VCell Published Models 2017-08-22T19:01:21+00:00

A Reaction-Diffusion Model Explains Amplification of the PLC/PKC Pathway in Fibroblast Chemotaxis.
Mohan,K1, Nosbisch,JL, Elston,TC, Bear,JE, Haugh,JM
Biophys J. 2017 Jul 11;113(1):185-194.
PUBMED:28700916      doi:10.1016/j.bpj.2017.05.035
   VCell BioModels referenced in publication:
   user: jnosbis,   model name: Mohan chemotaxis 2017

Activation of the contact pathway of blood coagulation on the circulating microparticles may explain blood plasma coagulation induced by dilution
Chelushkin,MA, Panteleev,MA, Sveshnikova,AN
Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology. 2017;11(2):130–143

Cell shape information is transduced through tension-independent mechanisms
Ron, A., Azeloglu, E.U., Calizo, R.C., Hu, M., Bhattacharya, S., Chen, Y., Jayaraman, G., Lee, S., Neves-Zaph, S.R., Li, H., Gordon, R.E.
Nature communications. 2017; 8(1), p.2145.
PUBMED:28652372      doi:10.1038/s41467-017-02218-4

Fission yeast myo2: Molecular organization and diffusion in the cytoplasm
Friend, J. E., Sayyad, W. A., Arasada, R., McCormick, C. D., Heuser, J. E., Pollard, T. D.
Cytoskeleton. 2017 Dec 4.
PUBMED:29205883      doi:10.1002/cm.21425
   VCell BioModels referenced in publication:
   user: Wasim,   model name: Yeast 3D_FRAP

Fragility of foot process morphology in kidney podocytes arises from chaotic spatial propagation of cytoskeletal instability
Falkenberg,CV, Azeloglu,EU, Stothers,M, Deerinck,TJ, Chen,Y, He,JC, Ellisman,MH, Hone,JC, Iyengar,R, Loew,LM
PLoS Comput Biol. 2017 Mar 16;13(3):e1005433.
PUBMED:28301477      doi:10.1371/journal.pcbi.1005433
   VCell BioModels referenced in publication:
   user: falkenbe,   model name: Falkenberg_PodocyteStability

Muscarinic receptor regulates extracellular signal regulated kinase by two modes of arrestin binding
Jung, S. R., Kushmerick, C., Seo, J. B., Koh, D. S., Hille, B.
Proceedings of the National Academy of Sciences, 201700331
PUBMED:28652372      doi:10.1073/pnas.1700331114
   VCell BioModels referenced in publication:
   user: jsr007,   model name: Jung_PNAS_2017_BiasedM1R_Figure4
   user: jsr007,   model name: Jung_PNAS_2017_wildtypeM1R_figure5

Plant potassium channels are in general dual affinity uptake systems
AIMS Biophysics, 2017, 4(1): 90-106.

Src Homology 2 domains enhance tyrosine phosphorylation in vivo by protecting binding sites in their target proteins from dephosphorylation
Jadwin, J. A., Curran, T. G., Lafontaine, A. T., White, F. M., Mayer, B. J.
Journal of Biological Chemistry (2017) 293.2: 623-637
PUBMED:29162725      doi:10.1074/jbc.M117.794412
   VCell BioModels referenced in publication:
   user: jjadwin,   model name: spatial protection test- no flux two way competition orginal – paper model-shared
   user: jjadwin,   model name: spatial protection test- two way competition orginal – paper model shared

The fungal UmSrt1 and maize ZmSUT1 sucrose transporters battle for plant sugar resources
Wittek,A, Dreyer,I, Al-Rasheid,KAS, Sauer,N, Hedrich,R, Geiger,D
J Integr Plant Biol. 2017 Jun;59(6):422-435.
PUBMED:28296205      doi:10.1111/jipb.12535
VCell BioModels referenced in publication:
user: idreyer,   model name: Wittek_et_al_JIntegrPlantBiol_2017_Phloem Fungus

