Plant Systems Biology, 2009
Methods in Molecular Biology Series, Vol. 553

Part I: Systems Biology of Plant Gene Expression 1. Gene-Specific and Genome-Wide ChIP Approaches to Study Plant Transcriptional Networks Kengo Moroashi, Zidian Xie, and Erich Grotewold 2. Genome-Wide Analysis of RNA-Protein Interactions in Plants Alice Barkan 3. Whole-Genome Microarrays: Applications and Technical Issues Brian D. Gregory and Dmitry A. Belostotsky 4. Manipulating Large Scale Arabidopsis Microarray Expression Data: Identifying Dominant Expression Patterns and Biological Process Enrichment David A. Orlando, Siobhan M. Brady, Jeremy D. Koch, José R. Dinneny, and Philip N. Benfey 5. Applications of Ultra-High Throughput Sequencing Samuel Fox, Sergei Filichkin, and Todd C. Mockler 6. Isolation of Plant Polysomal mRNA by Differential Centrifugation and Ribosome Immunopurification Methods Angelika Mustroph, Piyada Juntawong, and Julia Bailey-Serres 7. Chromatin Charting: Global Mapping of Epigenetic Effects Chongyuan Luo and Eric Lam 8. Clone-Based Functional Genomics Annick Bleys, Mansour Karimi, and Pierre Hilson Part II: Networks, Pathways, Statistical Issues, and Novel Computational Tools 9. Challenges and Approaches to Statistical Design and Inference in High Dimensional Investigations Gary L. Gadbury, Karen A. Garrett, and David B. Allison 10. Discrete Dynamic Modeling with Asynchronous Update, or How to Model Complex Systems in the Absence of Quantitative Information Sarah M. Assmann and Réka Albert 11. Quantification of Variation in Expression Networks Daniel J. Kliebenstein 12. Coexpression Analysis of Metabolic Pathways in Plants Ann Loraine 13. Integration of Metabolic Reactions and GeneRegulation Chen-Hsiang Yeang 14. Applying Word-Based Algorithms: The IMEter Ian F. Korf and Alan B. Rose Part III: Imaging 15. Live-Imaging and Image Processing of Shoot Apical Meristems of Arabidopsis thaliana G. Venugopala Reddy and A. Roy-Chowdhury 16. Computer Vision as a Tool to Study Plant Development Edgar P. Spalding Part IV: Chemical Genetic, Metabolomic, and Integrative Methods for Plant Systems Biology 17. Metabolomics of Plant Volatiles Anthony V. Qualley and Natalia Dudareva 18. Chemical Genomics Approaches in Plant Biology Lorena Norambuena, Natasha V. Raikhel, and Glenn R. Hicks 19. Comparison of Quantitative Metabolite Imaging Tools and Carbon-13 Techniques for Fluxomics Totte Niittylae, Bhavna Chaudhuri, Uwe Sauer, and Wolf B. Frommer 20. Democratization and Integration of Genomic Profiling Tools Michael R. Sussman, Edward L. Huttlin, and Dana J. Wohlbach