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™ 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 WojciechRychlik



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 Brejová, Tomás 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

"...contains very valuable information on a wide range of topics related to bioinformatics research." - Heredity