Umfang:
Online-Ressource (X, 228p. 52 illus., 35 illus. in color, digital)
ISBN:
9781461403203
,
1283352087
,
9781283352086
Serie:
SpringerLink
Inhalt:
A fundamental problem in life sciences is the characterization of biological function. In medical sciences, understanding the bases of functional anomalies holds the key to effective diagnosis, treatment, ¡ and prognosis; in genetics, functional annotation of genetic variability uncovers the complex relationship between genotype and phenotype; in evolutionary biology, functional differences between diverse organisms highlight the evolutionary mechanisms that underlie the complexity of biological systems. With the successful completion of the human genome project and recent technological advances in biological data collection, it has become possible to study biological function from a systems perspective. Today, Systems Biology is established as a fundamental interdisciplinary science, which focuses on systematic study of the complex mechanisms that orchestrate the cooperation between diverse molecules that compose life. In the study of biological systems, the complex interactions between biomolecules are often abstracted using network models. Molecular networks provide descriptions of the organization of various biological processes, including cellular signaling, metabolism, and genetic regulation. Knowledge on molecular networks provides the basis for systems level analysis of biological function. Research and method development for such analyses has grown tremendously in the past few years. This volume provides a detailed overview of existing knowledge on the functional characterization of biological networks. In eight chapters authored by an international group of systems biology and bioinformatics researchers, functional coherence of molecular networks is comprehensively explored from various perspectives, including network topology, modularity, functional inference, evolution, phenotype, disease, network dynamics, and molecular kinetics
Inhalt:
Molecular networks provide descriptions of the organization of various biological processes, including cellular signaling, metabolism, and genetic regulation. Knowledge on molecular networks is commonly used for systems level analysis of biological function; research and method development in this area has grown tremendously in the past few years. This book will provide a detailed review of existing knowledge on the functional characterization of biological networks. In 15 chapters authored by an international group of prolific systems biology and bioinformatics researchers, it will organize
Anmerkung:
Includes bibliographical references and index
,
Functional Coherence of MolecularNetworks in Bioinformatics; Preface; Contents; Contributors; Chapter 1 Introduction to Network Biology; 1 Systems Biology; 2 Molecular Interaction Networks; 2.1 Protein-Protein Interaction Networks; 2.2 Metabolic Networks; 2.3 Gene Regulatory Networks; 2.4 Other Abstractions; 3 Molecular Networks and Biological Function; 4 Functional Coherence of Molecular Networks; References; Chapter 2 Topological Characteristics of Molecular Networks; 1 Biological Networks: Motivation, Data Sets, and Challenges; 2 Network Analysis: Measures of Network Structure
,
2.1 Global Network Properties2.2 Local Network Properties; 2.3 Node Centralities; 3 Network Modeling; 3.1 Network Models; 3.2 Biological Applications; 4 Network Alignment; 4.1 Local Network Alignments; 4.2 Global Network Alignments; 4.2.1 Topological Network Alignments; 5 Interplay Between Network Topology and Biological Function and Disease; 5.1 From PPI Networks to Biological Function; 5.2 PPI Networks in Disease and Pharmacology; 6 Future Prospects and Concluding Remarks; References; Chapter 3 Function Annotation in Gene Networks; 1 Computational Function Prediction and Gene Networks
,
2 Network Synthesis and Annotation3 Techniques for Computational Annotation in Networks; 3.1 Direct Approaches; 3.2 Module-Assisted Approaches; 3.3 Probabilistic Approaches; 3.4 Pattern-Based Approaches; 4 Network Annotation Prediction as a Framework; 4.1 Interaction Network Synthesis; 4.2 Network Feature Extraction; 4.3 Classification; 5 Accuracy Comparison of Existing Methods; 6 Annotation in Multiple Genome Networks; 6.1 Hypothesis A: Orthologs Share Annotations; 6.2 Hypothesis B: Orthologs Share Annotations and Annotation Profiles
,
6.3 Hypothesis C: Similar Functional Profiles Imply Shared Annotations7 Conclusion; References; Chapter 4 Proteome Network Emulating Models; 1 Proteome Network Emulation Models; 1.1 Preferential Attachment Models; 1.2 Geometric Random Model; 1.3 Gene Duplication-Based Models; 1.3.1 Parameter Selection in the Generalized Duplication Model; 2 Assessing Network Evolution Models; 2.1 Graph Isomorphism; 2.2 Network Features; 2.2.1 Degree Distribution; 2.2.2 k-hop Reachability; 2.2.3 Betweenness Distribution; 2.2.4 Closeness Distribution; 2.2.5 Subgraph Frequency
,
2.2.6 Robustness of Network Features2.3 Emulating PPI Networks; 2.3.1 Generalized Duplication Model: The Importance of Seed Network Selection; 2.3.2 Comparing PPI Networks of Varying Size; 2.4 PPI Network Emulation: Further Challenges; 3 Discussion; References; Chapter 5 Biological Network Alignment; 1 Introduction; 2 Definitions and Notations; 2.1 Network Alignment Problems; 3 Algorithms and Methods; 3.1 Local Alignment; 3.1.1 The Blast Family: PathBlast, NetworkBlast, and NetworkBlast-M; 3.1.2 MaWISh: Alignment Based on Network Evolution Models
,
3.1.3 Graemlin: Alignment with Equivalence Classes
Weitere Ausg.:
ISBN 9781461403197
Weitere Ausg.:
Buchausg. u.d.T. ISBN 9781461403197
Sprache:
Englisch
Fachgebiete:
Biologie
Schlagwort(e):
Bioinformatik
;
Netzwerk
DOI:
10.1007/978-1-4614-0320-3
URL:
Volltext
(lizenzpflichtig)
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