to the Nucleus Requires a Novel CaMKIIα-Shank3 Interaction. PMID:32019829
α-Actinin-1 promotes activity of the L-type Ca2+ channel Cav 1.2. PMID:31985069
In Vivo Imaging of the Coupling between Neuronal and CREB Activity in the Mouse Brain. PMID:31883788
Inhibition of NR2B-containing NMDA receptors during nitrogen narcosis. PMID:31828746
Kv2.1 mediates spatial and functional coupling of L-type calcium channels and ryanodine receptors in mammalian neurons. PMID:31663850
Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers. PMID:31585079
Functional Consequences of Calcium-Dependent Synapse-to-Nucleus Communication: Focus on Transcription-Dependent Metabolic Plasticity. PMID:31570333
CaM Kinase: Still Inspiring at 40. PMID:31394063
Opsin 3 is a key regulator of ultraviolet A-induced photoageing in human dermal fibroblast cells. PMID:31380578
CAMK2-Dependent Signaling in Neurons Is Essential for Survival. PMID:31064859
How can memories last for days, years, or a lifetime? Proposed mechanisms for maintaining synaptic potentiation and memory. PMID:30992383
Synapse-to-Nucleus Communication through NFAT Is Mediated by L-type Ca2+ Channel Ca2+ Spike Propagation to the Soma. PMID:30917310
Podocyte histone deacetylase activity regulates murine and human glomerular diseases. PMID:30776024
Procyanidins and Alzheimer's Disease. PMID:30649713
CaMKII Isoforms in Learning and Memory: Localization and Function. PMID:30564099
Activity-Regulated Transcription: Bridging the Gap between Neural Activity and Behavior. PMID:30359600
The C-terminus of NMDAR GluN1-1a Subunit Translocates to Nucleus and Regulates Synaptic Function. PMID:30333730
The intellectual disability-associated CAMK2G p.Arg292Pro mutation acts as a pathogenic gain-of-function. PMID:30184290
β-Subunit of the voltage-gated Ca2+ channel Cav1.2 drives signaling to the nucleus via H-Ras. PMID:30150369
Activity-dependent Signaling and Epigenetic Abnormalities in Mice Exposed to Postnatal Ethanol. PMID:30031835
Ischemic Injury-Induced CaMKIIδ and CaMKIIγ Confer Neuroprotection Through the NF-κB Signaling Pathway. PMID:29992531
Calmodulin shuttling mediates cytonuclear signaling to trigger experience-dependent transcription and memory. PMID:29934532
High-Frequency Repetitive Magnetic Stimulation Enhances the Expression of Brain-Derived Neurotrophic Factor Through Activation of Ca2+-Calmodulin-Dependent Protein Kinase II-cAMP-Response Element-Binding Protein Pathway. PMID:29867712
A novel role for CAMKIIβ in the regulation of cortical neuron migration: implications for neurodevelopmental disorders. PMID:29712998
Improved calcium sensor GCaMP-X overcomes the calcium channel perturbations induced by the calmodulin in GCaMP. PMID:29666364
Analysis of the CaMKIIα and β splice-variant distribution among brain regions reveals isoform-specific differences in holoenzyme formation. PMID:29615706
Multifactorial Modes of Action of Arsenic Trioxide in Cancer Cells as Analyzed by Classical and Network Pharmacology. PMID:29535630
Memory formation depends on both synapse-specific modifications of synaptic strength and cell-specific increases in excitability. PMID:29434376
Biophysical attributes that affect CaMKII activation deduced with a novel spatial stochastic simulation approach. PMID:29401454
Physiological and Pathological Roles of CaMKII-PP1 Signaling in the Brain. PMID:29271887
Was the Watchmaker Blind? Or Was She One-Eyed? PMID:29261138
Highlights for the 6th International Ion Channel Conference: ion channel structure, function, disease and therapeutics. PMID:29159026
A novel mechanism for Ca2+/calmodulin-dependent protein kinase II targeting to L-type Ca2+ channels that initiates long-range signaling to the nucleus. PMID:28916724
Evolution viewed from physics, physiology and medicine. PMID:28839924
A T-type channel-calmodulin complex triggers αCaMKII activation. PMID:28800734
α-Actinin Promotes Surface Localization and Current Density of the Ca2+ Channel CaV1.2 by Binding to the IQ Region of the α1 Subunit. PMID:28613835
Conserved properties of Drosophila Insomniac link sleep regulation and synaptic function. PMID:28558011
Regulated transport of signaling proteins from synapse to nucleus. PMID:28502891
