Bioinformatics

Structures.- UNAFold.- Protein Structure Prediction.- An Introduction to Protein Contact Prediction.- Analysis of Mass Spectrometry Data in Proteomics.- The Classification of Protein Domains.- Inferring Function.- Inferring Function from Homology.- The Rosetta Stone Method.- Inferring Functional Relationships from Conservation of Gene Order.- Phylogenetic Profiling.- Phylogenetic Shadowing.- Prediction of Regulatory Elements.- Expression and Microarrays.- Identifying Components of Complexes.- Integrating Functional Genomics Data.- Applications and Disease.- Computational Diagnostics with Gene Expression Profiles.- Analysis of Quantitative Trait Loci.- Molecular Similarity Concepts and Search Calculations.- Optimization of the MAD Algorithm for Virtual Screening.- Combinatorial Optimization Models for Finding Genetic Signatures from Gene Expression Datasets.- Genetic Signatures for a Rodent Model of Parkinson's Disease Using Combinatorial Optimization Methods.- Analytical and Computational Methods.- Developing Fixed-Parameter Algorithms to Solve Combinatorially Explosive Biological Problems.- Clustering.- Visualization.- Constructing Computational Pipelines.- Text Mining.