A Primer of Genome Science
Authors: Greg Gibson & Spencer V. Muse
Publisher: Sinauer, Sunderland, Massachusetts, 2002
Contents:
1. Genome Projects: Organization and Objectives -- 2. Genome Sequencing and Annotation -- 3. Gene Expression and the Transcriptome -- 4. Proteomics and Functional Genomics -- 5. SNPs and Variation -- 6. Integrative Genomics

Bioinformatics : A Practical Guide to the Analysis of Genes and Proteins
Editors: Andreas D. Baxevanis & B.F. Francis Ouellette
Publisher: John Wiley, 1998
Contents:
1. The Internet and the Biologist -- 2. The GenBank Sequence Database -- 3. Structure Databases -- 4. Sequence Analysis Using GCG -- 5. Information Retrieval from Biological Databases -- 6. The NCBI Data Model -- 7.Sequence Alignment and Database Searching -- 8. Prical Aspects of Multiple Sequence Alignment -- 9. Phylogenetic Analysis -- 10. Predictive Methods Using Nucleotide Sequences -- 11. Predictive Methods Using Protein Sequences -- 12. Of Mice and Men: Navigation Public Physical Mapping Databases -- 13. ACEDB: A Database for Genome Information -- 14. Submitting DNA Sequence to the Databases

Bioinformatics and Functional Genomics
Author: Johnathan Pevsner
Publisher: Wiley-Liss, Hoboken, New Jersey, 2003
Contents:
1. Introduction -- 2. Access to Sequence and Literature Databases -- 3. Pairwise Sequence Alignment -- 4. Basic Local Alignment Search Tool (BLAST) -- 5. Advanced BLAST Searching -- 6. Genome-Wide Analysis of Gene Expression -- 7. Gene Expression: Microarrays -- 8. Protein Analysis and Proteomics -- 9. Protein Structure -- 10. Multiple Sequence Alignment -- 11. Molecular Phylogeny -- 12. Completed Genomes and the Tree of Life -- 13. Completed Genomes: Viruses -- 14. Completed Genomes: Bacteria and Archaea -- 15. Eukaryotic Genomes: Fungi -- 16. Eukaryotic Genomes: From Parasites to Primates -- 17. The Human Genome -- 18. Human Disease

Bioinformatics for Dummies
Authors: Jean-Michel Claverie & Cedric Notredame
Publisher: Wiley, 2003
Contents:
1. Finding Out What Bioinformatics Can Do for You -- 2. How Most People Use Bioinfomatics -- 3. Using Nucleotide Sequence Databases -- 4. Using Protein and Specialized Sequence Databases -- 5. Working with a Single DNA Sequence -- 6. Working with a Single Protein Sequence -- 7. Similarity Searches on Sequence Databases -- 8. Comparing Two Sequences -- 9. Building a Multiple Sequence Alignment -- 10. Editing and Publishing Alignments -- 11. Working with Protein 3-D Structures -- 12. Working with RNA -- 13. Building Phylogenetic Trees -- 14. The Ten Commandments When Using Servers -- 15. Some Useful Bioinformatics Resources

Bioinformatics for Geneticists
Authors: Michael R. Barnes & Ian C. Gray
Publisher: Wiley, West Sussex, 2003
Contents:
1. Introduction: The Role of Genetic Bioinformatics -- 2. Internet Resources for the Geneticist -- 3. Human Genetic Variations: Databases and Concepts -- 4. Finding, Delineating and Analysing Genes -- 5. Assembling a View of the Human Genome -- 6. Mouse and Rat Genome Informatics -- 7. Genetic and Physical Map Resources -- An Integrated View -- 8. From Linkage Peak to Culprit Gene: Following Up Linkage Analysis of Complex Phenotypes with Population-based Association Studies -- 9. Genetic Studies from Genomic Sequence -- 10. SNP Discovery and PCR-based Assay Design: From In Silico Data to the Laboratory Experiment -- 11. Tools for Statistical Analysis of Genetic Data -- 12. Predictive Functional Analysis of Polymorphisms: An Overview -- 13. Functional In Silico Analysis of Non-coding SNPs -- 14. Amino Acid Properties and Consequences of Substitutions -- 15. Gene Expression Informatics and Analysis -- 16. Proteomic Informatics -- 17. Concluding Remarks: Final Thoughts and Future Trends