From Gene to Behavior: L-Type Calcium Channel Mechanisms Underlying Neuropsychiatric Symptoms. PMID:28497380
The calcium-cancer signalling nexus. PMID:28386091
Densin-180 Controls the Trafficking and Signaling of L-Type Voltage-Gated Cav1.2 Ca2+ Channels at Excitatory Synapses. PMID:28363979
Phosphorylation of Ser1928 mediates the enhanced activity of the L-type Ca2+ channel Cav1.2 by the β2-adrenergic receptor in neurons. PMID:28119465
Translation reprogramming is an evolutionarily conserved driver of phenotypic plasticity and therapeutic resistance in melanoma. PMID:28096186
Wnt5a is essential for hippocampal dendritic maintenance and spatial learning and memory in adult mice. PMID:28069946
Detecting stoichiometry of macromolecular complexes in live cells using FRET. PMID:27922011
Neuronal Gene Targets of NF-κB and Their Dysregulation in Alzheimer's Disease. PMID:27881951
NMDA receptors in mouse anterior piriform cortex initialize early odor preference learning and L-type calcium channels engage for long-term memory. PMID:27739540
Evidence for evolutionary divergence of activity-dependent gene expression in developing neurons. PMID:27692071
Synaptic GluN2B/CaMKII-α Signaling Induces Synapto-Nuclear Transport of ERK and Jacob. PMID:27559307
The CaM Kinase CMK-1 Mediates a Negative Feedback Mechanism Coupling the C. elegans Glutamate Receptor GLR-1 with Its Own Transcription. PMID:27462879
Electroacupuncture improves cognitive ability following cerebral ischemia reperfusion injury via CaM-CaMKIV-CREB signaling in the rat hippocampus. PMID:27446275
Decreased Caffeine-Induced Locomotor Activity via Microinjection of CART Peptide into the Nucleus Accumbens Is Linked to Inhibition of the pCaMKIIa-D3R Interaction. PMID:27404570
Store-operated Ca2+ channels in airway epithelial cell function and implications for asthma. PMID:27377718
Tau accumulation induces synaptic impairment and memory deficit by calcineurin-mediated inactivation of nuclear CaMKIV/CREB signaling. PMID:27298345
CaMKII mediates stimulus specificity in early odor preference learning in rats. PMID:27121578
Phosphorylation of Cav1.2 on S1928 uncouples the L-type Ca2+ channel from the β2 adrenergic receptor. PMID:27103070
Chromatin Modulatory Proteins and Olfactory Receptor Signaling in the Refinement and Maintenance of Fruitless Expression in Olfactory Receptor Neurons. PMID:27093619
Excitation-Transcription Coupling in Parvalbumin-Positive Interneurons Employs a Novel CaM Kinase-Dependent Pathway Distinct from Excitatory Neurons. PMID:27041500
Unifying Views of Autism Spectrum Disorders: A Consideration of Autoregulatory Feedback Loops. PMID:26985722
Sequential ionic and conformational signaling by calcium channels drives neuronal gene expression. PMID:26912895
NF-KappaB in Long-Term Memory and Structural Plasticity in the Adult Mammalian Brain. PMID:26635522
Ca2+/calmodulin-dependent protein kinase II-γ (CaMKIIγ) negatively regulates vascular smooth muscle cell proliferation and vascular remodeling. PMID:26567004
Coordination of Protein Phosphorylation and Dephosphorylation in Synaptic Plasticity. PMID:26453308
Cell biological mechanisms of activity-dependent synapse to nucleus translocation of CRTC1 in neurons. PMID:26388727
Regulation of BDNF chromatin status and promoter accessibility in a neural correlate of associative learning. PMID:26336984
Differential CaMKII regulation by voltage-gated calcium channels in the striatum. PMID:26255006
Importance of being Nernst: Synaptic activity and functional relevance in stem cell-derived neurons. PMID:26240679
Nuclear Translocation of Calcium/Calmodulin-dependent Protein Kinase IIδ3 Promoted by Protein Phosphatase-1 Enhances Brain-derived Neurotrophic Factor Expression in Dopaminergic Neurons. PMID:26163515
Evolutionary and functional perspectives on signaling from neuronal surface to nucleus. PMID:25998737
Differential expression of CaMKII isoforms and overall kinase activity in rat dorsal root ganglia after injury. PMID:25982557
Heterogeneity of Calcium Channel/cAMP-Dependent Transcriptional Activation. PMID:25966705
A transcriptional reporter of intracellular Ca(2+) in Drosophila. PMID:25961791
