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
