Literature DB >> 20801417

Use of virtual cell in studies of cellular dynamics.

Boris M Slepchenko1, Leslie M Loew.   

Abstract

The Virtual Cell (VCell) is a unique computational environment for modeling and simulation of cell biology. It has been specifically designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. The models created with VCell can range from the simple, to evaluate hypotheses or to interpret experimental data, to complex multilayered models used to probe the predicted behavior of spatially resolved, highly nonlinear systems. In this chapter, we discuss modeling capabilities of VCell and demonstrate representative examples of the models published by the VCell users. Copyright 2010 Elsevier Inc. All rights reserved.

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Year:  2010        PMID: 20801417      PMCID: PMC3519358          DOI: 10.1016/S1937-6448(10)83001-1

Source DB:  PubMed          Journal:  Int Rev Cell Mol Biol        ISSN: 1937-6448            Impact factor:   6.813


  137 in total

1.  Determination of time-dependent inositol-1,4,5-trisphosphate concentrations during calcium release in a smooth muscle cell.

Authors:  C C Fink; B Slepchenko; L M Loew
Journal:  Biophys J       Date:  1999-07       Impact factor: 4.033

Review 2.  On the edge: modeling protrusion.

Authors:  Alex Mogilner
Journal:  Curr Opin Cell Biol       Date:  2005-11-28       Impact factor: 8.382

3.  Tools for kinetic modeling of biochemical networks.

Authors:  Rui Alves; Fernando Antunes; Armindo Salvador
Journal:  Nat Biotechnol       Date:  2006-06       Impact factor: 54.908

4.  In vivo dynamics of Rac-membrane interactions.

Authors:  Konstadinos Moissoglu; Boris M Slepchenko; Nahum Meller; Alan F Horwitz; Martin A Schwartz
Journal:  Mol Biol Cell       Date:  2006-04-05       Impact factor: 4.138

Review 5.  Quantitative fluorescent speckle microscopy of cytoskeleton dynamics.

Authors:  Gaudenz Danuser; Clare M Waterman-Storer
Journal:  Annu Rev Biophys Biomol Struct       Date:  2006

6.  A general computational framework for modeling cellular structure and function.

Authors:  J Schaff; C C Fink; B Slepchenko; J H Carson; L M Loew
Journal:  Biophys J       Date:  1997-09       Impact factor: 4.033

7.  An amplified sensitivity arising from covalent modification in biological systems.

Authors:  A Goldbeter; D E Koshland
Journal:  Proc Natl Acad Sci U S A       Date:  1981-11       Impact factor: 11.205

8.  Phosphoinositides and Rho proteins spatially regulate actin polymerization to initiate and maintain directed movement in a one-dimensional model of a motile cell.

Authors:  Adriana T Dawes; Leah Edelstein-Keshet
Journal:  Biophys J       Date:  2006-11-10       Impact factor: 4.033

9.  A model of action potentials and fast Ca2+ dynamics in pancreatic beta-cells.

Authors:  L E Fridlyand; D A Jacobson; A Kuznetsov; L H Philipson
Journal:  Biophys J       Date:  2009-04-22       Impact factor: 4.033

10.  A signal transduction pathway model prototype II: Application to Ca2+-calmodulin signaling and myosin light chain phosphorylation.

Authors:  Thomas J Lukas
Journal:  Biophys J       Date:  2004-09       Impact factor: 4.033

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  18 in total

1.  Developing models in virtual cell.

Authors:  Susana R Neves
Journal:  Sci Signal       Date:  2011-09-20       Impact factor: 8.192

2.  Diffusion amid random overlapping obstacles: similarities, invariants, approximations.

Authors:  Igor L Novak; Fei Gao; Pavel Kraikivski; Boris M Slepchenko
Journal:  J Chem Phys       Date:  2011-04-21       Impact factor: 3.488

3.  Redundant mechanisms for stable cell locomotion revealed by minimal models.

Authors:  Charles W Wolgemuth; Jelena Stajic; Alex Mogilner
Journal:  Biophys J       Date:  2011-08-03       Impact factor: 4.033

Review 4.  Modeling cellular processes in 3D.

Authors:  Alex Mogilner; David Odde
Journal:  Trends Cell Biol       Date:  2011-10-27       Impact factor: 20.808

5.  The emergence of sarcomeric, graded-polarity and spindle-like patterns in bundles of short cytoskeletal polymers and two opposite molecular motors.

Authors:  E M Craig; S Dey; A Mogilner
Journal:  J Phys Condens Matter       Date:  2011-08-23       Impact factor: 2.333

Review 6.  Virtual Cell: computational tools for modeling in cell biology.

Authors:  Diana C Resasco; Fei Gao; Frank Morgan; Igor L Novak; James C Schaff; Boris M Slepchenko
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2011-12-02

7.  Spatial modeling of cell signaling networks.

Authors:  Ann E Cowan; Ion I Moraru; James C Schaff; Boris M Slepchenko; Leslie M Loew
Journal:  Methods Cell Biol       Date:  2012       Impact factor: 1.441

8.  Mad dephosphorylation at the nuclear pore is essential for asymmetric stem cell division.

Authors:  Justin Sardi; Muhammed Burak Bener; Taylor Simao; Abigail E Descoteaux; Boris M Slepchenko; Mayu Inaba
Journal:  Proc Natl Acad Sci U S A       Date:  2021-03-30       Impact factor: 11.205

9.  Computational investigation of the dynamic control of cAMP signaling by PDE4 isoform types.

Authors:  Dean Paes; Sammy Hermans; Daniel van den Hove; Tim Vanmierlo; Jos Prickaerts; Aurélie Carlier
Journal:  Biophys J       Date:  2022-06-18       Impact factor: 3.699

10.  Computational analysis of Rho GTPase cycling.

Authors:  Cibele Vieira Falkenberg; Leslie M Loew
Journal:  PLoS Comput Biol       Date:  2013-01-10       Impact factor: 4.475

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