Preface; Contents; 1 Global Nonlinear Fitness Function for Protein Structures; Abstract; Introduction; Theory and Models; Modeling Protein Fitness Function; Two Geometric Views of Linear Protein Potentials; Optimal Linear Fitness Function; Relation to Support Vector Machines; Nonlinear Scoring Function; Optimal Nonlinear Fitness Function; Rectangle Kernel and Reduced Support Vector Machine (RSVM); Smooth Newton Method; Computational Procedures; Protein Data; Contact Maps and Sequence Decoys; Learning Linear Fitness Function; Learning Full Nonlinear Fitness Function

Learning Simplified Nonlinear Fitness FunctionResults; Linear Fitness Functions; Full Nonlinear Fitness Function; Results of Simplified Nonlinear Fitness Function; Discussion; References; 2 Computational Methods for Mass Spectrometry Imaging: Challenges, Progress, and Opportunities; Abstract; Introduction; Challenges; Challenge 1: Integration of MSI Data with Complementary Imaging Modalities; Challenge 2: Movement Toward MSI from Three-Dimensional Samples; Challenge 3: Reproducibility, Data Standardization, and Community Resources; Current Techniques in MSI Analysis; Case Study; Conclusion

AcknowledgementsReferences; 3 Identification and Functional Annotation of LncRNAs in Human Disease; Abstract; Background; Current Bioinformatics Methods; Identify Associated lncRNAs in Human Diseases; By Microarray; By RNA-seq; Annotated the Functions of Associated lncRNAs in Human Diseases Based on Co-expression Network; Further Analysis of LncRNAs After Identification and Functional Annotation; Challenges and Current Problems; Example; Identification of Differentially Expressed lncRNAs in Gastric Cancer; Conclusion; References; 4 Metabolomics Characterization of Human Diseases; Abstract

BackgroundChallenges; Current Techniques; Example One-Pathway Analysis To Understand the Change of Pattern in Metabolomics Profiles; Example Two-Development of a Classification Model Using Metabolite Biomarkers for Discriminating Disease Samples from Controls; Conclusions; References; 5 Metagenomics for Monitoring Environmental Biodiversity: Challenges, Progress, and Opportunities; Abstract; Introduction; Sampling and Experimental Design; Metagenomic Sequencing and Preprocessing; Metagenomic Data Analyses; Platforms; Example: Bacteria 16S RRNA Metagenomics Pipeline; Conclusion; References

6 Clinical Assessment of Disease Risk Factors Using SNP Data and Bayesian MethodsAbstract; Promise and Complexity of Personalized Medicine; Whole-Genome Association Studies; Beyond Single-Locus Analysis; Modern Bioinformatics Approaches; Bayesian Data Analysis Methods; Overview of Bayesian Data Analysis; Overview of Bayesian Variable Partition; Epistasis Analysis Methods; Incorporating Block-Type Genome Structure; Detailed Interaction Partition Structure Determination; Bayesian Graph Models and Networks; Clinical Applications of Bayesian Methodology; Conclusions and Future Prospects