Virtual Cell - Publications

Quantitative analysis of G-actin transport in motile cells
I.L. Novak, B.M. Slepchenko, A. Mogilner
Biophysical Journal, 95(4):1627-38, 2008
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Dynamics of Cdc42 network embodies a Turing-type mechanism of yeast cell polarity
A.B. Goryachev, and A.V. Pokhilkos
FEBS Letters, v. 582, p.1437, (2008)
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Analysis of phosphatidylinositol-4,5-bisphosphate signaling in cerebellar Purkinje spines.
Brown, S., F. Morgan, J. Watras, and L.M. Loew.
Biophys J. 95:1795-1812,2008.
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Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks.
Neves SR, Tsokas P, Sarkar A, Grace EA, Rangamani P, Taubenfeld SM, Alberini CM, Schaff JC, Blitzer RD, Moraru II, Iyengar R.
Cell. 2008 May 16;133(4):666-80.
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The tight junction protein complex undergoes rapid and continuous molecular remodeling at steady state.
Shen L, Weber CR, Turner JR.
J Cell Biol. 2008 May 19;181(4):683-95. Epub 2008 May 12.
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Calcium Transport Mechanisms of PC12 Cells.
Duman, J.G., L. Chen, and B. Hille.
J. Gen. Physiol. 131:307-323, 2008.
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Calcium signal transmission in chick sensory neurones is diffusion based.
Coatesworth W, Bolsover S.
Cell Calcium. 2008 Mar;43(3):236-49. Epub 2007 Jul 12
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The role of the FH1 domain and profilin in formin-mediated actin-filament elongation and nucleation.
Paul, A., Pollard, T.
Current Biology, 2008 Jan 8;18(1):9-19.
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Pathway of actin filament branch formation by Arp2/3 complex.
Beltzner CC, Pollard TD.
J Biol Chem 283: 7135-7144.2008.
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Coordination of Chromosome Alignment and Mitotic Progression Chromosome-Based Ran Signal
Hoi Y. Li, Win Pin Ng, Wong Chi Hang, Pablo A. Iglesias and Yixian Zheng
Cell Cycle. 6(15):1886-1895, 2007.
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Membrane-binding/modification model of signaling protein activation and analysis of its control by cell morphology.
Haugh, J.M.
Biophys J 92, L93-95, 2007.
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Switching of membrane organelles between cytoskeletal transport systems is determined by regulation of the microtubule-based transport.
Slepchenko, B.M., Semenova, I., Zaliapin, I., and Rodionov, V.
J. Cell Biol., jcb.200705146, 2007.
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Regulation of cAMP dynamics by Ca2+ and G-protein coupled receptors in the pancreatic beta-cell: A computational approach.
Fridlyand, L.E., M.C. Harbeck, M.W. Roe, and L.H. Philipson
Am J Physiol Cell Physiol:293:C1924-C1933, 2007.
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Compartment-Specific Feedback Loop and Regulated Trafficking Can Result in Sustained Activation of Ras at the Golgi.
Narat J. Eungdamrong and Ravi Iyengar
Biophys. J. 2007; 92(3): p. 808-815
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Rapid redistribution of synaptic PSD-95 in the neocortex in vivo.
Gray, N, Weimer R.M., Bureau, I. Svoboda, K
PLoS, v4, Iss 11, e370, 2006.
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Does diacylglycerol regulate KCNQ channels?
Suh, B.-C., and B. Hille.
Pflügers Archiv European Journal of Physiology. 453:293-301,2006.
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Modeling the impact of store-operated Ca2+ entry on intracellular Ca2+ oscillations.
Kowalewski, J.M., P. Uhlen, H. Kitano, and H. Brismar.
Mathematical Biosciences. 204:232-249, 2006.

In vivo dynamics of Rac-membrane interactions.
Moissoqlu K, Slepchenko BM, Meller N, Horwitz AF, Schwartz, MAA
Mol Biol Cell. 2006 Jun; 17(6):2770-9. Epub 2006 Apr.5
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Systems analysis of PKA-mediated phosphorylation gradients in live cardiac myocytes.
J.J. Saucerman, J. Zhang, J.C. Martin, L.X. Peng, A.E. Stenbit, R.Y. Tsien, and A.D. McCulloch..
Proceedings of the National Academy of Sciences. 103:12923-12928.
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Analysis of a RanGTP-regulated gradient in mitotic somatic cells.
Kalab, P., A. Pralle, E.Y. Isacoff, R. Heald, and K. Weis.
Nature 2006. 440:(7084)697-701.
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Quantitative elucidation of a distinct spatial gradient-sensing mechanism in fibroblasts.
Schneider, I.C. and Haugh, J.M.
J.Cell B 171:883-892 (2005)
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Modeling and Analysis of Calcium Signaling Events Leading to Long-Term Depression in Cerebellar Purkinje Cells.
N. Hernjak, B. M. Slepchenko, K. Fernald, C.C. Fink, D. Fortin, I.I. Moraru, J. Watras, and L.M. Loew.
Biophysical Journal Volume 89, Dec. 2005, pp. 3790-3806
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STAT module can function as a biphasic amplitude filter.
V. Mayya and L.M. Loew.
IEE Proceedings Systems Biology, March 2005, Volume 2, Issue 1, p. 43-52
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Phospholipase C in living cells: activation, inhibition, Ca2+ requirement, and regulation of M current.
Horowitz LF, Hirdes W, Suh B-C, Hilgemann DW, Mackie K, Hille B.
J. Gen. Physiol. 2005. 126(3):243-262.
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Rearrangement of the endoplasmic reticulum and calcium transient formation: The computational approach.
Pomorski P, Targos B, Baranska J.
Biochem Biophys Res Commun. 2005 Mar 25;328(4):1126-32.

