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Modeling - Resources

Publications - last updated February, 2014

2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002

  • Hang TC, Tedford NC, Reddy RJ, Rimchala T, Wells A, White FM, Kamm RD, Lauffenburger DA. Vascular Endothelial Growth Factor and Platelet Factor 4 Inputs Modulate Human Microvascular Endothelial Signaling in a Three-Dimensional Matrix Migration Context. Mol. Cell Proteomics 2013; PubMed.
  • Zawistowski JS, Sabouri-Ghomi M, Danuser G, Hahn KM, Hodgson L. A RhoC Biosensor Reveals Differences in the Activation Kinetics of RhoA and RhoC in Migrating Cells. PLoS ONE 2013; 8:e79877 Full Text | CMC Update Article.

2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002

  • Lacayo CI, Soneral PA, Zhu J, Tsuchida MA, Footer MJ, Soo FS, Lu Y, Xia Y, Mogilner A, Theriot JA. Choosing orientation: influence of cargo geometry and ActA polarization on actin comet tails. Mol. Biol. Cell 2012; 23:614-29 Full Text.
  • Loerke D, le Duc Q, Blonk I, Kerstens A, Spanjaard E, Machacek M, Danuser G, de Rooij J. Quantitative imaging of epithelial cell scattering identifies specific inhibitors of cell motility and cell-cell dissociation. Sci Signal 2012; 5:rs5 PubMed | CMC Update Article.
  • Meyer AS, Hughes-Alford SK, Kay JE, Castillo A, Wells A, Gertler FB, Lauffenburger DA. 2D protrusion but not motility predicts growth factor-induced cancer cell migration in 3D collagen. J. Cell Biol. 2012; 197:721-9 Full Text.
  • Ng MR, Besser A, Danuser G, Brugge JS. Substrate stiffness regulates cadherin-dependent collective migration through myosin-II contractility. J. Cell Biol. 2012; 199:545-63 PubMed | CMC Update Article.
  • Stains CI, Tedford NC, Walkup TC, Luković E, Goguen BN, Griffith LG, Lauffenburger DA, Imperiali B. Interrogating signaling nodes involved in cellular transformations using kinase activity probes. Chem. Biol. 2012; 19:210-7 Full Text | CMC Update Article.
  • Welf ES, Ahmed S, Johnson HE, Melvin AT, Haugh JM. Migrating fibroblasts reorient directionality by a metastable, PI3K-dependent mechanism. J. Cell Biol. 2012; 197:105-14 Full Text | CMC Update Article.
  • Welf ES, Haugh JM. Stochastic models of cell protrusion arising from spatiotemporal signaling and adhesion dynamics. Methods Cell Biol. 2012; 110:223-41 PubMed.

