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Modeling - Resources

Publications - last updated December, 2008

2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002

  • Barua D, Faeder JR, Haugh JM. Computational models of tandem Src homology 2 domain interactions and application to phosphoinositide 3-kinase. J Biol Chem 2008; 283 (12):7338-45 PubMed | CMC Update article.
  • Choi CK, Vicente-Manzanares M, Zareno J, Whitmore LA, Mogilner A, Horwitz AR. Actin and alpha-actinin orchestrate the assembly and maturation of nascent adhesions in a myosin II motor-independent manner. Nat Cell Biol. 2008; 36(Pt 2):263-6 PubMed | CMC Update article.
  • Fass J, Pak C, Bamburg J, Mogilner A. Stochastic simulation of actin dynamics reveals the role of annealing and fragmentation. J Theor Biol 2008; 252:173-83 PubMed | CMC Update article.
  • Harley BA, Kim HD, Zaman MH, Yannas IV, Lauffenburger DA, Gibson LJ. Micro-architecture of three-dimensional scaffolds influences cell migration behavior via junction interactions. Biophys J 2008;(8):4013-24 PubMed | CMC Update article.
  • Ji L, Lim J, Danuser G. Fluctuations of intracellular forces during cell protrusion. Nat Cell Biol. 2008 Nov 16. [Epub ahead of print] PubMed | CMC Update article.
  • Kapustina M, Weinreb GE, Costigliola N, Rajfur Z, Jacobson K, Elston TC. Mechanical and biochemical modeling of cortical oscillations in spreading cells. Biophys J 2008; 94 (12):4605-20 PubMed | CMC Update article.
  • Keren K, Pincus Z, Allen GM, Barnhart EL, Marriott G, Mogilner A, Theriot JA. Mechanism of shape determination in motile cells. Nature 2008; 453 (7194):475-80 PubMed | CMC Update article.
  • Kim HD, Guo TW, Wu AP, Wells A, Gertler FB, Lauffenburger DA. EGF-induced Enhancement of Glioblastoma Cell Migration in 3D Arises from Intrinsic Increase in Speed but Extrinsic Matrix- and Proteolysis-dependent Increase in Persistence. Mol Biol Cell 2008; Jul 16. [Epub ahead of print] PubMed | CMC Update article.
  • Kraikivski P, Slepchenko BM, Novak IL. Actin Bundling: Initiation Mechanisms and Kinetics. Phys. Rev. Lett. 2008; 101, 128102. link | CMC Update article.
  • Monine MI, Haugh JM. Signal Transduction at Point-blank Range: Analysis of a Spatial Coupling Mechanism for Pathway Crosstalk. Biophys J 2008; (5):2172-82 PubMed | CMC Update article.
  • Mogilner A. Mathematics of cell motility: have we got its number? J Math Biol 2008; May 7. [Epub ahead of print] PubMed | CMC Update article.
  • Novak I, Slepchenko B, Mogilner A. Quantitative analysis of G-actin transport in motile cells. Biophys J 2008; (4):1627-38 PubMed | CMC Update article.
  • Schaefer AW, Schoonderwoert VT, Ji L, Mederios N, Danuser G, Forscher P. Coordination of actin filament and microtubule dynamics during neurite outgrowth. Dev Cell 2008; 15 (1):146-62 PubMed | CMC Update article.

