Abstract
Systems biology can be defined as the analysis of interactions with different biological systems at different complex levels by using different network approaches. Such advances have permeated to different fields, including those of health known as systems medicine. Such a novel tool has been defined as a holistic approach where human health is integrated from different perspectives, from biomedical to environmental and social. Interestingly, nowadays, there are several examples of applications of such technologies to clinics, for instance, whole-genome association studies or digital health applications that have shown to be quite helpful to public health. Therefore, in the present chapter, we resume some of the main tools of systems biology and its applications to health through systems medicine.
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Abbreviations
- ODEs:
-
Ordinary differential equations
- GRNs:
-
Gene regulatory networks
References
Ideker T, Galitski T, Hood L. A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet. 2001;2:343–72.
Kitano H. Systems biology: a brief overview. Science. 2002;295:1662–4.
Trewavas A. A brief history of systems biology: “Every object that biology studies is a system of systems.” Francois Jacob (1974). Plant Cell. 2006;18:2420–30.
Jensen HJ. Self-organized criticality: emergent complex behavior in physical and biological systems. Cambridge University Press, Cambridge, UK; 1998.
Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science. 2001;292:929–34.
Bhalla US, Iyengar R. Emergent properties of networks of biological signaling pathways. Science. 1999;283:381–7.
Tyson JJ, Chen KC, Novak B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol. 2003;15(2):221–31. https://doi.org/10.1016/s0955-0674(03)00017-6. PMID: 12648679.
Breitling R. What is systems biology? Front Physiol. 2010;1:9.
Lynch M. The evolution of genetic networks by non-adaptive processes. Nat Rev Genet. 2007;8:803–13.
Lynch M. The frailty of adaptive hypotheses for the origins of organismal complexity. Proceedings of the National Academy of Sciences. (2007), 104 (suppl 1). 8597–8604; https://doi.org/10.1073/pnas.0702207104.
Tavassoly I, Goldfarb J, Iyengar R. Systems biology primer: the basic methods and approaches. Essays Biochem. 2018;62:487–500.
Chuang H-Y, Hofree M, Ideker T. A decade of systems biology. Annu Rev Cell Dev Biol. 2010;26:721–44.
Zhu X, Gerstein M, Snyder M. Getting connected: analysis and principles of biological networks. Genes Dev. 2007;21:1010–24.
Barabási A-L, Oltvai ZN. Network biology: understanding the cell’s functional organization. Nat Rev Genet. 2004;5:101–13.
Ryan CJ, Roguev A, Patrick K, et al. Hierarchical modularity and the evolution of genetic interactomes across species. Mol Cell. 2012;46:691–704.
Han J-DJ, Bertin N, Hao T, et al. Evidence for dynamically organized modularity in the yeast protein–protein interaction network. Nature. 2004;430:88–93.
Sachs K, Perez O, Pe’er D, Lauffenburger DA, Nolan GP. Causal protein-signaling networks derived from multiparameter single-cell data. Science. 2005;308:523–9.
Sachs K, Gifford D, Jaakkola T, Sorger P, Lauffenburger DA. Bayesian network approach to cell signaling pathway modeling. Sci STKE. 2002;2002:e38.
Needham CJ, Bradford JR, Bulpitt AJ, Westhead DR. A primer on learning in Bayesian networks for computational biology. PLoS Comput Biol. 2007;3:e129.
Jha SK, Clarke EM, Langmead CJ, Legay A, Platzer A, Zuliani P. A Bayesian approach to model checking biological systems. Comput Meth Syst Biol. 2009;5688:218–34.
Albert R. Scale-free networks in cell biology. J Cell Sci. 2005;118:4947–57.
Barabási A-L. Scale-free networks: a decade ``and beyond. Science. 2009;325:412–3.
Hornung G, Barkai N. Noise propagation and signaling sensitivity in biological networks: a role for positive feedback. PLoS Comput Biol. 2008;4:e8.
Milgram S. The small-world problem. PsycEXTRA Dataset. 1967; https://doi.org/10.1037/e400002009-005.
Rives AW, Galitski T. Modular organization of cellular networks. Proc Natl Acad Sci U S A. 2003;100:1128–33.
Newman MEJ. Modularity and community structure in networks. Proc Natl Acad Sci. 2006;103:8577–82.
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Network motifs: simple building blocks of complex networks. Science. 2002;298:824–7.
