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

Multi-condensate state as a functional strategy to optimize the cell signaling output.
Chattaraj, A., & Shakhnovich, E. I.
Nat Commun. 2024 Jul 25;15(1):6268.
PUBMED:39054333
https://www.nature.com/articles/s41467-024-50489-5

Comparative Investigation of the Mechanisms of Calcium Response in Human and Murine Spermatozoa.
Korobkina, J. D., Panteleev, M. A., & Sveshnikova, A. N.
Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology, 18(2), 110-126.

https://link.springer.com/article/10.1134/S1990747824700132

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.
PUBMED:38857179
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.
PUBMED:38744819
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.
PUBMED:38017688
doi:10.1111/nph.19436
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.
PUBMED:37737289
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.
PUBMED:37644720
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
PUBMED:37391402
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
PUBMED:37353932/
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
PUBMED:37216041
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.
PUBMED:36841229
doi:10.1093/jambio/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.
PUBMED:36463416
doi:10.1113/JP283966
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.
PUBMED:36724373
doi:10.1021/acs.biomac.2c00961

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.
PUBMED:36879764
doi:10.1016/j.mex.2023.102070

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.
PUBMED:36279957
doi:10.1016/j.jtbi.2022.111326

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.
PUBMED:35715404
doi:10.1038/s41467-022-31070-4

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
PUBMED:35644176
https://doi.org/10.1016/bs.mie.2021.09.014

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.
PUBMED:35717559
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.
PUBMED:35378857
doi:10.1016/j.isci.2022.104078
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
PUBMED:35344653
doi:10.1021/jacs.1c12064

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.
PUBMED:35367415
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.
PUBMED:35110734
doi:10.1038/s41586-021-04392-4

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.
doi:10.35459/tbp.2021.000198
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
doi:10.1038/s41467-021-26839-y

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.
PUBMED:34765087
doi:10.1016/j.csbj.2021.10.003
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
doi:10.3390/toxins13100674
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.
PUBMED:34509508
doi:10.1016/j.bpj.2021.09.009
VCell MathModels referenced in publication
user: kerbai,
Mathmodel names:
Kerbai_BiophysJ_2021_YAPTAZ_Ksf_case3
Kerbai_BiophysJ_2021_YAPTAZ_Ksf_case4
Kerbai_BiophysJ_2021_YAPTAZ_Ksf_case5
Kerbai_BiophysJ_2021_YAPTAZ_noKsf_case1
Kerbai_BiophysJ_2021_YAPTAZ_noKsf_case2
Kerbai_BiophysJ_2021_YAPTAZ_noKsf_case3
Kerbai_BiophysJ_2021_YAPTAZ_noKsf_case4
Kerbai_BiophysJ_2021_YAPTAZ_noKsf_case5

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
PUBMED:34509503
doi:10.1016/j.bpj.2021.09.006
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.
doi:10.1016/j.finmec.2021.100041

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
PUBMED:34360784
doi:10.3390/ijms22158018
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.
PUBMED:33990464
doi:10.1073/pnas.2021571118
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.
PUBMED:33753475
doi:10.1073/pnas.2006786118
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.
PUBMED:33063731
doi:10.4103/1673-5374.295332

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
PUBMED:34396153
doi:10.1016/j.crphys.2021.03.005
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.
PUBMED:33735291
doi:10.1371/journal.pone.0248293
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.
PUBMED:33237849
doi:10.1091/mbc.E20-08-0530

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.
PUBMED:33186442
doi:10.1085/jgp.202012627
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.
PUBMED:33201801
doi:10.7554/eLife.55013
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.
PUBMED:33199589
doi:10.1073/pnas.2010801117
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.
PUBMED:33161320
doi:110.1016/j.biomaterials.2020.120412

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.
PUBMED:33082406
doi:10.1038/s41598-020-74700-x

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.
PUBMED:33063731
doi:10.4103/1673-5374.295332

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.
PUBMED:32881857
doi:10.1371/journal.pbio.3000866
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.
PUBMED:32754013
doi:10.3389/fncel.2020.00180

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
PUBMED:32255775
doi:10.1371/journal.pcbi.1007708
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
PUBMED:32155414
doi:10.1016/j.cub.2019.12.067
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.
PUBMED:32082350
doi:10.3389/fpls.2019.01797

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
DOI:10.1007/s42452-019-1757-9

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.
PUBMED:31774078
doi:10.1039/c9cc07197k

Notch Pathway: A Bistable Inducer of Biological Noise?
Vujovic, F.; Hunter, N.; Farahani, R. M.
Cell Communication and Signaling 2019, 17 (1), 133.
PUBMED:31640734
DOI:10.1186/s12964-019-0453-0

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.
PUBMED:31017840
doi:10.1091/mbc.E18-10-0630
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.
PUBMED:30565261
doi:10.1111/nph.15646
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
PUBMED:31164479
doi:10.1126/scisignal.aap7584
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.
PUBMED:30622132
doi:10.1085/jgp.201812260
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.
doi:10.1016/j.msec.2018.10.048

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.
PUBMED:
doi:10.15252/embr.201847430
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

