Data Mining for Systems Biology

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.