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

Reaction-diffusion modeling provides insights into biophysical carbon concentrating mechanisms in land plants.
Kaste, J. A., Walker, B. J., & Shachar-Hill, Y.
Plant Physiol. 2024 Jun 10:kiae324.
doi: 10.1093/plphys/kiae324

Dynamin1 long-and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters.
Jiang, A., Kudo, K., Gormal, R.S., Ellis, S., Guo, S., Wallis, T.P., Longfield, S.F., Robinson, P.J., Johnson, M.E., Joensuu, M. and Meunier, F.A..
Nature Communications. 2024 May 14;15(1):4060.
doi: 10.1038/s41467-024-47677-8

K+ and pH homeostasis in plant cells is controlled by a synchronized K+ /H+ antiport at the plasma and vacuolar membrane.
Li, K., Grauschopf, C., Hedrich, R., Dreyer, I. & Konrad, K.R.
New Phytologist. 2024 Feb;241(4):1525-1542.
VCell BioModels referenced in the publication
user: idreyer
biomodel name: Li_et_al_2024_NewPhytol_Guard_Cell_Homeostats

Computational evidence for multi-layer crosstalk between the cadherin-11 and PDGFR pathways.
Karagöz, Z., Passanha, F. R., Robeerst, L., van Griensven, M., LaPointe, V. L. S., Carlier, A.
Sci Rep 13, 15804 2023.
doi: 10.1038/s41598-023-42624-x
VCell BioModels referenced in the publication
user: ra_mb_jb_jmh
biomodel name: cdh11-pdgfr-erk-feedback-v2

G-actin diffusion is insufficient to achieve F-actin assembly in fast-treadmilling protrusions.
Appalabhotla, R., Butler, M. T., Bear, J. E., & Haugh, J. M.
Biophys J. 2023 Aug 28;S0006-3495(23)00553-2.
doi: 10.1016/j.bpj.2023.08.022
VCell BioModels referenced in the publication
user: ra_mb_jb_jmh
biomodel name: Figure 4
biomodel name: Figure 6 – Cytochalasin D Simulations
biomodel name: Figure S1 – G-actin diffusion 3D
biomodel name: Figure S4
biomodel name: Figure S5
mathmodel name: Figure 3 – Simulation Image and Line Scan; Figure 5 – Leading Edge Recovery and Line Scan (mathmodel-259882543)
mathmodel name: Figure 4 – Variable Diffusion (mathmodel-259882423)
mathmodel name: Figure S3B – DG01 (mathmodel-260439082)
mathmodel name: Figure S3B – DG03 (mathmodel-260439125)
mathmodel name: Figure S3B – DG05 (mathmodel-260438575)
mathmodel name: Figure S3B = DG02 (mathmodel-260439104)
mathmodel name: Figure S3D (mathmodel-260438471)
mathmodel name: Figure S6 – Exp. 1 (mathmodel-260474144)
mathmodel name: Figure S6 – Exp. 2 (mathmodel-260474263)
mathmodel name: Figure S6 – Exp. 3 (mathmodel-260474383)
mathmodel name: Figure S6 – Exp. 4 (mathmodel-260474568)
mathmodel name: Figure S6 – Exp. 5 (mathmodel-260474758)
mathmodel name: Figure S6 – Exp. 6 (mathmodel-260474808)
mathmodel name: Figure S7B (mathmodel-260438368)

Nuclear lamina strain states revealed by intermolecular force biosensor.
Danielsson, B.E., George Abraham, B., Mäntylä, E., Cabe, J.I., Mayer, C.R., Rekonen, A., Ek, F., Conway, D.E. and Ihalainen, T.O.
Nat Commun. 2023 Jun 30;14(1):3867
doi: 10.1038/s41467-023-39563-6

Beyond analytic solution: Analysis of FRAP experiments by spatial simulation of the forward problem.
Cowan, A.E. & Loew, L.M.
Biophys J. 2023 Jun 23;S0006-3495(23)00401-0
doi: 10.1016/j.bpj.2023.06.013
VCell BioModels referenced in publication
user: les
biomodel name: FRAP_Membrane_Rel
biomodel name: FRAP_Cyt
biomodel name: FRAP_Cyt_Membrane_Binding
biomodel name: FRAP Condensate Droplet

Dynamic model assuming mutually inhibitory biomarkers of frailty suggests bistability with contrasting mobility phenotypes.
Schaumburger N, Pally J, Moraru II, Kositsawat J, Kuchel GA, Blinov ML.
Frontiers in Network Physiology, 2023 May 4; 3, 1079070
doi: 10.3389/fnetp.2023.1079070
VCell BioModels referenced in publication
user: aging_project
biomodel name: Aging_Phenotypes

Expression of the 2Duf protein in wild-type Bacillus subtilis spores stabilizes inner membrane proteins and increases spore resistance to wet heat and hydrogen peroxide.
Korza G, DePratti S, Fairchild D, Wicander J, Kanaan J, Shames H, Nichols FC, Cowan A, Brul S, Setlow P.
Journal of Applied Microbiology. 2023 Mar 1;134(3):lxad040.
VCell BioModels referenced in publication
user: dfairchild
biomodel name: Bacillus Spore Membrane FRAP Analysis

Mechanisms underlying divergent relationships between Ca2+ and YAP/TAZ signalling.
Khalilimeybodi, A., Fraley, S.I. & Rangamani, P.
J Physiol. 2023 Feb;601(3): 483-515.
VCell BioModels referenced in the publication
user: prangamani
biomodel name: Khalilimeybodi et al. 2022 J Physiol

Optimization of Media Change Intervals through Hydrogels Using Mathematical Models.
Ruiter FA, King J, Swapnasrita S, Giselbrecht S.
Biomacromolecules. 2023 Feb 13;24(2):604-612.

Methodology for development of single cell dendritic spine (SCDS) synaptic tagging and capture model using Virtual Cell (VCell)
Khan R, Kulasiri D, Samarasinghe S.
MethodsX. 2023 Feb 11;10:102070.

A multifarious exploration of synaptic tagging and capture hypothesis in synaptic plasticity: Development of an integrated mathematical model and computational experiments
Khan R, Kulasiri D, Samarasinghe S.
Journal of Theoretical Biology. 2022 Oct 21:111326.

Asynchronous glutamate release is enhanced in low release efficacy synapses and dispersed across the active zone.
Mendonça PR, Tagliatti E, Langley H, Kotzadimitriou D, Zamora-Chimal CG, Timofeeva Y, Volynski KE.
Nature communications. 2022 Jun 17;13(1):1-7.

