COPASI's Use In Cell Biology


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Irgen-Gioro S, Yoshida SR, Walling V, Chong S (2022) Fixation can change the appearance of phase separation in living cells. eLife 11:e79903 Cell Biology Biophysics Link

1 publication
Castro M, Lythe G, Smit J, Molina-París C (2021) Fusion and fission events regulate endosome maturation and viral escape. Scientific Reports 11:7845 Cell Biology Link
Dalle Pezze P, Karanasios E, Kandia V, Manifava M, Walker SA, Le Novère NG, Ktistakis NT (2021) ATG13 dynamics in nonselective autophagy and mitophagy: insights from live imaging studies and mathematical modeling. Autophagy 17:1131–1141 Cell Biology Signaling Link
Guhe V, Soni B, Ingale P, Singh S (2021) Autophagy proteins and its homeostasis in cellular environment. Advances in Protein Chemistry and Structural Biology 123:73–93 Cell Biology Signaling Link
Hetmanski JHR, Jones MC, Chunara F, Schwartz J-M, Caswell PT (2021) Combinatorial mathematical modelling approaches to interrogate rear retraction dynamics in 3D cell migration. PLoS Computational Biology 17:e1008213 Cell Biology Signaling Link
Quiros DN, Nieto F, Mayorga LS (2021) From cartoons to quantitative models in Golgi transport. Biology of the Cell 113:146–164 Cell Biology Link
Rosenbloom AD (2021) Mechanism of Actin Filament Nucleation. Ph.D. Thesis, Yale University, New Haven, CT, USA. Macromolecular Biochemistry Cell Biology Link
Tisi R, Spinelli M, Palmioli A, Airoldi C, Cazzaniga P, Besozzi D, Nobile MS, Mazzoleni E, Arnhold S, De Gioia L, Grandori R, Peri F, Vanoni M, Sacco E (2021) The Multi-Level Mechanism of Action of a Pan-Ras Inhibitor Explains its Antiproliferative Activity on Cetuximab-Resistant Cancer Cells. Frontiers in Molecular Biosciences 8:625979 Signaling Cell Biology Link
Yahya G, Pérez AP, Mendoza MB, Parisi E, Moreno DF, Artés MH, Gallego C, Aldea M (2021) Stress granules display bistable dynamics modulated by Cdk. Journal of Cell Biology 220:jcb202005102 Cell Biology Signaling Link
Zweifel ME, Sherer LA, Mahanta B, Courtemanche N (2021) Nucleation limits the lengths of actin filaments assembled by formin. Biophysical Journal 120:4442–4456 Macromolecular Biochemistry Cell Biology Link

9 publications
Balzer CJ, James ML, Narvaez-Ortiz HY, Helgeson LA, Sirotkin V, Nolen BJ (2020) Synergy between Wsp1 and Dip1 may initiate assembly of endocytic actin networks. eLife 9:e60419 Cell Biology Macromolecular Biochemistry Link
Dalle Pezze P, Karanasios E, Kandia V, Manifava M, Walker SA, Le Novère NG, Ktistakis NT (2020) ATG13 dynamics in nonselective autophagy and mitophagy: insights from live imaging studies and mathematical modeling. Autophagy 17:1131-1141 Cell Biology Link
Howell RSM, Klemm C, Thorpe PH, Csikász-Nagy A (2020) Unifying the mechanism of mitotic exit control in a spatiotemporal logical model. PLoS Biology 18:e3000917 Cell Biology Link
Meyer K, Morales-Navarrete H, Seifert S, Wilsch-Braeuninger M, Dahmen U, Tanaka EM, Brusch L, Kalaidzidis Y, Zerial M (2020) Bile canaliculi remodeling activates YAP via the actin cytoskeleton during liver regeneration. Molecular Systems Biology 16:e8985 Signaling Cell Biology Link
Mondeel TDGA, Ivanov O, Westerhoff HV, Liebermeister W, Barberis M (2020) Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs. npj Systems Biology and Applications 6:8 Cell Biology Link
Sumi T, Harada K (2020) Mechanism underlying hippocampal long-term potentiation and depression based on competition between endocytosis and exocytosis of AMPA receptors. Scientific Reports 10:14711 Signaling Cell Biology Link
Zweifel ME, Courtemanche N (2020) Profilin’s Affinity for Formin Regulates the Availability of Filament Ends for Actin Monomer Binding. Journal of Molecular Biology 432:166688 Cell Biology Link