A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation
Yang, P. C., Boras, B. W., Jeng, M. T., Docken, S. S., Lewis, T. J., McCulloch, A. D., Harvey, R. D., Clancy, C. E.
PLoS Comput Biol. 2016;12(7):e1005005.
PUBMED:27409243      doi:10.1371/journal.pcbi.1005005
   VCell BioModels referenced in publication:
   user: bboras,   model name: Boras-Diffusional Study-1000xPDEtest4
   user: bboras,   model name: Boras-Diffusional Study-250xPDEtest4
   user: bboras,   model name: Boras-Diffusional Study No geometry1x larger
   user: bboras,   model name: Boras-Diffusional Study No geometry10x larger
   user: bboras,   model name: Boras-Diffusional Study-25xPDEtest4
   user: bboras,   model name: Boras-Diffusional Study-100xPDEtest7
   user: bboras,   model name: Boras-Diffusional Study-10xPDEtest5
   user: bboras,   model name: Boras-Diffusional Study-100xPDEtest5
   user: bboras,   model name: Boras-Diffusional Study-100xPDEtest6 for images
   user: bboras,   model name: Boras-Diffusional Study-1xPDEtest5

Contributions of protein kinases and beta-arrestin to termination of protease-activated receptor 2 signaling
Jung, S. R., Seo, J. B., Deng, Y., Asbury, C. L., Hille, B., Koh, D. S.
J Gen Physiol. 2016;147(3):255-71.
PUBMED:26927499      doi:10.1085/jgp.201511477
   VCell BioModels referenced in publication:
   user: jsr007,   model name: hillelab: JungSR_PAR2_desensitization2015

Cooperation through Competition—Dynamics and Microeconomics of a Minimal Nutrient Trade System in Arbuscular Mycorrhizal Symbiosis
Schott, Stephan, Valdebenito, Braulio, Bustos, Daniel, Gomez-Porras, Judith L., Sharma, Tripti, Dreyer, Ingo
Front Plant Sci. 2016 Jun 27;7:912.
PUBMED:27446142      doi:10.3389/fpls.2016.00912
   VCell BioModels referenced in publication:
   user: idreyer,   model name: AMF Symbiosis with SWEET

Cross-regulation of phosphodiesterase-1 and phosphodiesterase-2 activities controls dopaminemediated striatal alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (ampa) receptor trafficking.
Song, R.S., Tolentino, R., Sobie, E.A., Neves-Zaph, S.R.
J Biol Chem. 2016 Sep 7. pii: jbc.M116.749747
PUBMED:27605670      doi:10.1074/jbc.M116.749747
   VCell BioModels referenced in publication:
   user: rsong,   model name: RS_JBC2016

Dynamics of Phosphoinositide-Dependent Signaling in Sympathetic Neurons
Kruse, M., Vivas, O., Traynor-Kaplan, A., Hille, B.
J Neurosci. 2016;36(4):1386-400.
PUBMED:26818524      doi:10.1523/JNEUROSCI.3535-15.2016
   VCell BioModels referenced in publication:
   user: mkruse,   model name: hillelab: KruseVivasTraynorKaplanHille_PI-metabolism_SCG_2015

Hysteresis-like binding of coagulation factors X/Xa to procoagulant activated platelets and phospholipids results from multistep association and membrane-dependent multimerization
Podoplelova, N. A., Sveshnikova, A. N., Kurasawa, J. H., Sarafanov, A. G., Chambost, H., Vasil&apos, ev, S. A., Demina, I. A., Ataullakhanov, F. I., Alessi, M. C., Panteleev, M. A.
Biochim Biophys Acta. 2016;1858(6):1216-27.
PUBMED:26874201      doi:10.1016/j.bbamem.2016.02.008
   VCell BioModels referenced in publication:
   user: agolomy,   model name: fX_platelet_binding
   user: agolomy,   model name: fX_thrombus_binding

Modeling Excitable Dynamics of Chemotactic Networks
Bhattacharya, S., Iglesias, P. A.
Methods Mol Biol. 2016;1407:397-415.
PUBMED:27271916      doi:10.1007/978-1-4939-3480-5_27
   VCell BioModels referenced in publication:
   user: sayak66,   model name: BEN
   user: sayak66,   model name: Smoldyn

Neighboring phosphoSer-Pro motifs in the undefined domain of IRAK1 impart bivalent advantage for Pin1 binding
Rogals, M. J., Greenwood, A. I., Kwon, J., Lu, K. P., Nicholson, L. K.
The FEBS journal, 2016; 283(24), 4528-4548
PUBMED:28652372      doi:10.1111/febs.13943
   VCell BioModels referenced in publication:
   user: mjr323,   model name: Pin1_2Domains(diffKds)_monovalentligand
   user: mjr323,   model name: Pin1_2domain(diffKds)_w_Bivalentligand(diffKds)
   user: mjr323,   model name: Pin1_2domain(diffKds)_w_Bivalentligand(diffKds)

Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology
Schaff, J.C., Gao, F., Li, Y., Novak, I.L., Slepchenko, B.M.
PLoS Comput Biol. 2016 Dec 13;12(12):e1005236.
PUBMED:27959915      doi:10.1371/journal.pcbi.1005236
   VCell MathModels referenced in publication:
   user: boris,   model name: Hybrid_cell_polarity_public

On the importance of modelling the internal spatial dynamics of biological cells
Sayyid, F., Kalvala, S.
Biosystems. 2016 Jul;145:53-66.
PUBMED:27262415      doi:10.1016/j.biosystems.2016.05.012

Pancreatic Beta Cell G-Protein Coupled Receptors and Second Messenger Interactions: A Systems Biology Computational Analysis
Fridlyand, L. E., Philipson, L. H.
PLoS ONE. 2016;11(5):e0152869.
PUBMED:27138453      doi:10.1371/journal.pone.0152869
   VCell MathModels referenced in publication:
   user: Fridlyand,   model name: Messengers interaction

Paradoxical signaling regulates structural plasticity in dendritic spines
Rangamani, P., Levy, MG, Khan, S., Oster, G.
Proc Natl Acad Sci USA. 2016;113(36):E5298-307.
PUBMED:27551076      doi:10.1073/pnas.1610391113
   VCell BioModels referenced in publication:
   user: prangamani,   model name: Spine Model Final Rangamani et al PNAS 2016

Phosphoinositide 5- and 3-phosphatase activities of a voltage-sensing phosphatase in living cells show identical voltage dependence
Keum, D., Kruse, M., Kim, D. I., Hille, B., Suh, B. C.
Proc Natl Acad Sci USA. 2016;113(26):E3686-95.
PUBMED:27222577      doi:10.1073/pnas.1606472113
   VCell BioModels referenced in publication:
   user: hillelab,   model name: KeumKruseKimHilleSuh_2016

Regulation of quantal currents determines synaptic strength at neuromuscular synapses in larval Drosophila
Powers, Andrew S., Grizzaffi, Jeffrey, Ribchester, Richard, Lnenicka, Gregory A.
Pflugers Arch. 2016 Nov;468(11-12):2031-2040.
PUBMED:27783155      doi:10.1007/s00424-016-1893-7
   VCell BioModels referenced in publication:
   user: gregl,   model name: minepsp

Simultaneous quantification of actin monomer and filament dynamics with modelling assisted analysis of photoactivation
Kapustina, M., Read, T. A., Vitriol, E. A.
J Cell Sci. 2016 Dec 15;129(24):4633-4643
PUBMED:27831495      doi:10.1242/jcs.194670
   VCell BioModels referenced in publication:
   user: marynka,   model name: GF-actin FDAP
   user: marynka,   model name: Axon_FDAP

Analysis of AKAP7gamma Dimerization
Singh, A., Rigatti, M., Le, A. V., Carlson, C. R., Moraru,, II, Dodge-Kafka, K. L.
J Signal Transduct. 2015;2015:371626.
PUBMED:26417456      doi:10.1155/2015/371626

Bridging scales through multiscale modeling: a case study on protein kinase A
Boras, B. W., Hirakis, S. P., Votapka, L. W., Malmstrom, R. D., Amaro, R. E., McCulloch, A. D.
Front Physiol. 2015;6:250.
PUBMED:26441670      doi:10.3389/fphys.2015.00250

Calmodulin as a major calcium buffer shaping vesicular release and short-term synaptic plasticity: facilitation through buffer dislocation
Timofeeva, Y., Volynski, K. E.
Front Cell Neurosci. 2015;9:239.
PUBMED:26190970      doi:10.3389/fncel.2015.00239

Computational neurobiology is a useful tool in translational neurology: the example of ataxia
Brown, S. A., McCullough, L. D., Loew, L. M.
Front Neurosci. 2015;9:1.
PUBMED:25653585      doi:10.3389/fnins.2015.00001

Dendritic geometry shapes neuronal cAMP signalling to the nucleus
Li, L., Gervasi, N., Girault, J. A.
Nat Commun, 2015/02/18
PUBMED:25692798      doi:10.1038/ncomms7319
   VCell BioModels referenced in publication:
   user: luli,   model name: Li2015_geometryCreatesNonlinearNuclearPKA