Purification and characterization of sequential cobalamin-dependent radical SAM methylases ThnK and TokK in carbapenem β-lactam antibiotic biosynthesis
Sinner EK, Townsend CA.
Methods in Enzymology. 2022; 669:29–44

Computational investigation of the dynamic control of cAMP signaling by PDE4 isoform types.
Paes, D., Hermans, S., van den Hove, D., Vanmierlo, T., Prickaerts, J., & Carlier, A.
Biophys J. 2022 Jul 19;121(14):2693-2711.
doi: 10.1016/j.bpj.2022.06.019
VCell BioModels referenced in the publication
user: aureliecarlier
biomodel name: Carlier_cAMP_isoforms_v2
biomodel name: Carlier_cAMP_isoforms_cyclic_v2

Transporter networks can serve plant cells as nutrient sensors and mimic transceptor-like behavior.
Dreyer I, Li K, Riedelsberger J, Hedrich R, Konrad KR, Michard E.
iScience. 2022 Apr 15;25(4):104078.
VCell BioModels referenced in publication
user: idreyer
Biomodel name: Dreyer_et_al_2022_iScience

The Atypical Cobalamin-Dependent S-Adenosyl-l-Methionine Nonradical Methylase TsrM and Its Radical Counterparts.
Ulrich EC, Drennan CL
J Am Chem Soc. 2022 Apr 6;144(13):5673-5684

A kinetic model of phospholipase C-γ1 linking structure-based insights to dynamics of enzyme autoinhibition and activation. 
Nosbisch JL, Bear JE, Haugh JM.
J Biol Chem. 2022 May;298(5):101886.
doi: 10.1016/j.jbc.2022.101886
VCell BioModels referenced in publication
user: jnosbis
biomodel name: Nosbisch PLCgamma1 2021
biomodel name: Nosbisch PLCgamma1 + polarization 2021

Structure of a B12-dependent radical SAM enzyme in carbapenem biosynthesis.
Knox HL, Sinner EK, Townsend CA, Boal AK, Booker SJ.
Nature. 2022 Feb 10;602(7896):343–348.

Teaching Mathematical Modeling of Cellular Systems with the VCell MathModel.
King J, Eroumé KS, Truckenmüller R, Giselbrecht S, Cowan A, Loew LM, Carlier A.
The Biophysicist [Internet]. 2021 Dec 3.
VCell BioModels referenced in publication
user: tutorial
biomodel name: Tutorial_MultiApp

Nuclear-capture of endosomes depletes nuclear G-actin to promote SRF/MRTF activation and cancer cell invasion.
Marco S, Neilson M, Moore M, Perez-Garcia A, Hall H, Mitchell L, Lilla S, Blanco GR, Hedley A, Zanivan S, Norman JC.
Nat Commun. 2021 Nov 24;12(1):6829.
PUBMED: 34819513

Computational Modeling of RNase, Antisense ORF0 RNA, and Intracellular Compartmentation and their Impact on the Life Cycle of the LINE Retrotransposon.
David Martin M, Brown DN, Ramos KS.
Computational and Structural Biotechnology Journal. 2021 19:5667-5677.
VCell BioModels referenced in publication
user: seriously
Biomodel names:
biomodel name: Line1Activity_Full_July10_0202
biomodel name: Dicer_Check_MassAction
biomodel name: Dicer_Check_Michaelis_new
biomodel name: Exosome_Processing_Bodies_Continuous
biomodel name: Exosome_ReactionRules
biomodel name: RISC_mRNA_Deg_MassAction
biomodel name: RISC_mRNA_Deg_Michaelis_Menten
biomodel name: RNA Interference Mass Action

The Influence of OAT1 Density and Functionality on Indoxyl Sulfate Transport in the Human Proximal Tubule: An Integrated Computational and In Vitro Study.
King J, Mihaila SM, Ahmed S, Truckenmüller R, Giselbrecht S, Masereeuw R, Carlier A.
Toxins. 2021 Sep 22;13(10):674.
PUBMED: 34678967
VCell BioModels referenced in publication
user: JasiaKing
biomodel name: OD_IS_only
biomodel name: OD_Full_3compartment_IS_

Exploring the influence of cytosolic and membrane FAK activation on YAP/TAZ nuclear translocation.
Eroumé KS; Cavill R; Staňková K; de Boer J; Carlier A
Biophys J. 2021 Sep 10;S0006-3495(21)00743–8.
VCell MathModels referenced in publication
user: kerbai,
Mathmodel names:

Mechanism of actin filament nucleation.
Rosenbloom, AD; Kovar, EW; Kovar, DR; Loew, LM; Pollard, TD;
Biophys J. 2021 Sep 10;S0006-3495(21)00740-2
VCell BioModels referenced in publication
user: AaronRosenbloom, biomodel name: NucleationMechanism

A three-dimensional finite element model of cAMP signals.
Warren R, Rich TC, Leavesley SJ, Phan A-V
Forces in Mechanics. 2021 Oct;4:100041.

Occurrence of Calcium Oscillations in Human Spermatozoa Is Based on Spatial Signaling Enzymes Distribution.
Korobkin J; Balabin FA; Yakovenko SA; Simonenko EY; Sveshnikova AN;
Int J Mol Sci. 22(15):8018
VCell BioModels referenced in publication
user: Juliajessica, biomodel name: SpermCalcium

A spatial model of YAP/TAZ signaling reveals how stiffness, dimensionality, and shape contribute to emergent outcomes.
Scott, K.E.; Fraley, S.I.;Rangamani, P.
Proc Natl Acad Sci U S A 2021, 118 (20): e2021571118.
VCell BioModels referenced in publication
user: prangamani, biomodel name: Scott_Fraley_Rangamani_YAP_TAZ_model_2021(Rho and FAK confined simulations (true 2D)
user: prangamani, biomodel name: Scott_Fraley_Rangamani_YAP_TAZ_model_2021(2D and 3D simulations)

Mad Dephosphorylation at the Nuclear Pore Is Essential for Asymmetric Stem Cell Division.
Sardi, J.; Bener, M. B.; Simao, T.; Descoteaux, A. E.; Slepchenko, B. M.; Inaba, M.
Proc Natl Acad Sci U S A 2021, 118 (13): e2006786118.
VCell MathModels referenced in publication
user: boris, model name: Inaba_Model_public_final

Modeling protein-protein interactions in axon initial segment to understand their potential impact on action potential initiation.
Bhardwaj, P.; Kulasiri, D.; Samarasinghe, S.
Neural Regen Res 2021, 16 (4), 700–706.

Effect of crista morphology on mitochondrial ATP output: A computational study.
Afzal N; Lederer WJ; Jafri MS; Mannella CA;
Curr Res Physiol. 4:163–176
VCell BioModels referenced in publication
user: nasrin, biomodel name: Energy-production-pathway-reduced-model-01132021

On the influence of cell shape on dynamic reaction-diffusion polarization patterns.
Eroumé, K.; Vasilevich, A.; Vermeulen, S.; de Boer, J.; Carlier, A.
PLoS One 2021, 16 (3), e0248293.
VCell BioModels referenced in publication:
user: KerbaicBITE, model name: Kerbai_PLoSone_2021_teardrop_polarization_minimal
user: KerbaicBITE, model name: Kerbai_PLoSone_2021_teardrop_polarization_extended

Quantifying the Roles of Space and Stochasticity in Computer Simulations for Cell Biology and Cellular Biochemistry.
Johnson, M. E.; Chen, A.; Faeder, J. R.; Henning, P.; Moraru, I. I.; Meier-Schellersheim, M.; Murphy, R. F.; Prüstel, T.; Theriot, J. A.; Uhrmacher, A. M.
Mol Biol Cell 2021, 32 (2), 186–210.

