Biomolecular networks : methods and applications in systems biology / / Luonan Chen, Rui-Sheng Wang, Xiang-Sun Zhang

• Record Nr.: UNINA9910823650003321
• Autore: Chen Luonan <1962->
• Pubbl/distr/stampa: Hoboken, NJ, : Wiley, c2009
• ISBN: 9786612186028; 9781282186026; 1282186027; 9780470488065; 0470488069; 9780470488058; 0470488050
• Edizione: [1st ed.]
• Descrizione fisica: 1 online resource (420 p.)
• Collana: Wiley series on bioinformatics
• Altri autori (Persone): WangRui-Sheng; ZhangXiang-Sun <1943->
• Disciplina: 572.80285
• Soggetti: Molecular biology - Data processing; Computational biology; Bioinformatics; Biological systems - Research - Data processing
• Lingua di pubblicazione: Inglese
• Formato: Materiale a stampa
• Livello bibliografico: Monografia
• Note generali: Description based upon print version of record.
• Nota di bibliografia: Includes bibliographical references and index.
• Nota di contenuto: BIOMOLECULAR NETWORKS; CONTENTS; PREFACE; ACKNOWLEDGMENTS; LIST OF ILLUSTRATIONS; ACRONYMS; 1 Introduction; 1.1 Basic Concepts in Molecular Biology; 1.1.1 Genomes, Genes, and DNA Replication Process; 1.1.2 Transcription Process for RNA Synthesis; 1.1.3 Translation Process for Protein Synthesis; 1.2 Biomolecular Networks in Cells; 1.3 Network Systems Biology; 1.4 About This Book; I GENE NETWORKS; 2 Transcription Regulation: Networks and Models; 2.1 Transcription Regulation and Gene Expression; 2.1.1 Transcription and Gene Regulation; 2.1.2 Microarray Experiments and Databases; 2.1.3 ChIP-Chip Technology and Transcription Factor Databases2.2 Networks in Transcription Regulation; 2.3 Nonlinear Models Based on ; Biochemical Reactions; 2.4 Integrated Models for Regulatory Networks; 2.5 Summary; 3 Reconstruction of Gene Regulatory Networks; 3.1 Mathematical Models of Gene Regulatory Network; 3.1.1 Boolean Networks; 3.1.2 Bayesian Networks; 3.1.3 Markov Networks; 3.1.4 Differential Equations; 3.2 Reconstructing Gene Regulatory Networks; 3.2.1 Singular Value Decomposition; 3.2.2 Model-Based Optimization; 3.3 Inferring Gene Networks from Multiple Datasets; 3.3.1 General Solutions and a Particular Solution of Network Structures for Multiple Datasets3.3.2 Decomposition Algorithm; 3.3.3 Numerical Validation; 3.4 Gene Network-Based Drug Target Identification; 3.4.1 Network Identification Methods; 3.4.2 Linear Programming Framework; 3.5 Summary; 4 Inference of Transcriptional Regulatory Networks; 4.1 Predicting TF Binding Sites and Promoters; 4.2 Inference of Transcriptional Interactions; 4.2.1 Differential Equation Methods; 4.2.2 Bayesian Approaches; 4.2.3 Data Mining and Other Methods; 4.3 Identifying Combinatorial Regulations of TFs; 4.4 Inferring Cooperative Regulatory Networks4.4.1 Mathematical Models; 4.4.2 Estimating TF Activity; 4.4.3 Linear Programming Models; 4.4.4 Numerical Validation; 4.5 Prediction of Transcription Factor Activity; 4.5.1 Matrix Factorization; 4.5.2 Nonlinear Models; 4.6 Summary; II PROTEIN INTERACTION NETWORKS; 5 Prediction of Protein-Protein Interactions; 5.1 Experimental Protein-Protein Interactions; 5.2 Prediction of Protein-Protein Interactions; 5.2.1 Association Methods; 5.2.2 Maximum-Likelihood Estimation; 5.2.3 Deterministic Optimization Approaches; 5.3 Protein Interaction Prediction Based on Multidomain Pairs5.3.1 Cooperative Domains, Strongly Cooperative Domains, Superdomains; 5.3.2 Inference of Multidomain Interactions; 5.3.3 Numerical Validation; 5.3.4 Reconstructing Complexes by Multidomain Interactions; 5.4 Domain Interaction Prediction Methods; 5.4.1 Statistical Method; 5.4.2 Domain Pair Exclusion Analysis; 5.4.3 Parsimony Explanation Approaches; 5.4.4 Integrative Approaches; 5.5 Summary; 6 Topological Structure of Biomolecular Networks; 6.1 Statistical Properties of Biomolecular Networks; 6.2 Evolution of Protein Interaction Networks
• Sommario/riassunto: Alternative techniques and tools for analyzing biomolecular networks With the recent rapid advances in molecular biology, high-throughput experimental methods have resulted in enormous amounts of data that can be used to study biomolecular networks in living organisms. With this development has come recognition of the fact that a complicated living organism cannot be fully understood by merely analyzing individual components. Rather, it is the interactions of components or biomolecular networks that are ultimately responsible for an organism's form and function. This book addresses the impor