24小时热门版块排行榜

返回列表

【奖励】本帖被评价3次，作者xiemin217增加金币 2.4 个

xiemin217

木虫 (正式写手)

APEPI: 1
应助: 23 (小学生)
金币: 1841.3
帖子: 319
在线: 190小时
虫号: 1319439

[资源] Plant Systems Biology-ANNUAL PLANT REVIEWS 2009

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 ]

回复此楼