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University of Connecticut Health Center - Know Better Care VCell - The Virtual Cell

VCell Publications

  • NRCAM Publications
  • VCell Reviews to Cite
  • Reviews Featuring VCell
Computational analysis of calcium signaling and membrane electrophysiology in cerebellar Purkinje neurons associated with ataxia.
BMC Syst Biol. 2012 Jun 15;6:70. doi: 10.1186/1752-0509-6-70.
Brown SA, Loew LM.

CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation.
Phys Biol. 2012 Jun 8;9(3):036010. [Epub ahead of print]
Michalski PJ, Loew LM.

Stoichiometry of Nck-dependent actin polymerization in living cells
J Cell Biol 197 (5): 643-658, May 21, 2012
Ditlev, J.A., Michalski, P.J., Huber, G., Rivera, G.M., Mohler, W.A., Loew, L.M., Mayer, B.J.

Spatial modeling of cell signaling networks
Methods Cell Biol. 2012;110:195-221
Cowan AE, Moraru II, Schaff JC, Slepchenko BM, Loew LM.

Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling.
J Comput Neurosci. 2011 Feb 22. [Epub ahead of print]
Brown SA, Moraru II, Schaff JC, Loew LM.

Effects of excluded volume due to internal membranes and cytoskeletal structures.
Biophysical Journal (2009) 97(3): 758-767.
Novak, I.L., Kraikivski, P., Slepchenko, B.M.

An open model of actin dendritic nucleation.
Biophys J.2009,96:3529-3542.
Ditlev, J.A., N.M. Vacanti, I.L. Novak, and L.M. Loew.

Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation.
IET Syst Biol. 2008 Sep;2(5):363-8.
Blinov ML,Ruebenacker O,Moraru II.

Quantitative analysis of G-actin transport in motile cells.
Biophysical Journal, 2008, 95(4):1627-38,
I.L. Novak, B.M. Slepchenko, A. Mogilner

Analysis of phosphatidylinositol-4,5-bisphosphate signaling in cerebellar Purkinje spines.
Biophys J. (2008.) 95:1795-1812.
Brown, S., F. Morgan, J. Watras, and L.M. Loew.

Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks.
Cell, May 2008 16;133(4):666-80.
Neves SR, Tsokas P, Sarkar A, Grace EA, Rangamani P, Taubenfeld SM, Alberini CM, Schaff JC, Blitzer RD, Moraru II, Iyengar R.

Diffusion on a Curved Surface Coupled to diffusion in the Volume: Application to Cell Biology.
J. Comput. Phys.,2007, 226: 1271-1290.
Novak, I. L., Gao, F., Choi, Y.-S., Resasco, D., Schaff, J. C., Slepchenko B. M.

Switching of membrane organelles between cytoskeletal transport systems is determined by the regulation of the microtubule-based transport.
J. Cell Biol.,2007, 179: 635-641.
Slepchenko B. M., Semenova, I., Zaliapin, I., Rodionov V.

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

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.
Moraru, I. I., J. C. Schaff and L. M. Loew.

In vivo dynamics of Rac-membrane interactions. Mol. Biol. Cell., 2006, 17: 2770-2779.
Moissoglu, K., Slepchenko, B. M., Meller, N., Horwitz, A. F., Schwartz M. A.

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

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

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

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

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

Bio-switches: what makes them robust? Curr.
Opin. Genet. Dev. 14/4: 428-434, 2004.
Slepchenko, B. M. and Terasaki, M.

Cyclin aggregation and robustness of bio-switching.
Mol. Biol. Cell (2003)14: 4695 - 4706.
Slepchenko, B. M. and Terasaki, M.

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

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

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

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

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

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

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

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.
Slepchenko, B. M., and Felix Bronner.

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

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

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

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

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

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

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

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

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. (1999) 228-239.
Schaff, J., and L. M. Loew.

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, 1998.
Shin, D.-G., L. Liu, L. M. Loew, and J. Schaff.

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

Spatial modeling of cell signaling networks
Methods Cell Biol. 2012;110:195-221
Cowan AE, Moraru II, Schaff JC, Slepchenko BM, Loew LM.

Use of Virtual Cell in Studies of Cellular Dynamics.
In Kwang W. Jeon, editor: International Review of Cell and Molecular Biology, Vol. 283, Burlington: Academic Press, 2010, pp. 1-56. ISBN: 978-0-12-381254-4 © Copyright 2010 Elsevier Inc. Academic Press.
Boris M. Slepchenko and Leslie M. Loew

Using the Virtual Cell Simulation Environment for Extracting Quantitative Parameters from Live Cell Fluorescence Imaging Data.
Microscopy Today. 17:36-39
Cowan, A.E., Y. li, F.R. Morgan, D.E. Koppel, B.M. Slepchenko, L.M. Loew, and J. Schaff. 2009.

Virtual Cell modelling and simulation software environment.
IET Syst Biol. 2008 Sep;2(5):352-62.
Moraru II, Schaff JC, Slepchenko BM, Blinov ML, Morgan F, Lakshminarayana A, Gao F, Li Y, Loew LM.

Think simulation - think experiment: the Virtual Cell paradigm.
In Proceedings of the 2006 Winter Simulation Conference. Vol. 38. L.F. Perrone, F. Wieland, J. Liu, B. Lawson, D. Nicol, and R. Fujimoto, editors. IEEE Proceedings, Monterey, CA. 1713-1719.
Moraru, I., J.C. Schaff, and L.M. Loew. 2006.

