Preface... Table of Contents... Contributing Authors...Part I Structure, Function, Pathways and Networks1. 3D Computational Modeling of Proteins Using Sparse Paramagnetic NMR DataKala Bharath Pilla, Gottfried Otting, and Thomas Huber2. Inferring Function from HomologyTom C. Giles and Richard D. Emes3. Inferring Functional Relationships from Conservation of Gene OrderGabriel Moreno-Hagelsieb4. Structural and Functional Annotation of Long Non-Coding RNAsMartin A. Smith and John S. Mattick5. Construction of Functional Gene Networks Using Phylogenetic ProfilesJunha Shin and Insuk Lee6. Inferring Genome-Wide Interaction NetworksGoekmen Altay and Onur Mendi7. Integrating Heterogeneous Datasets for Cancer Module IdentificationA.K.M. Azad8. Metabolic Pathway MiningJan M. Czarnecki and Adrian J. ShepherdPart II Applications9. Analysis of Genome-Wide Association DataAllan F. McRae10. Adjusting for Familial Relatedness in the Analysis of GWAS DataRussell Thomson and Rebekah McWhirter11. Analysis of Quantitative Trait LociDavid L. Duffy12. High-Dimensional Profiling for Computational DiagnosisClaudio Lottaz, Wolfram Gronwald, Rainer Spang, and Julia C. Engelmann13. Molecular Similarity Concepts for Informatics ApplicationsJurgen Bajorath14. Compound Data Mining for Drug DiscoveryJurgen Bajorath15. Studying Antibody Repertoires with Next-Generation SequencingWilliam D. Lees and Adrian J. Shepherd16. Using the QAPgrid Visualization Approach for Biomarker Identification of Cell-Specific Transcriptomic SignaturesChloe Warren, Mario Inostroza-Ponta, and Pablo Moscato17. Computer-Aided Breast Cancer Diagnosis with Optimal Feature Sets: Reduction Rules and Optimization TechniquesLuke Mathieson, Alexandre Mendes, John Marsden, Jeffrey Pond, and Pablo MoscatoPart III Computational Methods18. Inference Method for Developing Mathematical Models of Cell Signaling Pathways Using Proteomic DatasetsTianhai Tian and Jiangning Song19. ClusteringGeoffrey J. McLachlan, Richard W. Bean and Shu-Kay Ng20. Parameterized Algorithmics for Finding Exact Solutions of NP-Hard Biological ProblemsFalk Huffner, Christian Komusiewicz, Rolf Niedermeier, and Sebastian Wernicke21. Information Visualization for Biological DataTobias Czauderna and Falk Schreiber