Using process diagrams for the graphical representation of biological networks

By Hiroaki Kitano, Akira Funahashi, Yukiko Matsuoka, Kanae Oda. Nature Biotechnology, 2005

494 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/3571bea7b40928e8c03949be2f01432a55eaee1a

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In Molecular Biology

Citations in the corpus

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks (2008, methodology): “The main standardized features that CellDesigner supports are summarized as Bgraphical notation, [B model description,[ and Bapplication integration environment.[ The standard for graphical notation plays an important role for efficient and accurate dissemination of knowledge [ 7 ], and these standa”
Systems medicine: the future of medical genomics and healthcare (2009, unknown): “and dynamic models [101-105].”
PANTHER Pathway: an ontology-based pathway database coupled with data analysis tools (2009, methodology): “First, the pathway diagrams are drawn with CellDesigner software (Kitano 2003; Kitano et al. 2005).”
BioPAX – A community standard for pathway data sharing (2010, unknown): “The Pathway Tools software 21 and CellDesigner pathway editor 54 are developing support for BioPAX-based data exchange.”
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).”
Modeling metabolic response to changes of enzyme amount in yeast glycolysis (2010, methodology): “2 (Kitano et al., 2005) (http://www.”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “…Longabaugh, 2012 BisoGenet http://bio.cigb.edu.cu/bisogenet-cytoscape Martin et al., 2010 CellDesigner http://www.celldesigner.org Kitano et al., 2005 Cell Illustrator http://www.cellillustrator.com Nagasaki et al., 2011 CFinder http://www.cfinder.org Adamcsek et al., 2006…”
Combining Machine Learning Systems and Multiple Docking Simulation Packages to Improve Docking Prediction Reliability for Network Pharmacology (2013, background): “[32], enabling molecular docking simulations to be performed with specified molecules in a network loaded to CellDesigner (Figure 4).”
OptFlux: an open-source software platform for in silico metabolic engineering (2010, methodology): “It should be mentioned that efforts such as Cytoscape [37], Cell Designer [20] and Systems Biology Workbench [38] are considered by the authors as very important projects, although orthogonal to our work, and ways to integrate OptFlux with those tools are being considered.”
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways (2015, methodology): “Thus, Escher uses a well-defined representation of the biochemical network, but the scope of the Escher notation is much more specific than community standards such as Systems Biology Graphical Notation (SBGN) [34] and Systems Biology Markup Language (SBML) with the lay-out extension [35 – 37].”
Presenting and exploring biological pathways with PathVisio (2008, background): “There are certain conventions for this, as well as several published formalized symbolic languages [14-16].”
Seeded Bayesian Networks: Constructing genetic networks from microarray data (2008, background): “In order to address these issues the groups of Kohn and Kitano began to devise new approaches to pathway notation using many ideas adopted from the electronics industry [1-3].”
The Edinburgh human metabolic network reconstruction and its functional analysis (2007, methodology): “The Edinburgh human metabolic network reconstruction and its functional analysis”
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways (2006, methodology): “The molecule subclasses are those supported by CellDesigner: proteins, genes/DNA, RNA, small organic or inorganic molecules and ions.”
A Correction to the Review Titled "Rules for Modeling Signal-Transduction Systems" by W. S. Hlavacek et al. (2006, background): “Rules can also be made more readable by enhancing them with graphical notation developed for annotating protein-protein interactions (49, 53) (http://www.”