From START to FINISH: computational analysis of cell cycle control in budding yeast
Kraikivski, Pavel, Chen, Katherine C., Laomettachit, Teeraphan, Murali, T. M., Tyson, John J.
npj Systems Biology and Applications 1 (2015) 15016
PUBMED:25790189      doi:10.1038/npjsba.2015.16

In silico spatial simulations reveal that MCC formation and excess BubR1 are required for tight inhibition of the anaphase-promoting complex
Ibrahim, B.
Mol Biosyst. 2015;11(11):2867-77.
PUBMED:26256776      doi:10.1039/c5mb00395d

Integration of SBML models for the description of biological system in a lab-on-chip
Rezgui, A., Madec, M., Lallement, C., Haiech, J.
Mixed Design of Integrated Circuits & Systems (MIXDES), 2015 22nd International Conference, Torun, 2015, pp. 165-170.

Non-structural proteins P17 and P33 are involved in the assembly of the internal membrane-containing virus PRD1
Karttunen, J., Mantynen, S., Ihalainen, T. O., Bamford, J. K., Oksanen, H. M.
Virology. 2015;482:225-33.
PUBMED:25880114      doi:10.1016/j.virol.2015.03.049

Phosphorylation state-dependent interaction between AKAP7delta/gamma and phospholamban increases phospholamban phosphorylation
Rigatti, M., Le, A. V., Gerber, C., Moraru,, II, Dodge-Kafka, K. L.
Cellular Signaling, June 3rd 2015
PUBMED:26027516      doi:10.1016/j.cellsig.2015.05.016
   VCell BioModels referenced in publication:
   user: Marc.Rigatti,   model name: AKAP7_PLB_Binding_2PKA

Platelet surface-associated activation and secretion-mediated inhibition of coagulation factor XII
Zakharova, N. V., Artemenko, E. O., Podoplelova, N. A., Sveshnikova, A. N., Demina, I. A., Ataullakhanov, F. I., Panteleev, M. A.
Journal: PLoS ONE 10(2): e0116665. doi:10.1371/journal.pone.0116665 Publication Date: February 17, 2015
PUBMED:25688860      doi:10.1371/journal.pone.0116665
   VCell BioModels referenced in publication:
   user: agolomy,   model name: fXii_activation

Spindle assembly checkpoint is sufficient for complete Cdc20 sequestering in mitotic control
Ibrahim, B.
Comput Struct Biotechnol J. 2015;13:320-8.
PUBMED:25977749      doi:10.1016/j.csbj.2015.03.006

Symmetry and scale orient Min protein patterns in shaped bacterial sculptures
Wu, F., van Schie, B. G., Keymer, J. E., Dekker, C.
Nat Nanotechnol. 2015;10(8):719-26.
PUBMED:26098227      doi:10.1038/nnano.2015.126

Synaptic activity regulates the abundance and binding of complexin
Wragg, R. T., Gouzer, G., Bai, J., Arianna, G., Ryan, T. A., Dittman, J. S.
Biophysical Journal, Volume 108, Issue 6, p1318-1329, 24 March 2015
PUBMED:25809246      doi:10.1016/j.bpj.2014.12.057
   VCell BioModels referenced in publication:
   user: jdittman,   model name: CPX Binding

The Nectin-4/Afadin Protein Complex and Intercellular Membrane Pores Contribute to Rapid Spread of Measles Virus in Primary Human Airway Epithelia
Singh, B. K., Hornick, A. L., Krishnamurthy, S., Locke, A. C., Mendoza, C. A., Mateo, M., Miller-Hunt, C. L., Cattaneo, R., Sinn, P. L.
J Virol. 2015;89(14):7089-96.
PUBMED:25926640      doi:10.1128/JVI.00821-15

Two functionally distinct sources of actin monomers supply the leading edge of lamellipodia
Vitriol, E. A., McMillen, L. M., Kapustina, M., Gomez, S. M., Vavylonis, D., Zheng, J. Q.
Cell Rep. 2015;11(3):433-45.
PUBMED:25865895      doi:10.1016/j.celrep.2015.03.033
   VCell BioModels referenced in publication:
   user: marynka,   model name: FDAP diffusion

A synaptic mechanism for temporal filtering of visual signals
Baden, T., Nikolaev, A., Esposti, F., Dreosti, E., Odermatt, B., Lagnado, L.
PLoS Biol. 2014;12(10):e1001972.
PUBMED:25333637      doi:10.1371/journal.pbio.1001972

