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NRCAM news items.


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Current information on Release and Beta versions.


Seminars
CCAM Seminar schedule.


Symposium
International Symposium on Computational Cell Biology.


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Current listing of NRCAM publications.


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Presentation of the Virutal Cell.


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NRCAM Publications

Schaff, J., C. C. Fink, B. Slepchenko, J. H. Carson, and L. M. Loew. 1997. A general computational framework for modeling cellular structure and function. Biophys. J. 73:1135-1146.

Shin, D.-G., L. Liu, L. M. Loew, and J. Schaff. 1998. Virtual Cell: a general framework for simulating and visualizing cellular physiology. In Proc. of 4th IFIP 2.6 Working Conference on Visual Database Systems,. L'Aquila, Italy.

Schaff, J., and L. M. Loew. 1999. The Virtual Cell. In Biocomputing: Proceedings of the 1999 Pacific Symposium. R. B. Altman, A. K. Dunker, L. Hunter, T. E. Klein and K. Lauderdale, editors. World Scientific, Singapore. 228-239.

Fink, C. C., B. Slepchenko, and L. M. Loew. 1999. Determination of time-dependent inositol-1,4,5-trisphosphate concentrations during calcium release in a smooth muscle cell. Biophys. J. 77: 617-628.

Fink, C. C., B. Slepchenko, I. I. Moraru, J. Schaff, J. Watras, and L. M. Loew. 1999. Morphological control of inositol-1,4,5-trisphosphate-dependent signals. J. Cell Biol. 147:929-935.

Fink, C. C., B. Slepchenko, I. I. Moraru, J. Watras, J. Schaff, and L. M. Loew. 2000. An image-based model of calcium waves in differentiated neuroblastoma cells. Biophys. J. 2000 79:163-183.

Schaff, J. C., B. M. Slepchenko, and L. M. Loew. 2000. Physiological modeling with the Virtual Cell framework. In Methods in Enzymology. Vol. 321, M. Johnson and L. Brand, eds. Academic Press, San Diego. 1-26.

Schaff, J. C., B. M. Slepchenko, Y. Choi, J. M. Wagner, D. Resasco, and L.M. Loew. 2001. Analysis of non-linear dynamics on arbitrary geometries withthe Virtual Cell. Chaos 11:115-131.

Carson, J.H., A. Cowan, L. M. Loew. 2001. Computational cell biologists snowed in at Cranwell. Trends in Cell Biology 11:236-238.

Roy, P., Z. Rajfur, D. Jones, G. Marriott, L. Loew, and K. Jacobson. 2001. Local Photorelease of Caged Thymosin beta4 in Locomoting Keratocytes Causes Cell Turning. J. Cell Biol. 153:1035-1048.

Loew, L. M., and J. C. Schaff. 2001. The Virtual Cell: A software environment for computational cell biology. Trends in Biotechnology 19:401-406.

Terasaki, M., Campagnola, P., Rolls, M.M., Stein, P., Ellenberg, J., Hinkle, B., and Slepchenko, B. 2001. A new model for nuclear envelope breakdown. Mol. Biol. Cell 12: 503-510.

Mannella, C. A., D. R. Pfeiffer, P. C. Bradshaw, I. I. Moraru, B.Slepchenko, L. M. Loew, C. Hsieh, K. Buttle, and M. Marko. 2001.Topology of the mitochondrial inner membrane: dynamics and bioenergetic implications. IUBMB Life 52(2,4,5).

Slepchenko, B. M., and Felix Bronner. Modeling of transcellular Ca transport in rat duodenum points to coexistence of two mechanisms of apical entry. Am. J. Physiol., Cell Physiology 2001, v. 281, issue 1, pp. C270-C281.

Roy, P., Z. Rajfur, D. Jones, G. Marriott, L. Loew, and K. Jacobson. 2001. Local Photorelease of Caged Thymosin beta4 in Locomoting Keratocytes Causes Cell Turning. Journal of Cell Biology. 153:1035-1048.

Slepchenko B, Schaff JC, Carson JH, Loew LM. 2002. Computational cell biology: spatiotemporal simulation of cellular events. Annual Review of Biophysics & Biomolecular Structure 31:423-441.

Smith AE, Slepchenko BM, Schaff JC, Loew LM, Macara IG. 2002. Systems analysis of Ran transport. Science 295:488-491.

Loew, LM. 2002. The Virtual Cell Project. Novartis Foundation Symposium 247 - In silico Simulation of Biological Processes, Wiley, Chichester, UK, pp. 151-161.

Moraru, II, Schaff JC, Slepchenko BM, Loew LM. 2002. The virtual cell: an integrated modeling environment for experimental and computational cell biology. Ann N Y Acad Sci 971:595-6.

Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A and others. 2003. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4):524-531.

Xu, C., J. Watras, and L. M. Loew. 2003. Kinetic analysis of receptor activated phosphoinositide turnover. J. Cell Biol. 161:779-791.

Slepchenko BM, Schaff J, Macara IG, Loew LM. 2003. Quantitative Cell Biology with the Virtual Cell. Trends in Cell Biology 13:pp. 570 - 576.

Slepchenko, B. M. and Terasaki, M. 2003. Cyclin aggregation and robustness of bio-switching. Mol. Biol. Cell 14: 4695 - 4706.
See Applications for information regarding the models.

Slepchenko, B. M. and Terasaki, M. 2004. Bio-switches: what makes them robust? Curr. Opin. Genet. Dev. 14/4: 428-434.
See Applications for information regarding the models.

Novak IL, Slepchencko BM, Mogilner A, and Loew LM. 2004. Cooperativity between Cell Contratility and Adhesion. Phys Rev Lett. 93:268109-1-4.

Mayya V., and Loew LM. March 2005, STAT module can function as a biphasic amplitude filter. IEE Prodeedings Sytems Biology. Volume 2, Issue 1, p43-52.

Burakov, A., E. Nadezhdina, B. Slepchenko, and V. Rodionov. 2003. Centrosome positioning in interphase cells. J. Cell Biol. 162:963-969.

Carson JH, Barbarese E. 2005. Systems analysis of RNA trafficking in neural cells. Biol Cell 97(1):51-62.

Hernjak, N., B. M. Slepchenko, K. Fernald, C. C. Fink, D. Fortin, I. I. Moraru, J. Watras, and L. M. Loew. 2005. Modeling and Analysis of Calcium Signaling Events Leading to Long-Term Depression in Cerebellar Purkinje Cells. Biophys. J. 89:3790-3806.

Moissoglu, K., B. M. Slepchenko, N. Meller, A. F. Horwitz, and M. A. Schwartz. 2006. In Vivo Dynamics of Rac-Membrane Interactions. Mol. Biol. Cell:E06-01-0005.

Moraru, I.I., and L.M. Loew. 2005. Intracellular signaling: spatial and temporal control. Physiology. 20:169-179.

Moraru, I. I., J. C. Schaff and L. M. Loew. 2006. Think simulation-think experiment: the Virtual Cell paradigm. Proceedings of the 2006 Winter Simulation Conference. L. F. Perrone, F. P. Wieland, J. Liu, B. G. Lawson, D. M. Nicol, and R. M. Fujimoto, eds. IEEE Proceedings, in press.

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