Bioinformatics : Genes, Proteins, and Computers
Editors: Christine Orengo, David Jones & Janet Thornton
Publisher: Oxford : BIOS Scientific ; New York : Distributed in the U.S. by Springer-Verlag, 2003
Contents:
1. Molecular Evolution (Sylvia Nagl) -- 2. Gene Finding (John G.Sgouros and Richard M. Twyman) -- 3. Sequence Comparison Methods (Christine Orengo) -- 4. Amino Acid Residue Conservation (William S.J. Valdar and David T. Jones) -- 5. Function Prediction from Protein Sequence (Sylvia B. Nagl) -- 6. Protein Structure Comparison (Ian Sillitoe and Christine Orengo) -- 7. Protein Structure Classifications (Frances Pearl and Christine Orengo) -- 8. Comparative Modeling (Andrew C.R. Martin) -- 9. Protein Structure Prediction (David T. Jones) -- 10. From Protein Structure to Function (Annabel E. Todd) -- 11. From Structure-Based Genome Annotation to Understanding Genes and Proteins (Sarah A. Teichmann) -- 12. Global Approaches for Studying Protein-Protein Interactions (Sarah A. Teichmann) -- 13. Predicting the Structure of Protein-Biomolecular Interactions (Richard M. Jackson) -- 14. Experimental Use of DNA Arrays (Paul Kellam and Xiaohui Liu) -- 15. Mining Gene Expression Data (Xiaohui Liu and Paul Kellam) -- 16. Proteomics (Malcolm P. Weir, Walter P. Blackstock and Richard M. Twyman) -- 17. Data Managament of Biological Information (Nigel J. Martin) -- 18. Internet Technologies for Bioinformatics (Andrew C. R. Martin)

Bioinformatics Methods and Protocols
Editors: Stephen Misener & Stephen A. Krawetz
Publisher: Humana Press, Totowa, NJ, 2000
Contents:
1. GCG: The Wisconsin Package of Sequence Analysis Programs (David D. Womble) -- 2. Web-Based Interfaces for the GCG Sequence Analysis Programs (David D. Womble) -- 3. Omiga: A PC-Based Sequence Analysis Tool (Jeffrey A. Kramer) -- 4. MacVector: Integrated Sequence Analysis for the Macintosh (Promila A. Rastogi) -- 5. DNASTAR's Lasergene Sequence Analysis Software (Timothy G. Burland) -- 6. PepTool and GeneTool: Platform-Independent Tools for Biological Sequence Analysis (David S. Wishart, Paul Stothard, and Gary H. Van Domselaar -- 7. The Staden Package, 1998 (Rodger Staden, Kathryn F. Beal, and James K. Bonfield -- 8. Building a Multiuser Sequence Analysis Facility Using Freeware (Brian Fristensky) -- 9. Free Software in Molecular Biology for Macintosh and MS Windows Computers (Don Gilbert) -- 10. Flexible Sequence Similarity Searching with the FASTA3 Program Package (William R. Pearson) -- 11. The Use of CLUSTAL W and CLUSTAL X for Multiple Sequence Alignment (Ashok Alyar) -- 12. Phylogenetic Analysis Using PHYLIP (Jacques D. Retlef) -- 13. Annotating Sequence Data Using Genotator (Nomi L. Harris) -- 14. Low Cost Gel Analysis (Jeffry A. Reidler) -- 15. Computer Resources for the Clinical and Molecular Geneticist (Yuval Yaron and Avi Orr-Urtreger) -- 16. The NCBI: Publicly Available Tools and Resources on the Web (Jack P. Jenuth) -- 17 Resources at EBI (Patricia Rodriguez-Tome) -- 18 Computer-Assisted Analysis of Transcription Control Regions: MatInspector and Other Programs (Thomas Werner) -- 19. Computational Approaches for Gene Identification (Gautam B. Singh) -- 20. Primer3 on the WWW for General Users and for Biologist Programmers (Steve Rozena and Helen Skaletsky) -- 21. Using the WWW to Supply the Molecular Biology Lab (MaryAnn Labant and Roger Anderson) -- 22. Network Computing: Restructuring How Scientists Use Computers and What We Get Out of Them (Brian Fristensky) -- 23. Computing with DNA (Lila Kari and Laura F. Landweber) -- 24 Detecting Biological Petterns: The Integration of Databases, Models, and Algorithms (Gautam B. Singh) -- 25. Design and Implementation of an Introductory Course for Computer Applications in Molecular Biology and Genetics (Stephen A. Krawetz) -- 26. The Virtual Library I: Searching MEDLINE (Keir Reavie) -- 27. The Virtual Library II: Science Citation Index and Current Awareness Services (Keir Reavie) -- 28. The Virtual Library III: Electronic Journals, Grants, and Funding Information (Keir Reavie)

