Introduction to Bioinformatics

Part I. Biochemistry, Cell, and Molecular Biology A. The Cell Nucleic Acids and Proteins: Modern Linguistics for the Genomics and Bioinformatics Era Bradley C. Hyman Structure and Function of Cell Organelles Jon Holy Cell Signaling Daniel A. Rappolee B. Transcription and Translation DNA Replication, Repair, and Recombination Linda B. Bloom Transcription, RNA Processing, and Translation Thomas P. Yang and Thomas W. O'Brien Part II. Molecular Genetics A. Genomics Epigenetic Mechanisms Regulating Gene Expression John R. McCarrey Gene Families and Evolution Ben F. Koop Repetitive DNA: Detection, Annotation, and Analysis Jerzy Jurka Molecular Genetics of Disease and the Human Genome Project Paromita Deb-Rinker and Stephen W. Scherer B. Clinical Human Genetics Heredity C. A. Rupar The Clinical Genetics Databases Peter J. Bridge Population Genetics Jill S. Barnholtz-Sloan Part III. The UNIX Operating System A. Basics and Installation Introduction to UNIX for Biologists David D. Womble Installation of the Sun Solaris(t) Operating Environment Bryon Campbell Sun System Administration Bryon Campbell B. Managing Bioinformatics Tools Installing Bioinformatics Software in a Server-Based Computing Environment Brian Fristensky Management of a Server-Based Bioinformatics Resource Brian Fristensky C. Command Line Sequence Analysis GCG File Management Sittichoke Saisanit GCG Sequence Analysis Sittichoke Saisanit Part IV. Computer Applications A. Management and Analysis of DNA Sequencing Projects and Sequences Managing Sequencing Projects in the GAP4 Environment Rodger Staden, David P. Judge, and James K. Bonfield OLIGO Primer Analysis Software John D. Offerman and Wojciech Rychlik Statistical Modeling of DNA Sequences and Patterns Gautam B. Singh Statistical Mining of the Matrix Attachment Regions in Genomic Sequences Gautam B. Singh Analyzing Sequences Using the Staden Package and EMBOSS Rodger Staden, David P. Judge, and James K. Bonfield B. The Genome Database: Analysis and Similarity Searching Ensembl: An Open-Source Software Tool for Large-Scale Genome Analysis James W. Stalker and Anthony V. Cox The PIR for Functional Genomics and Proteomics Cathy H. Wu Sequence Similarity and Database Searching David S. Wishart GCG Database Searching David J. Heard C. Identifying Functional and Structural Sequence Elements Pattern Discovery: Methods and Software Brona Brejova, Tomas Vinar, and Ming Li The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection Thomas Werner An Introduction to Multiple Sequence Alignment and Analysis Steven M. Thompson 3D Molecular Visualization with Protein Explorer Eric Martz Multiple Sequence Alignment and Analysis: The SeqLab Interface: A Practical Guide Steven M. Thompson D. Analysis of Gene Expression: Microarrays and Other Tools Overview of the Tools for Microarray Analysis: Transcription Profiling, DNA Chips, and Differential Display Jeffrey A. Kramer Microarrays: Tools for Gene Expression Analysis Sorin Draghici Knowledge Discovery from the Human Transcriptome Kousaku Okubo and Teruyoshi Hishiki Part V. Appendices Appendix 1: CD Contents Appendix 2: A Collection of Useful Bioinformatic Tools and Molecular Tables Appendix 3: Simple UNIX Commands Index