2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002

  • Au A, Boehm CA, Mayes AM, Muschler GF, Griffith LG. Formation of osteogenic colonies on well-defined adhesion peptides by freshly isolated human marrow cells. Biomaterials 2007; 28 (10):1847-61 PubMed | CMC Update article.
  • Delorme V, Machacek M, Dermardirossian C, Anderson KL, Wittmann T, Hanein D, Waterman-Storer C, Danuser G, Bokoch GM. Cofilin activity downstream of pak1 regulates cell protrusion efficiency by organizing lamellipodium and lamella actin networks. Dev Cell 2007; 13 (5):646-62 PubMed | CMC Update article.
  • Fan VH, Tamama K, Au A, Littrell R, Richardson LB, Wright JW, Wells A, Griffith LG. Tethered EGF Provides a Survival Advantage to Mesenchymal Stem Cells. Stem Cells 2007; 25(5):1241-51 PubMed | CMC Update article.
  • Haugh JM. Membrane-binding/modification model of signaling protein activation and analysis of its control by cell morphology. Biophys J 2007; 92 (11):L93-5 PubMed | CMC Update article.
  • Hu K, Ji L, Applegate KT, Danuser G, Waterman-Storer CM. Differential transmission of actin motion within focal adhesions. Science 2007; 315 (5808):111-5 PubMed | CMC Update article.
  • Ji L, Loerke D, Gardel M, Danuser G. Probing intracellular force distributions by high-resolution live cell imaging and inverse dynamics. Methods Cell Biol. 2007; 83:199-235. PubMed | CMC Update article
  • Kharait S, Hautaniemi S, Wu S, Iwabu A, Lauffenburger DA, Wells A. Decision tree modeling predicts effects of inhibiting contractility signaling on cell motility. BMC Syst Biol 2007; 1:9 PubMed | CMC Update article.
  • Kuhlman W, Taniguchi I, Griffith LG, Mayes AM. Interplay Between PEO Tether Length and Ligand Spacing Governs Cell Spreading on RGD-Modified PMMA-g-PEO Comb Copolymers. Biomacromolecules 2007; 8(10):3206-13 PubMed | CMC Update article.
  • Kozlov MM, Mogilner A. Model of polarization and bi-stability of cell fragments. Biophys J 2007 93 (11):3811-9 PubMed | CMC Update article.
  • Lacayo CI, Pincus Z, VanDuijn MM, Wilson CA, Fletcher DA, Gertler FB, Mogilner A, Theriot JA. Emergence of large-scale cell morphology and movement from local actin filament growth dynamics. PLoS Biol 2007; 5 (9):e233 PubMed | CMC Update article.
  • Yam PT, Wilson CA, Ji L, Hebert B, Barnhart EL, Dye NA, Wiseman PW, Danuser G, Theriot JA. Actin-myosin network reorganization breaks symmetry at the cell rear to spontaneously initiate polarized cell motility. J Cell Biol 2007; 178 (7):1207-21 PubMed | CMC Update article.

2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002

  • Bohnet S, Ananthakrishnan R, Mogilner A, Meister JJ, Verkhovsky AB. Weak force stalls protrusion at the leading edge of the lamellipodium. Biophys J 2006; 90 (5):1810-20 PubMed.
  • Haugh JM, Schneider IC. Effectiveness factor for spatial gradient sensing in living cells. Chem Eng Sci. 2006; 61 (17):5603-11.
  • Karakozova M, Kozak M, Wong CC, Bailey AO, Yates Iii JR, Mogilner A, Zebroski H, Kashina A.Arginylation of Beta Actin Regulates Actin Cytoskeleton and Cell Motility.Science. 2006; 313 (5784):192-6PubMed | CMC Update article.
  • Larripa K, Mogilner A. Transport of a 1D viscoelastic actin-myosin strip of gel as a model of a crawling cell. Physica A 2006; 372:113-23 PDF.
  • Machacek M, Danuser G. Morphodynamic profiling of protrusion phenotypes. Biophys J. 2006; 90(4):1439-52 PubMed | CMC Update article.
  • Mogilner A. On the edge: modeling protrusion. Curr Opin Cell Biol 2006; 18 (1):32-9 PubMed | CMC Update article.
  • Mogilner A, Wollman R, Marshall WF. Quantitative modeling in cell biology: what is it good for? Dev Cell 2006; 11 (3):279-87 PubMed | CMC Update article.
  • Moissoglu K, Slepchenko BM, Meller N, Horwitz AF, Schwartz MA. In vivo dynamics of Rac-membrane interactions. Mol Biol Cell 2006; 17 (6):2770-9 PubMed
  • Prass M, Jacobson K, Mogilner A., Radmacher M. Direct measurement of the lamellipodial protrusive force in a migrating cell J Cell Biol 2006; 174 (6):767-72 PubMed | CMC Update article.
  • Schneider IC, Haugh JM. Mechanisms of gradient sensing and chemotaxis: conserved pathways, diverse regulation. Cell Cycle 2006; 5 (11):1130-4. PubMed
  • Smith KD, Wells A, Lauffenburger DA. Multiple signaling pathways mediate compaction of collagen matrices by EGF-stimulated fibroblasts. Exp Cell Res. 2006; 312 (11):1970-82 PubMed | CMC Update article.
  • Zaman MH, Matsudaira P, Lauffenburger DA. Understanding Effects of Matrix Protease and Matrix Organization on Directional Persistence and Translational Speed in Three-Dimensional Cell Migration. Ann Biomed Eng 2006; 35(1):91-100 PubMed | CMC Update article.
  • Zaman MH, Trapani LM, Siemeski A, Mackellar D, Gong H, Kamm RD, Wells A, Lauffenburger DA, Matsudaira P. Migration of tumor cells in 3D matrices is governed by matrix stiffness along with cell-matrix adhesion and proteolysis. Proc Natl Acad Sci U S A 2006; 103 (29):10889-94 PubMed | CMC Update article.

