COPASI's Use In Theory


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Holzheu P, Großeholz R, Kummer U (2021) Impact of explicit area scaling on kinetic models involving multiple compartments. BMC Bioinformatics 22:21 Theory Link
Ritis D, Boulougouris GC (2021) On the hierarchical design of biochemical-based digital computations. Computers in Biology and Medicine 135:104630 Computational Method Theory Link

2 publications
Cho D-J, Függer M, Hopper C, Kushwaha M, Nowak T, Soubeyran Q (2020) Distributed Computation with Continual Population Growth. In: Attiya H (ed) 34th International Symposium on Distributed Computing (DISC 2020). Dagstuhl, Germany: Schloss Dagstuhl–Leibniz-Zentrum für Informatik, 7:1-7:17. Theory Link
Erlendsson S, Teilum K (2020) Binding Revisited-Avidity in Cellular Function and Signaling. Frontiers in Molecular Biosciences 7:615565 Signaling Theory Link
Ribó JM, Hochberg D (2020) Spontaneous mirror symmetry breaking: an entropy production survey of the racemate instability and the emergence of stable scalemic stationary states. Physical Chemistry Chemical Physics 22:14013–14025 Chemistry Theory Link

3 publications

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Silva LHG (2018) Self-Replication and Non-enzymatic Catalytic Networks subject to Open Flow. MS Thesis, University of Porto, Portugal. Biochemistry Theory Link

1 publication
Badet T, Peyraud R, Mbengue M, Navaud O, Derbyshire M, Oliver RP, Barbacci A, Raffaele S (2017) Codon optimization underpins generalist parasitism in fungi. eLife 6:e22472 Genomics Theory Macromolecular Biochemistry Link
Martin RR, Montero S, Silva E, Bizzarri M, Cocho G, Mansilla R, Nieto-Villar JM (2017) Phase transitions in tumor growth: V what can be expected from cancer glycolytic oscillations? Physica A 486:762–771 Metabolism Theory Link
Roy RD, Rosenmund C, Stefan MI (2017) Cooperative binding mitigates the high-dose hook effect. BMC Systems Biology 11:74 Theory Macromolecular Biochemistry Link
Wong ASY, Huck WTS (2017) Grip on complexity in chemical reaction networks. Beilstein Journal of Organic Chemistry 13:1486–1497 Chemistry Theory Link

4 publications

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Karapetyan S, Buchler NE (2015) Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators. Physical Review E 92:062712 Macromolecular Biochemistry Theory Link
Paul D, Dasgupta A, De RK (2015) Exploring the Altered Dynamics of Mammalian Central Carbon Metabolic Pathway in Cancer Cells: A Classical Control Theoretic Approach. PLoS One 10:e0137728. Theory Link
Samal SS, Grigoriev D, Fröhlich H, Weber A, Radulescu O (2015) A Geometric Method for Model Reduction of Biochemical Networks with Polynomial Rate Functions. Bulletin of Mathematical Biology 77:2180-211. Computational Method Theory Link

3 publications

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Cornish-Bowden A, Piedrafita G, Morán F, Cárdenas ML, Montero F (2013) Simulating a model of metabolic closure. Biological Theory 8:383-390 Theory Link
Kourdis PD, Goussis DA (2013) Glycolysis in Saccharomyces cerevisiae: Algorithmic exploration of robustness and origin of oscillations. Mathematical Biosciences 243:190-214 Theory Link
Tapinos A, Mendes P (2013) A Method for Comparing Multivariate Time Series with Different Dimensions. PLoS One 8:e54201 Computational Method Theory Link

3 publications
Bodenstein C, Heiland I, Schuster S (2012) Temperature compensation and entrainment in circadian rhythms. Physical Biology 9:036011 Theory Link

1 publication
Hinze T, Schumann M, Bodenstein C, Heiland I, Schuster S (2011) Biochemical Frequency Control by Synchronisation of Coupled Repressilators: An In Silico Study of Modules for Circadian Clock Systems. Computational Intelligence and Neuroscience 2011:1–9 Theory Link
Kolodkin AN (2011) Emergence of design. PhD Thesis, Vrije Universiteit Amsterdam, The Netherlands. Theory Metabolism Link
Li Y, Cucinotta FA (2011) Modeling non-homologous end joining. Journal of Theoretical Biology 283:122–135 Genetics Theory Macromolecular Biochemistry Link
Liu B, Hsu D, Thiagarajan PS (2011) Probabilistic approximations of ODEs based bio-pathway dynamics. Theoretical Computer Science 412:2188–2206 Theory Link

4 publications
Flach EH, Schnell S (2010) Stability of open pathways. Mathematical Biosciences 228:147–152 Theory Metabolism Link
Piedrafita G, Montero F, Morán F, Cárdenas ML, Cornish-Bowden A (2010) A Simple Self-Maintaining Metabolic System: Robustness, Autocatalysis, Bistability. PLoS Computational Biology 6:e1000872 Metabolism Theory Link

2 publications
Magarkar A, Banerji A, Kolhi S (2009) Quantification of Biological Robustness at the Systemic Level. arXiv preprint arXiv:0903.4844 Theory Link

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