Active transport can greatly enhance Cdc20:Mad2 formation
Ibrahim, B., Henze, R.
Int J Mol Sci. 2014;15(10):19074-91.
PUBMED:25338047      doi:10.3390/ijms151019074

Dynamic metabolic control of an ion channel
Hille, B., Dickson, E., Kruse, M., Falkenburger, B.
Prog Mol Biol Transl Sci. 2014;123:219-47.
PUBMED:24560147      doi:10.1016/b978-0-12-397897-4.00008-5

Integrating fluorescent biosensor data using computational models
Greenwald, E. C., Polanowska-Grabowska, R. K., Saucerman, J. J.
Methods Mol Biol. 2014;1071:227-48.
PUBMED:24052393      doi:10.1007/978-1-62703-622-1_18

Interconnected network motifs control podocyte morphology and kidney function
Azeloglu, E. U., Hardy, S. V., Eungdamrong, N. J., Chen, Y., Jayaraman, G., Chuang, P. Y., Fang, W., Xiong, H., Neves, S. R., Jain, M. R., Li, H., Ma&apos, ayan, A., Gordon, R. E., He, J. C., Iyengar, R.
Sci. Signal., 4 February 2014 Vol. 7, Issue 311, p. ra12 [DOI: 10.1126/scisignal.2004621]
PUBMED:24497609      doi:10.1126/scisignal.2004621
   VCell BioModels referenced in publication:
   user: sihar,   model name: Podocyte Nested FFM model (copy sensitivity)
   user: sihar,   model name: Podocyte Nested FFM model

Structural basis of thymosin-beta4/profilin exchange leading to actin filament polymerization
Xue, B., Leyrat, C., Grimes, J. M., Robinson, R. C.
Proc Natl Acad Sci USA. 2014;111(43):E4596-605.
PUBMED:25313062      doi:10.1073/pnas.1412271111

Synaptic excitation is regulated by the postsynaptic dSK channel at the Drosophila larval NMJ
Gertner, D. M., Desai, S., Lnenicka, G. A.
Journal of NeurophysiologyPublished 15 June 2014Vol. 111no. 2533-2543 DOI: 10.1152/jn.00903.2013
PUBMED:24671529      doi:10.1152/jn.00903.2013
   VCell BioModels referenced in publication:
   user: gregl,   model name: epsp_gcs

Using Markov state models to develop a mechanistic understanding of protein kinase A regulatory subunit RIalpha activation in response to cAMP binding
Boras, B. W., Kornev, A., Taylor, S. S., McCulloch, A. D.
J Biol Chem. 2014 Sep 8. pii: jbc.M114.568907
PUBMED:25202018      doi:10.1074/jbc.M114.568907
   VCell BioModels referenced in publication:
   user: bboras,   model name: Boras_PKA-Dimer
   user: bboras,   model name: Boras_PKA-CBD-A
   user: bboras,   model name: Boras_PKA-Unconstrained
   user: bboras,   model name: Boras_PKA_Dimer_mutant_B-inhibited
   user: bboras,   model name: Boras_PKA_CBD-A_mutant_B-inhibited
   user: bboras,   model name: Boras_PKA-CBD-A
   user: bboras,   model name: Boras_PKA_Dual_mutant_B-inhibited
   user: bboras,   model name: Boras_PKA-CBD-B
   user: bboras,   model name: Boras_PKA-Dual
   user: bboras,   model name: Boras_PKA-Dimer_mutant_A-inhibited
   user: bboras,   model name: Boras_PKA_CBD-A_mutant_A-inhibited
   user: bboras,   model name: Boras_PKA_CBD-B_mutant_A-inhibited
   user: bboras,   model name: Boras_PKA_Dual_mutant_A-inhibited

Computational Analysis of Rho GTPase Cycling
Cibele V Falkenberg, Leslie M Loew
PLoS Comput Biol. 2013 9(1): e1002831. doi:10.1371/journal.pcbi.1002831 PLoS Comput Biol 9(1): e1002831. doi:10.1371/journal.pcbi.1002831
PUBMED:23326220      doi:10.1371/journal.pcbi.1002831
   VCell BioModels referenced in publication:
   user: falkenbe,   model name: Falkenberg_GTPases_Rac_betaCell