7 publications
Bell M, Bartol T, Sejnowski T, Rangamani P (2019) Dendritic spine geometry and spine apparatus organization govern the spatiotemporal dynamics of calcium. Journal of General Physiology 151:1017–1034 Cell Biology Biophysics Signaling Link
Erlendsson S, Thorsen TS, Vauquelin G, Ammendrup-Johnsen I, Wirth V, Martinez KL, Teilum K, Gether U, Madsen KL (2019) Mechanisms of PDZ domain scaffold assembly illuminated by use of supported cell membrane sheets. eLife 8:e39180 Macromolecular Biochemistry Cell Biology Link
Getz M, Swanson L, Sahoo D, Ghosh P, Rangamani P (2019) A predictive computational model reveals that GIV/girdin serves as a tunable valve for EGFR-stimulated cyclic AMP signals. Molecular Biology of the Cell 30:1621–1633 Signaling Cell Biology Link
Hetmanski JHR, de Belly H, Busnelli I, Waring T, Nair RV, Sokleva V, Dobre O, Cameron A, Gauthier N, Lamaze C, Swift J, del Campo A, Starborg T, Zech T, Goetz JG, Paluch EK, Schwartz J-M, Caswell PT (2019) Membrane Tension Orchestrates Rear Retraction in Matrix-Directed Cell Migration. Developmental Cell 51:460-475.e10 Cell Biology Biophysics Link
Moreno DF, Jenkins K, Morlot S, Charvin G, Csikász-Nagy A, Aldea M (2019) Proteostasis collapse, a hallmark of aging, hinders the chaperone-Start network and arrests cells in G1. eLife 8:e48240 Signaling Cell Biology Link
Moreno DF, Parisi E, Yahya G, Vaggi F, Csikász-Nagy A, Aldea M (2019) Competition in the chaperone-client network subordinates cell-cycle entry to growth and stress. Life Science Alliance 2:e201800277 Signaling Cell Biology Link

6 publications
Dalle Pezze P, Karanasios E, Kandia V, Walker SA, Ktistakis NT, Le Novère N (2018) Dynamic modelling suggests differential mechanisms for initiation of non-selective autophagy and mitophagy. bioRxiv Preprint bioRxiv:370114 Cell Biology Link
Guerra A, Rodriguez DJ, Montero S, Betancourt-Mar JA, Martin RR, Silva E, Bizzarri M, Cocho G, Mansilla R, Nieto-Villar JM (2018) Phase transitions in tumor growth VI: Epithelial–Mesenchymal transition. Physica A 499:208–215 Physiology Cell Biology Link
Hantusch A (2018) Systems Biological Analysis of Bcl-2 Family Interactions and Effector Oligomerization. Ph.D. Thesis, University of Konstanz, Germany Cell Biology Macromolecular Biochemistry Link
Kosey D, Soni B, Nimsarkar P, Singh S (2018) Infection dynamics in L. major autophagic machinery is regulated by ATG9-PI3P negative feedback loop. bioRxiv Preprint bioRxiv:398545 Cell Biology Immunology Link
Kwon JS, Wang X, Yao G (2018) Study Quiescence Heterogeneity by Coupling Single-Cell Measurements and Computer Modeling. Methods in Molecular Biology 1686:287–299 Cell Biology Education Link
Mayorga LS, Cebrian I, Verma M, Hoops S, Bassaganya-Riera J (2018) Reconstruction of endosomal organization and function by a combination of ODE and agent-based modeling strategies. Biology Direct 13:25 Cell Biology Link