2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002

  • Civelekoglu-Scholey G, Orr AW, Novak I, Meister JJ, Schwartz MA, Mogilner A.Model of coupled transient changes of Rac, Rho, adhesions and stress fibers alignment in endothelial cells responding to shear stress. J Theor Biol. 2005; 232:569-85. PubMed
  • Hautaniemi S, Kharait S, Iwabu A, Wells A, Lauffenburger DA. Modeling of signal-response cascades using decision tree analysis. Bioinformatics. 2005; 21:2027-35. PubMed
  • Ji L, Danuser G. Tracking quasi-stationary flow of weak fluorescent signals by adaptive multi-frame correlation. J Microsc. 2005; 220(Pt 3):150-67. PubMed
  • Mogilner A and Rubinstein B. The physics of filopodial protrusion. Biophys J. 2005 89:782-95. PubMed
  • Monine MI, Haugh JM. Reactions on cell membranes: comparison of continuum theory and Brownian dynamics simulations. J Chem Phys. 2005; 123(7):074908. PubMed
  • Rubinstein B, Jacobson K, Mogilner A. Multiscale Two-Dimensional Modeling of a Motile Simple-Shaped Cell. SIAM J. MMS, 2005; 3:413-439.
  • Schneider IC, Haugh JM. Quantitative elucidation of a distinct spatial gradient-sensing mechanism in fibroblasts. J Cell Biol. 2005; 171(5):883-92. PubMed
  • Schneider IC, Parrish EM, Haugh JM. Spatial Analysis of 3' Phosphoinositide Signaling in Living Fibroblasts, III: Influence of Cell Morphology and Morphological Polarity. Biophys. J. 2005; 89:1420-1430. PubMed | CMC Update article.
  • Shemesh T, Geiger B, Bershadsky AD, Kozlov MM. Focal adhesions as mechanosensors: a physical mechanism. Proc Natl Acad Sci U S A. 2005; 102(35):12383-8. PubMed
  • Woolf PJ, Prudhomme W, Daheron L, Daley GQ, Lauffenburger DA. Bayesian Network Analysis of Signaling Networks Governing Stem Cell Fate Decisions. Bioinformatics. 2005; 21:741-53. PubMed
  • Zaman MH, Kamm RD, Matsudaira PT, Lauffenburger DA. Computational Model for Cell Migration in Three- Dimensional Matrices. Biophys J. 2005; 89:1389-97. PubMed

2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002

  • Cytrynbaum EN, Rodionov V, Mogilner A. Computational model of dynein-dependent self-organization of microtubule asters. J Cell Sci. 2004; 117(Pt 8):1381-97. PubMed
  • Janes KA, Kelly J, Gaudet S, Albeck J, Sorger PK, Lauffenburger DA. Cue-signal-response analysis of TNF-induced HT29 cell death using partial least squares regression of multivariate signaling network dynamics data. J Comput Biol. 2004; 11(4):544-61. PubMed
  • Maly IV, Wiley HS, Lauffenburger DA. Self-organization of polarized cell signaling via autocrine circuits: computational model analysis. Biophys J. 2004; 86(1 Pt 1):10-22. PubMed
  • Novak IL, Slepchenko BM, Mogilner A, Loew LM. Cooperativity between cell contractility and adhesion. Phys. Rev. Letts. 2003; 93:268109. PubMed
  • Wolgemuth CW, Mogilner A, Oster G. The hydration dynamics of polyelectrolyte gels with applications to cell motility and drug delivery. Eur Biophys J. 2004; 33(2):146-58. PubMed

