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Licensed Unlicensed Requires Authentication Published by De Gruyter Oldenbourg March 31, 2014

Enhanced Petri Net: elucidating the pathway-level mechanism of targeted-therapy drugs

Guangxu Jin

Dr. Jin is a Research Associate at the Translational Bioinformatics Lab under Dr. Stephen Wong at The Methodist Hospital Research Institute. He received his Ph.D degree from the Academy of Mathematics & Systems Science, Chinese Academy of Sciences in Beijing, in 2008. Dr. Jin's research focuses on the mathematical and computational biology models for translational studies. He has a long-term interest in the modeling of the effects of targeted therapy drugs at the molecular off-target level.

6565 Fannin Street, B5-041, Houston, Texas 77030-2707; Phone: 713-441-7268

and Stephen T. C. Wong

Dr. Wong is the Founding Chairman for Department of Systems Medicine and Bioengineering, The Methodist Hospital Research Institute. He holds the John S. Dunn, Sr. Distinguished Endowed Chair in Biomedical Engineering. Dr. Wong has more than twenty years of research and management experience in industry and academia. His research focuses on understanding health and disease from a systems perspective in order to generate cost-effective strategies and solutions for disease management.

6670 Bertner Ave., R2-216, Houston, Texas 77030-2707; Phone: 713-441-7885

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Abstract

Characterizing the dynamics of cellular signaling pathways with external simuli or drug treatment is critical for the understanding of mechanisms of cellular behavors. Petri Net, as a non-parametric approach, has been widely used for studying dynamics of a large scale of signaling network only based on the connections (interactions) within this network. In this article, we will describe an extension of the Petri net methods, called Enhanced Petri Net (EPN), specifcally designed for analyzing and modeling the dynamics of signaling pathways in order to predict the unknown signaling mechanisms of targeted-therapy drugs.

About the authors

Guangxu Jin

Dr. Jin is a Research Associate at the Translational Bioinformatics Lab under Dr. Stephen Wong at The Methodist Hospital Research Institute. He received his Ph.D degree from the Academy of Mathematics & Systems Science, Chinese Academy of Sciences in Beijing, in 2008. Dr. Jin's research focuses on the mathematical and computational biology models for translational studies. He has a long-term interest in the modeling of the effects of targeted therapy drugs at the molecular off-target level.

6565 Fannin Street, B5-041, Houston, Texas 77030-2707; Phone: 713-441-7268

Stephen T. C. Wong

Dr. Wong is the Founding Chairman for Department of Systems Medicine and Bioengineering, The Methodist Hospital Research Institute. He holds the John S. Dunn, Sr. Distinguished Endowed Chair in Biomedical Engineering. Dr. Wong has more than twenty years of research and management experience in industry and academia. His research focuses on understanding health and disease from a systems perspective in order to generate cost-effective strategies and solutions for disease management.

6670 Bertner Ave., R2-216, Houston, Texas 77030-2707; Phone: 713-441-7885

Received: 2013-7-9
Accepted: 2014-2-11
Published Online: 2014-3-31
Published in Print: 2014-4-28

©2014 Walter de Gruyter Berlin/Boston

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