2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002

  • Applegate KT, Besson S, Matov A, Bagonis MH, Jaqaman K, Danuser G. plusTipTracker: Quantitative image analysis software for the measurement of microtubule dynamics. J. Struct. Biol. 2011; 176:168-84 Full Text | CMC Update Article.
  • Barnhart EL, Lee KC, Keren K, Mogilner A, Theriot JA. An Adhesion-Dependent Switch between Mechanisms That Determine Motile Cell Shape. PLoS Biol. 2011; 9:e1001059 Full Text | CMC Update Article.
  • Gao RC, Zhang XD, Sun YH, Kamimura Y, Mogilner A, Devreotes PN, Zhao M. Different roles of membrane potentials in electrotaxis and chemotaxis of dictyostelium cells. Eukaryotic Cell 2011; 10:1251-6 Full Text.
  • Iwanicki MP, Davidowitz RA, Ng MR, Besser A, Muranen T, Merritt M, Danuser G, Ince TA, Ince T, Brugge JS. Ovarian cancer spheroids use myosin-generated force to clear the mesothelium. Cancer Discov 2011; 1:144-57 Full Text.
  • Mendoza MC, Er EE, Zhang W, Ballif BA, Elliott HL, Danuser G, Blenis J. ERK-MAPK Drives Lamellipodia Protrusion by Activating the WAVE2 Regulatory Complex. Mol. Cell 2011; 41:661-71 PubMed | CMC Update Article.
  • Novak IL, Gao F, Kraikivski P, Slepchenko BM. Diffusion amid random overlapping obstacles: similarities, invariants, approximations. J Chem Phys 2011; 134:154104 Full Text.
  • Novak, IL, Gao, F, Kraikivski, P, Slepchenko, BM. Erratum: "Diffusion amid random overlapping obstacles: Similarities, invariants, approximations'' [J. Chem. Phys. 134, 154104 (2011)]. J Chem Phys 2011; 135:039901 Full Text.
  • Novak, IL, Gao, F, Kraikivski, P, Slepchenko, BM. Erratum: "Diffusion amid random overlapping obstacles: Similarities, invariants, approximations'' [J. Chem. Phys. 134, 154104 (2011)]. J Chem Phys 2011; 135:039901 DOI.
  • Ofer N, Mogilner A, Keren K. Actin disassembly clock determines shape and speed of lamellipodial fragments. Proc Natl Acad Sci U S A 2011; PubMed.
  • Paradise RK, Lauffenburger DA, Van Vliet KJ. Acidic extracellular pH promotes activation of integrin α(v)β(3). PLoS ONE 2011; 6:e15746 Full Text | CMC Update Article.
  • Peyton SR, Kalcioglu ZI, Cohen JC, Runkle AP, Van Vliet KJ, Lauffenburger DA, Griffith LG. Marrow-Derived stem cell motility in 3D synthetic scaffold is governed by geometry along with adhesivity and stiffness. Biotechnol. Bioeng. 2011; 108:1181-93 PubMed | CMC Update Article.
  • Sun YH, Reid B, Fontaine JH, Miller LA, Hyde DM, Mogilner A, Zhao M. Airway Epithelial Wounds in Rhesus Monkey Generate Ionic Currents That Guide Cell Migration to Promote Healing. J Appl Physiol 2011; PubMed.
  • Tkachenko E, Sabouri-Ghomi M, Pertz O, Kim C, Gutierrez E, Machacek M, Groisman A, Danuser G, Ginsberg MH. Protein kinase A governs a RhoA-RhoGDI protrusion-retraction pacemaker in migrating cells. Nat. Cell Biol. 2011; 13:661-8 PubMed | CMC Update Article.
  • Welch CM, Elliott H, Danuser G, Hahn KM. Imaging the coordination of multiple signalling activities in living cells. Nat. Rev. Mol. Cell Biol. 2011; 12:749-56 PubMed.
  • Welf ES, Haugh JM. Signaling pathways that control cell migration: models and analysis. Wiley Interdiscip Rev Syst Biol Med 2011; 3:231-40 PubMed.
  • Wolgemuth CW, Stajic J, Mogilner A. Redundant mechanisms for stable cell locomotion revealed by minimal models. Biophys. J. 2011; 101:545-53 Full Text | CMC Update Article.
  • Wu S, Wells A, Griffith LG, Lauffenburger DA. Controlling multipotent stromal cell migration by integrating "course-graining" materials and "fine-tuning" small molecules via decision tree signal-response modeling. Biomaterials 2011; 32:7524-31 Full Text | CMC Update Article.