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

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

The Virtual Cell project.
Novartis Found Symp. 247:151-60; discussion 160-1, 198-206, 244-52. PMID 12539954
Loew, L.M. 2002.

Moraru, II, J.C. Schaff, B.M. Slepchenko, and L.M. Loew. 2002.
The virtual cell: an integrated modeling environment for experimental and computational cell biology.
Ann N Y Acad Sci. 971:595-6. PMID 12438191

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

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

Neves, S.R. 2011.
Modeling of spatially-restricted intracellular signaling.
Wiley Interdisciplinary Reviews: Systems Biology and Medicine:2011, July 15. WIREs Syst Biol Med 2011 DOI: 10.1002/wsbm.155

Brown, S.A., R.M. Holmes, and L.M. Loew. 2011.
Spatial organization and diffusion in neuronal signalling.
In Computational Systems Neurobiology. N. Le Novere, editor. Springer, New York. in press.

Cheong, R., S. Paliwal, and A. Levchenko. 2010.
Models at the single cell level.
Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2:34-48

Radhakrishnan, K., Á. Halász, D. Vlachos, and J.S. Edwards. 2010.
Quantitative understanding of cell signaling: the importance of membrane organization.
Current Opinion in Biotechnology. 21:677-682.

Neves, S.R., and R. Iyengar. 2009.
Models of Spatially Restricted Biochemical Reaction Systems.
Journal of Biological Chemistry. 284(9):5445-5449.

Csikász-Nagy, A. 2009.
Computational systems biology of the cell cycle.
Briefings in Bioinformatics. 10:424-434

Linderman, J.J. 2009.
Modeling of G-protein-coupled Receptor Signaling Pathways.
Journal of Biological Chemistry. 284:5427-5431

Gardner, M.K., D.J. Odde, and K. Bloom. 2007.
Hypothesis testing via integrated computer modeling and digital fluorescence microscopy.
Methods. 41:232-237

Wierling, C., R. Herwig, and H. Lehrach. 2007.
Resources, standards and tools for systems biology.
Briefings in Functional Genomics & Proteomics. 6:240-251

Alves, R., F. Antunes, and A. Salvador. 2006.
Tools for kinetic modeling of biochemical networks.
Nat Biotechnol. 24:667-72. PMID 16763599

Gilbert, D., H. Fuß, X. Gu, R. Orton, S. Robinson, V. Vyshemirsky, M.J. Kurth, C.S. Downes, and W. Dubitzky. 2006.
Computational methodologies for modelling, analysis and simulation of signalling networks.
Briefings in Bioinformatics. 7:339-353

Ridgway, D., G. Broderick, and M.J. Ellison. 2006.
Accommodating space, time and randomness in network simulation.
Current Opinion in Biotechnology. 17:493-498

Strömbäck, L., V. Jakoniene, H. Tan, and P. Lambrix. 2006.
Representing, storing and accessing molecular interaction data: a review of models and tools.
Briefings in Bioinformatics. 7:331-338

Ma'ayan, A., R.D. Blitzer, and R. Iyengar. 2005.
TOWARD PREDICTIVE MODELS OF MAMMALIAN CELLS.
Annual Review of Biophysics and Biomolecular Structure. 34:319-349

Orton, R.J., O.E. Sturm, V. Vyshemirsky, M. Calder, D.R. Gilbert, and W. Kolch. 2005.
Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway.
Biochem J. 392:249-61. PMID 16293107 1316260

Semple, J.L., N. Woolridge, and C.J. Lumsden. 2005.
Review: In Vitro, in Vivo, in Silico: Computational Systems in Tissue Engineering and Regenerative Medicine.
Tissue Engineering. 11:341-356

Sprague, B.L., and J.G. McNally. 2005.
FRAP analysis of binding: proper and fitting.
Trends in Cell Biology. 15:84-91

Takahashi, K., S.N.V. Arjunan, and M. Tomita. 2005.
Space in systems biology of signaling pathways - towards intracellular molecular crowding in silico.
FEBS Letters. 579:1783-1788

Eungdamrong, N.J., and R. Iyengar. 2004.
Computational approaches for modeling regulatory cellular networks.
Trends in Cell Biology. 14:661-669

Eungdamrong, N.J., and R. Iyengar. 2004.
Modeling Cell Signaling Networks.
Biology of the Cell. 96:355-362

Rice, J.J., and G. Stolovitzky. 2004.
Making the most of it: pathway reconstruction and integrative simulation using the data at hand.
Drug Discovery Today: BIOSILICO. 2:70-77

Armitage, J.P., C.J. Dorman, K. Hellingwerf, R. Schmitt, D. Summers, and B. Holland. 2003.
Thinking and decision making, bacterial style: Bacterial Neural Networks
Obernai, France, 7th-12th June 2002. Mol Microbiol. 47:583-93. PMID 12519207

Szallasi, Z. 2002.
Build your own (virtual) cell.
Trends Pharmacol Sci. 23:158-9. PMID 11931982

Gibas, C., and P. Jambeck. 2001.
Developing bioinformatics computer skills.
O'Reilly.

The Virtual Cell, a project of NRCAM, is developed by the Center for Cell Analysis & Modeling (CCAM)