COPASI's Use In Signaling

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
Hagen SJ, Son M (2017) Origins of heterogeneity in Streptococcus mutans competence: interpreting an environment-sensitive signaling pathway. Physical Biology 14:015001 Signaling Microbiology Link
Haurat MF, Figueiredo AS, Hoffmann L, Li L, Herr K, J Wilson A, Beeby M, Schaber J, Albers S-V (2017) ArnS, a kinase involved in starvation-induced archaellum expression. Molecular Microbiology 103:181–194 Microbiology Signaling Link
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

4 publications
2016
Andrews SS, Peria WJ, Richard CY, Colman-Lerner A, Brent R (2016) Push-pull and feedback mechanisms can align signaling system outputs with inputs. Cell Systems 3:444–455 Signaling Link
Beuke K (2016) TNF-induced NF-κB Signal Transduction in the Liver. PhD Thesis, Heidelberg University. Immunology Signaling Link
Bush A, Vasen G, Constantinou A, Dunayevich P, Patop IL, Blaustein M, Colman-Lerner A (2016) Yeast GPCR signaling reflects the fraction of occupied receptors, not the number. Molecular Systems Biology 12:898 Signaling Link
Dalle Pezze P, Ruf S, Sonntag AG, Langelaar-Makkinje M, Hall P, Heberle AM, Navas PR, Van Eunen K, Tölle RC, Schwarz JJ, Wiese H, Warscheid B, Deitersen J, Stork B, Fäßler E, Schäuble S, Horvatovich P, Shanley DP, Thedieck K (2016) A systems study reveals concurrent activation of AMPK and mTOR by amino acids. Nature Communications 7:13254 Signaling Link
Di Camillo B, Carlon A, Eduati F, Toffolo GM (2016) A rule-based model of insulin signalling pathway. BMC Systems Biology 10:38 Signaling Link
Dubey BN, Lori C, Ozaki S, Fucile G, Plaza-Menacho I, Jenal U, Schirmer T (2016) Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking. Science advances 2:e1600823 Biochemistry Signaling Link
Panchal C, Azimi S, Petre I (2016) Generating the Logicome of a Biological Network. International Conference on Algorithms for Computational Biology. Springer, 38–49 Computational Method Signaling Link
Pappalardo F, Russo G, Candido S, Pennisi M, Cavalieri S, Motta S, McCubrey JA, Nicoletti F, Libra M (2016) Computational Modeling of PI3K/AKT and MAPK Signaling Pathways in Melanoma Cancer. PLOS ONE 11:e0152104 Signaling 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
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
Tyc KM, Herwald SE, Hogan JA, Pierce JV, Klipp E, Kumamoto CA (2016) The game theory of Candida albicans colonization dynamics reveals host status-responsive gene expression. BMC Systems Biology 10:20 Microbiology Immunology Signaling 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

14 publications
2015
Amemiya T, Honma M, Kariya Y, Ghosh S, Kitano H, Kurachi Y, Fujita K, Sasaki Y, Homma Y, Abernethy DR, Kume H, Suzuki H (2015) Elucidation of the molecular mechanisms underlying adverse reactions associated with a kinase inhibitor using systems toxicology. npj Systems Biology and Applications 1:15005 Toxicology Signaling 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
Hamacher-Brady A, Brady NR (2015) Bax/Bak-Dependent, Drp1-Independent Targeting of XIAP into Inner-Mitochondrial Compartments Counteracts Smac-Dependent Effector Caspase Activation. J. Biol. Chem. 290:22005-18. 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
Marwaha S (2015) A Genomics and Mathematical Modeling Approach for the study of Helicobacter pylori associated Gastritis and Gastric Cancer. PhD Thesis, University of Cincinnati Immunology Signaling Link
Subramanian A, Sarkar RR (2015) Dynamics Of GLI Regulation And A Strategy To Control Cancerous Situation: Hedgehog Signaling Pathway Revisited. J. Biol. Systems 23:681-719 Signaling Link
Suwanmajo T, Krishnan J (2015) Mixed mechanisms of multi-site phosphorylation. J. Royal Soc. Interface 12:20141405 Signaling Link
Sveshnikova AN, Ataullakhanov FL, Panteleev MA (2015) Compartmentalized calcium signaling triggers subpopulation formation upon platelet activation through PAR1. Molecular BioSystems 11:1052-60 Signaling Link
Wang, H-Y, Huang Y-X, Zheng L-H, Bao Y-L, Sun L-G, Wu Y, Yu C-L, Song Z-B, Sun Y, Wang G-N, Ma Z-Q, Li Y-X Li (2015) Modelling Coupled Oscillations in the Notch, Wnt, and FGF Signaling Pathways during Somitogenesis: A Comprehensive Mathematical Model. Comput. Intelligence Neurosci. 2015:387409 Signaling Link
Willems PH, Pahle J, Stalpers XL, Mugahid D, Nikolaew A, Koopman WJ, Kummer U (2015) PKC-mediated inhibitory feedback of the cholecystokinin 1 receptor controls the shape of oscillatory Ca2+ signals. FEBS J. 282:2187-201 Signaling Link

