By Björn H. Junker, Falk Schreiber
An advent to organic networks and techniques for his or her analysisAnalysis of organic Networks is the 1st booklet of its sort to supply readers with a entire creation to the structural research of organic networks on the interface of biology and computing device technological know-how. The booklet starts with a quick assessment of organic networks and graph theory/graph algorithms and is going directly to discover: international community homes, community centralities, community motifs, community clustering, Petri nets, sign transduction and gene rules networks, protein interplay networks, metabolic networks, phylogenetic networks, ecological networks, and correlation networks.Analysis of organic Networks is a self-contained advent to this crucial examine subject, assumes no specialist wisdom in laptop technology or biology, and is out there to execs and scholars alike. every one bankruptcy concludes with a precis of details and with workouts for readers to check their knowing of the fabric offered. also, an FTP web site with hyperlinks to author-provided information for the booklet is accessible for deeper study.This ebook is acceptable as a source for researchers in desktop technological know-how, biology, bioinformatics, complex biochemistry, and the lifestyles sciences, and likewise serves as an incredible reference textual content for graduate-level classes in bioinformatics and organic study.
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Extra resources for Analysis of Biological Networks (Wiley Series in Bioinformatics)
Within the extensive literature on the shortest paths problem, the most common choices are the Dijkstra and the Floyd–Warshall algorithm . The Dijkstra algorithm returns the lowest cost path between a source vertex ni and all other vertices in the network in O(NV2 ) time. For efficiency reasons, the algorithm return just one shortest path; enumerating all shortest paths between two vertices is computationally more tricky and expensive. To calculate the all-to-all distances, the Floyd– Warshall algorithm is the method of choice.
Thompson, I. Simon, J. Zeitlinger, E. G. Jennings, H. L. Murray, D. B. Gordon, B. Ren, J. J. -B. Tagne, T. L. Volkert, W. Fraenkel, D. K. Gifford, and R. A. Young. Transcriptional regulatory networks in Saccharomyces cerivisiae. Science, 298:799–804, 2002. 24. J. Lisso, D. Steinhauser, T. Altmann, J. Kopka, and C. M¨ussig. Identification of brassinoidrelated genes by means of transcript co-response analyses. Nucleic Acids Research, 33:2685–2696, 2005. 14 NETWORKS IN BIOLOGY 25. -W. -P. Zeng. Phylogenetic comparison of metabolic capacities of organisms at genome level.
Nature Genetics, 35:176–179, 2003. 1 INTRODUCTION The term network is an informal description for a set of elements with connections or interactions between them. A typical example from biology is a protein interaction network. It consists of a set of proteins (elements) and a set of interactions between them (connections). The previous chapter introduced many different biological networks. Given such networks, we could be interested in questions such as Which protein has the highest number of interactions with other proteins in a protein interaction network?