- Course overview
- Search within this course
- What is a mathematical model?
- Introduction to networks and graphs
- How to get from biology to mathematics
- Introduction to three mathematical model formalisms
- Case study – Infectious diseases (SIR Models)
- Other modelling approaches
- Sustainable modelling and sharing
- Summary
- Check your learning
- Your feedback
- References
References
Banwarth-Kuhn M, Sindi S. How and why to build a mathematical model: A case study using prion aggregation. J Biol Chem. 2020 Apr 10;295(15):5022-5035. doi: 10.1074/jbc.REV119.009851. Epub 2020 Jan 31. PMID: 32005659; PMCID: PMC7152750.
Booth CS, Crowther A, Helikar R, Luong T, Howell ME, Couch BA, Roston RL, van Dijk K, Helikar T. 2021. Teaching advanced concepts in regulation of the lac operon with modeling and simulation. CourseSource. https://doi.org/10.24918/cs.2021.39
Bordbar, A., Monk, J., King, Z. et al. Constraint-based models predict metabolic and associated cellular functions. Nat Rev Genet 15, 107–120 (2014). https://doi.org/10.1038/nrg3643
Gunawardena J. Models in biology: ‘accurate descriptions of our pathetic thinking’. BMC Biology. 2014 Apr;12:29. DOI: 10.1186/1741-7007-12-29. PMID: 24886484; PMCID: PMC4005397.
Koutrouli M, Karatzas E, Paez-Espino D, Pavlopoulos GA. A Guide to Conquer the Biological Network Era Using Graph Theory. Frontiers in Bioengineering and Biotechnology. 2020 ;8:34. DOI: 10.3389/fbioe.2020.00034. PMID: 32083072; PMCID: PMC7004966.
Niarakis A, Helikar T. A practical guide to mechanistic systems modeling in biology using a logic-based approach. Brief Bioinform. 2021 Jul 20;22(4):bbaa236. doi: 10.1093/bib/bbaa236. PMID: 33064138; PMCID: PMC8293813.
Noordijk B, Garcia Gomez ML, ten Tusscher KHWJ, de Ridder D, van Dijk ADJ, Smith RW. The rise of scientific machine learning: a perspective on combining mechanistic modelling with machine learning for systems biology. Frontiers in Systems Biology [Internet]. 2024 Aug 2;4. Available from: http://dx.doi.org/10.3389/fsysb.2024.1407994
Porubsky VL, Goldberg AP, Rampadarath AK, Nickerson DP, Karr JR, Sauro HM. Best Practices for Making Reproducible Biochemical Models. Cell Syst. 2020 Aug 26;11(2):109-120. doi: 10.1016/j.cels.2020.06.012. PMID: 32853539; PMCID: PMC7480321.
Puniya BL, Verma M, Damiani C, Bakr S, Dräger A. Perspectives on computational modeling of biological systems and the significance of the SysMod community. Bioinformatics Advances. 2024 ;4(1):vbae090. DOI: 10.1093/bioadv/vbae090. PMID: 38948011.
Raia V, Schilling M, Böhm M, et al. Dynamic mathematical modeling of IL13-induced signaling in Hodgkin and primary mediastinal B-cell lymphoma allows prediction of therapeutic targets. Cancer Research. 2011 Feb;71(3):693-704. DOI: 10.1158/0008-5472.can-10-2987. PMID: 21127196.
Touré V, Le Novère N, Waltemath D, Wolkenhauer O (2018) Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. PLoS Comput Biol 14(2): e1005740. https://doi.org/10.1371/journal.pcbi.1005740
Ullah M, Wolkenhauer O. Stochastic approaches in systems biology. WIREs Systems Biology and Medicine [Internet]. 2010 Jun 15;2(4):385–97. Available from: http://dx.doi.org/10.1002/wsbm.78
Volkova S, Matos MRA, Mattanovich M, Marín de Mas I. Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis. Metabolites. 2020; 10(8):303. https://doi.org/10.3390/metabo10080303