11 publications
2014
Antunes G, Sebastião AM, de Souza FMS (2014) Mechanisms of regulation of olfactory transduction and adaptation in the olfactory cilium. PLoS One 9:e105531 Signaling Pharmacology Link
Dalle Pezze P, Nelson G, Otten EG, Korolchuk VI, Kirkwood TBL, von Zglinicki T, Shanley DP (2014) Dynamic Modelling of Pathways to Cellular Senescence Reveals Strategies for Targeted Interventions. PLoS Comput. Biol. 10:e1003728. Signaling Link
Graybill C, Prehoda KE (2014) Ordered multisite phosphorylation of lethal giant larvae by atypical protein kinase C. Biochemistry 53:4931-7 Signaling Link
Hui W, Young DA, Rowan AD, Xu X, Cawston TE, Proctor CJ (2014) Oxidative changes and signalling pathways are pivotal in initiating age-related changes in articular cartilage. Annals of the Rheumatic Diseases 75:449–458 Signaling Immunology Link
Kleppe R, Ghorbani S, Martinez A, Haavik J (2014) Modelling cellular signal communication mediated by phosphorylation dependent interaction with 14-3-3 proteins. FEBS Letters 588:92–98 Signaling Link
Marwaha S, Schumacher MA, Zavros Y, Eghbalnia HR (2014) Crosstalks between Cytokines and Sonic Hedgehog in Helicobacter pylori Infection: A Mathematical Model. PLoS ONE 9:e111338. Immunology Signaling Link
McAuley MT, Khalil R, Stockton DJ, Schilstra MJ (2014) Modelling the flagellar motor assembly process to help improve industrial operations systems design. Signaling Link
Schaber J, Lapytsko A, Flockerzi D (2014) Nested autoinhibitory feedbacks alter the resistance of homeostatic adaptive biochemical networks. J. Royal Soc. Interface 11:20130971 Signaling Link
Ventura AC, Bush A, Vasen G, Goldín MA, Burkinshaw B, Bhattacharjee N, Folch A, Brent R, Chernomoretz A, Colman-Lerner A (2014) Utilization of extracellular information before ligand-receptor binding reaches equilibrium expands and shifts the input dynamic range. Proceedings of the National Academy of Sciences 111:E3860–E3869 Signaling Link
Wang CCN, Chang P-C, Ng K-L, Chang C-M, Sheu PCY, Tsai JJP (2014) A model comparison study of the flowering time regulatory network in Arabidopsis. BMC Systems Biology 8:15 Signaling Link

10 publications
2013
Gow C-H (2013) Novel mechanisms of transcriptional regulation by leukemia fusion proteins. PhD Thesis, University of Cincinnati, Cincinnati, OH. Signaling Link
Helgeson LA, Nolen BJ (2013) Mechanism of synergistic activation of Arp2/3 complex by cortactin and N-WASP. eLife 2:e00884 Macromolecular Biochemistry Signaling Link
Kolodkin A, Sahin N, Phillips A, Hood SR, Bruggeman FJ, Westerhoff HV, Plant N (2013) Optimization of stress response through the nuclear receptor-mediated cortisol signalling network. Nature Communications 4:1792 Signaling Link
Ravichandran S, Rao KVS, Jain S (2013) Bistability in a model of early B cell receptor activation and its role in tonic signaling and system tunability. Molecular BioSystems 9:2498-2511 Signaling 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
Sharma V, Compagnoni A (2013) Computational and mathematical models of the JAK-STAT signal transduction pathway. Proceedings of the 2013 Summer Computer Simulation Conference 15 Computational Method Signaling Link
Sharp GC (2013) Comprehensive data analysis to study parturition. PhD Thesis, University of Edinburgh. Signaling Link
Sharp GC, Ma H, Saunders PTK, Norman JE (2013) A Computational Model of Lipopolysaccharide-Induced Nuclear Factor Kappa B Activation: A Key Signalling Pathway in Infection-Induced Preterm Labour. PLoS ONE 8:e70180 Signaling Link
Smith GR, Shanley, DP (2013) Computational modelling of the regulation of Insulin signalling by oxidative stress. BMC Systems Biol. 7:41 Signaling Link

