| Actin dynamics |
Physico-chemical - (mesoscopic model of force generation and symmetry breaking in actin gels) |
Completed - Dayel et al., 2009 |
Mogilner (Mullins) |
| Actin dynamics |
Virtual cell - (actin dynamics at the leading edger of locomoting cells) |
Completed - Novak et al., 2008 (CMC Update Article) |
Loew (Novak, Slepchecko) |
| Actin dynamics |
Virtual Cell - (actin dynamics at the leading edge of locomoting cells) |
Completed - Ditlev et al., 2009 (CMC Update Article) |
Loew (Novak, Slepchecko, Mogilner) |
| Actin dynamics |
Virtual Cell - (actin dynamics at the leading edge of locomoting cells) |
Completed - Kraikivski and Slepchenko, 2010 |
Loew |
| Actin dynamics |
Physico-chemical - (1-D model of actin transport in rapidly and steadily migrating cells using partial differential equations) |
Completed - Mogilner and Edelstein-Keshet, 2002 (CMC Update Article) |
Mogilner |
| Actin dynamics |
Physico-chemical - (model of actin dynamics and cell shape at the leading edge of the migrating keratocyte cell) |
Completed - Grimm et al., 2003 |
Mogilner |
| Actin dynamics |
Physico-chemical - (model of actin dynamics and cell shape at the leading edge of the migrating keratocyte cell) |
Completed - Lacayo et al., 2007 (CMC Update Article) |
Mogilner (Theriot) |
| Actin dynamics |
Physico-chemical - (model of actin dynamics in vitro) |
Completed - Fass et al., 2008 |
Mogilner (Bamburg) |
| Actin dynamics |
Physico-chemical - (model of adhesion dynamics) |
Completed - Choi et al., 2008 (CMC Update Article) |
Mogilner (Horwitz) |
| Actin dynamics |
Physico-chemical - (model of bi-stability of keratocyte lamellipodial fragments) |
Completed - Kozlov and Mogilner, 2007 (CMC Update Article) |
Mogilner |
| Actin dynamics |
Physico-chemical - (model of filopodial protrusion) |
Completed - Mogilner and Rubinstein, 2005 (CMC Update Article) |
Mogilner |
| Actin dynamics |
Physico-chemical - (tethered polymerization ratchet model of protrusive force generation) |
Completed - Mogilner and Oster, 2003 |
Mogilner |
| Adhesion |
Physico-chemical - (modeling of focal adhesion and stress fiber dynamics) |
Completed - Novak et al., 2004 |
Loew (Mogilner) |
| Adhesion, Actin dynamics |
Continuum mechanical model - (of integrated adhesion and contraction forces in lamella of migrating cells) |
Completed - Ji et al., 2007 (CMC Update Article); Ji et al., 2008 (CMC Update Article) |
Danuser |
| Adhesion, Protrusion |
Physico-chemical - (model of limiting role of adhesion in cell protrusion) |
Completed - Bohnet et al., 2006 |
Mogilner (Verkhovsky) |
| Adhesion signaling |
Physico-chemical - (model of cytoskeleton & Rho GTPase response to external force in endothelial cells using differential equations) |
Completed - Civelekoglu-Scholey et al., 2005 (CMC Update Article) |
Mogilner (Schwartz) |
| Cell migration |
Develop a basic graphic interface to build and simulate a CMAP based on cell biology data. |
Completed - software available, instructional video |
Jacobson (Weinreb) |
| Cell migration |
Causal mapping (CMAP) Semi-quantitative intermediate model for cytoskeletal oscillations. Develop ODE model to test CMAP formalism. Models applicable to mechano-chemical signaling in general. |
Completed - Weinreb et al., 2006 (CMC Update Article); Weinreb and Cao, 2007; Kapustina et al., 2008; Weinreb et al., 2009 (CMC Update Article) |
Jacobson (Weinreb, Elston) |
| Cell migration |
Development of materials that control ligand spacing independent of tether length |
Completed - Kuhlman et al., 2007 (CMC Update Article) |
Griffith (Mayes) |
| Cell migration |
Dynamical systems model for cell/substratum adhesion linkages |
Completed - Macdonald et al., 2008 (CMC Update Article) |
Lauffenburger (Horwitz) |
| Cell migration |
Experimental test of model for cell migration in 3-D environments |
Completed - Zaman et al., 2006 (CMC Update Article); Harley et al., 2008 (CMC Update Article) |
