publication

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