2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002

  • Barnhart, EL, Lee, KC, Keren, K, Mogilner, A, Theriot, JA. Rapidly locomoting fish keratocytes transition among three adhesion-dependent migration regimes.. PLoS Biology 2010; .
  • Cirit M, Krajcovic M, Choi CK, Welf ES, Horwitz AF, Haugh JM. Stochastic model of integrin-mediated signaling and adhesion dynamics at the leading edges of migrating cells. PLoS Comput. Biol. 2010; 6:e1000688 Full Text | CMC Update Article.
  • Kapustina M, Vitriol E, Elston TC, Loew LM, Jacobson K. Modeling capping protein FRAP and CALI experiments reveals in vivo regulation of actin dynamics. Cytoskeleton (Hoboken) 2010; 67:519-34 Full Text | CMC Update Article.
  • Kraikivski P, Slepchenko BM. Quantifying a pathway: kinetic analysis of actin dendritic nucleation. Biophys. J. 2010; 99:708-15 Full Text.
  • Mogilner A, Rubinstein B. Actin disassembly 'clock' and membrane tension determine cell shape and turning: a mathematical model. J Phys Condens Matter 2010; 22:194118 Full Text.
  • Weiger MC, Ahmed S, Welf ES, Haugh JM. Directional persistence of cell migration coincides with stability of asymmetric intracellular signaling. Biophys. J. 2010; 98:67-75 Full Text | CMC Update Article.
  • Welf ES, Haugh JM. Stochastic Dynamics of Membrane Protrusion Mediated by the DOCK180/Rac Pathway in Migrating Cells. Cell Mol Bioeng 2010; 3:30-39 Full Text | CMC Update Article.
  • Wilson CA, Tsuchida MA, Allen GM, Barnhart EL, Applegate KT, Yam PT, Ji L, Keren K, Danuser G, Theriot JA. Myosin II contributes to cell-scale actin network treadmilling through network disassembly. Nature 2010; 465:373-7 PubMed.
  • Wolgemuth CW, Zajac M. The Moving Boundary Node Method: A level set-based, finite volume algorithm with applications to cell motility. J Comput Phys 2010; 229:7287-7308 Full Text.

2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002

  • Dayel MJ, Akin O, Landeryou M, Risca V, Mogilner A, Mullins RD. In silico reconstitution of actin-based symmetry breaking and motility. PLoS Biol. 2009; 7:e1000201 Full Text.
  • Ditlev JA, Vacanti NM, Novak IL, Loew LM. An open model of actin dendritic nucleation. Biophys. J. 2009; 96:3529-42 Full Text | CMC Update Article.
  • Keren K, Yam PT, Kinkhabwala A, Mogilner A, Theriot JA. Intracellular fluid flow in rapidly moving cells. Nat. Cell Biol. 2009; 11:1219-24 Full Text | CMC Update Article.
  • Machacek M, Hodgson L, Welch C, Elliott H, Pertz O, Nalbant P, Abell A, Johnson GL, Hahn KM, Danuser G. Coordination of Rho GTPase activities during cell protrusion. Nature 2009; 461:99-103 Full Text | CMC Update Article.
  • Mogilner A. Mathematics of cell motility: have we got its number?. J Math Biol 2009; 58:105-34 Full Text | CMC Update Article.
  • Mogilner A, Keren K. The shape of motile cells. Curr. Biol. 2009; 19:R762-71 Full Text.
  • Novak IL, Kraikivski P, Slepchenko BM. Diffusion in cytoplasm: effects of excluded volume due to internal membranes and cytoskeletal structures. Biophys. J. 2009; 97:758-67 Full Text.
  • Rubinstein B, Fournier MF, Jacobson K, Verkhovsky AB, Mogilner A. Actin-myosin viscoelastic flow in the keratocyte lamellipod. Biophys. J. 2009; 97:1853-63 Full Text | CMC Update Article.
  • Stajic J, Wolgemuth CW. Biochemical mechanisms for regulating protrusion by nematode major sperm protein. Biophys. J. 2009; 97:748-57 Full Text.
  • Weiger MC, Wang CC, Krajcovic M, Melvin AT, Rhoden JJ, Haugh JM. Spontaneous phosphoinositide 3-kinase signaling dynamics drive spreading and random migration of fibroblasts. J. Cell. Sci. 2009; 122:313-23 Full Text.
  • Weinreb GE, Kapustina MT, Jacobson K, Elston TC. In silico generation of alternative hypotheses using causal mapping (CMAP). PLoS ONE 2009; 4:e5378 Full Text | CMC Update Article.