6 publications
Henze R, Dittrich P, Ibrahim B (2017) A Dynamical Model for Activating and Silencing the Mitotic Checkpoint. Scientific Reports 7:3865 Cell Biology Link
Kagan VE, Mao G, Qu F, Angeli JPF, Doll S, St Croix C, Dar HH, Liu B, Tyurin VA, Ritov VB, Kapralov AA, Amoscato AA, Jiang J, Anthonymuthu T, Mohammadyani D, Yang Q, Proneth B, Klein-Seetharaman J, Watkins S, Bahar I, Greenberger J, Mallampalli RK, Stockwell BR, Tyurina YY, Conrad M, Bayır H (2017) Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis. Nature Chemical Biology 13:81–90 Signaling Cell Biology Link
Zaccarin M, Bosello-Travain V, Di Paolo ML, Falda M, Maiorino M, Miotto G, Piccolo S, Roveri A, Ursini F, Venerando R, Toppo S (2017) Redox status in a model of cancer stem cells. Archives of Biochemistry and Biophysics 617:120–128 Biochemistry Cell Biology Link

3 publications
Emiola A, Andrews SS, Heller C, George J (2016) Crosstalk between the lipopolysaccharide and phospholipid pathways during outer membrane biogenesis in Escherichia coli. Proceedings of the National Academy of Sciences USA 113:3108–3113 Signaling Cell Biology Link
Kilner J, Corfe BM, McAuley MT, Wilkinson SJ (2016) A deterministic oscillatory model of microtubule growth and shrinkage for differential actions of short chain fatty acids. Molecular BioSystems 12:93-101 Cell Biology Link
Kollarovic G, Studencka M, Ivanova L, Lauenstein C, Heinze K, Lapytsko A, Talemi SR, Figueiredo AS, Schaber J (2016) To senesce or not to senesce: how primary human fibroblasts decide their cell fate after DNA damage. Aging 8:158 Cell Biology Link
Ouzounoglou E, Dionysiou D, Stamatakos GS (2016) Differentiation resistance through altered retinoblastoma protein function in acute lymphoblastic leukemia: in silico modeling of the deregulations in the G1/S restriction point pathway. BMC Systems Biology 10:23 Cell Biology Link

4 publications
Daneshjou N, Sieracki N, van Nieuw Amerongen GP, Schwartz MA, Komarova YA, Malik AB, Conway DE (2015) Rac1 functions as a reversible tension modulator to stabilize VE-cadherin trans-interaction. Journal of Cell Biology 208:23-32 Macromolecular Biochemistry Cell Biology Link
Everetts NJ (2015) Computational Analysis of the Control of Cell Cycle Entry. Bachelor's Thesis, Department of Molecular and Cellular Biology, University of Arizona, USA Cell Biology Signaling Link
Intosalmi J, Ahlfors H, Rautio S, Mannerstöm H, Chen ZJ, Lahesmaa R, Stockinger B, Lähdesmäki H (2015) Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data. BMC Systems Biology 9:81. Immunology Cell Biology Signaling Link
Li L, Gervasi N, Girault J-A (2015) Dendritic geometry shapes neuronal cAMP signalling to the nucleus. Nature Communications 6:6319 Cell Biology Signaling Link
Luna A, McFadden GB, Aladjem MI, Kohn KW (2015) Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response. PLoS Computational Biology 11:e1004144 Cell Biology Link
Zhou J, Aponte-Santamaría C, Sturm S, Bullerjahn JT, Bronowska A, Gräter F (2015) Mechanism of Focal Adhesion Kinase Mechanosensing. PLoS Computational Biology 11:e1004593 Macromolecular Biochemistry Cell Biology Link

