Data Mining for Systems Biology: Methods and Protocols

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

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