1.       Use of Genome Browsers to Locate your Favorite Genes  1

2.       Methods for Identifying and Mapping Recent Segmental and Gene Duplications in Eukaryotic Genomes  9

3.       Identification and Mapping of Paralogous Genes on a Known Genomic DNA Sequence  21

4.       Quantitative DNA Fiber Mapping in Genome Research and Construction of Physical Maps  31

5.       Prins for Mapping Single-Copy Genes  59

6.       VISTA Family of Computational Tools for Comparative Analysis of DNA Sequences and Whole Genomes  69

7.       Computational Prediction of cis-Regulatory Modules from Multispecies Alignments Using Galaxy, Table Brower, and GALA  91

8.       Comparative Promoter Analysis in Vertebrate Genomes with the CORG Workbench  105

9.       cis-Regulatory Region Analysis Using BEARR  119

10.   A Database of 9-Mers from Promoter Regions of Human Protein-Coding Genes  129

11.   A Program Toolkit for the Analysis of Regulatory Regions of Genes  135

12.   Analysis of Allele-Specific Gene Expression  153

13.   Construction of microRNA-Containing Vectors for Expression in Mammalian Cells  167

14.   Mining Microarray Data at NCBI’s Gene Expression Omnibus (GEO)  175

15.   The Stanford Microarray Database: A User’s Guide  191

16.   Detecting Nucleosome Ladders on Unique DNA Sequences in Mouse Liver Nuclei  209

17.   DNA Methyltransferase Probing of DNA-Protein Interactions  225

18.   Protein Binding Microarrays (PBMs) for Rapid, High-Through Characterization of the Sequence Specificities of  DNA Binding proteins  245

19.   Quantitative Profiling of Protein-DNA Binding on Microarrays  261

20.   Analysis of Protein-DNA Binding by Streptavidin-Agarose Pulldown  281

21.   Isolation and Mass Spectrometry of Specific DNA Binding Proteins  291

22.   Isolation of Transcription Factor Complexes by In Vivo Biotinylation Tagging and Direct Binding to Streptavidin Beads  305