Phosphatidylinositol 4,5-bisphosphate is regenerated by speeding of the PI 4-kinase pathway during long PLC activation.
Myeong, J.; de la Cruz, L.; Jung, R.; Yeon, J.-H.; Suh, B.-C.; Koh, D.-S.; Hille, B.
J Gen Physiol. 2020. 152 (12): e202012627.
VCell BioModels referenced in publication:
user: Myeong,   model name: PI cycle Figure 4 & S4
user: Myeong, model name: PI cycle Figure 6, 7 & S9

Spatially Compartmentalized Phase Regulation of a Ca2+-CAMP-PKA Oscillatory Circuit.
Tenner, B.; Getz, M.; Ross, B.; Ohadi, D.; Bohrer, C. H.; Greenwald, E.; Mehta, S.; Xiao, J.; Rangamani, P.; Zhang, J.
Elife 2020, 9.
VCell BioModels referenced in publication:
user: mgetz,   model name: Minimum Stochastic Model BetaCell

An inactive receptor-G protein complex maintains the dynamic range of agonist-induced signaling.
Jang, W.; Adams, C.E.; Liu, H.; Zhang, C. Levy; F.O.; Andressen, K.W.; Lambert, N.A.
Proc Natl Acad Sci U S A. 2020. 1172 (48): 30755-30762.
VCell BioModel referenced in publication:
user: wojang,   model name: 5HT7_Jang_2020

Breast cancer cells and macrophages in a paracrine-juxtacrine loop.
Onal, S.; Turker-Burhan, M.; Bati-Ayaz, G.; Yanik, H.; D. Pesen-Okvur, D.
Biomaterials. 2021. 267:120412.

Cell shape regulates subcellular organelle location to control early Ca2+ signal dynamics in vascular smooth muscle cells.
Calizo, R.C.; Bell, M.K.; Ron, A.; Hu, M.; Bhattacharya, S.; Wong, N.J.; Janssen, W.G.M.; Perumal, G.; Pederson, P.; Scarlata, S.; Hone, J.; Azeloglu, E.U.; Rangamani, P.; Iyengar, R.
Sci Rep. 2020 10:17866.

Modeling protein-protein interactions in axon initial segment to understand their potential impact on action potential initiation.
Bhardwaj, P.; Kulasiri, D.; Samarasinghe, S.
Neural Regen Res. 2021. 16:700–706.

Activation of RhoA Allows for Persistent RhoA Signaling.
EZhang, J. Z.; Nguyen, A. H.; Miyamoto, S.; Heller Brown, J.; McCulloch, A. D.; Zhang, J.
PLoS Biol 2020, 18 (9), e3000866.
VCell BioModels referenced in publication:
user: jzz002, model name: KHistamtine-RhoA- Model_Final3

Whole-Cell Photobleaching Reveals Time-Dependent Compartmentalization of Soluble Proteins by the Axon Initial Segment.
Nicholson, L., N. Gervasi, T. Falières, A. Leroy, D. Miremont, D. Zala, and C. Hanus.
Front Cell Neurosci. 2020 14:180.

Mechanistic Models of PLC/PKC Signaling Implicate Phosphatidic Acid as a Key Amplifier of Chemotactic Gradient Sensing.
Nosbisch, J.L., A. Rahman, M. Krithika, T.C. Elston, J.E. Bear, and J. M. Haugh
PLoS Comput. Biol. 2020. 16(4):e1007708
VCell BioModels referenced in publication:
user: jnosbis,   model name: Nosbisch chemotaxis 2020

Two MYB Proteins in a Self-Organizing Activator-Inhibitor System Produce Spotted Pigmentation Patterns.
Ding, B., E.L. Patterson, S.V. Holalu, J. Li, G.A. Johnson, L.E. Stanley, A.B. Greenlee, F. Peng, H.D. Bradshaw, M.L. Blinov, B.K. Blackman, and Y.-W. Yuan
Current Biology. 30:802-814.e8
VCell BioModels referenced in publication:
user: colreeze,   model name: Monkeyflower_pigmentation_v2

High- and Low-Affinity Transport in Plants From a Thermodynamic Point of View.
Dreyer, I., and E. Michard
Front. Plant Sci. 10: 17497.

Notch Pathway: A two-dimensional finite element model of cyclic adenosine monophosphate (cAMP) intracellular signaling
Stone, N., S. Shettlesworth, T.C. Rich, S.J. Leavesley, and A.-V. Phan
SN Appl. Sci. 2019 1:1713

Methylations in complex carbapenem biosynthesis are catalyzed by a single cobalamin-dependent radical S-adenosylmethionine enzyme.
Sinner EK, Lichstrahl MS, Li R, Marous DR, Townsend CA
Chem Commun (Camb). 2019 Dec 10;55(99):14934-14937.

Notch Pathway: A Bistable Inducer of Biological Noise?
Vujovic, F.; Hunter, N.; Farahani, R. M.
Cell Communication and Signaling 2019, 17 (1), 133.

A predictive computational model reveals that giv/girdin serves as a tunable valve for egfr-stimulated cyclic amp signals.
Getz, M., L. Swanson, D. Sahoo, P. Ghosh, and P. Rangamani
Mol Biol Cell. 2019 30: 1621-1633.
VCell BioModels referenced in publication:
user: mgetz,   model name: A predictive computational model reveals that GIV/Girdin serves as a tunable valve for EGFR-stimulated Cyclic AMP Signals

Nutrient exchange in arbuscular mycorrhizal symbiosis from a thermodynamic point of view.
Dreyer, I., O. Spitz, K. Kanonenberg, K. Montag, M.R. Handrich, S. Ahmad, S. Schott-Verdugo, C. Navarro-Retamal, M.E. Rubio-Melendez, J.L. Gomez-Porras, J. Riedelsberger, M.A. Molina-Montenegro, A. Succurro, A. Zuccaro, S.B. Gould, P. Bauer, L. Schmitt, and H. Gohlke
New Phytol. 2019 222: 1043-1053.
VCell BioModels referenced in publication:
user: idreyer,   model name: AMF Symbiosis with SWEET

Design and evaluation of engineered protein biosensors for live-cell imaging of EGFR phosphorylation.
Tiruthani, K., A. Mischler, S. Ahmed, J. Mahinthakumar, J.M. Haugh, and B.M. Rao
Science Signaling 2019, 12 (584), eaap7584
VCell BioModels referenced in publication:
user: jmhaugh,   model name: SH2 biosensor

Reinterpretation of the substrate specificity of the voltage-sensing phosphatase during dimerization
Kruse, M., S.C. Kohout, and B. Hille
J Gen Physiol. 2019 151(2): 258-263.
VCell BioModels referenced in publication:
user: mkruse,   model name: Kruse_Kohout_Hille_CiVSP

Characterization of the microstructure of hydrazone crosslinked polysaccharide-based hydrogels through rheological and diffusion studies
Karvinen, J., T.O. Ihalainen, M.T. Calejo, I. Jönkkäri, and M. Kellomäki
Materials Science and Engineering: C.2019; 94:1056-1066.