9 publications
2012
Betney R, de Silva E, Mertens C, Knox Y, Krishnan J, Stansfield I (2012) Regulation of release factor expression using a translational negative feedback loop: A systems analysis. RNA 18:2320-2334 Signaling Link
Dalle Pezze P, Sonntag AG, Thien A, Prentzell MT, Godel M, Fischer S, Neumann-Haefelin E, Huber TB, Baumeister R, Shanley DP, Thedieck K (2012) A Dynamic Network Model of mTOR Signaling Reveals TSC-Independent mTORC2 Regulation. Science Signaling 5:ra25-ra25 Signaling Link
Heiland I, Bodenstein C, Hinze T, Weisheit O, Ebenhoeh O, Mittag M, Schuster S (2012) Modeling temperature entrainment of circadian clocks using the Arrhenius equation and a reconstructed model from Chlamydomonas reinhardtii. Journal of Biological Physics 38:449-464 Signaling Link
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
Leach MD, Tyc KM, Brown AJP, Klipp E (2012) Modelling the Regulation of Thermal Adaptation in Candida albicans, a Major Fungal Pathogen of Humans. PLoS ONE 7:e32467 Signaling Link
Li Y, Wang M, Carra C, Cucinotta FA (2012) Modularized Smad-regulated TGFβ signaling pathway. Mathematical Biosciences 240:187-200 Signaling Link
Maiwald, Tim (2012) Computational Analysis of The Interferon Alpha Signalling Using a Systems Biology Modelling Approach Pathway. PhD Thesis, Heidelberg University. Signaling Link
Mazemondet O, John M, Leye S, Rolfs A, Uhrmacher AM (2012) Elucidating the Sources of β-Catenin Dynamics in Human Neural Progenitor Cells. PLoS ONE 7:e42792 Signaling Link
Pinna F, Sahle S, Beuke K, Bissinger M, Tuncay S, D’Alessandro LA, Gauges R, Raue A, Timmer J, Klingmüller U, Schirmacher P, Kummer U, Breuhahn K (2012) A Systems Biology Study on NFκB Signaling in Primary Mouse Hepatocytes. Frontiers in Physiology 3:466 Signaling Link
Piras V, Hayashi K, Tomita M, Selvarajoo K (2012) Investigation of stochasticity in TRAIL signaling cancer model. IEEE, 609-614. Signaling Link
Salvado B, Vilaprinyo E, Karathia H, Sorribas A, Alves R (2012) Two Component Systems: Physiological Effect of a Third Component. PLoS ONE 7:e31095 Signaling Link
Sarma U, Ghosh I (2012) Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade. BMC Systems Biology 6:82 Signaling Link
Sarma U, Ghosh I (2012) Oscillations in MAPK cascade triggered by two distinct designs of coupled positive and negative feedback loops. BMC Research Notes 5:287 Signaling Link
Sarma U, Sareen A, Maiti M, Kamat V, Sudan R, Pahari S, Srivastava N, Roy S, Sinha S, Ghosh I, Chande AG, Mukhopadhyaya R, Saha B (2012) Modeling and Experimental Analyses Reveals Signaling Plasticity in a Bi-Modular Assembly of CD40 Receptor Activated Kinases. PLoS ONE 7:e39898 Signaling Link
Schimek C, Vlaic S, Wöstemeyer J, Werner S, Schuster S, Schroeter A (2012) Model of the synthesis of trisporic acid in Mucorales showing bistability. IET Systems Biology 6:207-214 Signaling Link
Tiedemann MT, Heinrichs DE, Stillman MJ (2012) Multiprotein Heme Shuttle Pathway in Staphylococcus aureus : Iron-Regulated Surface Determinant Cog-Wheel Kinetics. Journal of the American Chemical Society 134:16578-16585 Signaling Link
Wegner K, Bachmann A, Schad J-U, Lucarelli P, Sahle S, Nickel P, Meyer C, Klingmüller U, Dooley S, Kummer U (2012) Dynamics and feedback loops in the transforming growth factor β signaling pathway. Biophysical Chemistry 162:22-34 Signaling Link

