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Multi-scale biosystems analysis of
Xenopus morphogenesis: |
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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
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Abstract |
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: 284-91. [PubMed]
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: 1-13. [PubMed
|
Abstract |
Full Text |
PDF]
Longo, D., S.M. Peirce, T.C. Skalak, L. Davidson, M.
Marsden, B. Dzamba, D.W. DeSimone. 2004. Multicellular computer
simulation of morphogenesis: blastocoel roof thinning and matrix
assembly in Xenopus laevis. Developmental Biology, 271:
210-22.
[PubMed]
Models:
| 1. |
NETLOGO simulation of mesendoderm migration [download] |
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| 2. |
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] |
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| 3. |
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: E10. [PubMed
|
Abstract |
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.
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