Lauffenburger (Zaman) |
| Cell migration |
Extension of model for cell migration in 3D environments to include matrix protease effects |
Completed - Zaman et al., 2006 (CMC Update Article); Kim et al., 2008 |
Lauffenburger (Zaman) |
| Cell migration |
Force-based - (model for cell migration through 3-D matrices to model effects of cell and matrix properties on migration speed) |
Completed - Zaman et al., 2005 (CMC Update Articles: 1, 2) |
Lauffenburger (Matsudaira, Kamm) |
| Cell migration |
Physico-chemical - (1-D model of crawling cell with visco-elastic contractile lamellipodium on a free boundary domain) |
Completed - Larripa and Mogilner, 2006 |
Mogilner (Larripa) |
| Cell migration |
Physico-chemical - (1-D model of crawling nematode sperm cell using partial differential equations on a free boundary domain) |
Completed - Mogilner and Verzi, 2003; Wolgemuth et al., 2004 |
Mogilner |
| Cell migration |
Physico-chemical - (2-D model of crawling keratocyte cell using Finite Element method on a free boundary domain) |
Completed - Rubinstein et al., 2005, view the movies (based on the model of this paper) of the motile lamellipodial fragment and of the turning lamellipodial fragment |
Mogilner (Jacobson) |
| Cell migration |
Physico-chemical - (2-D model of crawling nematode sperm cell using Monte Carlo simulations) |
Completed - Bottino et al., 2002 |
Mogilner |
| Cell Migration |
Modeling EGF signaling network using CMAP. Developing models binding and enzymatic reactions within CMAP approach. Use them as building blocks of a signaling network. |
Completed - manuscript in preparation |
Jacobson (Weinreb & Bankaitis) |
| Cell Migration |
Studying CMAP properties such as dependence of the simulation results on set size K, concept time response constant , etc. using CMAP model of cortical oscillation. |
Completed - web-posting of the results is underway Weinreb et al., 2009 (CMC Update Article) |
Jacobson (Weinreb) |
| Cell migration signaling |
Physico-chemical - (model of chemotactic collective cell movement using partial differential equations) |
Completed - Luca et al., 2003 |
Mogilner |
| Cell shape |
Physico-chemical - (model of the keratocyte cell shape) |
Completed - Keren et al., 2008 (CMC Update Article) |
Mogilner (Theriot) |
| Protrusion |
Level set/Motility of nematode sperm |
Completed - publications in progress Zajac et al., 2008; Stajic and Wolgemuth, 2009 |
Loew (Wolgemuth) |
| Protrusion |
Virtual cell - (Model of filopdia formation regulated by capping protein and Ena/VASP) |
Completed - Kapustina et al., 2010 (CMC Update Article) |
Loew (Jacobson) |
| Protrusion |
Biophysical measurement of lamellipodial protrusive force and force velocity relationship |
Completed - Prass et al., 2006 (CMC Update Article) |
Jacobson, Mogilner (Prass, Radmacher) |
| Protrusion |
Physico-chemical - (model of limiting role of arginylation of beta-actin in cell protrusion) |
Completed - Karakozova et al., 2006 (CMC Update Article) |
Mogilner (Kashina) |
| Protrusion, Actin transport |
Physico-chemical - (model of fluid flow of cytoplasm in migrating cells) |
Completed - Model in Virtual Cell |
Loew, Mogilner |
| Signaling |
Virtual Cell - (analysis of diffusion in crowded environments) |
Completed - Novak et al., 2009 |
Loew |
| Signaling |
Virtual Cell - (InsP3-mediated Ca++ release) |
Completed - Fink et al., 1999; Fink et al., 2000 |
Loew |
| Signaling |
Virtual Cell - (modeling of FRAP experiments for membrane translocation of Rac) |
Completed - Moissoglu et al., 2006 (CMC Update Article) |
Loew (Slepchenko, Schwartz) |
| Signaling |
Bayesian network - (modeling applied to signaling pathways to model cell differentiation regulatory networks) |
Completed - Sachs et al., 2002 (CMC Update Article); Woolf et al., 2005 (CMC Update Article) |
Lauffenburger |
| Signaling |
