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Plant Systems Biology / Edition 1

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Overview

As a fairly new and expansive area of study, plant systems biology has been approached by scientists from fields as varied as plant physiology and astrophysics, creating a wide variety of techniques and methods to further this vital research. In Plant Systems Biology, expert investigators provide cutting-edge chapters dealing with diverse subjects such as systems biology of plant gene expression to analysis of networks, pathways, specific statistical issues and novel computational tools, imaging-based tools as well as chemical genetic, metabolomic and integrative methods that cannot be easily pigeonholed. As a volume in the highly successful Methods in Molecular Biology™ series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results.

Authoritative and comprehensive, Plant Systems Biology is an ideal guide for all researchers who wish to contribute to the evolution of the vibrant field of plant biology.

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Editorial Reviews

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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)

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Product Details

  • ISBN-13: 9781603275620
  • Publisher: Springer-Verlag New York, LLC
  • Publication date: 5/26/2009
  • Series: Methods in Molecular Biology Series , #553
  • Edition description: 2009
  • Edition number: 1
  • Pages: 408
  • Product dimensions: 7.60 (w) x 10.40 (h) x 1.20 (d)

Table of Contents

Foreword vii

Preface ix

Contributors xiii

Section I Systems Biology of Plant Gene Expression

1 Gene-Specific and Genome-Wide ChIP Approaches to Study Plant Transcriptional Networks Kengo Morohashi Zidian Xie Erich Grotewold 3

2 Genome-Wide Analysis of RNA-Protein Interactions in Plants Alice Barkan 13

3 Whole-Genome Microarrays: Applications and Technical Issues Brian D. Gregory Dmitry A. Belostotsky 39

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 Philip N. Benfey 57

5 Applications of Ultra-high-Throughput Sequencing Samuel Fox Sergei Filichkin Todd C. Mockler 79

6 Isolation of Plant Polysomal mRNA by Differential Centrifugation and Ribosome Immunopurification Methods Angelika Mustroph Piyada Juntawong Julia Bailey-Serres 109

7 Chromatin Charting: Global Mapping of Epigenetic Effects Chongyuan Luo Eric Lam 127

8 Clone-Based Functional Genomics Annick Bleys Mansour Karimi Pierre Hilson 141

Section 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 David B. Allison 181

10 Discrete Dynamic Modeling with Asynchronous Update, or How to Model Complex Systems in the Absence of Quantitative Information Sarah M. Assmann Réka Albert 207

11 Quantification of Variation in Expression Networks Daniel J. Kliebenstein 227

12 Co-expression Analysis of Metabolic Pathways in Plants Ann Loraine 247

13 Integration of Metabolic Reactions and Gene Regulation Chen-Hsiang Yeang 265

14 Applying Word-Based Algorithms: The IMEter Ian F. Korf Alan B. Rose 287

Section III Imaging

15 Live-Imaging and Image Processing of Shoot Apical Meristems of Arabidopsis thaliana G. Venugopala Reddy A. Roy-Chowdhury 305

16 Computer Vision as a Tool to Study Plant Development Edgar P. Spalding 317

Section IV Chemical Genetic, Metabolomic, and Integrative Methods for Plant Systems Biology

17 Metaboiomics of Plant Volatiles Anthony V. Qualley Natalia Dudareva 329

18 Chemical Genomics Approaches in Plant Biology Lorena Norambuena Natasha V. Raikhel Glenn R. Hicks 345

19 Comparison of Quantitative Metabolite Imaging Tools and Carbon-13 Techniques for Fluxomics Totte Niittylae Bhavna Chaudhuri Uwe Sauer Wolf B. Frommer 355

20 Democratization and Integration of Genomic Profiling Tools Michael R. Sussman Edward L. Huttlin Dana J. Wohlbach 373

Index 395

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