Localization dynamics of endogenous fluorescently labeled raf1 in egf-stimulated cells
Surve, S. V., Myers, P. J., Clayton, S. A., Watkins, S. C., Lazzara, M. J., and Sorkin, A.J Gen Physiol. 2019; 30(4): 506-523.
PUBMED:30586319 doi:10.1091/mbc.E18-08-0512
VCell BioModels referenced in publication:
user: pmyers1995,   model name: Surve_et_al_RAF1

Serendipita indica e5′nt modulates extracellular nucleotide levels in the plant apoplast and affects fungal colonization.
Nizam, S., X. Qiang, S. Wawra, R. Nostadt, F. Getzke, F. Schwanke, I. Dreyer, G. Langen, and A. Zuccaro
EMBO reports. 2019 20: e47430.
VCell BioModels referenced in publication:
user: idreyer,   model name: Schott_et_al_2016 AMF Symbiosis with SWEET

Mechanopharmaceutical Device (1): Measuring the Cargo Capacity of Macrophages in a Living Organism.
Rzeczycki, P., T. Woldemichael, A. Willmer, M.D. Murashov, J. Baik, R. Keswani, G.S. Yoon, K.A. Stringer, N. Rodriguez-Hornedo, and G.R. Rosania.
Pharmaceutical Research 2018, 36 (1), 12.
doi: 10.1007/s11095-018-2539-6
VCell BioModels referenced in publication:
user: awillmer,   model name: Macrophage Cargo Capacity

Action potential counting at giant mossy fiber terminals gates information transfer in the hippocampus.
Chamberland, S., Y. Timofeeva, A. Evstratova, K. Volynski, and K. Toth
Proc Natl Acad Sci U S A. 2018 Jul 10 115: 7434-7439.
PUBMED:29946034      doi:10.1073/pnas.1720659115

Fission yeast myo2: Molecular organization and diffusion in the cytoplasm
Friend, J.E., W.A. Sayyad, R. Arasada, C.D. McCormick, J.E. Heuser, and T.D. Pollard
Cytoskeleton (Hoboken). 2018 Apr 75: 164-173.
PUBMED:29205883      doi:10.1002/cm.21425
VCell BioModels referenced in publication:
user: Wasim,   model name: Yeast 3D_FRAP

Src Characterization of cell boundary and confocal effects improves quantitative frap analysis
Kingsley, J.L., J.P. Bibeau, S.I. Mousavi, C. Unsal, Z. Chen, X. Huang, L. Vidali, and E. Tuzel
Biophys J. 2018 Mar 13 114: 1153-1164.
PUBMED:29539401      doi:10.1016/j.bpj.2018.01.013

Src homology 2 domains enhance tyrosine phosphorylation in vivo by protecting binding sites in their target proteins from dephosphorylation
Jadwin, J.A., T.G. Curran, A.T. Lafontaine, F.M. White, and B.J. Mayer
J Biol Chem. 2018 Jan 12 293: 623-637.
PUBMED:29162725      doi:10.1074/jbc.M117.794412
VCell BioModels referenced in publication:
user: jjadwin,   model name: spatial protection test- two way competition orginal – paper model shared
user: jjadwin,   model name:
spatial protection test- no flux two way competition orginal – paper model-shared

A Noncanonical Binding Site in the EVH1 Domain of Vasodilator-Stimulated Phosphoprotein Regulates Its Interactions with the Proline Rich Region of Zyxin
Acevedo, LA, Greenwood, AI, Nicholson, LK
Biochemistry 2017, 56 (35), 4626–4636.
PMID 28783324

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.

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: Schott_et_al_2016 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,   mathmodel 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
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
   VCell BioModels referenced in publication:
   user: bfalken,   model name: FalkenburgerDicksonHille2013

Recycling of kinesin-1 motors by diffusion after transport
Blasius, T. L., Reed, N., Slepchenko, B. M., Verhey, K. J.
PLoS ONE. 2013;8(9):e76081.
PUBMED:24098765      doi:10.1371/journal.pone.0076081

Tension modulates actin filament polymerization mediated by formin and profilin
Courtemanche, N., Lee, J. Y., Pollard, T. D., Greene, E. C.
Proc Natl Acad Sci USA. 2013;110(24):9752-7.
PUBMED:23716666      doi:10.1073/pnas.1308257110

There is more than one way to model an elephant. Experiment-driven modeling of the actin cytoskeleton
Ditlev, J. A., Mayer, B. J., Loew, L. M.
Biophys J. 2013;104(3):520-32.
PUBMED:23442903      doi:10.1016/j.bpj.2012.12.044

Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport
Rosania, G. R., Shedden, K., Zheng, N., Zhang, X.
J Cheminform. 2013;5(1):44.
PUBMED:24093553      doi:10.1186/1758-2946-5-44

A computational systems analysis of factors regulating alpha cell glucagon secretion
Fridlyand, L. E., Philipson, L. H.
Islets. 2012;4(4):262-83.
PUBMED:23093806      doi:10.4161/isl.22193
VCell MathModels referenced in publication:
user: Fridlyand,   model name: Alpha and beta cell glucose sensing
user: Fridlyand,   model name: Glucagon secretion

Assessment of cellular mechanisms contributing to cAMP compartmentalization in pulmonary microvascular endothelial cells
Feinstein, W. P., Zhu, B., Leavesley, S. J., Sayner, S. L., Rich, T. C.
Am J Physiol, Cell Physiol. 2012;302(6):C839-52.
PUBMED:22116306      doi:10.1152/ajpcell.00361.2011

CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation
Michalski, P. J., Loew, L. M.
Phys Biol. 2012 Jun 8;9(3):036010.
PUBMED:22683827      doi:10.1088/1478-3975/9/3/036010
   VCell BioModels referenced in publication:
   user: pjmichal,   model name: BioNetGen CaMKII – Trimer – 3 states – with phosphatase
   user: pjmichal,   model name: BioNetGen CaMKII – Trimer – 6 states – with phosphatase
   user: pjmichal,   model name: CaMKII – Infinite Lattice – 6 states
   user: pjmichal,   model name: BioNetGen CaMKII – Dimer – 3 states – with phosphatase
   user: pjmichal,   model name: BioNetGen CaMKII – Tetramer – 3 states – with phosphatase
   user: pjmichal,   model name: BioNetGen CaMKII – Pentamer – 3 states – with phosphatase
   user: pjmichal,   model name: BioNetGen CaMKII – Hexamer – 3 states – with phosphatase

Computational analysis of calcium signaling and membrane electrophysiology in cerebellar Purkinje neurons associated with ataxia
Brown, S. A., Loew, L. M.
BMC Syst Biol. 2012;6:70.
PUBMED:22703638      doi:10.1186/1752-0509-6-70

VCell BioModels referenced in publication:
user: Brown,   model name: Brown et al 2011 Analysis of SCA15-SCA16 with IC4 Peptide Application
user: Brown,   model name: Brown et al 2011 SCA1 Compensation Analysis
user: Brown,   model name: Brown et al 2011 Analysis of SCA1-SCA2-SCA3 with IC-G2736X Peptide
user: Brown,   model name: Brown et al 2011 Purkinje Biochem-Electrophysiol SCA
user: Brown,   model name: Brown et al 2011 Purkinje 3D Spine – Spinocerebellar Ataxia study
user: Brown,   model name: Brown et al 2010 Purkinje MultiCompartmental Combined Biochem and Electrophysiol

Determinants of Formin Homology 1 (FH1) domain function in actin filament elongation by formins.
Courtemanche N, Pollard TD.
J Biol Chem. 2012 Mar 2;287(10):7812-20. doi: 10.1074/jbc.M111.322958. Epub 2012 Jan 14.
VCell BioModels referenced in publication:
user: abiggiep,   model name: Formin FH1FH2-Profilin-Actin Elongation (public)

