Plant Systems Biology

Part I: Systems Biology of Plant Gene Expression1. Gene-Specific and Genome-Wide ChIP Approaches to Study Plant Transcriptional NetworksKengo Moroashi, Zidian Xie, and Erich Grotewold2. Genome-Wide Analysis of RNA-Protein Interactions in PlantsAlice Barkan3. Whole-Genome Microarrays: Applications and Technical IssuesBrian D. Gregory and Dmitry A. Belostotsky4. Manipulating Large Scale Arabidopsis Microarray Expression Data: Identifying Dominant Expression Patterns and Biological Process EnrichmentDavid A. Orlando, Siobhan M. Brady, Jeremy D. Koch, José R. Dinneny, and Philip N. Benfey5. Applications of Ultra-High Throughput SequencingSamuel Fox, Sergei Filichkin, and Todd C. Mockler6. Isolation of Plant Polysomal mRNA by Differential Centrifugation and Ribosome Immunopurification MethodsAngelika Mustroph, Piyada Juntawong, and Julia Bailey-Serres7. Chromatin Charting: Global Mapping of Epigenetic EffectsChongyuan Luo and Eric Lam8. Clone-Based Functional GenomicsAnnick Bleys, Mansour Karimi, and Pierre HilsonPart II: Networks, Pathways, Statistical Issues, and Novel Computational Tools9. Challenges and Approaches to Statistical Design and Inference in High Dimensional InvestigationsGary L. Gadbury, Karen A. Garrett, and David B. Allison10. Discrete Dynamic Modeling with Asynchronous Update, or How to Model Complex Systems in the Absence of Quantitative Information Sarah M. Assmann and Réka Albert11. Quantification of Variation in Expression Networks Daniel J. Kliebenstein12. Coexpression Analysis of Metabolic Pathways in PlantsAnn Loraine13. Integration of Metabolic Reactions and GeneRegulationChen-Hsiang Yeang14. Applying Word-Based Algorithms: The IMEterIan F. Korf and Alan B. RosePart III: Imaging15. Live-Imaging and Image Processing of Shoot Apical Meristems of Arabidopsis thalianaG. Venugopala Reddy and A. Roy-Chowdhury16. Computer Vision as a Tool to Study Plant DevelopmentEdgar P. SpaldingPart IV: Chemical Genetic, Metabolomic, and Integrative Methods for

From the reviews:"For researchers, Belostotsky (biological sciences, U. of Missouri-Kansas City) compiles 20 chapters on plant systems biology ... . Chapters describe how to identify cellular components, interactions among these components, and quantitative approaches to analyze and model interactions, emergent properties, and dynamics of the networks." (SciTech Book News, March, 2010)