2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002

  • Grimm HP, Verkhovsky AB, Mogilner A, Meister JJ. Analysis of actin dynamics at the leading edge of crawling cells: implications for the shape of keratocyte lamellipodia. Eur Biophys J. 2003; 32(6):563-77. PubMed
  • Janes KA, Albeck JG, Peng LX, Sorger PK, Lauffenburger DA, Yaffe MB. A High-throughput Quantitative Multiplex Kinase Assay for Monitoring Information Flow in Signaling Networks: Application to Sepsis-Apoptosis. Mol Cell Proteomics. 2003; 2(7):463-73. PubMed
  • Mogilner A, Oster G. Cell biology. Shrinking gels pull cells. Science. 2003; 302(5649):1340-1. PubMed
  • Mogilner A, Oster G. Force generation by actin polymerization II: the elastic ratchet and tethered filaments. Biophys J. 2003; 84(3):1591-605. PubMed
  • Mogilner A, Oster G. Polymer motors: pushing out the front and pulling up the back. Curr Biol. 2003; 13(18):R721-33. PubMed
  • Mogilner A, Verzi D. A simple 1-D physical model of the crawling nematode sperm cell. J. Stat. Phys. 2003; 110:1169-1189.
  • Slepchenko BM, Schaff JC, Macara I, Loew LM. Quantitative cell biology with the Virtual Cell. Trends Cell Biol. 2003; 13(11):570-6. PubMed
  • Xu C, Watras J, Loew LM. Kinetic analysis of receptor-activated phosphoinositide turnover. J Cell Biol. 2003; 161(4):779-91. PubMed

2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002

  • Bottino D, Mogilner A, Roberts T, Stewart M, Oster G. How nematode sperm craw. J Cell Sci. 2002; 115(Pt 2):367-84. PubMed
  • Mogilner A, Edelstein-Keshet L. Regulation of actin dynamics in rapidly moving cells: a quantitative analysis. Biophys J. 2002; 83(3):1237-58. PubMed
  • Moraru II, Schaff JC, Slepchenko BM, Loew LM. The virtual cell: an integrated modeling environment for experimental and computational cell biology. Ann N Y Acad Sci. 2002; 971:595-6. PubMed
  • Sachs K, Gifford D, Jaakkola T, Sorger P, Lauffenburger DA. Bayesian network approach to cell signaling pathway modeling. Sci STKE. 2002; 2002(148):PE38. PubMed
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Modeling Software

Danuser Models | Haugh Models | Lauffenburger Models| Loew VC Models | Mogilner Models

Lauffenburger laboratory

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Mogilner laboratory

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Loew laboratory

  • How to View the Virtual Cell Published Models
    • Login to the Virtual Cell (http://vcell.org/login/login.html)
    • Go to File>Open>BioModel>Shared Models or File>Open>MathModel>Shared Models and find the CMC username.
    • Double click the model you are interested in viewing.
    • If you wish to modify the model or run new simulations, you may copy it into your VC Workspace under your own User account.

The following are stored as BioModels under user CMC in the Virtual Cell Database:

  • Tutorial_FRAPbinding - A model corresponding to the online VCell FRAP Tutorials (http://www.nrcam.uchc.edu/login/frap.pdf; http://www.nrcam.uchc.edu/login/frap_binding.pdf)

  • FRAP of nuclear FR - This is an elaboration of the FRAP tutorial for a real image-based geometry

  • Ca_Release_Fink_et al_1999 & 2000 - An image-based model of calcium waves in differentiated neuroblastoma cells. Fink CC, Slepchenko B, Moraru II, Watras J, Schaff J, Loew LM. Biophys. J. 2000 79:163-183.2000 PubMed

  • Generic_Ras_cascade_1998 - Derived from the CellML model Repository and based on the paper: Increasing Complexity of the Ras Signaling Pathway, Vojtek AB, Ders CJ. J Biol Chem. 1998 273(32):19925-8 PubMed

