Statistical and evolutionary analysis of biological networks / editors, Michael P.H. Stumpf, Carsten Wiuf.

Format:

Book

Contributor:

Stumpf, M. P. H. (Michael P. H.)

Wiuf, Carsten.

Language:

English

Subjects (All):

Biometry.

Computational biology.

Graph theory.

Physical Description:

1 online resource (179 p.)

Edition:

1st ed.

Place of Publication:

London : Imperial College Press, c2010.

Language Note:

English

Summary:

Networks provide a very useful way to describe a wide range of different data types in biology, physics and elsewhere. Apart from providing a convenient tool to visualize highly dependent data, networks allow stringent mathematical and statistical analysis. In recent years, much progress has been achieved to interpret various types of biological network data such as transcriptomic, metabolomic and protein interaction data as well as epidemiological data. Of particular interest is to understand the organization, complexity and dynamics of biological networks and how these are influenced by ne

Contents:

Contents; Preface; 1. A Network Analysis Primer Michael P.H. Stumpf and Carsten Wiuf; 1.1. Introduction; 1.2. Types of Biological Networks; 1.3. A Primer on Networks; 1.3.1. Mathematical descriptions of networks; 1.3.1.1. Characteristics of a node; 1.3.1.2. Paths, components and trees; 1.3.1.3. Distance and diameter; 1.3.2. Network properties; 1.3.2.1. The degree distribution; 1.3.2.2. Clustering; 1.3.2.3. Average path length; 1.3.3. Mathematical representation of networks; 1.3.3.1. The adjacency matrix; 1.3.3.2. The adjacency list; 1.3.3.3. The edge list; 1.3.3.4. Some remarks on complexity

1.4. Comparing Biological Networks 1.4.1. Identity of networks; 1.4.2. Subnets and patterns; 1.4.3. The challenges of the data; References; 2. Evolutionary Analysis of Protein Interaction Networks Carsten Wiuf and Oliver Ratmann; 2.1. Introduction; 2.1.1. Molecular genetic uptake; 2.1.2. Expansion by gene duplication; 2.1.3. Redeployment of existing genetic systems; 2.2. Protein Interaction Network Data; 2.3. Mathematical Models of Networks and Network Growth; 2.3.1. Simplistic models of network growth; 2.3.2. Complex models of network growth by repeated node addition

2.3.3. Asymptotics of the node degree DD+RA and DD+PA2. 4. Inferring Evolutionary Dynamics in Terms of Mixture Models of Network Growth; 2.4.1. The likelihood of PIN data under DD+RA or DD+PA; 2.4.2. Simple methods to account for incomplete datasets; 2.4.3. Approximating the likelihood with many summaries; 2.4.4. Approximate Bayesian computation; 2.4.5. Evolutionary analysis of the PIN topologies of T. pallidum, H. pylori and P. falciparum; 2.4.6. The size of the interactome; 2.5. Conclusion; Acknowledgements; Appendix A. Proofs of Theorems.; References

3. Motifs in Biological Networks Falk Schreiber and Henning Schw obbermeyer 3.1. Introduction; 3.2. Characterisation of Network Motifs; 3.2.1. Definitions; 3.2.2. Modelling of biological data as graphs; 3.2.3. Complexity of motif search; 3.2.4. Frequency concepts; 3.2.5. Statistical significance of network motifs; 3.2.6. Randomisation algorithm for generation of null model networks; 3.2.7. Calculation of the P-value and Z-score; 3.3. Methods and Tools for the Analysis of Network Motifs; 3.3.1. Mfinder; 3.3.2. Pajek; 3.3.3. MAVisto; 3.4. Analyses of Motifs in Networks

3.4.1. Analysis of gene regulatory networks 3.4.2. Motifs in cortical networks; 3.4.3. Analysis of other networks; 3.4.4. Superstructures formed by overlapping motif matches; 3.4.5. Dynamic properties of network motifs; 3.4.6. Comparison of networks using motif distributions; 3.4.7. On the function of network motifs in biological networks; References; 4. Bayesian Analysis of Biological Networks: Clusters, Motifs, Cross- Species Correlations Johannes Berg and Michael Lassig; 4.1. Introduction; 4.2. Measuring Biological Networks; 4.3. Random Networks in Biology; 4.4. Network Clusters

4.4.1. Clusters in protein interaction networks

Notes:

Description based upon print version of record.

Includes bibliographical references and index.

ISBN:

9786612759987

9781282759985

1282759981

9781848164345

1848164343

OCLC:

729020361