COPASI's Use In Physiology

Mohapatra SR, Sadik A, Sharma S, Poschet G, Gegner HM, Lanz TV, Lucarelli P, Klingmüller U, Platten M, Heiland I, Opitz CA (2021) Hypoxia Routes Tryptophan Homeostasis Towards Increased Tryptamine Production. Frontiers in Immunology 12:590532 Metabolism Physiology Link
Zake DM, Kurlovics J, Zaharenko L, Komasilovs V, Klovins J, Stalidzans E (2021) Physiologically based metformin pharmacokinetics model of mice and scale-up to humans for the estimation of concentrations in various tissues. PLOS One 16:e0249594 Pharmacology Physiology Link

2 publications
Vargas-Villamil LM, Tedeschi LO, Medina-Peralta S, Izquierdo-Reyes F, Navarro-Alberto J, González-Garduño R (2020) A multi-inverse approach for a holistic understanding of applied animal science systems. Animal 14:s238–s249 Computational Method Physiology Link

1 publication
Anderson R, Lagnado A, Maggiorani D, Walaszczyk A, Dookun E, Chapman J, Birch J, Salmonowicz H, Ogrodnik M, Jurk D, Proctor C, Correia-Melo C, Victorelli S, Fielder E, Berlinguer-Palmini R, Owens A, Greaves LC, Kolsky KL, Parini A, Douin-Echinard V, LeBrasseur NK, Arthur HM, Tual-Chalot S, Schafer MJ, Roos CM, Miller JD, Robertson N, Mann J, Adams PD, Tchkonia T, Kirkland JL, Mialet-Perez J, Richardson GD, Passos JF (2019) Length-independent telomere damage drives post-mitotic cardiomyocyte senescence. The EMBO Journal 38:e100492 Genetics Physiology Link
Filkova AA, Martyanov AA, Dasgupta AKG, Panteleev MA, Sveshnikova AN (2019) Quantitative dynamics of reversible platelet aggregation: mathematical modelling and experiments. Scientific Reports 9:1–9 Physiology Link
Jaime JC, Mesa-Álvarez MD, Martin RR, Betancourt-Mar JA, Cocho G, Mansilla R, Nieto-Villar JM (2019) Chronotherapy of cancer: periodic perturbations in vascular growth and metastasis. Biological Rhythm Research 50:495–504 Physiology Link
Knight-Schrijver V (2019) Towards systems pharmacology models of druggable targets and disease mechanisms. Thesis, University of Cambridge Pharmacology Physiology Signaling Link
Krahmer J, Goralogia GS, Kubota A, Zardilis A, Johnson RS, Song YH, MacCoss MJ, Le Bihan T, Halliday KJ, Imaizumi T, Millar AJ (2019) Time-resolved interaction proteomics of the GIGANTEA protein under diurnal cycles in Arabidopsis. FEBS Letters 593:319–338 Physiology Link
Kühn C, Checa S (2019) Computational Modeling to Quantify the Contributions of VEGFR1, VEGFR2, and Lateral Inhibition in Sprouting Angiogenesis. Frontiers in Physiology 10:288 Signaling Physiology Link
Montero G, Silva E, Mansilla R (2019) Do mole-rats follow the same rules in their longevity and aging in nature? MOJ Gerontology & Geriatrics 4:259–263 Physiology Link
Morgan A (2019) Using Mathematical Modelling and Electrochemical Analysis to Investigate Age‐Associated Disease. Ph.D. Thesis, University of Chester, UK Physiology Link
Parmar JH, Mendes P (2019) A computational model to understand mouse iron physiology and disease. PLOS Computational Biology 15:e1006680 Physiology Link
Reader P (2019) in vitro Characterisation of the Complement Cascade for Predicting Patient Outcome Post-operatively. Ph.D. Thesis, University of Exeter Biochemistry Physiology Link
Singh A, Marcoline FV, Veshaguri S, Kao AW, Bruchez M, Mindell JA, Stamou D, Grabe M (2019) Protons in small spaces: Discrete simulations of vesicle acidification. PLOS Computational Biology 15:e1007539 Physiology Link