17 publications
2011
Bairy S, Wong CF (2011) Influence of kinetics of drug binding on EGFR signaling: A comparative study of three EGFR signaling pathway models. Proteins: Structure, Function, and Bioinformatics 79:2491–2504 Signaling Link
Danis J, Turányi T (2011) Sensitivity analysis of bacterial chemotaxis models. Procedia Computer Science 7:233–234 Signaling Microbiology Link
Iwasaki H, Takeuchi O, Teraguchi S, Matsushita K, Uehata T, Kuniyoshi K, Satoh T, Saitoh T, Matsushita M, Standley DM, Akira S (2011) The IkB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR-IL-1R by controlling degradation of regnase-1. Nature Immunology 12:1167-75 Immunology Signaling Link
Kleppe R, Martinez A, Døskeland SO, Haavik J (2011) The 14-3-3 proteins in regulation of cellular metabolism. Seminars in Cell & Developmental Biology. 22:713–719 Signaling Metabolism Link
Klipp E (2011) Computational yeast systems biology: a case study for the MAP kinase cascade. Methods in Molecular Biology 759:323–343 Signaling Link
Schweizer N (2011) Calcium signaling in fish cells. PhD Thesis, University of Heidelberg Signaling Link

6 publications
2010
Fujita KA, Toyoshima Y, Uda S, Ozaki Y, Kubota H, Kuroda S (2010) Decoupling of Receptor and Downstream Signals in the Akt Pathway by Its Low-Pass Filter Characteristics. Science Signaling 3:ra56-ra56 Signaling Link
Liu J, Mehdi S, Topping J, Tarkowski P, Lindsey K (2010) Modelling and experimental analysis of hormonal crosstalk in Arabidopsis. Molecular Systems Biology 6 Signaling Link
Maiwald T, Schneider A, Busch H, Sahle S, Gretz N, Weiss TS, Kummer U, Klingmüller U (2010) Combining theoretical analysis and experimental data generation reveals IRF9 as a crucial factor for accelerating interferon α-induced early antiviral signalling: IRF9 accelerates IFNα signal transduction. FEBS Journal 277:4741-4754 Signaling Link

3 publications
2009
Bauer-Mehren A, Furlong LI, Rautschka M, Sanz F (2009) From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways. BMC Bioinformatics 10:S6 Signaling Link
Figueiredo AS, Höfer T, Klotz C, Sers C, Hartmann S, Lucius R, Hammerstein P (2009) Modelling and simulating interleukin-10 production and regulation by macrophages after stimulation with an immunomodulator of parasitic nematodes: Modelling interleukin-10 production and regulation. FEBS Journal 276:3454-3469 Signaling Link
Goyal M, Rizzo M, Schumacher F, Wong CF (2009) Beyond thermodynamics: drug binding kinetics could influence epidermal growth factor signaling. J. Medicinal Chem. 52:5582-5585 Signaling Link
Ibrahim B, Schmitt E, Dittrich P, Diekmann S (2009) In silico study of kinetochore control, amplification, and inhibition effects in MCC assembly. Biosystems 95:35-50 Signaling Link
Menolascina F, Bellomo D, Maiwald T, Bevilacqua V, Ciminelli C, Paradiso A, Tommasi S (2009) Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering. BMC Bioinformatics 10:S4 Laboratory Method Signaling Link
Orton RJ, Adriaens ME, Gormand A, Sturm OE, Kolch W, Gilbert DR (2009) Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway. BMC Systems Biology 3:100 Signaling Link
Sun Y-C (2009) Examination of effects of GSK3β phosphorylation, β-catenin phosphorylation, and β-catenin degradation on kinetics of Wnt signaling pathway using computational method. Theoretical Biology and Medical Modelling 6:13 Signaling Link

7 publications
2008
Del Conte-Zerial P, Brusch L, Rink JC, Collinet C, Kalaidzidis Y, Zerial M, Deutsch A (2008) Membrane identity and GTPase cascades regulated by toggle and cut-out switches. Mol. Sys. Biol. 4:206 Signaling Link
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
Stefan MI, Edelstein SJ, Le Novère N (2008) An allosteric model of calmodulin explains differential activation of PP2B and CaMKII. PNAS 105:10768-73 Physiology Signaling Macromolecular Biochemistry Link

3 publications
2007
Kelly MP, Isiegas C, Cheung YF, Tokarczyk J, Yang X, Esposito MF, Rapoport DA, Fabian SA, Siegel SJ, Wand G, Houslay MD, Kanes SJ, Abel T (2007) Constitutive activation of Galphas within forebrain neurons causes deficits in sensorimotor gating because of PKA-dependent decreases in cAMP. Neuropsychopharmacology 32:577-88 Pharmacology Signaling Link

1 publication
2006
Frein D (2006) Signaling and Redox Regulation by Nitric Oxide, Superoxide and Carbon Monoxide. Signaling Link

1 publication