Gene mapping, discovery, and expression : methods and protocols

Use of genome browsers to locate your favorite genes / Minou Bina -- Methods for identifying and mapping recent segmental and gene duplications in eukaryotic genomes / Razi Khaja ... [et al.] -- Identification and mapping of paralogous genes on a known genomic DNA sequence / Minou Bina -- Quantitative DNA fiber mapping in genome research and construction of physical maps / Heinz-Ulrich G. Weier and Lisa W. Chu -- PRINS for mapping single copy genes / Avirachan T. Tharapel and Stephen S. Wachtel -- Vista family of computational tools for comparative analysis of DNA sequences and whole genomes / Inna Dubchak and Dmitriy V. Ryaboy -- Computational prediction of cis-regulatory modules from multispecies alignments using Galaxy, table browser, and GALA / Laura Elnitski, David King, and Ross C. Hardison -- Comparative promoter analysis in vertebrate genomes with the CORG workbench / Christoph Dieterich and Martin Vingron -- cis-regulatory region analysis using BEARR / Vinsensius Berlian Vega -- A database of 9-mers from promoter region of human protein-coding genes / Minou Bina, Phillip Wyss, and Syed Rehan Shah -- A program toolkit for the analysis of regulatory regions of genes / Phillip Wyss, Sheryl A. Lazarus, and Minou Bina. Analysis of allele-specific gene expression / Julian C. Knight -- Construction of micro-rna containing vectors for expression in mammalian cells / Yoko Fukuda, Hiroaki Kawasaki, and Kazunari Taira -- Mining microarray data at NCBI's gene expression omnibus (GEO) / Tanya Barrett and Ron Edgar -- The Stanford microarray database: a user's guide / Jeremy Gollub, Catherine A. Ball, and Gavin Sherlock -- Detecting nucleosome ladders on unique DNA sequences in mouse liver nuclei / Tomara J. Fleury, Alfred Cioffi, and Arnold Stein -- DNA methyltransferase probing of DNA-protein interactions / Scott A. Hoose and Michael P. Kladde -- Protein binding microarrays (PBMS) for the rapid, high-throughput characterization of the sequence specificities of DNA binding proteins / Michael F. Berger and Martha L. Bulyk -- Quantitative profiling of protein-DNA binding on microarrays / Jiannis Ragoussis, Simon Field, and Irina A. Udalova -- Analysis of protein-DNA binding by streptavidin-agarose pulldown / Kenneth K. Wu -- Isolation and mass spectrometry of specific DNA-binding proteins / Mariana Yaneva and Paul Tempst -- Isolation of transcription factor complexes by in vivo biotinylation tagging and direct binding to streptavidin beads / Patrick Rodriguez ... [et al.].