A Primer of Genome Science
Authors: Greg Gibson & Spencer V. Muse
Publisher: Sinauer, Sunderland, Massachusetts, 2009
Description:

Genome science has matured as a discipline to the point where it is now incorporated as a regular part of the genetics curriculum in universities. A Primer of Genome Science, Third Edition bridges the gap between standard genetics textbooks and highly specialized, technical, and advanced treatments of the subdisciplines. It provides an affordable and up-to-date introduction to the field that is suited to advanced undergraduate or early graduate courses.

Bioinformatic principles and experimental strategies are explained side-by-side with the experimental methods, establishing a framework that allows teachers to explore topics and the literature at their own pace. The Primer is organized into six chapters dealing with the scope of genomics, genome sequencing, variation and complex traits, gene expression, proteomics, and metabolomics. Each chapter includes several boxes explaining the theory behind bioinformatic methods, discussion questions, and a summary. This edition has been updated to include the latest developments in next-generation sequencing, high-volume genotyping and expression profiling, and advances in metabolomics.


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, 2009
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, 2006
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, 2007
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, 2007
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, 2010
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, 2004
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 & Debra T. Burhans
Publisher: O'Reilly, Beijing, 2013
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, 2010
Contents
1. Bioinformatics.Statistics.Computational Biology -- 2. Methods.Biometry -- 3. Methods.Data Interpretation, Statistical.Statistics -- 4. Methods.Medical Informatics -- 5. Methods.