Bioinformatics

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. Over 80 authors from around the globe have contributed.

In Bioinformatics, leading researchers 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. Over 80 authors from around the globe have contributed to the two volumes.

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