COPASI's Use In Biotechnology

Arya S, Williams A, Reina SV, Knapp CW, Kreft J-U, Hobman JL, Stekel DJ (2021) Towards a general model for predicting minimal metal concentrations co-selecting for antibiotic resistance plasmids. Environmental Pollution 275:116602 Microbiology Biotechnology Link
Farinelli G, Di Luca A, Kaila VRI, MacLachlan MJ, Tiraferri A (2021) Fe-chitosan complexes for oxidative degradation of emerging contaminants in water: Structure, activity, and reaction mechanism. Journal of Hazardous Materials 408:124662 Biotechnology Chemistry Link
Oliveira A, Rodrigues J, Ferreira EC, Rodrigues L, Dias O (2021) A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli. PLOS Computational Biology 17:e1008704 Biotechnology Metabolism Link

3 publications
Balasubramanian S, Chandrasekran P, Yesudhas AJR, Ganapathyraman P, Eiteman MA, Subramanian R (2020) In vivo interpretation of model predicted inhibition in acrylate pathway engineered Lactococcus lactis. Biotechnology and Bioengineering 117:3785–3798 Microbiology Metabolism Biotechnology Link
Zhou Q, Liu Y, Yuan W (2020) Kinetic modeling of butyric acid effects on butanol fermentation by Clostridium saccharoperbutylacetonicum. New Biotechnology 55:118–126 Biotechnology Microbiology Link

2 publications
Nguyen VD, Styevkó G, Madaras E, Haktanirlar G, Tran ATM, Bujna E, Dam MS, Nguyen QD (2019) Immobilization of β-galactosidase on chitosan-coated magnetic nanoparticles and its application for synthesis of lactulose-based galactooligosaccharides. Process Biochemistry 84:30–38 Biotechnology Link
Tapia F, Laske T, Wasik MA, Rammhold M, Genzel Y, Reichl U (2019) Production of defective interfering particles of influenza A virus in parallel continuous cultures at two residence times–insights from qPCR measurements and viral dynamics modeling. Frontiers in Bioengineering and Biotechnology 7:275 Biotechnology Link

2 publications
Nguyen VD, Styevkó G, Ta LP, Tran AT, Bujna E, Orbán P, Dam MS, Nguyen QD (2018) Immobilization and some properties of commercial enzyme preparation for production of lactulose-based oligosaccharides. Food and Bioproducts Processing 107:97–103 Biotechnology Enzymology Link
Vranish JN, Ancona MG, Oh E, Susumu K, Lasarte Aragonés G, Breger JC, Walper SA, Medintz IL (2018) Enhancing Coupled Enzymatic Activity by Colocalization on Nanoparticle Surfaces: Kinetic Evidence for Directed Channeling of Intermediates. ACS Nano 12:7911–7926 Biotechnology Enzymology Link
Wang M, Wölfer C, Otrin L, Ivanov I, Vidaković-Koch T, Sundmacher K (2018) Transmembrane NADH Oxidation with Tetracyanoquinodimethane. Langmuir 34:5435–5443 Biochemistry Biotechnology Link
Zhou Q, Liu Y, Yuan W (2018) Kinetic modeling of lactic acid and acetic acid effects on butanol fermentation by Clostridium saccharoperbutylacetonicum. Fuel 226:181–189 Metabolism Microbiology Biotechnology Link

4 publications
Komasilovs V, Pentjuss A, Elsts A, Stalidzans E (2017) Total enzyme activity constraint and homeostatic constraint impact on the optimization potential of a kinetic model. Biosystems 162:128-134 Computational Method Biotechnology Link
Stalidzans E, Mozga I, Sulins J, Zikmanis P (2017) Search for a Minimal Set of Parameters by Assessing the Total Optimization Potential for a Dynamic Model of a Biochemical Network. IEEE/ACM Transactions on Computational Biology and Bioinformatics 14:978–985 Computational Method Biotechnology Link
Vranish JN, Ancona MG, Oh E, Susumu K, Medintz IL (2017) Enhancing coupled enzymatic activity by conjugating one enzyme to a nanoparticle. Nanoscale 9:5172–5187 Enzymology Biotechnology Link

3 publications
Palai T, Kumar A, Bhattacharya PK (2016) Enzyme immobilization/bioconjugation in producing galactio-oligosaccharidies from lactose: developments of kinetic models and bio-reactors. Materials Today: Proceedings 3:3568–3586 Biotechnology Link
Salcedo-Sora JE, Mc Auley MT (2016) A mathematical model of microbial folate biosynthesis and utilisation: implications for antifolate development. Molecular BioSystems 12:923–933 Microbiology Metabolism Biotechnology Link

2 publications
Kashyap R, Palai T, Bhattacharya PK (2015) Kinetics and model development for enzymatic synthesis of fructo-oligosaccharides using fructosyltransferase. Bioprocess and Biosystems Engineering 38:2417-26 Biotechnology Metabolism Link
Palaia T, Kumarb A, Bhattacharyaa PK (2015) Kinetic studies and model development for the formation of galacto-oligosaccharides from lactose using synthesized thermo-responsive bioconjugate. Enzyme and Microbial Technology 70:42-49 Biotechnology Enzymology Link
Raganatia F, Procentese A, Olivieri G, Götzc P, Salatino P, Marzocchella A (2015) Kinetic study of butanol production from various sugars by Clostridium acetobutylicum using a dynamic model. Biochemical Engineering Journal 99:156-66. Biotechnology Metabolism Microbiology Link
Trausinger G, Gruber C, Krahulec S, Magnes C, Nidetzky B, Klimacek M (2015) Identification of novel metabolic interactions controlling carbon flux from xylose to ethanol in natural and recombinant yeasts. Biotechnology and Biofuels 8:157 Biotechnology Metabolism Link

4 publications
Khandekar DC, Palai T, Agarwal A, Bhattacharya PK (2014) Kinetics of sucrose conversion to fructo-oligosaccharides using enzyme (invertase) under free condition. Bioprocess and Biosystems Engineering 37:2529–2537 Enzymology Biotechnology Link
Palai T, Singh AK, Bhattacharya PK (2014) Enzyme, beta-galactosidase immobilized on membrane surface for galacto-oligosaccharides formation from lactose: kinetic study with feed flow under recirculation loop. Biochemical Engineering Journal 88:68-76 Biotechnology Enzymology Link
Raganati F (2014) Butanol production by fermentation of renewable feedstocks. PhD Thesis, Università di Napoli Federico II, Naples, Italy Biotechnology Link

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Casas A, Ramos MJ, Pérez Á (2011) Kinetics of chemical interesterification of sunflower oil with methyl acetate for biodiesel and triacetin production. Chemical Engineering Journal 171:1324–1332 Biotechnology Chemistry Link
Fedosov SN, Xu X (2011) Enzymatic synthesis of biodiesel from fatty acids. Kinetics of the reaction measured by fluorescent response of Nile Red. Biochemical Engineering Journal 56:172–183 Biotechnology Link

2 publications
Escuela G, Hinze T, Dittrich P, Schuster S, Moreno-Alvarez M (2010) Modelling Modified Atmosphere Packaging for Fruits and Vegetables using Membrane Systems. In Fred A, Filipe J Gamboa H. (Eds.), Proc. 3rd International Conference on Bio-inspired Systems and Signal Processing BIOSIGNALS 2010, pp. 306-311, INSTICC press Computational Method Biotechnology Link

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