Adenine nucleotide regulation in pancreatic beta cells: Modelling of ATP/ADP - Ca2+ interaction
Fridlyand L., Li Ma, Philipson LH.
Am J Physiol Endocrinol Metab. 289, E839-E848, 2005.
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Bio-switches: what makes them robust?
Slepchenko, B. M. and Terasaki, M.
Opin. Genet. Dev. 2004; 14/4: 428-434.
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A multi-enzyme model for pyrosequencing.
Ali Agah, Mariam Aghajan, Foad Mashayekhi, Sasan Amini, Ronald W. Davis, James D. Plummer, Mostafa Ronaghi, and Peter B. Griffin.
Nucleic Acids Research 2004 32(21):e166
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Two Complementary, Local Excitation, Global Inhibition Mechanisms Acting in Parallel Can Explain the Chemoattractant-Induced Regulation of PI(3,4,5)P₃ Response in Dictyostelium Cells.
Lan Ma, Chris Janetopoulos, Liu Yang, Peter N. Devreotes and Pablo A. Iglesias.
Biophys. J. 2004; 87(6): p. 3764-3774
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A Signal Transduction Pathway Model Prototype I: Application to Ca2+-Calmodulin Signaling and Myosin Light Chain Phosphorylation.
Lukas, TJ
Biophys. J. 2004;87 1417-1425
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A Signal Transduction Pathway Model Prototype I: From Agonist to Cellular Endpoint.
Lukas, TJ
Biophys. J. 2004; 87 1406-1416
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High Mobility of Vesicles Supports Continuous Exocytosis at a Ribbon Synapse.
Matthew Holt, Anne Cooke, Andreas Neef, and Leon Lagnado.
Current Biology, Vol. 14, 173-183, February 3, 2004
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Regulation of KCNQ2/KCNQ3 Current by G Protein Cycling: the kinetics of receptor-mediated signaling by Gq.
Byung-Chang Suh, Lisa R. Horowitz, Wiebke Hirdes, Ken Mackie and Bertil Hille.
Journal of General Physiology, Volume 123, Number 6, June 2004 663-683
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Cyclin aggregation and robustness of bio-switching.
Slepchenko, B. M. and Terasaki, M.
Mol. Biol. Cell 2003;14: 4695 - 4706.
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Kinetic analysis of receptor-activated phosphoinositide turnover
Chang Xu, James Watras and Leslie M. Loew
Journal of Cell Biology, vol. 161, no. 4, May 26, 2003
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Centrosome positioning in interphase cells.
Anton Burakov, Elena Nadezhdina, Boris Slepchenko, and Vladimir Rodionov
Journal of Cell Biology, 2003 Sep 15;162(6):963-9..
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Modeling Ca2+ flux in pancreatic B-cells: role of the plasma membrane and intracellular stores.
Leonid E. Fridlyand, Natalia Tamarina, and Louis H. Philipson
Am J Physiol Endocrinol Metab, Jul 2003;285: E138-154
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Systems Analysis of Ran Transport
Alicia E. Smith, Boris M. Slepchenko, James C. Schaff, Leslie M. Loew, Ian G. Macara.
Science. 2002 Jan 18;295(5554):488-91
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Targeting of rough endoplasmic reticulum membrane proteins and ribosomes in invertebrate neurons.
Rolls MM, Hall DH, Victor M, Stelzer EH, Rapoport TA.
Mol Biol Cell. 2002 May;13(5):1778-91.PMID: 12006669 [PubMed - indexed for MEDLINE]
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Distinct intracellular calcium transients in neurites and somata integrate neuronal signals.
Johenning FW, Zochowski M, Conway SJ, Holmes AB, Koulen P, Ehrlich BE.
J Neurosci 22: 5344-5353.2002.
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Computational Cell Biology
Christopher P. Fall, Eric S. Marland, John M. Wagner, John J. Tyson.
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