11 publications
Jaime J, Mesa-Álvarez M, Martin R, Betancourt-Mar J, Cocho G, Mansilla R, Nieto-Villar J (2018) Chronotherapy of cancer: periodic perturbations in vascular growth and metastasis. Biological Rhythm Research 50:495-504 Physiology Link
Martinez Guimera A (2018) Investigating homeostatic disruption by constitutive signals during biological ageing. Thesis, Newcastle University Signaling Physiology Link
Martinez Guimera A, Welsh CM, Proctor CJ, McArdle A, Shanley DP (2018) ‘Molecular habituation’as a potential mechanism of gradual homeostatic loss with age. Mechanisms of Ageing and Development 169:53–62 Physiology Link
Winter F, Bludszuweit-Philipp C, Wolkenhauer O (2018) Mathematical analysis of the influence of brain metabolism on the BOLD signal in Alzheimer’s disease. Journal of Cerebral Blood Flow & Metabolism 38:304–316 Physiology Metabolism Biophysics Link
Woller A, Gonze D (2018) Modeling clock-related metabolic syndrome due to conflicting light and food cues. Scientific Reports 8:13641 Physiology Metabolism Link

5 publications
Agrawal R, Kalmady SV, Venkatasubramanian G (2017) In Silico Model-driven Assessment of the Effects of Brain-derived Neurotrophic Factor Deficiency on Glutamate and Gamma-Aminobutyric Acid: Implications for Understanding Schizophrenia Pathophysiology. Clinical Psychopharmacology and Neuroscience 15:115 Physiology Signaling Link
Parmar JH, Davis G, Shevchuk H, Mendes P (2017) Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient. BMC Systems Biology 11:57 Physiology Link
Sier JH, Thumser AE, Plant NJ (2017) Linking physiologically-based pharmacokinetic and genome-scale metabolic networks to understand estradiol biology. BMC Systems Biology 11:141 Physiology Pharmacology Link
Sveshnikova AN, Panteleev MA, Dreval AV, Shestakova TP, Medvedev OS, Dreval OA (2017) Theoretical evaluation of the parameters of glucose metabolism on the basis of continuous glycemia monitoring data using mathematical modeling. Biophysics 62:842–847 Metabolism Physiology Link
Tikidji-Hamburyan A, Reinhard K, Storchi R, Dietter J, Seitter H, Davis KE, Idrees S, Mutter M, Walmsley L, Bedford RA, Ueffing M, Ala-Laurila P, Brown TM, Lucas RJ, Münch TA (2017) Rods progressively escape saturation to drive visual responses in daylight conditions. Nature Communications 8:1813 Biochemistry Biophysics Physiology Link
Tolleter D, Chochois V, Poiré R, Price GD, Badger MR (2017) Measuring CO2 and HCO3- permeabilities of isolated chloroplasts using a MIMS-18O approach. Journal of Experimental Botany 68:3915–3924 Laboratory Method Physiology Link

6 publications
Gerber S, Fröhlich M, Lichtenberg-Fraté H, Shabala S, Shabala L, Klipp E (2016) A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae. PLOS Computational Biology 12:e1004703 Metabolism Physiology Link
Proctor CJ, Gartland A (2016) Simulated interventions to ameliorate age-related bone loss indicate the importance of timing. Frontiers in Endocrinology 7:61 Physiology Signaling Link
Sano T, Kawata K, Ohno S, Yugi K, Kakuda H, Kubota H, Uda S, Fujii M, Kunida K, Hoshino D, Hatano, Atsushi, Matsuoka Y, Sato M, Suzuki Y, Kuroda S (2016) Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin. Science Signaling 9:ra112–ra112 Signaling Physiology Link
Shepelyuk TO, Panteleev MA, Sveshnikova AN (2016) Computational modeling of quiescent platelet energy metabolism in the context of whole-body glucose turnover. Mathematical Modelling of Natural Phenomena 11:91–101 Metabolism Physiology Link
Sluka JP, Fu X, Swat M, Belmonte JM, Cosmanescu A, Clendenon SG, Wambaugh JF, Glazier JA (2016) A Liver-Centric Multiscale Modeling Framework for Xenobiotics. PLOS One 11:e0162428 Physiology Pharmacology Link
Sveshnikova AN, Balatskiy AV, Demianova AS, Shepelyuk TO, Shakhidzhanov SS, Balatskaya MN, Pichugin AV, Ataullakhanov FI, Panteleev MA (2016) Systems biology insights into the meaning of the platelet’s dual-receptor thrombin signaling. Journal of Thrombosis and Haemostasis 14:2045–2057 Physiology Signaling Link
Valero E, Macià H, Ildefonso M, Hernández J-A, González-Sánchez M-I, García-Carmona F (2016) Modeling the ascorbate-glutathione cycle in chloroplasts under light/dark conditions. BMC Systems Biology 10:11 Metabolism Physiology Link
Woller A, Duez H, Staels B, Lefranc M (2016) A mathematical model of the liver circadian clock linking feeding and fasting cycles to clock function. Cell Reports 17:1087–1097 Metabolism Physiology Signaling Link
Xie Y (2016) Multi-scale modelling of the cellular and molecular mechanisms of hyperpolarisation mediated synaptic plasticity in the vestibular nuclei. MSc Thesis, The University of Edinburgh Signaling Physiology Link

