COPASI's Use In Cell Biology

2017
Kagan VE, Mao G, Qu F, Angeli JPF, Doll S, Croix CS, 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

2 publications
2016
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 Metabolism 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. Mol. 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
2015
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. J. Cell Biol. 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 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 Biol. 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 Comm. 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 Comput Biol 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 Comput. Biol. 11:e1004593 Macromolecular Biochemistry Cell Biology Link

6 publications
2014
Helgeson L (2014) Mechanisms of Branched Actin Network Formation through Coordinate Activation of Arp2/3 Complex. PhD Thesis, University of Oregon. 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
2013
Firczuk H, Kannambath S, Pahle J, Claydon A, Beynon R, Duncan J, Westerhoff H, 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
2012
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
Steinacher A, Leyser O, H. Clayton R (2012) A computational model of auxin and pH dynamics in a single plant cell. Journal of Theoretical Biology 296:84-94 Cell Biology Link

5 publications
2011
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. Mol. Systems Biol. 7:485 Cell Biology Link

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

1 publication
2009

0 publication
2008
Schmierer B, Tournier AL, Bates PA, Hill CS (2008) Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system. PNAS 105:6608-13 Cell Biology Signaling Link

1 publication
2007
Rippe K, Schrader A, Riede P, Strohner R, Lehmann E,Längst G (2007) DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. PNAS 104:15635-40 Macromolecular Biochemistry Cell Biology Link
Xie Z (2007) Modelling genetic regulatory networks: A new model for circadian rhythms in Drosophila and investigation of genetic noise in a viral infection process. PhD Thesis. Lincoln University, New Zealand Cell Biology Link

2 publications
2006

0 publication