  • InsP3 dependent Calcium Release - Morphological control of inositol-1,4,5-trisphosphate-dependent signals. Fink CC, Slepchenko B, Moraru II, Schaff J, Watras J, Loew LM. J Cell Biol. 1999 Nov 29;147(5):929-36 PubMed

  • Ma et al 2004 - local stimulation and Ma et al 2004 - mutant behavior - 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. Ma L, Janetopoulos C, Yang L, Devreotes PN, Iglesias PA. Biophys. J. 2004 87(6):3764-3774 PubMed

  • PI3 Kinase Signaling - Kinetic analysis of platelet-derived growth factor receptor/phosphoinositide 3-kinase/Akt signaling in fibroblasts. Park CS, Schneider IC, Haugh JM., J Biol Chem. 2003 278(39):37064-72 PubMed

  • PDGF gradient sensing - Quantitative elucidation of a distinct spatial gradient-sensing mechanism in fibroblasts. Schneider IC, Haugh JM. J.Cell Biol 2005 171:883-892 PubMed

  • MitoticExtract_added_ImportinB and MitoticExtract_added_RanQ69L - Analysis of a RanGTP-regulated gradient in mitotic somatic cells. Kaláb P, Pralle A, Isacoff EY, Heald R, Weis K. Nature 2006 440:(7084)697-701 PubMed

  • PIP2 Hydrolysis - Kinetic analysis of receptor-activated phosphoinositide turnover Xu C, Watras J, Loew LM. J Cell Biol. 2003 May 26;161(4):779-91 PubMed

  • Thymosin Photorelease - Local Photorelease of Caged Thymosin beta4 in Locomoting Keratocytes Causes Cell Turning. Roy P, Rajfur Z, Jones D, Marriott G, Loew L, Jacobson K. J Cell Biol. 2001 153(5):1035-48 PubMed

  • Cell Shape Control - Membrane-binding/modification model of signaling protein activation and analysis of its control by cell morphology. Haugh JM. Biophys J 92, L93-95, 2007. PubMed
  • Formin-PRF Polymerization and Formin-Profilin-Actin Polymerization models - 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. PubMed

The following are stored as MathModels under user CMC in the Virtual Cell Database:

  • Schwartz_2D_membrane_diffusion and Schwartz_3D_FLIP - In vivo dynamics of Rac-membrane interactions. Moissoglu K, Slepchenko BM, Meller N, Horwitz AF, Schwartz MA. Mol Biol Cell. 2006 17(6):2770-9 PubMed

  • EGFR_Bhalla_Iyengar - Emergent properties of networks of biological signaling pathways. Bhalla US, Iyengar R. Science 1999 283(5400): 381-387 PubMed

  • AnalysisAnalysis of G_actin transport in 2D fragment and Analysis of G_actin transport in keratocyte models- Novak I, Slepchenko B, Mogilner A. Quantitative analysis of G-actin transport in motile cells. Biophys J. 2008. May 23. [Epub ahead of print] PubMed

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Haugh laboratory

  • Modeling of realistic cell geometries in Schneider et al., 2005 was performed using FEMLAB, version 3. MATLAB was used to pass image data (acquired in MetaMorph) into FEMLAB for construction of the contact area geometry, and to interpolate FEMLAB output for generating virtual fluorescence images and direct comparison with experimental images. MATLAB files were authored by Ian Schneider and are available upon request.
  • Brownian dynamics algorithms for microscopic modeling of signaling interactions, described in Monine and Haugh, 2005, were implemented in C++ by Michael Monine (available upon request).
  • Membrane-binding/modification model of signaling protein activation and analysis of its control by cell morphology. Publicly available Virtual Cell models (go to File>Open>BioModel>Shared Models>jmhaugh).
    • pdgf gradient sensing (Schneider and Haugh), 2005)
    • Cell shape control (Haugh), 2007)

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Danuser laboratory

  • Cell edge tracking and mapping of protrusion and retraction activity as described in Machacek and Danuser, 2006 was implemented in MATLAB version 7 and newer. The software reads tiff series of fluorescence images and performs edge segmentation and tracking. It can also read edge definitions obtained by other segmentation algorithms and perform only the protrusion and retraction analysis according to Machacek and Danuser, 2006. MATLAB files were authored by Mathias Machacek and are available upon request (mailto: gdanuser@scripps.edu)

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