CellDesigner: a process diagram editor for gene-regulatory and biochemical networks
By Akira Funahashi, Mineo Morohashi, Hiroaki Kitano, Naoki Tanimura. 2003
656 citations recorded by the source corpus.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/e4637271b2a6ab6b1819c2c546919fca3a458d38
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In Molecular Biology
- Huaiyu Mi
- Paul D. Thomas
- Anushya Muruganujan
- Bernhard O. Palsson
- Dustin Ebert
- Tremayne Mushayahama
- Laurent-Philippe Albou
- Jens Nielsen
Citations in the corpus
- PANTHER: Making genome‐scale phylogenetics accessible to all (2021, methodology): “From 2003 to 2007, pathways were actively curated in PAN-THER using the CellDesigner software package, 13 and initially represented using Systems Biology Markup Language.”
- BisoGenet: a new tool for gene network building, visualization and analysis (2010, methodology): “CellDesigner [27] is a software suite that feature a friendly user interfaces for building gene-regulatory and biochemical models.”
- The PANTHER database of protein families, subfamilies, functions and pathways (2004, methodology): “Users can browse or query pathways associated with PANTHER families, subfamilies and training sequences (Figure 1). Pathway diagrams were drawn by expert curators using the CellDesigner software program ( 6 ), which supports Systems Biology Markup Language (SBML) standards (7) and uses the process n”
- Applications for protein sequence–function evolution data: mRNA/protein expression analysis and coding SNP scoring tools (2006, methodology): “(A) Mann‐WhitneyU-test results, and (B) CellDesigner ( 15 ) diagram of the T-cell activation signaling pathway from the PANTHER Pathway database (accession P00053, author Adam Douglass).”
- BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models (2010, methodology): “For example, tools such as the Virtual Cell [36], CellDesigner [64] or the Systems Biology Workbench [48] use these services to provide their users direct access (from within their tool) to hundreds of models.”
- A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology (2008, methodology): “We have also loaded the model successfully into some versions of Cytoscape 51 and CellDesigner 52 .”
- Presenting and exploring biological pathways with PathVisio (2008, methodology): “In the context of applications like CellDe-signer [21], SBML defines reactions and parameters necessary for computational modelling.”