Publications:
Robertson, S.H., C.K. Smith, A.L. Langhans, S.E. McLinden, M.A. Oberhardt, K.R. Jakab, B. Dzamba, D.W. DeSimone, J.A. Papin, and S.M. Peirce. 2007. Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior. BMC Systems Biology, 1:46. [PubMed | Full Text | PDF]
Gianchandani, E.P., D.L. Brautigan, and J.A. Papin. 2006. Systems analyses characterize integrated functions of biochemical networks. Trends in Biochemical Sciences, 31(5):284-291. [PubMed | Full Text | PDF]
Papin, J.A., T. Hunter, B.O. Palsson, and S. Subramaniam. 2005. Reconstruction of cellular signalling networks and analysis of their properties. Nature Reviews Molecular Cell Biology, 6(2): 99-111. [PubMed | Full Text | PDF]
Longo, D., S.M. Peirce, T.C. Skalak, L. Davidson, M. Marsden, B. Dzamba, and D.W. DeSimone. 2004. Multicellular computer simulation of morphogenesis: blastocoel roof thinning and matrix assembly in Xenopus laevis. Developmental Biology, 271(1):210-222. [PubMed | Full Text | PDF]
Models:
- NETLOGO simulation of mesendoderm migration [download]
-
Published NETLOGO simulations of BCR thinning
(a) patch of "red" cells implanted just under the superficial layer (blue) [download]
(b) patch of cells (pink) is extra "sticky" due to overexpressing VE-cadherin [download] -
MATLAB implementation of Wnt signaling model
[download]
Based on published work:
Lee, E., A. Salic, R. Kruger, R. Heinrich, and M.W. Kirschner. 2003. The roles of APC and Axin derived from experimental and theoretical analysis of the Wnt pathway. PLoS Biology, 1(1):E10. [PubMed | Full Text | PDF]
To view or modify these simulations, you must download and install the latest version of the freeware software NETLOGO.
Agent-Based Modeling:
A presentation providing an overview of agent-based modeling, the technique used here.