Live-cell fluorescence microscopy with molecular biosensors: what are we really measuring?
Haugh, J. M.
Biophys J, 102 (9): 2003-2011 (2012).
PUBMED:22824263      doi:10.1016/j.bpj.2012.03.055
   VCell BioModels referenced in publication:
   user: jmhaugh,   model name: Biosensor simple

Spatial modeling of cell signaling networks
Cowan, A. E., Moraru,, II, Schaff, J. C., Slepchenko, B. M., Loew, L. M.
Methods Cell Biol. 2012;110:195-221
PUBMED:22482950      doi:10.1016/B978-0-12-388403-9.00008-4
VCell BioModels referenced in publication:
user: les,   model name: Membrane Flux for meth cell biology

Spatiotemporal regulation of PKC via interactions with AKAP7 isoforms
Redden, J. M., Le, A. V., Singh, A., Federkiewicz, K., Smith, S., Dodge-Kafka, K. L.
Biochem J. 2012;446(2):301-9.
PUBMED:22670899      doi:10.1042/BJ20120366

Stoichiometry of Nck-dependent actin polymerization in living cells
Ditlev, J. A., Michalski, P. J., Huber, G., Rivera, G. M., Mohler, W. A., Loew, L. M., Mayer, B. J.
J Cell Biol 197 (5): 643-658, May 21, 2012
PUBMED:22613834      doi:10.1083/jcb.201111113
   VCell BioModels referenced in publication:
   user: JDitlev,   model name: Nck Induces Actin Comet Tail Formation – Single NWASP Activation of Arp2/3. Simplified Actin Dendritic Nucleation.
   user: JDitlev,   model name: Nck Induces Actin Comet Tail Formation – Dimer NWASP Activation of Arp2/3. Simplified Actin Dendritic Nucleation.
   user: JDitlev,   model name: Nck Induces Actin Comet Tail Formation – Dimer Nck Binds NWASP With Dimer NWASP Activation of Arp2/3. Simplified Actin Dendritic Nucleation.1

An Adhesion-Dependent Switch between Mechanisms That Determine Motile Cell Shape
Barnhart, E. L., Lee, K. C., Keren, K., Mogilner, A., Theriot, J. A.
PLoS Biol. 2011;9(5):e1001059.
PUBMED:21559321      doi:10.1371/journal.pbio.1001059

Astrocytes as regulators of synaptic function: a quest for the Ca2+ master key
Rusakov, D. A., Zheng, K., Henneberger, C.
Neuroscientist. 2011;17(5):513-23.
PUBMED:21536839      doi:10.1177/1073858410387304

Ca2+ buffering at a drosophila larval synaptic terminal
He, Tao, Lnenicka, Gregory A.
Synapse. 2011;65(7):687-93.
PUBMED:21218450      doi:10.1002/syn.20909

Cooperative Nuclear Localization Sequences Lend a Novel Role to the N-Terminal Region of MSH6
Gassman, Natalie R., Clodfelter, Jill E., McCauley, Anita K., Bonin, Keith, Salsbury, Freddie R., Jr., Scarpinato, Karin D.
PLoS ONE. 2011;6(3):e17907.
PUBMED:21437237      doi:10.1371/journal.pone.0017907

Coupling of metabolic, second messenger pathways and insulin granule dynamics in pancreatic beta-cells: a computational analysis
Fridlyand, L. E., Philipson, L. H.
Prog Biophys Mol Biol. 2011;107(2):293-303.
PUBMED:21920379      doi:10.1016/j.pbiomolbio.2011.09.001

Coupling of the phosphatase activity of Ci-VSP to its voltage sensor activity over the entire range of voltage sensitivity
Sakata, S., Hossain, M. I., Okamura, Y.
J Physiol. 589:2687-2705, 2011
PUBMED:21486809      doi: 10.1113/jphysiol.2011.208165
   VCell BioModels referenced in publication:
   user: ssvcell1548,   model name: Sakata_JP2011-Kir2.1
   user: ssvcell1548,   model name: Sakata_JP2011-PHDGFP

Potassium (K+) gradients serve as a mobile energy source in plant vascular tissues
Gajdanowicz, P., Michard, E., Sandmann, M., Rocha, M., Correa, L. G., Ramirez-Aguilar, S. J., Gomez-Porras, J. L., Gonzalez, W., Thibaud, J. B., van Dongen, J. T., Dreyer, I.
Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):864-9. Epub 2010 Dec 27.
PUBMED:21187374      doi:10.1073/pnas.1009777108
   VCell BioModels referenced in publication:
   user: IngoDreyer,   model name: Gajdanowicz_et_al_2011

Protein diffusion in mammalian cell cytoplasm
Kuhn, T., Ihalainen, T. O., Hyvaluoma, J., Dross, N., Willman, S. F., Langowski, J., Vihinen-Ranta, M., Timonen, J.
PLoS ONE. 2011;6(8):e22962.
PUBMED:21886771      doi:10.1371/journal.pone.0022962

Purification of actin from fission yeast Schizosaccharomyces pombe and characterization of functional differences from muscle actin
Ti, S. C., Pollard, T. D.
Journal of Biological Chemistry, 2011, 286(7), 5784-92 Publication Date: Dec 9, 2010
PUBMED:21148484      doi: 10.1074/jbc.M110.199794
   VCell BioModels referenced in publication:
   user: SCT,   model name: Pirelease 09/07

Quantifying the Waddington landscape and biological paths for development and differentiation
Wang, J., Zhang, K., Xu, L., Wang, E.
Proc Natl Acad Sci USA. 2011;108(20):8257-62.
PUBMED:21536909      doi:10.1073/pnas.1017017108

Signaling network triggers and membrane physical properties control the actin cytoskeleton-driven isotropic phase of cell spreading
Rangamani, P., Fardin, M. A., Xiong, Y., Lipshtat, A., Rossier, O., Sheetz, M. P., Iyengar, R.
Biophys J. 2011 Feb 16;100(4):845-57.
PUBMED:21320428      doi: 10.1016/j.bpj.2010.12.3732

Switching Cdk2 On or Off with Small Molecules to Reveal Requirements in Human Cell Proliferation
Merrick, Karl A, Wohlbold, Lara, Zhang, Chao, Allen, Jasmina J, Horiuchi, Dai, Huskey, Noelle E, Goga, Andrei, Shokat, Kevan M, Fisher, Robert P
Mol Cell. 2011;42(5):624-36.
PUBMED:21658603      doi:10.1016/j.molcel.2011.03.031

System analysis shows distinct mechanisms and common principles of nuclear envelope protein dynamics
Zuleger, N., Kelly, D. A., Richardson, A. C., Kerr, A. R., Goldberg, M. W., Goryachev, A. B., Schirmer, E. C.
J Cell Biol. 2011;193(1):109-23.
PUBMED:21444689      doi:10.1083/jcb.201009068

The effect of compressive deformations on the rate of build-up of oxygen in isolated skeletal muscle cells
Leopold, Efrat, Sopher, Ran, Gefen, Amit
Med Eng Phys. 2011;33(9):1072-8.
PUBMED:21600830      doi:10.1016/j.medengphy.2011.04.008