2013 | 2012 | 2011 | 2010 | 2009 | 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; 283:7338-45 Full Text.
  • 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; 10:1039-50 Full Text | 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 Full Text.
  • Harley BA, Kim HD, Zaman MH, Yannas IV, Lauffenburger DA, Gibson LJ. Microarchitecture of three-dimensional scaffolds influences cell migration behavior via junction interactions. Biophys. J. 2008; 95:4013-24 Full Text | CMC Update Article.
  • Ji L, Lim J, Danuser G. Fluctuations of intracellular forces during cell protrusion. Nat. Cell Biol. 2008; 10:1393-400 Full Text | 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; 94:4605-20 Full Text.
  • Keren K, Pincus Z, Allen GM, Barnhart EL, Marriott G, Mogilner A, Theriot JA. Mechanism of shape determination in motile cells. Nature 2008; 453:475-80 Full Text | CMC Update Article.
  • Kim HD, Guo TW, Wu AP, Wells A, Gertler FB, Lauffenburger DA. Epidermal growth factor-induced enhancement of glioblastoma cell migration in 3D arises from an intrinsic increase in speed but an extrinsic matrix- and proteolysis-dependent increase in persistence. Mol. Biol. Cell 2008; 19:4249-59 Full Text.
  • Kraikivski P, Slepchenko BM, Novak IL. Actin bundling: initiation mechanisms and kinetics. Phys. Rev. Lett. 2008; 101:128102 Full Text | CMC Update Article.
  • Macdonald A, Horwitz AR, Lauffenburger DA. Kinetic model for lamellipodal actin-integrin 'clutch' dynamics. Cell Adh Migr 2008; 2:95-105 Full Text | 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; 95:2172-82 Full Text | CMC Update Article.
  • Moraru II, Schaff JC, Slepchenko BM, Blinov ML, Morgan F, Lakshminarayana A, Gao F, Li Y, Loew LM. Virtual Cell modelling and simulation software environment. IET Syst Biol 2008; 2:352-62 Full Text.
  • Novak IL, Slepchenko BM, Mogilner A. Quantitative analysis of G-actin transport in motile cells. Biophys. J. 2008; 95:1627-38 Full Text | CMC Update Article.
  • Sabouri-Ghomi M, Wu Y, Hahn K, Danuser G. Visualizing and quantifying adhesive signals. Curr. Opin. Cell Biol. 2008; 20:541-50 Full Text | 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; 15:146-62 Full Text | CMC Update Article.
  • Zajac M, Dacanay B, Mohler WA, Wolgemuth CW. Depolymerization-driven flow in nematode spermatozoa relates crawling speed to size and shape. Biophys. J. 2008; 94:3810-23 Full Text.

2013 | 2012 | 2011 | 2010 | 2009 | 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; 28:1847-61 Full Text | CMC Update Article.
  • Burnette DT, Schaefer AW, Ji L, Danuser G, Forscher P. Filopodial actin bundles are not necessary for microtubule advance into the peripheral domain of Aplysia neuronal growth cones. Nat. Cell Biol. 2007; 9:1360-9 PubMed.
  • 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; 13:646-62 Full Text | CMC Update Article.
  • Fan VH, Tamama K, Au A, Littrell R, Richardson LB, Wright JW, Wells A, Griffith LG. Tethered epidermal growth factor provides a survival advantage to mesenchymal stem cells. Stem Cells 2007; 25:1241-51 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:L93-5 Full Text | CMC Update Article.
  • Hu K, Ji L, Applegate KT, Danuser G, Waterman-Storer CM. Differential transmission of actin motion within focal adhesions. Science 2007; 315:111-5 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 Full Text | CMC Update Article.
  • Kozlov MM, Mogilner A. Model of polarization and bistability of cell fragments. Biophys. J. 2007; 93:3811-9 Full Text | 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; 8:3206-13 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:e233 Full Text | CMC Update Article.
  • Weinreb, GE, Cao, Y. Fuzzy Causal Mapping (F-CMAP)-A Proposal To Develop A New Systems Biology Tool.. Information Science 2007; Proceedings of the 10th Joint Conference: DOI.
  • 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; 178:1207-21 Full Text | 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 2007; 35:91-100 PubMed | CMC Update Article.