Decoding information in cell shape
Rangamani, P., Lipshtat, A., Azeloglu, E. U., Calizo, R. C., Hu, M., Ghassemi, S., Hone, J., Scarlata, S., Neves, S. R., Iyengar, R.
Cell, 2013, 154:1356-1369.
PUBMED:24034255      doi:10.1016/j.cell.2013.08.026
   VCell BioModels referenced in publication:
   user: prangamani,   model name: EGF ras Sep 2012
   user: prangamani,   model name: PDGF Src March 2012
   user: prangamani,   model name: Rangamani Cell 2013 B2R signaling

Differential triggering of spontaneous glutamate release by P/Q-, N- and R-type Ca2+ channels
Ermolyuk, Y. S., Alder, F. G., Surges, R., Pavlov, I. Y., Timofeeva, Y., Kullmann, D. M., Volynski, K. E.
Nat Neurosci. 2013;16(12):1754-63.
PUBMED:24185424      doi:10.1038/nn.3563

ERK regulation of phosphodiesterase 4 enhances dopamine-stimulated AMPA receptor membrane insertion
Song, R. S., Massenburg, B., Wenderski, W., Jayaraman, V., Thompson, L., Neves, S. R.
Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):15437-42. doi: 10.1073/pnas.1311783110. Epub 2013 Aug 28.
PUBMED:23986500      doi:10.1073/pnas.1311783110
   VCell BioModels referenced in publication:
   user: rsong,   model name: Song_PNAS_2013

Guardians of the actin monomer
Xue, Bo, Robinson, Robert C.
Eur J Cell Biol. 2013;92(10-11):316-32.
PUBMED:24268205      doi:10.1016/j.ejcb.2013.10.012

Ion channels and regulation of insulin secretion in human beta-cells: a computational systems analysis
Fridlyand, L. E., Jacobson, D. A., Philipson, L. H.
Islets. 2013;5(1):1-15.
PUBMED:23624892      doi:10.4161/isl.24166
   VCell MathModels referenced in publication:
   user: Fridlyand,   model name: Humans_Beta_cell

Modeling and Simulation of Intracellular Drug Transport and Disposition Pathways with Virtual Cell
Baik, J., Rosania, G. R.
2013;1(1): 8., J Pharmaceu Pharmacol, June 2013 Vol.:1, Issue:1
PUBMED:24364041      doi:10.13188/2327-204X.1000004
   VCell BioModels referenced in publication:
   user: jsbaik,   model name: Baik & Rosania 2013 JPP – 01 Suspension model no lysosome
   user: jsbaik,   model name: Baik & Rosania 2013 JPP – 02 Transcellular model no lysosome
   user: jsbaik,   model name: Baik & Rosania 2013 JPP – 03 Transcellular model with lysosome

Mutations in DNA binding and transactivation domains affect the dynamics of parvovirus NS1 protein
Niskanen, E. A., Kalliolinna, O., Ihalainen, T. O., Hakkinen, M., Vihinen-Ranta, M.
J Virol. 2013;87(21):11762-74.
PUBMED:23986577      doi:10.1128/JVI.01678-13

Protein equilibration through somatic ring canals in Drosophila
McLean, P. F., Cooley, L.
Science. 2013 Jun 21;340(6139):1445-1447. Epub 2013 May 23.
PUBMED:23704373      doi:10.1126/science.1234887
   VCell BioModels referenced in publication:
   user: peterfoster,   model name: PAGFP Diffusion COMPARTMENTAL_4Cell_01
   user: peterfoster,   model name: PAGFP Diffusion COMPARTMENTAL_3Cell_02
   user: peterfoster,   model name: PAGFP Diffusion COMPARTMENTAL_3Cell_01
   user: peterfoster,   model name: 2 Cell Spatial CORR 1/4Cell_01

Quantitative properties and receptor reserve of the DAG and PKC branch of G(q)-coupled receptor signaling
Falkenburger, B. H., Dickson, E. J., Hille, B.
J. Gen. Physiol. 2013; 141:537-555
PUBMED:23630338      doi:10.1085/jgp.201210887
   VCell BioModels referenced in publication:
   user: bfalken,   model name: FalkenburgerDicksonHille2013