The emergence of sarcomeric, graded-polarity and spindle-like patterns in bundles of short cytoskeletal polymers and two opposite molecular motors
Craig, E. M., Dey, S., Mogilner, A.
J Phys Condens Matter. 2011;23(37):374102.
PUBMED:21862843      doi: 10.1088/0953-8984/23/37/374102

Triggering actin comets versus membrane ruffles: distinctive effects of phosphoinositides on actin reorganization
Ueno, T., Falkenburger, B. H., Pohlmeyer, C., Inoue, T.
Sci Signal. 2011;4(203):ra87.
PUBMED:22169478      doi:110.1126/scisignal.2002033
   VCell BioModels referenced in publication:
   user: bfalken,   model name: Ueno2011

Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling
Brown, S. A., Moraru,, II, Schaff, J. C., Loew, L. M.
J Comput Neurosci. 31:385-400, 2011
PUBMED:21340454      doi:10.1007/s10827-011-0317-0
   VCell BioModels referenced in publication:
   user: Brown,   model name: Brown et al 2011 Analysis of SCA15-SCA16 with IC4 Peptide Application

A mitotic kinesin-6, Pav-KLP, mediates interdependent cortical reorganization and spindle dynamics in Drosophila embryos
Sommi, P., Ananthakrishnan, R., Cheerambathur, D. K., Kwon, M., Morales-Mulia, S., Brust-Mascher, I., Mogilner, A.
J Cell Sci. 2010;123(Pt 11):1862-72.
PUBMED:20442250      doi:10.1242/jcs.064048

Caveolin-1-dependent occludin endocytosis is required for TNF-induced tight junction regulation in vivo
Marchiando, A. M., Shen, L., Graham, W. V., Weber, C. R., Schwarz, B. T., Austin, J. R., 2nd, Raleigh, D. R., Guan, Y., Watson, A. J., Montrose, M. H., Turner, J. R.
J Cell Biol. 2010;189(1):111-26.
PUBMED:20351069      doi:10.1083/jcb.200902153

Cingulin and paracingulin show similar dynamic behaviour, but are recruited independently to junctions
Paschoud, S., Yu, D., Pulimeno, P., Jond, L., Turner, J. R., Citi, S.
Mol Membr Biol. 2010 Dec 17.
PUBMED:21166484      doi:10.3109/09687688.2010.538937
   VCell BioModels referenced in publication:
   user: dyu,   model name: final cingulin model

Design of versatile biochemical switches that respond to amplitude, duration, and spatial cues
Lipshtat, Azi, Jayaraman, Gomathi, He, John Cijiang, Iyengar, Ravi
Proceedings of the National Academy of Sciences. 107:1247-1252, 2010.
PUBMED:20080566      doi:10.1073/pnas.0908647107
   VCell BioModels referenced in publication:
   user: azilipshtat,   model name: PNAS_switch
   user: azilipshtat,   model name: Rap1_switch

Effect of ATP binding and hydrolysis on dynamics of canine parvovirus NS1
Niskanen, E. A., Ihalainen, T. O., Kalliolinna, O., Hakkinen, M. M., Vihinen-Ranta, M.
J Virol. 2010;84(10):5391-403.
PUBMED:20219935      doi: 10.1128/JVI.02221-09

Kinetics of M1 muscarinic receptor and G protein signaling to phospholipase C in living cells
Falkenburger, Björn H., Jensen, Jill B., Hille, Bertil
J. Gen. Physiol. 2010; 135 81-97, Published online Jan 25 2010, 10.1085/jgp.200910344.
PUBMED:20100890      doi:10.1085/jgp.200910344
   VCell BioModels referenced in publication:
   user: hillelab,   model name: FalkenburgerJGP2010

Kinetics of PIP2 metabolism and KCNQ2/3 channel regulation studied with a voltage-sensitive phosphatase in living cells
Falkenburger, B. H., Jensen, J. B., Hille, B.
J. Gen. Physiol. 2010; 135 81-97, Published online Jan 25 2010, 10.1085/jgp.200910344.
VCell BioModels referenced in publication:
user: hillelab,   model name: FalkenburgerJGP2010

Long-term potentiation depends on release of D-serine from astrocytes
Henneberger, C., Papouin, T., Oliet, S. H., Rusakov, D. A.
Nature. 2010;463(7278):232-6.

Lysosomal Pathology and Osteopetrosis upon Loss of H+-Driven Lysosomal Cl– Accumulation
Weinert, Stefanie, Jabs, Sabrina, Supanchart, Chayarop, Schweizer, Michaela, Gimber, Niclas, Richter, Martin, Rademann, Jörg, Stauber, Tobias, Kornak, Uwe, Jentsch, Thomas J.
Science. 2010;328(5984):1401-3.
PUBMED:20430974      doi:10.1126/science.1188072

MLCK-dependent exchange and actin binding region-dependent anchoring of ZO-1 regulate tight junction barrier function
Yu, Dan, Marchiando, Amanda M., Weber, Christopher R., Raleigh, David R., Wang, Yingmin, Shen, Le, Turner, Jerrold R.
PNAS, vol. 107, no. 18, 8237-8241 (2010). Published online, April 19, 2010, doi:10.1072/pnas.0908869107.
PUBMED:20404178      doi:10.1073/pnas.0908869107
   VCell BioModels referenced in publication:
   user: dyu,   model name: cacodeltaABR
   user: dyu,   model name: mouseZO1control&PIK
   user: dyu,   model name: latrunculin

Modeling capping protein FRAP and CALI experiments reveals in vivo regulation of actin dynamics
Kapustina, M., Vitriol, E., Elston, T. C., Loew, L. M., Jacobson, K.
Cytoskeleton (Hoboken).2010 Aug;67(8):519-34.
PUBMED:20623665      doi:10.1002/cm.20463
   VCell BioModels referenced in publication:
   user: marynka,   model name: CALI

Putting one step before the other: Distinct activation pathways for Cdk1 and Cdk2 bring order to the mammalian cell cycle
Merrick, Karl A., Fisher, Robert P.
Cell Cycle. 2010;9(4):706-14.
PUBMED:20139727      doi:10.4161/cc.9.4.10732

Quantifying a pathway: kinetic analysis of actin dendritic nucleation
Kraikivski, P., Slepchenko, B. M.
Biophys J. 2010;99(3):708-15.

Quantitative Measurement of Ca2+ in the Sarcoplasmic Reticulum Lumen of Mammalian Skeletal Muscle
Ziman, Andrew P., Ward, Christopher W., Rodney, George G., Lederer, W. Jonathan, Bloch, Robert J.
Biophys J, 2010. 99(8): p. 2705-2714.
PUBMED:20959112      doi:10.1016/j.bpj.2010.08.032
   VCell BioModels referenced in publication:
   user: dyu,   model name: final cingulin model

The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation
Wang, J., Xu, L., Wang, E., Huang, S.
Biophys J. 2010;99(1):29-39.

