Data Mining for Systems Biology

1. Identifying Bacterial Strains from Sequencing Data



Tommi Maklin, Jukka Corander, and Antti Honkela







2. MetaVW: Large-Scale Machine Learning for Metagenomics Sequence Classification



Kevin Vervier, Pierre Mahe, and Jean-Philippe Vert







3. Online Interactive Microbial Classification and Geospatial Distributional Analysis Using BioAtlas



Jesper Lund, Qihua Tan, and Jan Baumbach







4. Generative Models for Quantification of DNA Modifications



Tarmo AEijoe, Richard Bonneau, and Harri Lahdesmaki







5. DiMmer: Discovery of Differentially Methylated Regions in Epigenome-Wide Association Study (EWAS) Data



Tobias Frisch, Jonatan Gottcke, Richard Roettger, Qihua Tan, and Jan Baumbach







6. Implementing a Transcription Factor Interaction Prediction System Using the GenoMetric Query Language



Stefano Perna, Arif Canakoglu, Pietro Pinoli, Stefano Ceri, and Limsoon Wong







7. Multiple Testing Tool to Detect Combinatorial Effects in Biology



Aika Terada and Koji Tsuda







8. 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, and Hiroshi Mamitsuka







9. Computing and Visualizing Gene Function Similarity and Coherence with NaviGO



Ziyun Ding, Qing Wei, and Daisuke Kihara







10. Analyzing Glycan Binding Profiles Using Weighted Multiple Alignment of Trees



Kiyoko F. Aoki-Kinoshita







11. Analysis of Fluxomic Experiments with Principal Metabolic Flux Mode Analysis



Sahely Bhadra and Juho Rousu







12. Analyzing Tandem Mass Spectra Using the DRIP Toolkit: Training, Searching, and Post-Processing



John T. Halloran







13. Sparse Modeling to Analyze Drug-Target Interaction Networks



Yoshihiro Yamanishi







14. DrugE-Rank: Predicting Drug-Target Interactions by Learning to Rank



Jieyao Deng, Qingjun Yuan, Hiroshi Mamitsuka, and Shanfeng Zhu







15. MeSHLabeler and DeepMeSH: Recent Progress in Large-Scale MeSH Indexing



Shengwen Peng, Hiroshi Mamitsuka, and Shanfeng Zhu







16. Disease Gene Classification with Metagraph Representations



Sezin Kircali Ata, Yuan Fang, Min Wu, Xiao-Li Li, and Xiaokui Xiao







17. Inferring Antimicrobial Resistance from Pathogen Genomes in KEGG



Minoru Kanehisa