9 publications
Dutta-Roy R, Rosenmund C, Edelstein SJ, Le Novère N (2015) Ligand-Dependent Opening of the Multiple AMPA Receptor Conductance States: A Concerted Model. PLOS One 10:e0116616 Physiology Macromolecular Biochemistry Link
Mendes P, Oliver SG, Kell DB (2015) Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly. Trends in Pharmacological Sciences 36:710-23 Physiology Pharmacology Link
Peñarrubia L, Romero P, Carrió-Seguí A, Andrés-Bordería A, Moreno J and Sanz A (2015) Temporal aspects of copper homeostasis and its crosstalk with hormones. Frontiers in Plant Science 6:255. Physiology Link
Sier JH (2015) Investigation of the impact of MRP3 and MRP4 on the disposition of drugs and conjugates in rat and human. Doctoral Thesis, University of Surrey Physiology Link

4 publications
Godfrey L, Yamada-Fowler N, Smith J, Thornalley PJ, Rabbani N (2014) Arginine-directed glycation and decreased HDL plasma concentration and functionality. Nutrition & Diabetes 4:e134 Physiology Link
Leal Denis MF (2014) Homeostasis de ATP extracelular en eritrocitos: interregulación y consecuencias funcionales. PhD Thesis, Universidad de Buenos Aires, Buenos Aires, Argentina. Physiology 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
Saller S, Kunz L, Berg D, Berg U, Lara H, Urra J, Hecht S, Pavlik R, Thaler CJ, Mayerhofer A (2014) Dopamine in human follicular fluid is associated with cellular uptake and metabolism-dependent generation of reactive oxygen species in granulosa cells: implications for physiology and pathology. Human Reproduction 29:555-67 Physiology Metabolism Link
Smallbone K, M Corfe B (2014) A mathematical model of the colon crypt capturing compositional dynamic interactions between cell types. International Journal of Experimental Pathology 95:1–7 Physiology Link

5 publications
Fröhlich M (2013) Computational and experimental investigation of the mechanisms involved in cellular water transport and (cat)ion homeostasis. Ph.D. Thesis, Department of Mathematics and Computer Science, Free University of Berlin Physiology Link

1 publication
Koval OM, Snyder JS, Wolf RM, Pavlovicz RE, Glynn P, Curran J, Leymaster ND, Dun W, Wright PJ, Cardona N, Qian L, Mitchell CC, Boyden PA, Binkley PF, Li C, Anderson ME, Mohler PJ, Hund TJ (2012) Ca2+/calmodulin-dependent protein kinase II-based regulation of voltage-gated Na+ channel in cardiac disease. Circulation 126:2084–2094 Physiology Signaling Link
Mc Auley MT, Wilkinson DJ, Jones JJ, Kirkwood TB (2012) A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. BMC Systems Biology 6:130 Metabolism Physiology Link

2 publications
Gerber S (2011) In silico modeling of cation homeostasis in Saccharomyces cerevisiae. PhD Thesis, Humboldt-University of Berlin. Physiology Link

1 publication
Adra S, Sun T, MacNeil S, Holcombe M, Smallwood R (2010) Development of a Three Dimensional Multiscale Computational Model of the Human Epidermis. PLOS One 5:e8511. Physiology Link
Nakano T, Doi T, Yoshimoto J, Doya K (2010) A Kinetic Model of Dopamine- and Calcium-Dependent Striatal Synaptic Plasticity. PLOS Computational Biology 6:e1000670. Physiology Link

2 publications

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Colvin RA, Bush AI, Volitakis I, Fontaine CP, Thomas D, Kikuchi K, Holmes WR (2008) Insights into Zn2+ homeostasis in neurons from experimental and modeling studies. American Journal of Physiology 294:C726-C742 Physiology Link
Stefan MI, Edelstein SJ, Le Novère N (2008) An allosteric model of calmodulin explains differential activation of PP2B and CaMKII. Proceedings of the National Academy of Sciences USA 105:10768-73 Physiology Signaling Macromolecular Biochemistry Link

2 publications

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