6 publications
Helgeson LA (2014) Mechanisms of Branched Actin Network Formation through Coordinate Activation of Arp2/3 Complex. Ph.D. Thesis, University of Oregon, USA. Cell Biology Link
Ligon TS, Leonhardt C, Rädler JO (2014) Multi-level kinetic model of mRNA delivery via transfection of lipoplexes. PLoS One 9:e107148 Cell Biology Genomics Link
Ouzounoglou E, Kalamatianos D, Emmanouilidou E, Xilouri M, Stefanis L, Vekrellis K, Manolakos ES (2014) In silico modeling of the effects of alpha-synuclein oligomerization on dopaminergic neuronal homeostasis. BMC Systems Biology 8:54 Physiology Cell Biology Link
Sosa CM, Pavarotti MA, Zanetti MN, Zoppino FCM, De Blas GA, Mayorga LS (2014) Kinetics of human sperm acrosomal exocytosis. MHR: Basic Science of Reproductive Medicine 21:244–254 Cell Biology Link

4 publications
Firczuk H, Kannambath S, Pahle J, Claydon A, Beynon R, Duncan J, Westerhoff HV, Mendes P, McCarthy JEG (2013) An in vivo control map for the eukaryotic mRNA translation machinery. Molecular Systems Biology 9:635 Macromolecular Biochemistry Cell Biology Link
Maccari G, Mori M, Rodríguez-Salarichs J, Fang W, Díaz JF, Botta M (2013) Free Energy Profile and Kinetics Studies of Paclitaxel Internalization from the Outer to the Inner Wall of Microtubules. Journal of Chemical Theory and Computation 9:698-706 Cell Biology Macromolecular Biochemistry Pharmacology Link
Sahaboglu A, Paquet-Durand O, Dietter J, Dengler K, Bernhard-Kurz S, Ekström PAR, Hitzmann B, Ueffing M, Paquet-Durand F (2013) Retinitis pigmentosa: rapid neurodegeneration is governed by slow cell death mechanisms. Cell Death & Disease 4:e488 Cell Biology Signaling Link

3 publications
Bortolussi L, Policriti A (2012) Studying cancer-cell populations by programmable models of networks. Network Modeling Analysis in Health Informatics and Bioinformatics 1:117-133 Cell Biology Link
Czeizler E, Mizera A, Czeizler E, Back R-J, Eriksson JE, Petre I (2012) Quantitative Analysis of the Self-Assembly Strategies of Intermediate Filaments from Tetrameric Vimentin. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9:885-898 Cell Biology Link
Kowald A, Hamann A, Zintel S, Ullrich S, Klipp E, Osiewacz HD (2012) A systems biological analysis links ROS metabolism to mitochondrial protein quality control. Mechanisms of Ageing and Development 133:331-337 Cell Biology Link
Mayorga LS, Lopez MJ, Becker WM (2012) Molecular Thermodynamics for Cell Biology as Taught with Boxes. Cell Biology Education 11:31-38 Cell Biology Education Link
Rahimi O, Phelix CF, Perry G (2012) Transcriptome-To-Reactome Biosimulation: Oxidative Pathways to Apoptotic Cell Death. Alzheimer’s & Dementia 8:P478–P479 Signaling Cell Biology Link
Steinacher A, Leyser O, Clayton RH (2012) A computational model of auxin and pH dynamics in a single plant cell. Journal of Theoretical Biology 296:84-94 Cell Biology Link

6 publications
Genc S, Kurnaz IA, Ozilgen M (2011) Astrocyte-neuron lactate shuttle may boost more ATP supply to the neuron under hypoxic conditions-in silico study supported by in vitro expression data. BMC Systems Biology 5:162 Cell Biology Metabolism Link
Rodriguez F, Bustos MA, Zanetti MN, Ruete MC, Mayorga LS, Tomes CN (2011) alpha-SNAP prevents docking of the acrosome during sperm exocytosis because it sequesters monomeric syntaxin. PLoS One 6:e21925 Cell Biology Macromolecular Biochemistry Link
Yao G, Tan C, West M, Nevins JR, You L (2011) Origin of bistability underlying mammalian cell cycle entry. Molecular Systems Biology 7:485 Cell Biology Link

3 publications
Brasen JC, Barington T, Olsen LF (2010) On the mechanism of oscillations in neutrophils. Biophysical Chemistry 148:82-92 Cell Biology Link

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