Functional Genomics

1. Front Matter

   Pages i-3

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2. Through a genome, darkly: comparative analysis of plant chromosomal DNA

   • Graham J. King

   Pages 5-20

3. Plant genome evolution: lessons from comparative genomics at the DNA level

   • Renate Schmidt

   Pages 21-37

4. Computational gene finding in plants

   • Mihaela Pertea, Steven L. Salzberg

   Pages 39-48

5. Computational modeling of gene structure in Arabidopsis thaliana

   • Volker Brendel, Wei Zhu

   Pages 49-58

6. Surviving in a sea of data: a survey of plant genome data resources and issues in building data management systems

   • Leonore Reiser, Lukas A. Mueller, Seung Yon Rhee

   Pages 59-74

7. Comprehensive gene expression analysis by transcript profiling

   • Jonathan Donson, Yiwen Fang, Gregg Espiritu-Santo, Weimei Xing, Andres Salazar, Susie Miyamoto et al.

   Pages 75-97

8. DNA microarrays for functional plant genomics

   • Asaph Aharoni, Oscar Vorst

   Pages 99-118

9. Microarray data quality analysis: lessons from the AFGC project

   • David Finkelstein, Rob Ewing, Jeremy Gollub, Fredrik Sterky, J. Michael Cherry, Shauna Somerville

   Pages 119-131

10. Large-scale plant proteomics

    • Birgit Kersten, Lukas Bürkle, Eckehard J. Kuhn, Patrick Giavalisco, Zoltan Konthur, Angelika Lueking et al.

    Pages 133-141

11. Proteomics and a future generation of plant molecular biologists

    • Justin K. M. Roberts

    Pages 143-154

12. Metabolomics — the link between genotypes and phenotypes

    • Oliver Fiehn

    Pages 155-171

13. Gene replacement by homologous recombination in plants

    • Holger Puchta

    Pages 173-182

14. Recombinase-directed plant transformation for the post-genomic era

    • David W. Ow

    Pages 183-200

15. Back Matter

    Pages 201-205

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This volume provides an overview of the current state of plant genomics using a number of different approaches at a time when we celebrate the completion of the Arabidopsis genome sequence and begin the transition from structural to functional studies of this and other plant genomes. Topics covered include comparative genomics, computational approaches to gene identification and annotation and data management, high throughput methodologies for functional analysis at the levels of transcript, protein and metabolite, and methods for genome modification by both homologous and site-specific recombination. The book will provide a good introduction to some of the many aspects of genomics both for established plant biologists who wish to understand this rapidly developing area and for scientists early in their careers. It is also very suitable for a one-semester course in Plant Genomics at the upper-level undergraduate/graduate student level, where the individual chapters provide a framework that can be readily expanded by use of some of the many articles in the bibliographies.

• DNA
• Microarray
• Proteomics
• arabidopsis thaliana
• evolution
• gene expression
• genes
• genotypes
• recombination

• The Institute for Genomic Research, Rockville, USA

  Chris Town

• Case Western Reserve University, Cleveland, USA

  Chris Town

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