Cue-signal-response - (model using PCA/PLS methodology in cell death to model apoptosis regulatory networks) |
Completed - Janes et al., 2003; Janes et al., 2004 |
Lauffenburger |
| Signaling |
Decision tree methodology for cue-signal-response - (analysis applied to signaling pathways to model cell migration responses to growth factors and extracellular matrix) |
Completed - Hautaniemi et al., 2005 (CMC Update Article) |
Lauffenburger (Wells) |
| Signaling |
Decision tree methodology for cue-signal-response |
Completed - Kharait et al., 2007 (CMC Update Article) |
Lauffenburger |
| Signaling |
Detailed, domain-based model of PI 3-kinase recruitment |
Completed - Barua et al., 2008 |
Haugh (Faeder) |
| Signaling |
Macroscopic model of cell morphology control of cell polarization/migration signaling |
Completed - Haugh, 2007 (CMC Update Article) |
Haugh |
| Signaling |
Microscopic model of PI 3 kinase/small GTPase signaling |
Completed - Codes Available, Monine and Haugh, 2008 (CMC Update Article) |
Haugh (Schwartz, Horwitz) |
| Signaling |
Microscopic model of reactions/interactions in cell membranes |
Completed - Codes Available, Monine and Haugh, 2005 (CMC Update Article) |
Haugh |
| Signaling |
Model of spatially defined growth factor receptor and integrin signaling |
Completed - Schneider and Haugh, 2005 (CMC Update Article) |
Haugh |
| Signaling |
Spatial model of PI 3-kinase signaling with realistic cell geometries |
Completed - Schneider et al., 2005 (CMC Update Article) |
Haugh |
| Signaling |
Virtual Cell - (PIP2 Turnover & PHd1-GFP translocation) |
Completed - Xu et al., 2003 |
Loew |
| Adhesion |
Physico-chemical - (model of adhesion dynamics) |
Completed, publication in progress |
Horwitz, Mogilner |
| Adhesion |
Physico-chemical - (stochastic modeling of the dynamics of focal adhesions and stress fibers) |
In progress |
Loew (Novak, Slepchenko) |
| Adhesion |
Virtual Cell - (analysis and modeling of quantitative imaging experiments on assembly/disassembly of adhesion complexes) |
In progress |
Loew (Horwitz) |
| Adhesion, Actin dynamics |
Computational image modeling of actin and adhesion dynamics in living cells |
In progress - Burnette et al., 2007; Delorme et al., 2007 (CMC Update Article); Hu et al., 2007 (CMC Update Article); Yam et al., 2007 (CMC Update Article); Schaefer et al., 2008 (CMC Update Article); Wilson et al., 2010 |
Danuser (Waterman, Bokoch, Theriot, Forscher) |
| Cell migration |
Apply 2-D cue-signal-response migration model |
In progress |
Griffith, Lauffenburger (Horwitz, Wells) |
| Cell migration |
Apply 3-D matrices to theory-experiment cycle |
In progress |
Griffith (Wells, Gertler) |
| Cell migration |
Develop synthetic 3-D matrices that control sterics/porosity, mechanics, adhesion, proteolysis |
In progress |
Griffith |
| Cell Migration |
Develop an algorithm to acquire and implement this algorithm within the basic software. Develop a Java-based web utility through the WWW. |
In progress |
Jacobson (Weinreb) |
| Cell Migration |
Developing two-sided CMAP to include spatial aspects of cell shape oscillations. The model is based on the CMAP published earlier. |
In progress - Web-posting of the results is underway |
Jacobson (Weinreb) |
| Signaling |
Macroscopic, Virtual Cell models of Rac/Pak signaling and adhesion/protrusion dynamics |
In progress |
Haugh (Horwitz, Schwartz, Hahn, Loew) |
| Signaling |
Stochastic models of Rac/Pak signaling and adhesion/protrusion dynamics |
In progress - Cirit et al., 2010 (CMC Update Article); Welf and Haugh, 2010 (CMC Update Article) |
Haugh (Horwitz) |
| Signaling Dynamics |
Statistical analysis - (of the causality between regulatory signals, cytoskeleton dynamics and cell protrusion) |
In progress - Machacek and Danuser, 2006 (CMC Update Article); Sabouri-Ghomi et al., 2008 (CMC Update Article); Machacek et al., 2009 (CMC Update Article) |
Danuser (Hahn, Ginsberg) |