Bioinformatics: Sequence and Genome Analysis
Author: David W. Mount
Publisher: Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2001
Contents:
1. Historical Introduction and Overview -- 2. Collecting and Storing Sequences in the Laboratory -- 3. Alignment of Pairs of Sequences -- 4. Multiple Sequence Alignment -- 5. Prediction of RNA Secondary Structure -- 6. Phylogenetic Prediction -- 7. Database Searching for Similar Sequences-- 8. Gene Prediction -- 9. Protein Classification and Structure Prediction -- 10. Genome Analysis.

Bioinformatics : The Machine Learning Approach
Authors: Pierre Baldi & Sren Brunak.
Publisher: MIT Press, Cambridge, Massachusetts, 1998
Contents:
1. Introduction -- 2. Machine Learning Foundations: The Probabilistic Framework -- 3. Probabilistic Modeling and Inference: Examples -- 4. Machine Learning Algorithms -- 5.Neural Networks: The Theory -- 6. Neural Networks: Applications -- 7. Hidden Markov Models: The Theory -- 8. Hidden Markov Models: Applications -- 9. Hybrid Systems: Hidden Markov Models and Neural Networks -- 10. Probabillistic Models of Evolution: Phylogenetic Trees -- 11. Stochastic Grammars and Linguistics -- 12. Internet Resources and Public Databases -- A. Statistics -- B. Information Theory, Entropy, and Relative Entropy -- C. Probabilistic Graphical Models -- D. HMM Technicalisities, Scaling, Periodic Architectures, State Functions, and Dirichlet Mixtures -- E. List of Main Symbols and Abbreviations

Developing Bioinformatics Computer Skills
Authors: Cynthia Gibas & Per Jambeck
Publisher: O'Reilly, Beijing, 2001
Contents:
1. Biology in the Computer Age -- 2. Computational Approaches to Biological Questions -- 3. Setting Up Your Workstation -- 4. Files and Directories in Unix -- 5. Working on a Unix System -- 6. Biological Research on the Web -- 7. Sequence Analysis, Pairwise Alignment, and Database Searching -- 8. Multiple Sequence Alignments, Trees, and Profiles -- 9. Visualizing Protein Structures and Computing Structural Properties -- 10. Predicting Protein Structure and Function from Sequence -- 11. Tools for Genomics and Proteomics -- 12. Automating Data Analysis with Perl -- 13. Building Biological Databases -- 14. Visualization and Data Mining

Dictionary of Bioinformatics and Computational Biology
Editors: John M. Hancock & Marketa J. Zvelebil
Publisher: Wiley, 2004

Statistical Methods in Bioinformatics : An Introduction
Author: Warren John Ewens
Publisher: Springer, New York, 2001
Contents
1. Bioinformatics.Statistics.Computational Biology -- 2. Methods.Biometry -- 3. Methods.Data Interpretation, Statistical.Statistics -- 4. Methods.Medical Informatics -- 5. Methods.