3D Computational Modeling of Proteins Using Sparse Paramagnetic NMR Data -- Inferring Function from Homology -- Inferring Functional Relationships from Conservation of Gene Order -- Structural and Functional Annotation of Long Non-Coding RNAs -- Construction of Functional Gene Networks Using Phylogenetic Profiles -- Inferring Genome-Wide Interaction Networks -- Integrating Heterogeneous Datasets for Cancer Module Identification -- Metabolic Pathway Mining -- Analysis of Genome-Wide Association Data -- Adjusting for Familial Relatedness in the Analysis of GWAS Data -- Analysis of Quantitative Trait Loci -- High-Dimensional Profiling for Computational Diagnosis -- Molecular Similarity Concepts for Informatics Applications -- Compound Data Mining for Drug Discovery -- Studying Antibody Repertoires with Next-Generation Sequencing -- Using the QAPgrid Visualization Approach for Biomarker Identification of Cell-Specific Transcriptomic Signatures -- Computer-Aided Breast Cancer Diagnosis with Optimal Feature Sets: Reduction Rules and Optimization Techniques -- Inference Method for Developing Mathematical Models of Cell Signaling Pathways Using Proteomic Datasets -- Clustering -- Parameterized Algorithmics for Finding Exact Solutions of NP-Hard Biological Problems -- Information Visualization for Biological Data.

This second edition provides updated and expanded chapters covering a broad sampling of useful and current methods in the rapidly developing and expanding field of bioinformatics. Bioinformatics, Volume II: Structure, Function, and Applications, Second Edition is comprised of three sections: Structure, Function, Pathways and Networks; Applications; and Computational Methods. The first section examines methodologies for understanding biological molecules as systems of interacting elements. The Applications section covers numerous applications of bioinformatics, focusing on analysis of genome-wide association data, computational diagnostic, and drug discovery. The final section describes four broadly applicable computational methods that are important to this field. These are: modeling and inference, clustering, parameterized algorithmics, and visualization. As a volume in the highly successful Methods in Molecular Biology series, chapters feature the kind of detail and expert implementation advice to ensure positive results. Comprehensive and practical, Bioinformatics, Volume II: Structure, Function, and Applications is an essential resource for graduate students, early career researchers, and others who are in the process of integrating new bioinformatics methods into their research. .