CellDesigner Papers

Here is the list of papers/documentation which refers to CellDesigner.

Referred Papers & Documentation

Using CellDesigner Models

  1. A Comprehensive Molecular Interaction Map for Rheumatoid Arthritis. Wu G et al, 2010, PLoS ONE
  2. Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation
  3. Gonadotropin-Releasing Hormone Receptor-Mediated Signaling Network in L{beta}T2 Cells: A Pathway-Based Web-Accessible Knowledgebase.
  4. A comprehensive molecular interaction map of the budding yeast cell cycle. Kaizu K et al, Mol Syst Biol (2010) vol. 6(1)
  5. Alzpathway: Mizuno S et al.  2012 May 30;6:52. doi: 10.1186/1752-0509-6-52.
  6. Parkinson's Disease: Fujita KA et al. (2013) Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map., Molecular Neurobiology doi:10.1007/s12035-013-8489-4
  7. FluMap - Influenza A Virus: Matsuoka Y et al. (2013) A comprehensive map of the influenza A virus replication cycle. BMC Syst Biol. Additional files
  8. LimeMap - Nishi, A. et al. LimeMap: a comprehensive map of lipid mediator metabolic pathways. (2021) npj Syst Biol Appl  7, 6.
  9. The Atlas of Inflammation-Resolution (AIR) Serhan C.N, et al. (2020) Mol Aspects Med .

Using CellDesigner Simulation

  1. Modelling of circadian rhythms in Drosophila incorporating the interlocked PER/TIM and VRI/PDP1 feedback loops
    Z. Xie and D. Kulasiri, Journal of Theoretical BiologyVolume 245, Issue 221 March 2007, Pages 290-304
  2. Signaling perturbations induced by invading H. pylori proteins in the host epithelial cells: A mathematical modeling approach, Dampier W and Tozeren A, Journal of Theoretical BiologyVolume 248, Issue 17 September 2007, Pages 130-144


  1. PRIME Pathway Repository: http://tsb.mssm.edu/pathwayPublisher/broadcast/
    by Center for Translational Systems Biology, Mount Sinai School of Medicine, New York
  2. The PANTHER database of protein families, subfamilies, functions and pathways, Mi et al.
    Nucl. Acids Res. (2005) 33 (suppl 1): D284-D288. doi: 10.1093/nar/gki078


  1. cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. Balaur I. et al. Bioinformatics . 2020 Apr 15;36(8):2620-2622.
  2. BioPP: a tool for web-publication of biological networks. Viswanathan GA, Nudelman G, Patil S, Sealfon SC. BMC Bioinformatics. 2007 May 22;8:168.
  3. Payao : A Community Platform for SBML Pathway Model Curation. Matsuoka et al. Bioinformatics 2010pp. btq143v1


Please check Plugins page.


  1. Experimental and mathematical approaches to modeling plant metabolic networks,
    Volume 68, Issues 16-18August-September 2007, Pages 2351-2374
    Rigoberto Rios-Estepa and Bernd Markus Lange
    SummaryPlus | Full Text + Links | PDF (625 K)
  2. A systems biology approach to developmental toxicology
    Reproductive ToxicologyVolume 19, Issue 3January-February 2005, Pages 281-290
    Audrey Cummings and Robert Kavlock
    SummaryPlus | Full Text + Links | PDF (353 K)
  3. Computational representation of developmental genetic regulatory networks
    Developmental Biology Volume 283, Issue 1, 1 July 2005, Pages 1-16
    William J.R. Longabaugh, Eric H. Davidson, and Hamid Bolouri
  4. Pathway databases and tools for their exploitation: benefits, current limitations and challenges.
    Mol Syst Biol (2009) vol. 5 (1) pp.
    Bauer-Mehren et al.

Book Chapter

  1. Methods for Simulating the Dynamics of Complex Biological Processes
    Methods in Cell BiologyVolume 842008, Pages 807-842
    Maria J. Schilstra, Stephen R. Martin and Sarah M. Keating
  2. Standards, Platforms, and Applications
    Computational Systems Biology2006, Pages 103-125
    Herbert M. Sauro
About Us | Site Map | Privacy Policy |Contact Us | ©2004-2022 The Systems Biology Institute. All rights reserved.