About the Book
1. Identifying Bacterial Strains from Sequencing Data
Tommi Mäklin, Jukka Corander, and Antti Honkela
2. MetaVW: Large-Scale Machine Learning for Metagenomics Sequence Classification
Kévin Vervier, Pierre Mahé, 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 Äijö, Richard Bonneau, and Harri Lähdesmäki
5. DiMmer: Discovery of Differentially Methylated Regions in Epigenome-Wide Association Study (EWAS) Data
Tobias Frisch, Jonatan Gøttcke, Richard Röttger, 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