A Tridimensional Model of Proangiogenic Calcium Signals in Endothelial Cells
Munaron, L.
The Open Biology Journal, 2009, 2, 114-129 Publication Date: October 2009
   VCell BioModels referenced in publication:
   user: Annalisa03,   model name: lmunaron

A genetically encoded reporter of synaptic activity in vivo
Dreosti, Elena, Odermatt, Benjamin, Dorostkar, Mario M., Lagnado, Leon
Nat Methods. 2009 Dec;6(12):883-9. Epub 2009 Nov 8.
PUBMED:19898484      doi:10.1038/nmeth.1399
VCell BioModels referenced in publication:
user: Leon,   model name: Fig.1v7
user: Leon,   model name: GECI_Synapse

A model of action potentials and fast Ca2+ dynamics in pancreatic beta-cells
Fridlyand, L. E., Jacobson, D. A., Kuznetsov, A., Philipson, L. H.
Biophys J. 2009;96(8):3126-39.
PUBMED:19383458      doi:10.1016/j.bpj.2009.01.029
VCell MathModels referenced in publication:
user: Fridlyand,   model name: MouseSpike

Affinity for phosphatidylinositol 4,5-bisphosphate determines muscarinic agonist sensitivity of Kv7 K+ channels
Hernandez, Ciria C., Falkenburger, Björn, Shapiro, Mark S.
J. Gen. Physiol. 2009;134 437-448, Published online Oct 26 2009, 10.1085/jgp.200910313.
PUBMED:19858360      doi:10.1085/jgp.200910313
   VCell BioModels referenced in publication:
   user: bfalken,   model name: Hernandez Falkenburger Shapiro 2009

An open model of actin dendritic nucleation
Ditlev, J. A., Vacanti, N. M., Novak, I. L., Loew, L. M.
Biophys J. 2009 96:3529-3542.
PUBMED:19413959      doi:10.1016/j.bpj.2009.01.037
VCell BioModels referenced in publication:
user: les,   model name: Actin Dendritic Nucleation
user: les,   model name: Actin Dendritic Nucleation_Detailed Branching
VCell MathModels referenced in publication:
user: les, model name: Actin Advection and Diffusion
user: les, model name: Actin Advection and Diffusion 2D Cylindrical Transform

Diffusion in Cytoplasm: Effects of Excluded Volume Due to Internal Membranes and Cytoskeletal Structures
Novak, Igor L., Kraikivski, Pavel, Slepchenko, Boris M.
Biophys J. 2009;97(3):758-67.
PUBMED:19651034      doi:10.1016/j.bpj.2009.05.036

Energetic requirements for processive elongation of actin filaments by FH1FH2-formins
Paul, A. S., Pollard, T. D.
J. Biol. Chem. 284:12533-40, 2009
PUBMED:19251693      doi:10.1074/jbc.M808587200
VCell BioModels referenced in publication:
user: abiggiep,   model name: Formin FH1FH2-Profilin-Actin Elongation (public)

Intracellular fluid flow in rapidly moving cells
Keren, Kinneret, Yam, Patricia T., Kinkhabwala, Anika, Mogilner, Alex, Theriot, Julie A.
Nat Cell Biol. 2009;11(10):1219-24.

Modeling spatial and temporal dynamics of chemotactic networks
Yang, L., Iglesias, P. A.
Chemotaxis: Methods and Protocols, Methods in Molecular Biology, vol. 571, pp. 489-505, 2009.
PUBMED:19763987      doi:10.1007/978-1-60761-198-1_32
   VCell BioModels referenced in publication:
   user: LiuYang,   model name: LEGI

Persistent cAMP-signals triggered by internalized G-protein-coupled receptors
Calebiro, D., Nikolaev, V. O., Gagliani, M. C., de Filippis, T., Dees, C., Tacchetti, C., Persani, L., Lohse, M. J.
PLoS Biol. 2009 Aug;7(8):e1000172 Publication Date: Epub 2009 Aug 18
   VCell BioModels referenced in publication:
   user: davide.calebiro,   model name: Calebiro_PLoS-Biol_2009

Phosphodiesterase 1C is dispensable for rapid response termination of olfactory sensory neurons
Cygnar, K. D., Zhao, H.
Nat Neurosci. 12:454-62, 2009. PMID 19305400 2712288.
PUBMED:19305400      doi:10.1038/nn.2289
VCell BioModels referenced in publication:
user: cygnar,   model name: NatureNeuroscience2009

Robustness and coherence of a three-protein circadian oscillator: landscape and flux perspectives
Wang, J., Xu, L., Wang, E.
Biophys J. 2009;97(11):3038-46.
PUBMED:19948134      doi:10.1016/j.bpj.2009.09.021

Subcellular Dynamics of Type II PKA in Neurons
Zhong, Haining, Sia, Gek-Ming, Sato, Takashi R., Gray, Noah W., Mao, Tianyi, Khuchua, Zaza, Huganir, Richard L., Svoboda, Karel
Neuron. 62:363-374, 2009
PUBMED:19447092      doi:10.1016/j.neuron.2009.03.013
   VCell BioModels referenced in publication:
   user: globus,   model name: RIIb 2D with AKAP
   user: globus,   model name: PKA 2D
   user: globus,   model name: CAT diffusion

A spatially restricted increase in receptor mobility is involved in directional sensing during Dictyostelium discoideum chemotaxis
de Keijzer, S., Serge, A., van Hemert, F., Lommerse, P. H. M., Lamers, G. E. M., Spaink, H. P., Schmidt, T., Snaar-Jagalska, B. E.
J Cell Sci. 2008;121(Pt 10):1750-7.
PUBMED:18469015      doi:10.1242/jcs.030692

Analog modulation of mossy fiber transmission is uncoupled from changes in presynaptic Ca2+
Scott, R., Ruiz, A., Henneberger, C., Kullmann, D. M., Rusakov, D. A.
J Neurosci. 2008;28(31):7765-73.
PUBMED:18667608      doi:10.1523/JNEUROSCI.1296-08.2008

Analysis of Phosphatidylinositol-4,5-bisphosphate Signaling in Cerebellar Purkinje Spines
Brown, S. A., Morgan, F., Watras, J., Loew, L. M.
Biophys J. 95:1795-1812,2008.
   VCell BioModels referenced in publication:
   user: Brown,   model name: Brown et al 2008 Purkinje Compartmental – adapted from Hernjak et al
   user: Brown,   model name: Brown et al 2008 Purkinje 1D
   user: Brown,   model name: Brown et al 2008 Purkinje 3D – 12 PF Stimuli
   user: Brown,   model name: Brown et al 2008 Purkinje 3D – 4 PF Stimuli
   user: Brown,   model name: Brown et al 2008 Purkinje 3D Several Spines – 12 PF Stimuli
   user: Brown,   model name: Brown et al 2008 PIP2 Diffusion 1D and 3D

Calcium signal transmission in chick sensory neurones is diffusion based
Coatesworth, W., Bolsover, S.
Cell Calcium. 2008 Mar;43(3):236-49. Epub 2007 Jul 12
PUBMED:17628664      doi:10.1016/j.ceca.2007.05.016
VCell BioModels referenced in publication:
user: coatesworth,   model name: 140105_SCAB100B
user: coatesworth,   model name: 190105_SCAB100B
user: coatesworth,   model name: 190105_SCAB100P
user: coatesworth,   model name: 240604_SCAB100B
user: coatesworth,   model name: 221204_SCAB100B
user: coatesworth,   model name: 120504_SCAB100B

