COPASI's Use In Physiology

2024

0 publication
2023
Davies C, Morgan AE, Mc Auley MT (2023) Computationally Modelling Cholesterol Metabolism and Atherosclerosis. Biology 12:1133 Metabolism Physiology Link
Schaumburger N, Pally J, Moraru II, Kositsawat J, Kuchel GA, Blinov ML (2023) Dynamic model assuming mutually inhibitory biomarkers of frailty suggests bistability with contrasting mobility phenotypes. Frontiers in Network Physiology 3:1079070 Signaling Physiology Link
Yalçınkaya BH, Genc S, Yılmaz B, Özilgen M (2023) How does exercise affect energy metabolism? An in silico approach for cardiac muscle. Heliyon 9:e17164 Biochemistry Physiology Link

3 publications
2022
Bauerstätter P (2022) Compartment Modeling of Overweight in Toddler Age: Modeling and Simulating a Diets Effect with COPASI. SNE Simulation Notes Europe 32:221–224 Physiology Computational Method Link
Chedere A, Mishra M, Kulkarni O, Sriraman S, Chandra N (2022) Personalized quantitative models of NAD metabolism in hepatocellular carcinoma identify a subgroup with poor prognosis. Frontiers in Oncology 12:954512 Metabolism Physiology Link
Esposito M, Picchiami L (2022) A Comparative Study of AI Search Methods for Personalised Cancer Therapy Synthesis in COPASI. In: Bandini S, Gasparini F, Mascardi V, Palmonari M and Vizzari G (eds) AIxIA 2021 – Advances in Artificial Intelligence. Lecture Notes in Computer Science 13196:638–654 Pharmacology Physiology Computational Method Link
Großeholz R, Wanke F, Rohr L, Glöckner N, Rausch L, Scholl S, Scacchi E, Spazierer A-J, Shabala L, Shabala S, Schumacher K, Kummer U, Harter K (2022) Computational modeling and quantitative physiology reveal central parameters for brassinosteroid-regulated early cell physiological processes linked to elongation growth of the Arabidopsis root. eLife 11:e73031 Signaling Physiology Plant Biology Link
Poucet T, Beauvoit B, González-Moro MB, Cabasson C, Pétriacq P, Flandin A, Gibon Y, Marino D, Dieuaide-Noubhani M (2022) Impaired cell growth under ammonium stress explained by modeling the energy cost of vacuole expansion in tomato leaves. The Plant Journal 112:1014–1028 Physiology Plant Biology Link
Xu Q, Rose JJ, Chen X, Wang L, DeMartino AW, Dent MR, Tiwari S, Bocian K, Huang XN, Tong Q, McTiernan CF, Guo L, Alipour E, Jones TC, Ucer KB, Kim-Shapiro DB, Tejero J, Gladwin MT (2022) Cell-free and alkylated hemoproteins improve survival in mouse models of carbon monoxide poisoning. JCI Insight 7:e153296 Biochemistry Toxicology Physiology Link

6 publications
2021
Esposito M, Picchiami L (2021) Intelligent Search for Personalized Cancer Therapy Synthesis: an Experimental Comparison. In: Benedictis RD, Maratea M, Micheli A, Scala E, Serina I, Vallati M, et al. (eds) Proceedings of the 9th Italian workshop on Planning and Scheduling (IPS’21) and the 28th International Workshop on “Experimental Evaluation of Algorithms for Solving Problems with Combinatorial Explosion” (RCRA’21) with CEUR-WS. Milan, Italy. Physiology Computational Method Link
King J, Mihaila SM, Ahmed S, Truckenmüller R, Giselbrecht S, Masereeuw R, Carlier A (2021) The Influence of OAT1 Density and Functionality on Indoxyl Sulfate Transport in the Human Proximal Tubule: An Integrated Computational and In Vitro Study. Toxins 13:674 Toxicology Physiology Link
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
Yang Y, Filipovic D, Bhattacharya S (2021) A Negative Feedback Loop and Transcription Factor Cooperation Regulate Zonal Gene Induction by 2, 3, 7, 8-Tetrachlorodibenzo-p-Dioxin in the Mouse Liver. Hepatology Communications 6:750-764 Signaling Physiology Toxicology 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

5 publications
2020
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
2019
Anderson R, Lagnado A, Maggiorani D, Walaszczyk A, Dookun E, Chapman J, Birch J, Salmonowicz H, Ogrodnik M, Jurk D, Proctor CJ, 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. EMBO Journal 38:e100492 Genetics Physiology Link
Filkova AA, Martyanov AA, Dasgupta AK, 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, UK 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
Mercadante CJ, Prajapati M, Parmar JH, Conboy HL, Dash ME, Pettiglio MA, Herrera C, Bu JT, Stopa EG, Mendes P, Bartnikas TB (2019) Gastrointestinal iron excretion and reversal of iron excess in a mouse model of inherited iron excess. Haematologica 104:678–689 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 AE (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, UK 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
Tjendana Tjhin V (2019) Brain iron trafficking in health and disease: a systems approach. Ph.D. Thesis, University of Warwick, UK Physiology Link

13 publications
2018
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
Guimera AM (2018) Investigating homeostatic disruption by constitutive signals during biological ageing. Thesis, Newcastle University Signaling Physiology Link
Guimera AM, 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
2017
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
Seitter H (2017) Retinal function of the voltage-gated calcium channel subunit α2δ-3 / Light-dependent effects in α2δ-3 mutant and in wild type retina. Ph.D. Thesis, Universität Tübingen, Germany. Biochemistry Biophysics 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

7 publications
2016
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
Llanos-Pérez JA, Betancourt-Mar JA, Cocho G, Mansilla R, Nieto-Villar JM (2016) Phase transitions in tumor growth: III vascular and metastasis behavior. Physica A 462:560–568 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 A, Ito 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, UK Signaling Physiology Link

10 publications
2015
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, Sanz A (2015) Temporal aspects of copper homeostasis and its crosstalk with hormones. Frontiers in Plant Science 6:255. Physiology Plant Biology 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, UK Physiology Link
Terentyeva VA, Sveshnikova AN, Panteleev MA (2015) Kinetics and mechanisms of surface-dependent coagulation factor XII activation. Journal of Theoretical Biology 382:235–243 Physiology Biophysics Link

5 publications
2014
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. Ph.D. Thesis, Universidad de 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, Corfe BM (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
2013
Fröhlich M (2013) Computational and experimental investigation of the mechanisms involved in cellular water transport and (cat)ion homeostasis. Ph.D. Thesis, Free University of Berlin, Germany Physiology Link
Phelix CF, Villareal G, LeBaron RG, Roberson DJ (2013) Molecular neural model recreates electrophysiology: Transcriptome-To-Physiome™ NeurobioSimulations using COPASI® software. Proceedings of the 2013 6th International IEEE/EMBS Conference on Neural Engineering (NER). San Diego, CA, 178–181 Physiology Link

2 publications
2012
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
McAuley MT, Wilkinson DJ, Jones JJ, Kirkwood TBL (2012) A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. BMC Systems Biology 6:130 Metabolism Physiology Link
Phelix CF, Villareal G, Perez-Cordova M, Hernandez S, Perry G, Colom L (2012) P3-395: Reanimating basal forebrain cholinergic neurons in electrophysiology biosimulations using COPASI software. Alzheimer’s & Dementia 8:P593–P594 Physiology Biophysics Link

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

1 publication
2010
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
2009

0 publication
2008