2013 | 2012 | 2011 | 2010 | 2009 | 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; 90:1810-20 Full Text.
  • Haugh, JM, Schneider, IC. Effectiveness factor for spatial gradient sensing in living cells.. Chem Eng Sci. 2006; 61:5603-5611 DOI.
  • Karakozova M, Kozak M, Wong CC, Bailey AO, Yates JR, Mogilner A, Zebroski H, Kashina A. Arginylation of beta-actin regulates actin cytoskeleton and cell motility. Science 2006; 313:192-6 PubMed | CMC Update Article.
  • Lagerholm BC, Averett L, Weinreb GE, Jacobson K, Thompson NL. Analysis method for measuring submicroscopic distances with blinking quantum dots. Biophys. J. 2006; 91:3050-60 Full Text | 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; 372:113-123 PubMed.
  • Machacek M, Danuser G. Morphodynamic profiling of protrusion phenotypes. Biophys. J. 2006; 90:1439-52 Full Text | CMC Update Article.
  • Mogilner A. On the edge: modeling protrusion. Curr. Opin. Cell Biol. 2006; 18:32-9 PubMed | CMC Update Article.
  • Mogilner A, Wollman R, Marshall WF. Quantitative modeling in cell biology: what is it good for?. Dev. Cell 2006; 11:279-87 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; 17:2770-9 Full Text | CMC Update Article.
  • Prass M, Jacobson K, Mogilner A, Radmacher M. Direct measurement of the lamellipodial protrusive force in a migrating cell. J. Cell Biol. 2006; 174:767-72 Full Text | CMC Update Article.
  • Schneider IC, Haugh JM. Mechanisms of gradient sensing and chemotaxis: conserved pathways, diverse regulation. Cell Cycle 2006; 5:1130-4 PubMed.
  • Smith KD, Wells A, Lauffenburger DA. Multiple signaling pathways mediate compaction of collagen matrices by EGF-stimulated fibroblasts. Exp. Cell Res. 2006; 312:1970-82 PubMed | CMC Update Article.
  • Taniguchi, I, Kuhlman, WA, Griffith, LG, Mayes, AM. Macromonomer purification strategy for well-defined polymer amphiphiles incorporating poly(ethylene glycol) monomethacrylate.. Macromol. 2006; 27:631-636 DOI.
  • Weinreb GE, Elston TC, Jacobson K. Causal mapping as a tool to mechanistically interpret phenomena in cell motility: application to cortical oscillations in spreading cells. Cell Motil. Cytoskeleton 2006; 63:523-32 PubMed | CMC Update Article.
  • Zaman MH, Trapani LM, Sieminski AL, 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; 103:10889-94 Full Text | CMC Update Article.

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  • 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 | CMC Update Article.
  • 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 | CMC Update Article.
  • Ji L, Danuser G. Tracking quasi-stationary flow of weak fluorescent signals by adaptive multi-frame correlation. J Microsc 2005; 220:150-67 PubMed.
  • Mogilner A, Rubinstein B. The physics of filopodial protrusion. Biophys. J. 2005; 89:782-95 Full Text | CMC Update Article.
  • Monine MI, Haugh JM. Reactions on cell membranes: comparison of continuum theory and Brownian dynamics simulations. J Chem Phys 2005; 123:074908 Full Text | CMC Update Article.
  • Rubinstein, B, Jacobson, K, Mogilner, A. Multiscale Two-Dimensional Modeling of a Motile Simple-Shaped Cell.. SIAM J. MMS, 2005; 3:413-439 Full Text.
  • Schneider IC, Haugh JM. Quantitative elucidation of a distinct spatial gradient-sensing mechanism in fibroblasts. J. Cell Biol. 2005; 171:883-92 Full Text | CMC Update Article.
  • 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; 89:1420-30 Full Text | CMC Update Article.
  • Taniguchi, I, Mayes, AM, Chan, EWL, Griffith, LG. A chemoselective approach to grafting biodegradable polyesters. Macromolecules 2005; 38:216-219 DOI.
  • Woolf PJ, Prudhomme W, Daheron L, Daley GQ, Lauffenburger DA. Bayesian analysis of signaling networks governing embryonic stem cell fate decisions. Bioinformatics 2005; 21:741-53 PubMed | CMC Update Article.
  • Zaman MH, Kamm RD, Matsudaira P, Lauffenburger DA. Computational model for cell migration in three-dimensional matrices. Biophys. J. 2005; 89:1389-97 Full Text | CMC Update Article.

