Bioinformatics: Volume II: Structure, Function and Applications / Edition 1

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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 bio-informatics algorithms. As a volume of the highly successful Methods in Molecular Biology TM series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results.
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Editorial Reviews

Doody's Review Service
Reviewer: Basabi Rana, Ph.D.(Loyola University Stritch School of Medicine)
Description: In general, this book describes some of the most useful and widely used techniques in the field of bioinformatics. With a significant number of contributing authors, it covers a wide variety of topics to satisfy the large audience involved in using and developing bioinformatics. Of particular interest are the clinical correlations and the possible implication of bioinformatics in diagnostics and drug design.
Purpose: As indicated by the editor, the authors of this book provide a "detailed description and implementation advice" for a variety of techniques used in the field of molecular biology. These will be of extreme importance to those involved in utilization and development of bioinformatics methods.
Audience: The book is written for students and beginning level bioinformatics researchers. The authors are authorities in the fields of molecular biology and bioinformatics.
Features: The first section on structures focuses primarily on methods used for prediction of protein structure and classification of protein domains. Section II, on inferring function, includes some of the well established techniques based on homology, "Rosetta stone" method, phylogenetic profiling, and phylogenetic shadowing. It also describes methods for predicting regulatory elements, expression patterns, complex formation, and integration of genomics data. Section III, on applications and disease, contains more applied diagnostic aspects and drug discovery. The topics in this section include the importance of microarray data in diagnostics, combinatorial optimization models for finding genetic signatures from gene expression datasets, and utilization in a rodent model of Parkinson's disease. The final section describes analytical and computational methods, which are composed of meta-methods that could be very important for the users and developers of bioinformatics. Inclusion of more illustrations would facilitate understanding.
Assessment: This is a good reference in the field of bioinformatics, particularly for those who are just starting out.
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Product Details

  • ISBN-13: 9781617378959
  • Publisher: Springer-Verlag New York, LLC
  • Publication date: 5/26/2011
  • Series: Methods in Molecular Biology Series , #453
  • Edition description: Softcover reprint of hardcover 1st ed. 2008
  • Edition number: 1
  • Pages: 506
  • Product dimensions: 7.09 (w) x 9.89 (h) x 1.11 (d)

Table of Contents

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 MarioFalchi Chapter 17. Molecular Similarity Concepts and Search Calculations Jens Auer and Jürgen Bajorath Chapter 18. Optimization of the MAD Algorithm for Virtual Screening Hanna Eckert and Jürgen 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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