Bina, Minou

Gene Mapping, Discovery, and Expression : Methods and Protocols

Preface v Contributors xiii Use of Genome Browsers to Locate Your Favorite Genes 1(8) Minou Bina Methods for Identifying and Mapping Recent Segmental and Gene Duplications in Eukaryotic Genomes 9(12) Razi Khaja Jeffrey R. MacDonald Junjun Zhang Stephen W. Scherer Identification and Mapping of Paralogous Genes on a Known Genomic DNA Sequence 21(10) Minou Bina Quantitative DNA Fiber Mapping in Genome Research and Construction of Physical Maps 31(28) Heinz-Ulrich G. Weier Lisa W. Chu PRINS for Mapping Single-Copy Genes 59(10) Avirachan T. Tharapel Stephen S. Wachtel Vista Family of Computational Tools for Comparative Analysis of DNA Sequences and Whole Genomes 69(22) Inna Dubchak Dmitriy V. Ryaboy Computational Prediction of cis-Regulatory Modules from Multispecies Alignments Using Galaxy, Table Browser, and Gala 91(14) Laura Elnitski David King Ross C. Hardison Comparative Promoter Analysis in Vertebrate Genomes with the CORG Workbench 105(14) Christoph Dieterich Martin Vingron cis-Regulatory Region Analysis Using BEARR 119(10) Vinsensius Berlian Vega A Database of 9-Mers from Promoter Regions of Human Protein-Coding Genes 129(6) Minou Bina Phillip Wyss Syed Rehan Shah A Program Toolkit for the Analysis of Regulatory Regions of Genes 135(18) Phillip Wyss Sheryl A. Lazarus Minou Bina Analysis of Allele-Specific Gene Expression 153(14) Julian C. Knight Construction of microRNA-Containing Vectors for Expression in Mammalian Cells 167(8) Yoko Fukuda Hiroaki Kawasaki Kazunari Taira Mining Microarray Data at NCBI's Gene Expression Omnibus (GEO) 175(16) Tanya Barrett Ron Edgar The Stanford Microarray Database: A User's Guide 191(18) Jeremy Gollub Catherine A. Ball Gavin Sherlock Detecting Nucleosome Ladders on Unique DNA Sequences in Mouse Liver Nuclei 209(16) Tomara J. Fleury Alfred Cioffi Arnold Stein DNA Methyltransferase Probing of DNA--Protein Interactions 225(20) Scott A. Hoose Michael P. Kladde Protein Binding Microarrays (PBMs) for Rapid, High-Throughput Characterization of the Sequence Specificities of DNA Binding Proteins 245(16) Michael F. Berger Martha L. Bulyk Quantitative Profiling of Protein-DNA Binding on Microarrays 261(20) Jiannis Ragoussis Simon Field Irina A. Udalova Analysis of Protein-DNA Binding by Streptavidin--Agarose Pulldown 281(10) Kenneth K. Wu Isolation and Mass Spectrometry of Specific DNA Binding Proteins 291(14) Mariana Yaneva Paul Tempst Isolation of Transcription Factor Complexes by In Vivo Biotinylation Tagging and Direct Binding to Streptavidin Beads 305(20) Patrick Rodriguez Harald Braun Katarzyna E. Kolodziej Ernie de Boer Jennifer Campbell Edgar Bonte Frank Grosveld Sjaak Philipsen John Strouboulis Index 325