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A Noncanonical Binding Site in the EVH1 Domain of Vasodilator-Stimulated Phosphoprotein Regulates Its Interactions with the Proline Rich Region of Zyxin
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A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation
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Cooperation through Competition—Dynamics and Microeconomics of a Minimal Nutrient Trade System in Arbuscular Mycorrhizal Symbiosis
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Cross-regulation of phosphodiesterase-1 and phosphodiesterase-2 activities controls dopaminemediated striatal alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (ampa) receptor trafficking.
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Dynamics of Phosphoinositide-Dependent Signaling in Sympathetic Neurons
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Hysteresis-like binding of coagulation factors X/Xa to procoagulant activated platelets and phospholipids results from multistep association and membrane-dependent multimerization
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Modeling Excitable Dynamics of Chemotactic Networks
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Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology
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Pancreatic Beta Cell G-Protein Coupled Receptors and Second Messenger Interactions: A Systems Biology Computational Analysis
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Phosphoinositide 5- and 3-phosphatase activities of a voltage-sensing phosphatase in living cells show identical voltage dependence
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Regulation of quantal currents determines synaptic strength at neuromuscular synapses in larval Drosophila
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Computational neurobiology is a useful tool in translational neurology: the example of ataxia
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Dendritic geometry shapes neuronal cAMP signalling to the nucleus
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From START to FINISH: computational analysis of cell cycle control in budding yeast
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In silico spatial simulations reveal that MCC formation and excess BubR1 are required for tight inhibition of the anaphase-promoting complex
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Integration of SBML models for the description of biological system in a lab-on-chip
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Non-structural proteins P17 and P33 are involved in the assembly of the internal membrane-containing virus PRD1
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Platelet surface-associated activation and secretion-mediated inhibition of coagulation factor XII
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Symmetry and scale orient Min protein patterns in shaped bacterial sculptures
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Synaptic activity regulates the abundance and binding of complexin
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The Nectin-4/Afadin Protein Complex and Intercellular Membrane Pores Contribute to Rapid Spread of Measles Virus in Primary Human Airway Epithelia
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Two functionally distinct sources of actin monomers supply the leading edge of lamellipodia
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Integrating fluorescent biosensor data using computational models
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Interconnected network motifs control podocyte morphology and kidney function
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Structural basis of thymosin-beta4/profilin exchange leading to actin filament polymerization
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Synaptic excitation is regulated by the postsynaptic dSK channel at the Drosophila larval NMJ
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Using Markov state models to develop a mechanistic understanding of protein kinase A regulatory subunit RIalpha activation in response to cAMP binding
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Computational Analysis of Rho GTPase Cycling
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Decoding information in cell shape
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Differential triggering of spontaneous glutamate release by P/Q-, N- and R-type Ca2+ channels
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ERK regulation of phosphodiesterase 4 enhances dopamine-stimulated AMPA receptor membrane insertion
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Ion channels and regulation of insulin secretion in human beta-cells: a computational systems analysis
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Modeling and Simulation of Intracellular Drug Transport and Disposition Pathways with Virtual Cell
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Mutations in DNA binding and transactivation domains affect the dynamics of parvovirus NS1 protein
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Protein equilibration through somatic ring canals in Drosophila
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Calcium transport mechanisms of PC12 cells
Duman, J. G., Chen, L., Hille, B.
J. Gen. Physiol. 131:307-323, 2008.
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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.
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Dynamics of Cdc42 network embodies a Turing-type mechanism of yeast cell polarity
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Pathway of actin filament branch formation by Arp2/3 complex
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Potential landscape and flux framework of nonequilibrium networks: robustness, dissipation, and coherence of biochemical oscillations
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Quantitative analysis of G-actin transport in motile cells
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Robustness, dissipations and coherence of the oscillation of circadian clock: potential landscape and flux perspectives
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The role of the FH1 domain and profilin in formin-mediated actin-filament elongation and nucleation
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The tight junction protein complex undergoes rapid and continuous molecular remodeling at steady state
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Compartment-specific feedback loop and regulated trafficking can result in sustained activation of Ras at the Golgi
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Coordination of chromosome alignment and mitotic progression by the chromosome-based Ran signal
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Regulation of cAMP dynamics by Ca2+ and G-protein coupled receptors in the pancreatic beta-cell: A computational approach
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Switching of membrane organelles between cytoskeletal transport systems is determined by regulation of the microtubule-based transport
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Analysis of a RanGTP-regulated gradient in mitotic somatic cells
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Does diacylglycerol regulate KCNQ channels?
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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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In vivo dynamics of Rac-membrane interactions
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Systems analysis of PKA-mediated phosphorylation gradients in live cardiac myocytes
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Adenine nucleotide regulation in pancreatic ?-cells: modeling of ATP/ADP-Ca2+ interactions
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Modeling and analysis of calcium signaling events leading to long-term depression in cerebellar Purkinje cells
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Phospholipase C in living cells: activation, inhibition, Ca2+ requirement, and regulation of M current
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STAT module can function as a biphasic amplitude filter
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A multi-enzyme model for Pyrosequencing
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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
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Regulation of KCNQ2/KCNQ3 Current by G Protein Cycling: The Kinetics of Receptor-mediated Signaling by Gq
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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
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Centrosome positioning in interphase cells
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Cyclin aggregation and robustness of bio-switching
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Kinetic analysis of receptor-activated phosphoinositide turnover
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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
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Distinct Intracellular Calcium Transients in Neurites and Somata Integrate Neuronal Signals
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Systems analysis of Ran transport
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Targeting of Rough Endoplasmic Reticulum Membrane Proteins and Ribosomes in Invertebrate Neurons
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Local photorelease of caged thymosin beta4 in locomoting keratocytes causes cell turning
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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
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Determination of time-dependent inositol-1,4,5-trisphosphate concentrations during calcium release in a smooth muscle cell
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