2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002

  • Janes KA, Kelly JR, Gaudet S, Albeck JG, Sorger PK, Lauffenburger DA. Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of dynamic multivariate data. J. Comput. Biol. 2004; 11:544-61 PubMed.
  • Lu H, Koo LY, Wang WM, Lauffenburger DA, Griffith LG, Jensen KF. Microfluidic shear devices for quantitative analysis of cell adhesion. Anal. Chem. 2004; 76:5257-64 PubMed.
  • Novak IL, Slepchenko BM, Mogilner A, Loew LM. Cooperativity between cell contractility and adhesion. Phys. Rev. Lett. 2004; 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; 33:146-58 PubMed.

2013 | 2012 | 2011 | 2010 | 2009 | 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; 32:563-77 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; 2:463-73 PubMed.
  • Mogilner A, Oster G. Force generation by actin polymerization II: the elastic ratchet and tethered filaments. Biophys. J. 2003; 84:1591-605 Full Text.
  • Mogilner, A, Verzi, D. A simple 1-D physical model of the crawling nematode sperm cell.. J. Stat. Phys. 2003; 110:1169-1189 Full Text.
  • Slepchenko BM, Schaff JC, Macara I, Loew LM. Quantitative cell biology with the Virtual Cell. Trends Cell Biol. 2003; 13:570-6 PubMed.
  • Xu C, Watras J, Loew LM. Kinetic analysis of receptor-activated phosphoinositide turnover. J. Cell Biol. 2003; 161:779-91 Full Text.

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  • Bottino D, Mogilner A, Roberts T, Stewart M, Oster G. How nematode sperm crawl. J. Cell. Sci. 2002; 115:367-84 PubMed.
  • Griffith LG. Emerging design principles in biomaterials and scaffolds for tissue engineering. Ann. N. Y. Acad. Sci. 2002; 961:83-95 PubMed.
  • Koo LY, Irvine DJ, Mayes AM, Lauffenburger DA, Griffith LG. Co-regulation of cell adhesion by nanoscale RGD organization and mechanical stimulus. J. Cell. Sci. 2002; 115:1423-33 PubMed.
  • Mogilner A, Edelstein-Keshet L. Regulation of actin dynamics in rapidly moving cells: a quantitative analysis. Biophys. J. 2002; 83:1237-58 Full Text | CMC Update Article.
  • 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:pe38 PubMed | CMC Update Article.
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Modeling Software

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

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: gdanuser@scripps.edu
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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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Jacobson laboratory

  • Weinreb and Jacobson have developed a basic graphic interface software to build and simulate a CMAP model based on cell biology data. This has been based on an earlier work: Weinreb, G.E., T.C. Elston, and K. Jacobson. The Causal Map as a Tool to Mechanistically Interpret Phenomena in Cell Motility: Application to Cortical Oscillations in Spreading Cells. Cell Motility and Cytosceleton, 2006; 63 (9):523-32 PubMed | CMC Update article, and the software is available, as well as an instructional video (alternate link).

Lauffenburger laboratory

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Loew laboratory

How to View the Virtual Cell Published Models
  • Login to the Virtual Cell (http://vcell.org/vcell_software/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: SimpleFRAP, FRAP binding

  • 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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Mogilner laboratory

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