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

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*Encompasses topics from across the diverse field of bioinformatics through its broad scope approach *Over 80 authors from around the globe contribute to the two volumes, including many leading experts *An inter-disciplinary collaboration involving biologists, biochemists, physicists, mathematicians, statisticians and computer scientists *Contains simplified descriptions, requiring a minimum of background knowledge, amenable to students and beginners in bioinformatics *References a wide variety of software tools and scripts, available online 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. As a volume of the highly successful Methods in Molecular BiologyT series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Comprehensive and cutting-edge, Bioinformatics: Volume II: Structure, Function and Applications is an ideal reference for all scientists involved with the ever-growing array of data in the expanding field of life science. Written for: Molecular biologists, bioinformaticians, geneticists, microbiologi

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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: 9781603274289
  • Publisher: Springer-Verlag New York, LLC
  • Publication date: 5/22/2008
  • Series: Methods in Molecular Biology Series, #453
  • Edition description: 2008
  • Edition number: 1
  • Pages: 506
  • Product dimensions: 7.30 (w) x 10.20 (h) x 1.40 (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

Mario Falchi

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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