Calcium transport mechanisms of PC12 cells
Duman, J. G., Chen, L., Hille, B.
J. Gen. Physiol. 131:307-323, 2008.
PUBMED:18347082      doi:10.1085/jgp.200709915
VCell BioModels referenced in publication:
user: hillelab,   model name: DumanJGP2008Fig9undiff
user: hillelab,   model name: DumanJGP2008Fig9diff
user: hillelab,   model name: DumanJGP2008Fig1A-control
user: hillelab,   model name: DumanJGP2008Fig1A-4block

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.
   VCell BioModels referenced in publication:
   user: susana,   model name: neves_cell_2008

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)
PUBMED:18381072      doi:10.1016/j.febslet.2008.03.029
VCell BioModels referenced in publication:
user: alex1,   model name: full01

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
Wang, J., Xu, L., Wang, E.
Proc Natl Acad Sci USA. 2008;105(34):12271-6.
PUBMED:18719111      doi:10.1073/pnas.0800579105

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
Wang, J., Xu, L., Wang, E.
PMC Biophys. 2008;1(1):7.
PUBMED:19351381      doi:10.1186/1757-5036-1-7

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.
   VCell BioModels referenced in publication:
   user: abiggiep,   model name: Formin-Profilin-Actin Polymerization

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.
   VCell BioModels referenced in publication:
   user: leshen,   model name: intracellular bleach FLIP
   user: leshen,   model name: large area membrane bleach FRAP
   user: leshen,   model name: membrane bleach FLIP
   user: leshen,   model name: small area membrane bleach FRAP

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
   VCell BioModels referenced in publication:
   user: eungdamr,   model name: eungdamrong and Iyengar BiophysJ

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.
PUBMED:17671426      doi:10.4161/cc.6.15.4487
VCell BioModels referenced in publication:
user: piglesias,   model name: Gorlich6

Membrane-binding/modification model of signaling protein activation and analysis of its control by cell morphology
Haugh, J. M.
Biophys J 92, L93-95, 2007.
   VCell BioModels referenced in publication:
   user: jmhaugh,   model name: Cell shape control

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.
VCell MathModels referenced in publication:
user: Fridlyand,   model name: cAMP

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.
   VCell BioModels referenced in publication:
   user: Pralle,   model name: MitoticExtract_added_RanQ69L
   user: Pralle,   model name: MitoticExtract_added_ImportinB

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.
PUBMED:16721610      doi:10.1007/s00424-006-0092-3
   VCell BioModels referenced in publication:
   user: hillelab,   model name: SuhHilleEJP2006Fig1b

Hallucinogen actions on 5-HT receptors reveal distinct mechanisms of activation and signaling by G protein-coupled receptors
Weinstein, H.
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.
PUBMED:16807336      doi:10.1523/jneurosci.0946-06.2006

Modeling the impact of store-operated Ca2+ entry on intracellular Ca2+ oscillations
Kowalewski, J. M., Uhlen, P., Kitano, H., Brismar, H.
Math Biosci. 2006;204(2):232-49.
PUBMED:16620876      doi:10.1016/j.mbs.2006.03.001

Rapid redistribution of synaptic PSD-95 in the neocortex in vivo
Gray, N. W., Weimer, R. M., Bureau, I., Svoboda, K.
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.
Proceedings of the National Academy of Sciences. 103:12923-12928.
   VCell BioModels referenced in publication:
   user: jsaucer,   model name: AKARmyocyte
   user: jsaucer,   model name: AKARmyocyte_2compart
   user: jsaucer,   model name: AKARmyocyte_no_cAMP_buffering

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.
PUBMED:15985450      doi:10.1152/ajpendo.00595.2004
VCell MathModels referenced in publication:
user: Fridlyand,   model name: Chicago 2

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
   VCell BioModels referenced in publication:
   user: hernjak,   model name: purkinje_2D
   user: hernjak,   model name: purkinje_compartmental

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.
   VCell BioModels referenced in publication:
   user: hillelab,   model name: Horowitz2005JGPprobes

Quantitative elucidation of a distinct spatial gradient-sensing mechanism in fibroblasts
Schneider, I. C., Haugh, J. M.
J.Cell B 171:883-892 (2005)
   VCell BioModels referenced in publication:
   user: jmhaugh,   model name: PDGF gradient sensing

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
   VCell BioModels referenced in publication:
   user: mayya,   model name: STATmodulePaper

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
   VCell BioModels referenced in publication:
   user: foad,   model name: pyroseq_fin

A signal transduction pathway model prototype I: From agonist to cellular endpoint
Lukas, T. J.
Biophys. J. 2004; 87 1406-1416
   VCell BioModels referenced in publication:
   user: tjlukas,   model name: Ca_Release_Coupled_MLC

A signal transduction pathway model prototype II: Application to Ca2+-calmodulin signaling and myosin light chain phosphorylation
Lukas, T. J.
Biophys. J. 2004;87 1417-1425
   VCell BioModels referenced in publication:
   user: tjlukas,   model name: Ca_Release_Coupled_MLC

Bio-switches: what makes them robust?
Slepchenko, B. M., Terasaki, M.
Opin. Genet. Dev. 2004; 14/4: 428-434.
   VCell BioModels referenced in publication:
   user: boris,   model name: Terasaki_MPF1

High mobility of vesicles supports continuous exocytosis at a ribbon synapse
Holt, M., Cooke, A., Neef, A., Lagnado, L.
Current Biology, Vol. 14, 173-183, February 3, 2004
   VCell BioModels referenced in publication:
   user: Lagnado Lab,   model name: TIR_FRAP

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
PUBMED:15173220      doi:10.1085/jgp.200409029
   VCell BioModels referenced in publication:
   user: hillelab,   model name: SuhJGP2004Fig11A
   user: hillelab,   model name: SuhJGP2004Fig12
   user: hillelab,   model name: SuhJGP2004Fig13B
   user: hillelab,   model name: SuhJGP2004Fig15

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
Slepchenko, B. M., Terasaki, M.
Mol. Biol. Cell 2003;14: 4695 – 4706.
   VCell BioModels referenced in publication:
   user: boris,   model name: Terasaki_MPF1

Kinetic analysis of receptor-activated phosphoinositide turnover
Xu, C., Watras, J., Loew, L. M.
Journal of Cell Biology, vol. 161, no. 4, May 26, 2003
   VCell BioModels referenced in publication:
   user: les,   model name: PIP2 Hydrolysis JCB Submission

Modeling of Ca2+ flux in pancreatic beta-cells: role of the plasma membrane and intracellular stores
Fridlyand, L. E., Tamarina, N., Philipson, L. H.
Am J Physiol Endocrinol Metab. 2003;285(1):E138-54.
VCell MathModels referenced in publication:
user: Fridlyand,   model name: Chicago 1

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.
   VCell BioModels referenced in publication:
   user: CompCell,   model name: Chay-Keizer ER
   user: CompCell,   model name: Hodgkin-Huxley
   user: CompCell,   model name: Keizer-Levine Open-Cell
   user: CompCell,   model name: L-Type Calcium Channels
   user: CompCell,   model name: Morris-Lecar Coincidence Detection
   user: CompCell,   model name: Morris-Lecar Type II
   user: CompCell,   model name: Morris-Lecar Mutual Inhibition
   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
   VCell BioModels referenced in publication:
   user: les,   model name: Smith et al 2002 Systems Analysis of Ran Transport

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
   VCell BioModels referenced in publication:
   user: partharoy,   model name: 7_12_00_model1

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.