COPASI's Use In Theory

2022

0 publication
2021
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
2020
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
2019

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

1 publication
2017
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
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

3 publications
2016

0 publication
2015
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
2014

0 publication
2013
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
2012
Bodenstein C, Heiland I, Schuster S (2012) Temperature compensation and entrainment in circadian rhythms. Physical Biology 9:036011 Theory Link

1 publication
2011
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
Liu B, Hsu D, Thiagarajan PS (2011) Probabilistic approximations of ODEs based bio-pathway dynamics. Theoretical Computer Science 412:2188–2206 Theory Link

3 publications
2010
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

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

1 publication
2008

0 publication
2007

0 publication
2006

0 publication