COPASI's Use In Theory

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

1 publication
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
da 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

2 publications
2016

0 publication
2015
Karapetyan S, Buchler NE (2015) Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators. Physical Reviews 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

2 publications
2010

0 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