CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks
By Akira Funahashi, Yukiko Matsuoka, Akiya Jouraku, Mineo Morohashi, Norihiro Kikuchi, Hiroaki Kitano. Proceedings of the IEEE, 2008
481 citations recorded by the source corpus.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/47f23e3ff38bd1c54f0ad5e1b3cd1553d6b04ce2
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In Molecular Biology
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Citations in the corpus
- The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease (2018, methodology): ““ReconMaps” resource The ReconMaps resource consists of seven human metabolic maps drawn manually using CellDesigner21 and hosted within the web service Molecular Interaction NEtwoRks VisuAlization (MINERVA)22.”
- The Systems Biology Graphical Notation (2009, methodology): “The process diagram draws its inspiration from process-style notations, borrowing ideas from the work of CellDesigner 28 and EPE 22 .”
- The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum (2013, background): “The CellDesigner file is available in Dataset S1.”
- RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units) (2010, methodology): “The graphs were generated using the CellDesigner editor (2,3), the html maps were developed in java, and the resizing image map uses a javascript taken from http:// home.”
- BioModels—15 years of sharing computational models in life science (2019, methodology): “An extensive suite of well-established software tools, including CellDesigner (22), VCell (23), iBioSim (24), Tellurium (25), libRoadRunner (26) and SemGen (27), integrates the BioModels API into their business functionality, allowing their users to load models of interest remotely.”
- Large-scale gene function analysis with PANTHER Classification System (2013, methodology): “These pathways were curated from the literature by expert biologists, and diagrams were drawn with CellDesigner, a pathway-editing tool that uses controlled graphical notations to represent pathway knowledge 8 .”
- PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees (2012, methodology): “The current release of PANTHER Pathways includes 176 pathways, generated using the CellDesigner tool (21).”
- Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways (2015, methodology): “Briefly, these tools include Omix [8], Cytoscape [5], CellDesigner [9], Vanted [10] with the SBGN-ED add-on [11], VisAnt [12] and PathVisio [13].”
- RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond (2015, methodology): “Images comply with the Cell Designer (7) graphical notation (8).”