Quantitative properties and receptor reserve of the IP(3) and calcium branch of G(q)-coupled receptor signaling
Dickson, E. J., Falkenburger, B. H., Hille, B.
J. Gen. Physiol. 2013; 141:521-535.
PUBMED:23630337      doi:10.1085/jgp.201210886
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Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks
Neves, S. R., Tsokas, P., Sarkar, A., Grace, E. A., Rangamani, P., Taubenfeld, S. M., Alberini, C. M., Schaff, J. C., Blitzer, R. D., Moraru,, II, Iyengar, R.
Cell. 2008 May 16;133(4):666-80.
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Dynamics of Cdc42 network embodies a Turing-type mechanism of yeast cell polarity
Goryachev, A. B., Pokhilko, A. V.
FEBS Letters, v. 582, p.1437, (2008)
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Pathway of actin filament branch formation by Arp2/3 complex
Beltzner, C. C., Pollard, T. D.
J Biol Chem. 2008;283(11):7135-44.
PUBMED:18165685      doi:10.1074/jbc.M705894200

Potential landscape and flux framework of nonequilibrium networks: robustness, dissipation, and coherence of biochemical oscillations
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Proc Natl Acad Sci USA. 2008;105(34):12271-6.
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Quantitative analysis of G-actin transport in motile cells
Novak, I. L., Slepchenko, B. M., Mogilner, A.
Biophys J. 2008;95(4):1627-38.

Robustness, dissipations and coherence of the oscillation of circadian clock: potential landscape and flux perspectives
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PMC Biophys. 2008;1(1):7.
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The role of the FH1 domain and profilin in formin-mediated actin-filament elongation and nucleation
Paul, A. S., Pollard, T. D.
Current Biology, 2008 Jan 8;18(1):9-19.
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The tight junction protein complex undergoes rapid and continuous molecular remodeling at steady state
Shen, L., Weber, C. R., Turner, J. R.
J Cell Biol. 2008 May 19;181(4):683-95. Epub 2008 May 12.
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Compartment-specific feedback loop and regulated trafficking can result in sustained activation of Ras at the Golgi
Eungdamrong, N. J., Iyengar, R.
Biophys. J. 2007; 92(3): p. 808-815
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Coordination of chromosome alignment and mitotic progression by the chromosome-based Ran signal
Li, H. Y., Ng, W. P., Wong, C. H., Iglesias, P. A., Zheng, Y.
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
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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., Harbeck, M. C., Roe, M. W., Philipson, L. H.
Am J Physiol, Cell Physiol. 2007;293(6):C1924-33.
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Switching of membrane organelles between cytoskeletal transport systems is determined by regulation of the microtubule-based transport
Slepchenko, Boris M., Semenova, Irina, Zaliapin, Ilya, Rodionov, Vladimir
J Cell Biol. 2007;179(4):635-41.
PUBMED:17998399      doi:10.1083/jcb.200705146

Analysis of a RanGTP-regulated gradient in mitotic somatic cells
Kalab, P., Pralle, A., Isacoff, E. Y., Heald, R., Weis, K.
Nature 2006. 440:(7084)697-701.
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Ca2+-dependent mechanisms of presynaptic control at central synapses
Rusakov, D. A.
Neuroscientist. 2006;12(4):317-26.
PUBMED:16840708      doi:10.1177/1073858405284672

Does diacylglycerol regulate KCNQ channels?
Suh, Byung-Chang, Hille, Bertil
Pflügers Archiv European Journal of Physiology. 453:293-301,2006.
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Hallucinogen actions on 5-HT receptors reveal distinct mechanisms of activation and signaling by G protein-coupled receptors
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AAPS J. 2005;7(4):E871-84.

In vivo dynamics of Rac-membrane interactions
Moissoglu, K., Slepchenko, B. M., Meller, N., Horwitz, A. F., Schwartz, M. A.
Mol Biol Cell. 2006;17(6):2770-9.

Main determinants of presynaptic Ca2+ dynamics at individual mossy fiber-CA3 pyramidal cell synapses
Scott, R., Rusakov, D. A.
J Neurosci. 2006;26(26):7071-81.
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Modeling the impact of store-operated Ca2+ entry on intracellular Ca2+ oscillations
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Rapid redistribution of synaptic PSD-95 in the neocortex in vivo
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PLoS Biol. 2006;4(11):e370.

