Data Mining for Systems Biology Methods and Protocols

This fully updated book collects numerous data mining techniques, reflecting the acceleration and diversity of the development of data-driven approaches to the life sciences. The first half of the volume examines genomics, particularly metagenomics and epigenomics, which promise to deepen our knowledge of genes and genomes, while the second half of the book emphasizes metabolism and the metabolome as well as relevant medicine-oriented subjects. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that is useful for getting optimal results. 

Identifying Bacterial Strains from Sequencing Data.- MetaVW: Large-Scale Machine Learning for Metagenomics Sequence Classification.- Online Interactive Microbial Classification and Geospatial Distributional Analysis Using BioAtlas.- Generative Models for Quantification of DNA Modifications.- DiMmer: Discovery of Differentially Methylated Regions in Epigenome-Wide Association Study (EWAS) Data.- Implementing a Transcription Factor Interaction Prediction System Using the GenoMetric Query Language.- Multiple Testing Tool to Detect Combinatorial Effects in Biology.- SiBIC: A Tool for Generating a Network of Biclusters Captured by Maximal Frequent Itemset Mining.- Computing and Visualizing Gene Function Similarity and Coherence with NaviGO.- Analyzing Glycan Binding Profiles Using Weighted Multiple Alignment of Trees.- Analysis of Fluxomic Experiments with Principal Metabolic Flux Mode Analysis.- Analyzing Tandem Mass Spectra Using the DRIP Toolkit: Training, Searching, and Post-Processing.- Sparse Modeling to Analyze Drug-Target Interaction Networks.- DrugE-Rank: Predicting Drug-Target Interactions by Learning to Rank.- MeSHLabeler and DeepMeSH: Recent Progress in Large-Scale MeSH Indexing.- Disease Gene Classification with Metagraph Representations.- Inferring Antimicrobial Resistance from Pathogen Genomes in KEGG.