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Subnetwork hierarchies of biochemical pathways
Umeå University, Faculty of Science and Technology, Department of Physics.ORCID iD: 0000-0003-2156-1096
2003 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1460-2059, Vol. 19, no 4, 532-538 p.Article in journal (Refereed) Published
Abstract [en]

Motivation: The vastness and complexity of the biochemical networks that have been mapped out by modern genomics calls for decomposition into subnetworks. Such networks can have inherent non-local features that require the global structure to be taken into account in the decomposition procedure. Furthermore, basic questions such as to what extent the network (graph theoretically) can be said to be built by distinct subnetworks are little studied.

Results: We present a method to decompose biochemical networks into subnetworks based on the global geometry of the network. This method enables us to analyze the full hierarchical organization of biochemical networks and is applied to 43 organisms from the WIT database. Two types of biochemical networks are considered: metabolic networks and whole-cellular networks (also including for example information processes). Conceptual and quantitative ways of describing the hierarchical ordering are discussed. The general picture of the metabolic networks arising from our study is that of a few core-clusters centred around the most highly connected substances enclosed by other substances in outer shells, and a few other well-defined subnetworks.

Place, publisher, year, edition, pages
2003. Vol. 19, no 4, 532-538 p.
URN: urn:nbn:se:umu:diva-3821DOI: 10.1093/bioinformatics/btg033OAI: diva2:142701
Available from: 2004-03-26 Created: 2004-03-26 Last updated: 2013-09-06Bibliographically approved
In thesis
1. Form and function of complex networks
Open this publication in new window or tab >>Form and function of complex networks
2004 (English)Doctoral thesis, comprehensive summary (Other academic)
Alternative title[sv]
Form och funktion i komplexa nätverk
Abstract [en]

Networks are all around us, all the time. From the biochemistry of our cells to the web of friendships across the planet. From the circuitry of modern electronics to chains of historical events. A network is the result of the forces that shaped it. Thus the principles of network formation can be, to some extent, deciphered from the network itself. All such information comprises the structure of the network. The study of network structure is the core of modern network science. This thesis centres around three aspects of network structure: What kinds of network structures are there and how can they be measured? How can we build models for network formation that give the structure of networks in the real world? How does the network structure affect dynamical systems confined to the networks? These questions are discussed using a variety of statistical, analytical and modelling techniques developed by physicists, mathematicians, biologists, chemists, psychologists, sociologists and anthropologists. My own research touches all three questions. In this thesis I present works trying to answer: What is the best way to protect a network against sinister attacks? How do groups form in friendship networks? Where do traffic jams appear in a communication network? How is cellular metabolism organised? How do Swedes flirt on the Internet? . . . and many other questions.

Place, publisher, year, edition, pages
Umeå: Umeå universitet, 2004. 104 p.
Theoretical physics, complex networks, complexity, small-world networks, scale-free networks, graph theory, Teoretisk fysik
National Category
Physical Sciences
Research subject
Theoretical Physics
urn:nbn:se:umu:diva-222 (URN)91-7305-629-4 (ISBN)
Public defence
2004-05-07, N430, Naturvetarhuset, Umeå Universitet, Umeå, 14:00
Available from: 2004-03-26 Created: 2004-03-26 Last updated: 2013-09-06Bibliographically approved

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