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This website comes online on 09/10/2007.

 

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Selected peer-reviewed publications

  1. J. Yang, W.S. Hlavacek. A rejection-free stochastic simulation method for multivalent biomolecular interactions. (submitted) [arxiv:0812.4619]

  2. J. Yang, W.S. Hlavacek. Scaffold-mediated nucleation of protein signaling complexes: elementary principles. (submitted)

  3. J. Yang, M.I. Monine, J.R. Faeder, and W.S. Hlavacek. Kinetic Monte Carlo method for rule based modeling of biochemical networks. Phys. Rev. E., 78, 031910, 2008. [Pubmed][arxiv:0712.3773]

  4. E. Shudo, J. Yang, Akihiko Yoshimura, and Yoh Iwasa. Robustness of the signal transduction system of the mammalian JAK/STAT pathway and dimerization steps. J. Theor. Biol. 246, 1, 2007. [Pubmed]

  5. M.L. Blinov, J. Yang, J.R. Faeder, and W.S. Hlavacek. Graph theory for rule-based modeling of biochemical networks. Trans. Comput. Sys. Biol. LNCS 4230, 89, 2006. [Springer]

  6. J. Yang, W.J. Bruno, W.S. Hlavacek, and J.E. Pearson. On imposing detailed balance to complex reaction networks, Biophys. J.. 91: 1136, 2006. [Pubmed]

  7. M.L. Blinov, J. Yang, J.R. Faeder and W.S. Hlavacek. Depicting signaling cascades, Nat. Biotechnol. 24., 137, 2006. [NPG/NBT]

  8. J. Yang, J.W. Clark, R.M. Bryan, and C.S. Robertson. Mathematical modeling of the nitric oxide/cGMP pathways in the vascular smooth muscle cell, Am. J. Physiol. Heart Circ. Physiol., 289(2), H886, 2005. [Pubmed]

  9. M.L. Blinov, J.R. Faeder, J. Yang, B. Goldstein, and W.S. Hlavacek. "On-the-fly" or "Generate first" modeling, Nat. Biotechnol. 23, 1344, 2005. [NPG/NBT]

  10. W.J. Bruno, J. Yang, J.E. Pearson. Using the number of independent open-to-closed transitions to simplify the identification of models for ion channel gating kinetics. Proc. Natl. Acad. Sci., U.S.A., 102(18), 6326, 2005. [Pubmed]

  11. J. Yang, J.W. Clark, R.M. Bryan, and C.S. Robertson. The myogenic response in isolated rat cerebrovascular arteries: smooth muscle cell model, Med. Eng. Phys., 25(8), 691, 2003. . [Pubmed]. Model available at: Cellml.Org

  12. J. Yang, J.W. Clark, R.M. Bryan, and C.S. Robertson. The myogenic response in isolated rat cerebrovascular arteries: vessel model, Med. Eng. Phys., 25(8), 711, 2003. [Pubmed].