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[资源]
Plant Systems Biology-ANNUAL PLANT REVIEWS 2009
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Part I Systems Biology: An Overview 1 Systems Biology: Principles and Applications in Plant Research 3 G.M. Coruzzi, A. Burga, M.S. Katari and R.A. Guti´errez 1.1 Introduction 4 1.2 Network biology 6 1.3 Experimental approaches for plant systems biology 10 1.4 Strategies for genomic data integration 21 1.5 Systems biology in plant research 26 1.6 Conclusion 31 2 An Overview of Systems Biology 41 R. Albert and S.M. Assmann 2.1 Systems theory and biology 41 2.2 Graph elements and network attributes 42 2.3 Building biological networks: identifying nodes and mapping interactions 47 2.4 Building biological networks: computational methods for network inference 52 2.5 Biological network models: data integration 54 2.6 Biological network models: from network structure to dynamics 56 2.7 Perspectives 57 3 Prokaryotic Systems Biology 67 T. Kacmarczyk, P. Waltman and R. Bonneau 3.1 Introduction 67 3.2 Types of questions 68 3.3 A typical prokaryotic systems biology project 70 3.4 Global models 70 3.5 Comparative functional genomics of prokaryotes 71 3.6 Review of core technologies for prokaryotic systems biology 72 3.7 Caulobacter crescentus 77 3.8 Bacillus subtilis 86 3.9 Escherichia coli 95 3.10 Halobacterium salinarium NRC-1 109 3.11 Conclusion 122 4 Animal Systems Biology: Towards a Systems View of Development in C. Elegans 137 A. Fernandez, F. Piano and K.C. Gunsalus 4.1 Why C. elegans as a model for developmental systems biology? 138 4.2 Defining in vivo functions during development: towards a phenome map of C. elegans embryogenesis 140 4.3 Data integration: towards a systems view of early embryogenesis 151 4.4 Conclusion 159 Part II Plant Systems Biology: Enumerating and Integrating the System Components 5 Software Tools for Systems Biology: Visualizing the Outcomes of N Experiments on M Entities 169 C. Poultney and D. Shasha 5.1 The worthwhile challenge of interdisciplinary work 169 5.2 Sungear design principles 171 5.3 Combining visualization tools for plant systems biology 182 5.4 MapMan 183 5.5 Genevestigator 185 5.6 Cytoscape 187 5.7 VirtualPlant 189 5.8 Conclusion 192 6 The Plant Genome: Decoding the Transcriptional Hardwiring 196 E. Grotewold and N. Springer 6.1 Introduction 196 6.2 The plant basal transcriptional apparatus 197 6.3 Plant transcription factors 201 6.4 Hard wiring of regulatory sequences 207 6.5 Plant transcriptional regulatory motifs, modules and networks 216 6.6 Conclusion 217 7 The RNAWorld: Identifying miRNA-Target RNA Pairs as Possible Missing Links in Multi-Network Models 229 P.J. Green and B.C. Meyers 7.1 Introduction 230 7.2 Sequencing of small RNAs 232 7.3 Identification of miRNAs 233 7.4 Identification of miRNA targets 235 7.5 MicroRNA-target mRNA pairs: missing links in multi-network models? 236 8 Proteomics: Setting the Stage for Systems Biology 243 S.C. Peck 8.1 Introduction: the need for proteomics in systems biology 243 8.2 Determination of protein location in the cell 244 8.3 Identification of different protein forms 246 8.4 Quantitation 248 8.5 Conclusion 254 9 Metabolomics: Integrating the Metabolome and the Proteome for Systems Biology 258 W. Weckwerth 9.1 The molecular hierarchy in biochemical networks, the concept of systems biology and functional genomics in the post-genome era 259 9.2 Metabolomics and proteomics: post-genome disciplines intimately bound to mass spectrometric techniques 261 9.3 Metabolomics: global analysis of rapid metabolic responses combined with computer-aided iterative metabolic modelling 261 9.4 Application of metabolomics in molecular plant physiology and biochemistry 269 9.5 Measuring the key players: proteomics 273 9.6 Combining metabolomics, proteomics and multivariate data mining: a systems biology approach 279 9.7 Conclusion 281 10 From the Ionome to the Genome: Identifying the Gene Networks that Control the Mineral Content of Plants 290 M.L. Guerinot, I. Baxter and D.E. Salt 10.1 Introduction 290 10.2 Analytical platforms for ionomics 291 10.3 Bioinformatics platforms for ionomics 294 10.4 Arabidopsis as a model system for ionomics 295 10.5 Evolutionary context for ionomics 298 11 Development and Systems Biology: Riding the Genomics Wave Towards a Systems Understanding of Root Development 304 S.M. Brady and P.N. Benfey 11.1 Roots and systems biology 304 11.2 Why study roots? 305 11.3 Root development in the model plant, Arabidopsis thaliana 305 11.4 Systems biology at the molecular level: modelling a root transcriptional network 308 11.5 Identification of components 309 11.6 Component modelling 314 11.7 Systems biology at the cellular level: modelling root growth and the dynamic behaviour of its component cells 317 11.8 Systems biology: modelling the root physical network 323 11.9 Future directions 327 12 Perspectives on Ecological and Evolutionary Systems Biology 331 C.L. Richards, Y. Hanzawa, M.S. Katari, I.M. Ehrenreich, K.E. Engelmann and M.D. Purugganan 12.1 Emergent properties of systems biology, ecology and evolution 332 12.2 Complex environments and ecological systems biology 332 12.3 Gene networks and the ecological transcriptome 333 12.4 Analysis of systems biology data: the role of ecological and evolutionary methods 335 12.5 The ecological and evolutionary context of model organisms: the example of Arabidopsis and beyond 336 12.6 Natural variation in genomes and gene networks 339 12.7 The future of ecological and evolutionary systems biology 343 Index 351 Color plate (between pages 176 and 177)  http://dl.dbank.com/c0ejwoyao0 [ Last edited by xiemin217 on 2011-10-29 at 12:11 ] |
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