Abstract
Modern biology has decisively moved in a direction where we scrutinise systems holistically rather than looking at entities in different levels discretely or in isolation. Unlike previous reductionist approaches; in this new approach called Systems Biology, networks play a crucial role in arriving at and summing up the holistic picture and in understanding the emergent properties of the system. In this chapter, we give an overview of how network approaches are useful at various levels in biology. After a conceptual introduction to networks and various network metrics used to quantify networks; we discuss various concepts like network motifs and random networks. We then examine at length about how networks shed insight at virtually every layer of life like gene regulatory networks, networks involving proteins and metabolic networks. We end the chapter with a discussion of the application of networks to epidemiology.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Albert R, Barabasi A-L (2002) Statistical mechanics of complex networks. Rev Mod Phys 74:47–97
Albert R, Jeong H, Barabasi A-L (2000) Error and attack tolerance of complex networks. Nature 406:378–382
Amaral LAN, Scala A, Barthelemy M, Stanley HE (2000) Classes of small-world networks. Proc Natl Acad Sci U S A 97:11149–11152
Banerjee SJ, Roy S (2012) Key to network controllability arxiv:1209.3737
Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cells functional organization. Nat Rev: Genet 5:101–113
Bhattacharyya M, Vishveshwara S (2011) Probing the allosteric mechanism in Pyrrolysyl-tRNA synthetase using energy-weighted network formalism. Biochem 50:6225–6236
Brinda KV, Vishveshwara S (2005) A network representation of protein structures: implications for protein stability. Biophys J 89:4159–4170
Filkov V, Saul ZM, Roy S, D’Souza RM, Devanbu PT (2009) Modeling and verifying a broad array of network properties. EPL (Europhys Lett) 86:28003
Freeman LC (1977) A set of measures of centrality based on betweenness. Sociometry 40:35–41
Goodey NM, Benkovic SJ (2008) Allosteric regulation and catalysis emerge via a common route. Nat Chem Biol 4:474–482
Greene LH, Higman VA (2003) Uncovering network systems within protein structures. J Mol Biol 334:781–791
Hongwu M, An-Ping Z (2003) Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19:270–277
Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL (2000) The large-scale organization of metabolic networks. Nature 407:651–654
Jeong H, Mason SP, Barabasi A-L, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411:41–42
Kannan N, Vishveshwara S (1999) Identification of side-chain clusters in protein structures by a graph spectral method. J Mol Biol 292:441–464
Kitano H (2002) Systems biology: a brief overview. Science 295(5560):1662–1664
Kitsak M, Gallos L, Havlin S, Liljeros F, Muchnik L, Stanley HE, Makse HA (2010) Identification of influential spreaders in complex networks. Nat Phys 6:888–893
Lee TI et al (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298(5594):799–804
Ma H et al (2003) Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinfomatics 19:270–277
Milo R et al (2002) Network motifs: simple building blocks of complex networks. Science 298(5594):824–827
Newman MEJ (2002) Assortative mixing in networks. Phys Rev Lett 89:208701
Newman MEJ (2010) Networks: an introduction. Oxford University Press, Oxford
Roy S (2012) Systems biology beyond degree, hubs and scale-free networks. Syst Synth Biol 6:31–34. doi:10.1007/s11693-012-9094-y
Roy S (2014) Networks, metrics and systems biology. In Kulkarni V, Stan G-B, Raman K (eds) A systems theoretic approach to systems and synthetic biology I: models and system characterizations. Springer, Heidelberg. DOI:http://dx.doi.org/10.1007/978-94-017-9041-3_8
Roy S, Filkov V (2009) Strong associations between microbe phenotypes and their network architecture. Phys Rev E 80:040902 (R)
Scala A et al (2001) Small-world networks and the conformation space of a short lattice polymer chain. Europhys Lett 55:59–4
Vendruscolo M, Dokholyan NV, Paci E, Karplus M (2002) Small-world view of the amino acids that play a key role in protein folding. Phys Rev E 65:061910
Vijayabaskar MS, Vishveshwara S (2010) Interaction energy based protein structure networks. Biophys J 99:3704–3715
Wagner A, Fell D (2001) The small world inside large metabolic networks. Proc Roy Soc London Series B 268:1803–1810
Wuchty S, Almaas E (2005) Peeling the yeast protein network. Proteomics 5:444–449
Wuellner DR, Roy S, D’Souza RM (2010) Resilience and rewiring of the passenger airline networks in the United States. Phys Rev E 82:056101
Wunderlich Z, Mirny LA (2006) Using the topology of metabolic networks to predict viability of mutant strains. Biophys J 91:2304–2311
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Roy, U., Grewal, R., Roy, S. (2015). Complex Networks and Systems Biology. In: Singh, V., Dhar, P. (eds) Systems and Synthetic Biology. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9514-2_7
Download citation
DOI: https://doi.org/10.1007/978-94-017-9514-2_7
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-017-9513-5
Online ISBN: 978-94-017-9514-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)