Data Mining for Systems Biology

Front Matter ....Pages i-xi
 Identifying Bacterial Strains from Sequencing Data  (Tommi Mäklin, Jukka Corander, Antti Honkela)....Pages 1-7
 MetaVW: Large-Scale Machine Learning for Metagenomics Sequence Classification  (Kévin Vervier, Pierre Mahé, Jean-Philippe Vert)....Pages 9-20
 Online Interactive Microbial Classification and Geospatial Distributional Analysis Using BioAtlas  (Jesper Lund, Qihua Tan, Jan Baumbach)....Pages 21-35
 Generative Models for Quantification of DNA Modifications  (Tarmo Äijö, Richard Bonneau, Harri Lähdesmäki)....Pages 37-50
 DiMmer: Discovery of Differentially Methylated Regions in Epigenome-Wide Association Study (EWAS) Data  (Tobias Frisch, Jonatan Gøttcke, Richard Röttger, Qihua Tan, Jan Baumbach)....Pages 51-62
 Implementing a Transcription Factor Interaction Prediction System Using the GenoMetric Query Language  (Stefano Perna, Arif Canakoglu, Pietro Pinoli, Stefano Ceri, Limsoon Wong)....Pages 63-81
 Multiple Testing Tool to Detect Combinatorial Effects in Biology  (Aika Terada, Koji Tsuda)....Pages 83-94
 SiBIC: A Tool for Generating a Network of Biclusters Captured by Maximal Frequent Itemset Mining  (Kei-ichiro Takahashi, David A. duVerle, Sohiya Yotsukura, Ichigaku Takigawa, Hiroshi Mamitsuka)....Pages 95-111
 Computing and Visualizing Gene Function Similarity and Coherence with NaviGO  (Ziyun Ding, Qing Wei, Daisuke Kihara)....Pages 113-130
 Analyzing Glycan-Binding Profiles Using Weighted Multiple Alignment of Trees  (Kiyoko F. Aoki-Kinoshita)....Pages 131-140
 Analysis of Fluxomic Experiments with Principal Metabolic Flux Mode Analysis  (Sahely Bhadra, Juho Rousu)....Pages 141-161
 Analyzing Tandem Mass Spectra Using the DRIP Toolkit: Training, Searching, and Post-Processing  (John T. Halloran)....Pages 163-180
 Sparse Modeling to Analyze Drug–Target Interaction Networks  (Yoshihiro Yamanishi)....Pages 181-193
 DrugE-Rank: Predicting Drug-Target Interactions by Learning to Rank  (Jieyao Deng, Qingjun Yuan, Hiroshi Mamitsuka, Shanfeng Zhu)....Pages 195-202
 MeSHLabeler and DeepMeSH: Recent Progress in Large-Scale MeSH Indexing  (Shengwen Peng, Hiroshi Mamitsuka, Shanfeng Zhu)....Pages 203-209
 Disease Gene Classification with Metagraph Representations  (Sezin Kircali Ata, Yuan Fang, Min Wu, Xiao-Li Li, Xiaokui Xiao)....Pages 211-224
 Inferring Antimicrobial Resistance from Pathogen Genomes in KEGG  (Minoru Kanehisa)....Pages 225-239
Back Matter ....Pages 241-243