Carotid body overactivity induces respiratory neurone channelopathy contributing to neurogenic hypertension. PMID:25900825
Dynamic visualization of calcium-dependent signaling in cellular microdomains. PMID:25703691
Distinct roles of multiple isoforms of CaMKII in signaling to the nucleus. PMID:25700840
The impact of NMDA receptor hypofunction on GABAergic neurons in the pathophysiology of schizophrenia. PMID:25583246
Targeting novel signaling pathways for resistant acute myeloid leukemia. PMID:25533111
Past experience resets behavior: CaMK takes the heat. PMID:25475181
Mission CaMKIIγ: shuttle calmodulin from membrane to nucleus. PMID:25303520 -
Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2
PubMed citations: 17.
17 articles citing: Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2
Exploring the evolution of biochemical models at the network level. PMID:35312734
Specifications of standards in systems and synthetic biology: status and developments in 2021. PMID:34674411
A detailed map of coupled circadian clock and cell cycle with qualitative dynamics validation. PMID:33975535
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. PMID:33758926
Specifications of standards in systems and synthetic biology: status and developments in 2020. PMID:32598316
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. PMID:31301675
Mental-Map Preserving Visualisation of Partitioned Networks in Vanted. PMID:31199771
A logic-based method to build signaling networks and propose experimental plans. PMID:29777117
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. PMID:29596055
Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. PMID:29447151
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. PMID:28187405
STON: exploring biological pathways using the SBGN standard and graph databases. PMID:27919219
Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants. PMID:26557642
Improving collaboration by standardization efforts in systems biology. PMID:25538939
A framework for mapping, visualisation and automatic model creation of signal-transduction networks. PMID:22531118
A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. PMID:21586134 -
Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2
PubMed citations: 14.
14 articles citing: Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2
Exploring the evolution of biochemical models at the network level. PMID:35312734
Specifications of standards in systems and synthetic biology: status and developments in 2021. PMID:34674411
A detailed map of coupled circadian clock and cell cycle with qualitative dynamics validation. PMID:33975535
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. PMID:33758926
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). PMID:32598315
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. PMID:31301675
Mental-Map Preserving Visualisation of Partitioned Networks in Vanted. PMID:31199771
A logic-based method to build signaling networks and propose experimental plans. PMID:29777117
Community-driven roadmap for integrated disease maps. PMID:29688273
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. PMID:29596055
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. PMID:28187405
Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants. PMID:26557642
Translation of SBGN maps: Process Description to Activity Flow. PMID:24176088
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enzymatic reaction
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mathematical model
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network model
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pathway model
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enzymatic reaction
metasource: Fairsharing.orgversion: FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
mathematical model
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molecular entity
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network model
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pathway model
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enzymatic reaction mathematical model molecular entity network model pathway model
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