Not only is the quantity of life science data expanding, but new types of biological data continue to be introduced as a result of technological development and a growing understanding of biological systems. Methods for analyzing these data are an increasingly important component of modern biological research. In Bioinformatics, leading researchers in the field provide a selection of the most useful and widely applicable methods, able to be applied as is, or with minor variations, to many specific problems.
Volume II: Structure, Function and Applications contains methods pertinent to the prediction of protein and RNA structures and the analysis and classification of structures, methods for inferring the function of previously identified genomic elements, chiefly protein-coding genes, medical applications in diagnostics and drug discovery, and "meta-methods" for developers of bioinformatics algorithms.
From the reviews: "In general, this book describes some of the most useful and widely used techniques in the field of bioinformatics. ! it covers a wide variety of topics to satisfy the large audience involved in using and developing bioinformatics. ! These will be of extreme importance to those involved in utilization and development of bioinformatics methods. The book is written for students and beginning level bioinformatics researchers. ! This is a good reference in the field of bioinformatics, particularly for those who are just starting out." (Basabi Rana, Doody's Review Service, September, 2008) "Bioinformatics is presented ! with a total of 51 chapters. ! successfully cover the wide field of bioinformatics, providing many useful methods, the majority of which are accessible to the non-specialist. ! will serve as a valuable reference and therefore may be most appropriate as an institutional purchase." (Conrad Nieduszynski, Microbiology Today, February, 2009) "Volume II contains 25 chapters that cover computational approaches and theory in analyzing function and structure of protein and nucleic acid sequences. ! give relatively in-depth coverage of many concepts that are applied by bioinformatics specialists. ! Many of the chapters are example driven, with basic forays into bioinformatics analyses that will educate readers in both the theory and practical matter of running the analyses." (Jason E. Stajich, The Quarterly Review of Biology, Vol. 84, September, 2009) "This volume emphasizes protein analysis and function recognition. ! In summary, this book presents a number of bioinformatics tools and methods, ranging from protein structure prediction, to gene function inference, to microarray data profiling. ! The book is very suitable for entry-level bioinformaticians and clinical researchers." (Hsun-Hsien Chang, ACM Computing Reviews, August, 2009)
Bioinformatics: Volume II: Structure, Function and Applications Section I: Structures Chapter 1. UNAFold: Software for Nucleic Acid Folding and Hybridization Nicholas R. Markham and Michael Zuker Chapter 2. Protein Structure Prediction Bissan Al-Lazikani, Emma E. Hill and Veronica Morea Chapter 3. An Introduction to Protein Contact Prediction Nicholas Hamilton and Thomas Huber Chapter 4. Analysis of Mass Spectrometry Data in Proteomics Rune Matthiesen and Ole N. Jensen Chapter 5. The Classification of Protein Domains Russell L. Marsden and Christine A. Orengo Section II: Inferring Function Chapter 6. Inferring Function from Homology Richard D. Emes Chapter 7. The Rosetta Stone Method Shailesh V. Date Chapter 8. Inferring Functional Relationships from Conservation of Gene Order Gabriel Moreno-Hagelsieb Chapter 9. Phylogenetic Profiling Shailesh V. Date, Jose M Peregrin-Alvarez Chapter 10. Phylogenetic Shadowing: Sequence Comparisons of Multiple Primate Species Dario Boffelli Chapter 11. Prediction of Regulatory Elements Albin Sandelin Chapter 12. Expression and Microarrays Joaquin Dopazo and Fatima Al-Shahrour Chapter 13. Identifying Components of Complexes Nicolas Goffard and Georg Weiller Chapter 14. Integrating Functional Genomics Data Insuk Lee and Edward M. Marcotte Section III: Applications and Disease Chapter 15. Computational Diagnostics with Gene Expression Profiles Claudio Lottaz, Dennis Kostka, Florian Markowetz and Rainer Spang Chapter 16. Analysis of Quantitative Trait Loci Mario Falchi Chapter 17. Molecular Similarity Concepts and Search Calculations Jens Auer and Jurgen Bajorath Chapter 18. Optimization of the MAD Algorithm for Virtual Screening Hanna Eckert and Jurgen Bajorath Chapter 19. Combinatorial Optimization Models for Finding Genetic Signatures from Gene Expression Datasets Regina Berretta, Wagner Costa and Pablo Moscato Chapter 20. Genetic Signatures for a Rodent Model of Parkinson's Disease Using Combinatorial Optimization Methods Mou'ath Hourani, Regina Berretta, Alexandre Mendes and Pablo Moscato Section IV: Analytical and Computational Methods Chapter 21. Developing Fixed-Parameter Algorithms to Solve Combinatorially Explosive Biological Problems Falk Huffner, Rolf Niedermeier and Sebastian Wernicke Chapter 22. Clustering Geoffrey J. McLachlan, R. W. Bean and S. K. Ng Chapter 23. Visualization Falk Schreiber Chapter 24. Constructing Computational Pipelines Mark Halling-Brown and Adrian J. Shepherd Chapter 25. Text mining Andrew B. Clegg and Adrian J. Shepherd
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