Referred Papers & Documentation

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. BMC Syst Biol. 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 .

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 Biology, Volume 245, Issue 2, 21 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 Biology, Volume 248, Issue 1, 7 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

1. Experimental and mathematical approaches to modeling plant metabolic networks,
   Phytochemistry, Volume 68, Issues 16-18, August-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 Toxicology, Volume 19, Issue 3, January-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.

1. Methods for Simulating the Dynamics of Complex Biological Processes
   Methods in Cell Biology, Volume 84, 2008, Pages 807-842
   Maria J. Schilstra, Stephen R. Martin and Sarah M. Keating
   Abstract
2. Standards, Platforms, and Applications
   Computational Systems Biology, 2006, Pages 103-125
   Herbert M. Sauro
   Abstract