Biomolecular Networks: Methods and Applications in Systems Biology
Biomolecular Networks: Methods and Applications in Systems Biology
复制标题
DOI：
10.1002/9780470488065
复制
发表时间：
2009-07
期刊：
影响因子：
--
通讯作者：
Luonan Chen;Rui-Sheng Wang;Xiang-Sun Zhang
中科院分区：
文献类型：
--
作者：
Luonan Chen;Rui-Sheng Wang;Xiang-Sun Zhang
前言。致谢。插图列表。缩写词。1绪论。1.1分子生物学基本概念。1.2细胞中的生物分子网络。1.3网络系统生物学。1.4本书简介。基因网络。2转录调控：网络与模型。2.1转录调控与基因表达。2.2转录调控网络。2.3基于生化反应的非线性模型。2.4调控网络集成模型。2.5综述。3基因调控网络重构。3.1基因调控网络数学模型。3.2基因调控网络重构。3.3多数据集基因网络推断。3.4基于基因网络的药物靶点鉴定。3.5综述。4转录调控网络。4.1预测TF结合位点和启动子。4.2转录相互作用的推断。4.3鉴定TF的组合调控。4.4推断协同调控网络。4.5预测转录因子活性。4.6总结。蛋白质相互作用网络。5蛋白质-蛋白质相互作用的预测。5.1蛋白质-蛋白质相互作用的实验。5.2蛋白质-蛋白质相互作用的预测。5.3基于多结构域对的蛋白质相互作用预测。5.4结构域相互作用预测方法。5.5综述。6生物分子网络的拓扑结构。6.1生物分子网络的统计性质。6.2蛋白质相互作用网络的进化。6.3枢纽，基序，6.4枢纽和网络基序的探索作用。6.5生物分子网络的模块化评价。6.6综述。7生物分子网络的比对。7.1来自多物种的生物分子网络。7.2生物分子网络的成对比对。7.3网络的数学规划比对。7.4生物分子网络的多重比对。7.5子网络和途径查询。7.6综述。8基于网络的蛋白质功能预测。8.1蛋白质功能与标注。8.2蛋白质功能模块检测。8.3蛋白质功能标注的功能链接。8.4高通量数据的蛋白质功能预测。8.5结构域的功能标注方法。8.6摘要。代谢网络和信号网络。9代谢网络：分析、重构与应用。9.1细胞代谢与代谢途径。9.2代谢网络分析与建模。9.3代谢网络重构。9.4代谢网络中药物靶点检测。9.5综述。10信号网络：建模和推理。10.1细胞系统中的信号转导。10.2信号转导途径的建模。10.3从高通量数据推断信号网络。10.4通过线性规划推断信号网络。10.5从实验证据推断信号网络。10.6总结。11其他主题和新趋势。11.1基于网络的蛋白质结构分析。11.2生物分子网络的整合。11.3非编码rna的转录后调控。11.4生物分子相互作用与人类疾病。11.5综述。参考文献。索引。
PREFACE. ACKNOWLEDGMENTS. LIST OF ILLUSTRATIONS. ACRONYMS. 1 Introduction. 1.1 Basic Concepts in Molecular Biology. 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. 2.2 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. 3.2 Reconstructing Gene Regulatory Networks. 3.3 Inferring Gene Networks from Multiple Datasets. 3.4 Gene Network-Based Drug Target Identification. 3.5 Summary. 4 Inference of Transcriptional Regulatory Networks. 4.1 Predicting TF Binding Sites and Promoters. 4.2 Inference of Transcriptional Interactions. 4.3 Identifying Combinatorial Regulations of TFs. 4.4 Inferring Cooperative Regulatory Networks. 4.5 Prediction of Transcription Factor Activity. 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. 5.3 Protein Interaction Prediction Based on Multidomain Pairs. 5.4 Domain Interaction Prediction Methods. 5.5 Summary. 6 Topological Structure of Biomolecular Networks. 6.1 Statistical Properties of Biomolecular Networks. 6.2 Evolution of Protein Interaction Networks. 6.3 Hubs, Motifs, and Modularity in Biomolecular Networks. 6.4 Explorative Roles of Hubs and Network Motifs. 6.5 Modularity Evaluation of Biomolecular Networks. 6.6 Summary. 7 Alignment of Biomolecular Networks. 7.1 Biomolecular Networks from Multiple Species. 7.2 Pairwise Alignment of Biomolecular Networks. 7.3 Network Alignment by Mathematical Programming. 7.4 Multiple Alignment of Biomolecular Networks. 7.5 Subnetwork and Pathway Querying. 7.6 Summary. 8 Network-Based Prediction of Protein Function. 8.1 Protein Function and Annotation. 8.2 Protein Functional Module Detection. 8.3 Functional Linkage for Protein Function Annotation. 8.4 Protein Function Prediction from High-Throughput Data. 8.5 Function Annotation Methods for Domains. 8.6 Summary. III METABOLIC NETWORKS AND SIGNALING NETWORKS. 9 Metabolic Networks: Analysis, Reconstruction, and Application. 9.1 Cellular Metabolism and Metabolic Pathways. 9.2 Metabolic Network Analysis and Modeling. 9.3 Reconstruction of Metabolic Networks. 9.4 Drug Target Detection in Metabolic Networks. 9.5 Summary. 10 Signaling Networks: Modeling and Inference. 10.1 Signal Transduction in Cellular Systems. 10.2 Modeling of Signal Transduction Pathways. 10.3 Inferring Signaling Networks from High-Throughput Data. 10.4 Inferring Signaling Networks by Linear Programming. 10.5 Inferring Signaling Networks from Experimental Evidence. 10.6 Summary. 11 Other Topics and New Trends. 11.1 Network-Based Protein Structural Analysis. 11.2 Integration of Biomolecular Networks. 11.3 Posttranscriptional Regulation of Noncoding RNAs. 11.4 Biomolecular Interactions and Human Diseases. 11.5 Summary. REFERENCES. INDEX.