Use of CellNetAnalyzer in biotechnology and metabolic engineering

Journal of Biotechnology
Axel von KampSteffen Klamt

Abstract

Mathematical models of the cellular metabolism have become an essential tool for the optimization of biotechnological processes. They help to obtain a systemic understanding of the metabolic processes in the used microorganisms and to find suitable genetic modifications maximizing the production performance. In particular, methods of stoichiometric and constraint-based modeling are frequently used in the context of metabolic and bioprocess engineering. Since metabolic networks can be complex and comprise hundreds or even thousands of metabolites and reactions, dedicated software tools are required for an efficient analysis. One such software suite is CellNetAnalyzer, a MATLAB package providing, among others, various methods for analyzing stoichiometric and constraint-based metabolic models. CellNetAnalyzer can be used via command-line based operations or via a graphical user interface with embedded network visualizations. Herein we will present key functionalities of CellNetAnalyzer for applications in biotechnology and metabolic engineering and thereby review constraint-based modeling techniques such as metabolic flux analysis, flux balance analysis, flux variability analysis, metabolic pathway analysis (elementary flux modes)...Continue Reading

References

Apr 6, 2007·BMC Systems Biology·Steffen KlamtErnst D Gilles
Jan 7, 2014·PLoS Computational Biology·Axel von Kamp, Steffen Klamt
Aug 1, 2014·BMC Biotechnology·Verena LohrUdo Reichl

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Citations

Jul 28, 2018·Bioinformatics·Iñigo ApaolazaFrancisco J Planes
Jan 17, 2019·Bioinformatics·Philipp Schneider, Steffen Klamt
Mar 1, 2019·Scientific Reports·Jorgelindo da Veiga MoreiraSabine Peres
Dec 17, 2019·Biotechnology and Bioengineering·Lisa Katharina SchuhElmar Heinzle
Jun 4, 2019·Frontiers in Microbiology·Sören WeinrichFlorian Centler
Dec 16, 2018·Nature Communications·Naveen VenayakRadhakrishnan Mahadevan
Jul 14, 2020·Frontiers in Bioengineering and Biotechnology·Denny Popp, Florian Centler
Sep 4, 2020·PLoS Computational Biology·Susanne HollmannUNKNOWN Cost Action CA15110
Jun 26, 2020·Frontiers in Bioengineering and Biotechnology·Javad Aminian-DehkordiIvan Mijakovic
Jan 16, 2020·BMC Bioinformatics·Pavlos Stephanos Bekiaris, Steffen Klamt
Oct 12, 2020·Cell Biochemistry and Biophysics·Olga Dotsenko, Dmytro Shtofel
Jan 11, 2021·Briefings in Bioinformatics·Jana Musilova, Karel Sedlar
Dec 15, 2020·Metabolic Engineering·Irene Otero-Muras, Pablo Carbonell
Jan 16, 2021·International Journal of Molecular Sciences·Laura BaumgartnerJérôme Noailly
May 1, 2021·Metabolites·Eunice van Pelt-KleinJanBas Teusink
Aug 24, 2021·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Rudolfs PetrovsAgris Pentjuss
Feb 19, 2020·ACS Synthetic Biology·Axel von Kamp, Steffen Klamt
Dec 21, 2021·Molecular Systems Biology·Simon BoeckerSteffen Klamt

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