Systems analysis of PKA-mediated phosphorylation gradients in live cardiac myocytes
Saucerman, J. J., Zhang, J., Martin, J. C., Peng, L. X., Stenbit, A. E., Tsien, R. Y., McCulloch, A. D.
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Adenine nucleotide regulation in pancreatic ?-cells: modeling of ATP/ADP-Ca2+ interactions
Fridlyand, Leonid E., Ma, Li, Philipson, Louis H.
Am J Physiol Endocrinol Metab. 2005;289(5):E839-48.
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Modeling and analysis of calcium signaling events leading to long-term depression in cerebellar Purkinje cells
Hernjak, N., Slepchenko, B. M., Fernald, K., Fink, C. C., Fortin, D., Moraru,, II, Watras, J., Loew, L. M.
Biophysical Journal Volume 89, Dec. 2005, pp. 3790-3806
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Phospholipase C in living cells: activation, inhibition, Ca2+ requirement, and regulation of M current
Horowitz, L. F., Hirdes, W., Suh, B. C., Hilgemann, D. W., Mackie, K., Hille, B.
J. Gen. Physiol. 2005. 126(3):243-262.
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Quantitative elucidation of a distinct spatial gradient-sensing mechanism in fibroblasts
Schneider, I. C., Haugh, J. M.
J.Cell B 171:883-892 (2005)
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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;328(4):1126-32.

STAT module can function as a biphasic amplitude filter
Mayya, V., Loew, L. M.
IEE Proceedings Systems Biology, March 2005, Volume 2, Issue 1, p. 43-52
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A multi-enzyme model for Pyrosequencing
Agah, A., Aghajan, M., Mashayekhi, F., Amini, S., Davis, R. W., Plummer, J. D., Ronaghi, M., Griffin, P. B.
Nucleic Acids Research 2004 32(21):e166
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A signal transduction pathway model prototype I: From agonist to cellular endpoint
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A signal transduction pathway model prototype II: Application to Ca2+-calmodulin signaling and myosin light chain phosphorylation
Lukas, T. J.
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Bio-switches: what makes them robust?
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High mobility of vesicles supports continuous exocytosis at a ribbon synapse
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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
Suh, BC, Horowitz, L. F., Hirdes, W., Mackie, K., Hille, B.
Journal of General Physiology, Volume 123, Number 6, June 2004 663-683
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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
Ma, L., Janetopoulos, C., Yang, L., Devreotes, P. N., Iglesias, P. A.
Biophys. J. 2004; 87(6): p. 3764-3774

Centrosome positioning in interphase cells
Burakov, A., Nadezhdina, E., Slepchenko, B., Rodionov, V.
J Cell Biol. 2003;162(6):963-9.

Cyclin aggregation and robustness of bio-switching
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Kinetic analysis of receptor-activated phosphoinositide turnover
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Journal of Cell Biology, vol. 161, no. 4, May 26, 2003
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Modeling of Ca2+ flux in pancreatic beta-cells: role of the plasma membrane and intracellular stores
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Computational Cell Biology
Fall, C. P., Marland, E.S., Wagner, J. M., Tyson, J. J.
The models from the text were implemented into the Virtual Cell by Johann Frederick Cutiongco.
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   user: CompCell,   model name: L-Type Calcium Channels
   user: CompCell,   model name: Morris-Lecar Coincidence Detection
   user: CompCell,   model name: Morris-Lecar Type II
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   user: CompCell,   model name: Morris-Lecar Mutual Excitation

Distinct Intracellular Calcium Transients in Neurites and Somata Integrate Neuronal Signals
Johenning, Friedrich W., Zochowski, Michal, Conway, Stuart J., Holmes, Andrew B., Koulen, Peter, Ehrlich, Barbara E.
J Neurosci. 2002;22(13):5344-53.

Systems analysis of Ran transport
Smith, A. E., Slepchenko, B. M., Schaff, J. C., Loew, L. M., Macara, I. G.
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, Melissa M., Hall, David H., Victor, Martin, Stelzer, Ernst H. K., Rapoport, Tom A.
Mol Biol Cell. 2002;13(5):1778-91.
PUBMED:12006669      doi:10.1091/mbc.01-10-0514

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 May 28;153(5):1035-48
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An image-based model of calcium waves in differentiated neuroblastoma cells
Fink, C. C., Slepchenko, B., Moraru,, II, Watras, J., Schaff, J. C., Loew, L. M.
Biophys J. 2000;79(1):163-83.

Determination of time-dependent inositol-1,4,5-trisphosphate concentrations during calcium release in a smooth muscle cell
Fink, C. C., Slepchenko, B., Loew, L. M.
Biophys J. 1999;77(1):617-28.