Tyson JJ, Novák B. Functional motifs in biochemical reaction networks. Annu Rev Phys Chem. 2010;61:219–40.
Alon U. Network motifs: theory and experimental approaches. Nat Rev Genet. 2007;8:450–61.
Tyson JJ, Chen K, Novak B. Network dynamics and cell physiology. Nat Rev Mol Cell Biol. 2001;2:908–16.
Jones PA, Baylin SB. The epigenomics of cancer. Cell. 2007;128:683–92.
Rual J-F, Venkatesan K, Hao T, et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature. 2005;437:1173–8.
Kauffman SA. Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol. 1969;22:437–67.
Thomas R, Kaufman M. Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior. Chaos. 2001;11:170–9.
Thomas R, Kaufman M. Multistationarity, the basis of cell differentiation and memory. II. Logical analysis of regulatory networks in terms of feedback circuits. Chaos. 2001;11:180–95.
Bartocci E, Lió P. Computational modeling, formal analysis, and tools for systems biology. PLoS Comput Biol. 2016;12:e1004591.
Schaub MA, Henzinger TA, Fisher J. Qualitative networks: a symbolic approach to analyze biological signaling networks. BMC Syst Biol. 2007;1:4.
Alur R, Courcoubetis C, Henzinger TA, Ho P-H. Hybrid automata: an algorithmic approach to the specification and verification of hybrid systems. Hybrid Syst. 1993;736:209–29.
Fromentin J, Eveillard D, Roux O. Hybrid modeling of biological networks: mixing temporal and qualitative biological properties. BMC Syst Biol. 2010; https://doi.org/10.1186/1752-0509-4-79.
Boran ADW, Iyengar R. Systems approaches to polypharmacology and drug discovery. Curr Opin Drug Discov Devel. 2010;13:297–309.
Hansen J, Zhao S, Iyengar R. Systems pharmacology of complex diseases. Ann N Y Acad Sci. 2011;1245:E1–5.
Wolkenhauer O. Systems Medicine: Integrative, Qualitative and Computational Approaches. 1st Ed. 2020 Academic Press. Cambridge, Massachusetts US.
Kanodia AK, Kim I, Sturmberg JP. A personalized systems medicine approach to refractory rumination. J Eval Clin Pract. 2011;17:515–9.
Wang L, Eftekhari P, Schachner D, et al. Novel interactomics approach identifies ABCA1 as direct target of evodiamine, which increases macrophage cholesterol efflux. Sci Rep. 2018;8:11061.
Fisher CP, Plant NJ, Moore JB, Kierzek AM. QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells. Bioinformatics. 2013;29:3181–90.
Hartung T, FitzGerald RE, Jennings P, Mirams GR, Peitsch MC, Rostami-Hodjegan A, Shah I, Wilks MF, Sturla SJ. Systems toxicology: real world applications and opportunities. Chem Res Toxicol. 2017;30:870–82.
Nikpay M, Goel A, Won H-H, et al. A comprehensive 1,000 genomes-based genome-wide association meta-analysis of coronary artery disease. Nat Genet. 2015;47:1121–30.
Mäkinen V-P, Civelek M, Meng Q, et al. Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease. PLoS Genet. 2014;10:e1004502.
Smith JA, Ware EB, Middha P, Beacher L, Kardia SLR. Current applications of genetic risk scores to cardiovascular outcomes and subclinical phenotypes. Curr Epidemiol Rep. 2015;2:180–90.
Fiandaca MS, Mapstone M, Connors E, Jacobson M, Monuki ES, Malik S, Macciardi F, Federoff HJ. Systems healthcare: a holistic paradigm for tomorrow. BMC Syst Biol. 2017;11:142.
Oh S-H, Lee SY, Han C. The effects of social media use on preventive behaviors during infectious disease outbreaks: the mediating role of self-relevant emotions and public risk perception. Health Commun. 2020:1–10.
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This chapter is part of a registered project at the Instituto Nacional de Geriatría with the number DI-PI-003/2018.
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Yustis-Rubio, J.C., Gomez-Verjan, J.C. (2022). Systems Medicine Applied to Epidemiology. In: Gomez-Verjan, J.C., Rivero-Segura, N.A. (eds) Principles of Genetics and Molecular Epidemiology. Springer, Cham. https://doi.org/10.1007/978-3-030-89601-0_16
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DOI: https://doi.org/10.1007/978-3-030-89601-0_16
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