1. Use of Genome Browsers to Locate Your Favorite Genes
Minou Bina
pp. 1-8
2. Methods for Identifying and Mapping Recent Segmental and Gene Duplications in Eukaryotic Genomes
Razi Khaja; Jeffrey R. MacDonald; Junjun Zhang; Stephen W. Scherer
pp. 9-20
3. Identification and Mapping of Paralogous Genes on a Known Genomic DNA Sequence
Minou Bina
pp. 21-30
4. Quantitative DNA Fiber Mapping in Genome Research and Construction of Physical Maps
Heinz-Ulrich G. Weier; Lisa W. Chu
pp. 31-58
5. PRINS for Mapping Single-Copy Genes
Avirachan T. Tharapel; Stephen S. Wachtel
pp. 59-68
6. VISTA Family of Computational Tools for Comparative Analysis of DNA Sequences and Whole Genomes
Inna Dubchak; Dmitriy V. Ryaboy
pp. 69-90
7. Computational Prediction of cis-Regulatory Modules from Multispecies Alignments Using Galaxy, Table Browser, and GALA
Laura Elnitski; David King; Ross C. Hardison
pp. 91-104
8. Comparative Promoter Analysis in Vertebrate Genomes With the CORG Workbench
Christoph Dieterich; Martin Vingron
pp. 105-118
9. cis-Regulatory Region Analysis Using BEARR
Vinsensius Berlian Vega
pp. 119-128
10. A Database of 9-Mers from Promoter Regions of Human Protein-Coding Genes
Minou Bina; Phillip Wyss; Syed Rehan Shah
pp. 129-134
11. A Program Toolkit for the Analysis of Regulatory Regions of Genes
Phillip Wyss; Sheryl A. Lazarus; Minou Bina
pp. 135-152
12. Analysis of Allele-Specific Gene Expression
Julian C. Knight
pp. 153-166
13. Construction of microRNA-Containing Vectors for Expression in Mammalian Cells
Yoko Fukuda; Hiroaki Kawasaki; Kazunari Taira
pp. 167-174
14. Mining Microarray Data at NCBI's Gene Expression Omnibus (GEO)*
Tanya Barrett; Ron Edgar
pp. 175-190
15. The Stanford Microarray Database: A User's Guide
Jeremy Gollub; Catherine A. Ball; Gavin Sherlock
pp. 191-208
16. Detecting Nucleosome Ladders on Unique DNA Sequences in Mouse Liver Nuclei
Tomara J. Fleury; Alfred Cioffi; Arnold Stein
pp. 209-224
17. DNA Methyltransferase Probing of DNA-Protein Interactions
Scott A. Hoose; Michael P. Kladde
pp. 225-244
18. Protein Binding Microarrays (PBMs) for Rapid, High-Throughput Characterization of the Sequence Specificities of DNA Binding Proteins
Michael F. Berger; Martha L. Bulyk
pp. 245-260
19. Quantitative Profiling of Protein-DNA Binding on Microarrays
Jiannis Ragoussis; Simon Field; Irina A. Udalova
pp. 261-280
20. Analysis of Protein-DNA Binding by StreptavidinAgarose Pulldown
Kenneth K. Wu
pp. 281-290
21. Isolation and Mass Spectrometry of Specific DNA Binding Proteins
Mariana Yaneva; Paul Tempst
pp. 291-304
22. Isolation of Transcription Factor Complexes by In Vivo Biotinylation Tagging and Direct Binding to Streptavidin Beads
Patrick Rodriguez; Harald Braun; Katarzyna E. Kolodziej; Ernie de Boer; Jennifer Campbell; Edgar Bonte; Frank Grosveld; Sjaak Philipsen; John Strouboulis
pp. 305-323