Data Mining for Systems Biology

1. Dense Module Enumeration in Biological Networks Koji Tsuda and Elisabeth Georgii 2. Discovering Interacting Domains and Motifs in Protein-Protein Interactions Hugo Willy, Wing-Kin Sung, and See-Kiong Ng. 3. Global Alignment of Protein-Protein Interaction Networks Misael Mongiov__ Roded Sharan 4. Structure Learning for Bayesian Networks as Models of Biological Networks Antti Larjo, Ilya Shmulevich, and Harri Lahdesmaki 5. Supervised Inference of Gene Regulatory Networks from Positive Examples Fantine Mordelet and Jean-Phillippe Vert 6. Mining Regulatory Network Connections by Ranking Transcription Factor Target Genes using Time Series Expression Data Annti Honkela, Magnus Rattray, and Neil D. Lawrence 7. Identifying Pathways of Co-ordinated Gene Expression Timothy Hancock, Ichigaku Takigawa, and Hiroshi Mamitsuka 8. Mining Frequent Subtrees in Glcan Data using the RINGS Glycan Miner Tool Kiyoko Flora Aoki-Kinoshita 9. Chemogenomic Approaches to Infer Drug-target Interaction Networks Yoshihiro Yamanishi 10. Localization Prediction and Structure-based in Silico Analysis of Bacterial Proteins- with Emphasis on Outer Membrane Proteins Kenichiro Imai, Sikander Hayat, Noriyuki Sakiyama, Naoya Fujita, Kentaro Tomii, Arne Elofsson, and Paul Horton 11. Analysis Strategy of Protein-Protein Interaction Networks Zhenjun Hu 12. Data Mining in the MetaCyc Family of Pathway Databases Peter D. Karp, Suzanne Paley, and Tomer Altman 13. Gene Set/Pathway Enrichment Analysis Jui-Hung Hung 14. Construction of Functional Linkage Gene Networks by Data Integration Bolan Linghu, Eric A. Franzosa, Yu Xia 15. Genome-Wide Association Studies Tun-Hsiang Yang, Mark Kon, Charles DeLisi 16. Viral Genome Analysis and Knowledge Management Carla Kuiken, Hyejin Yoon, Werner Abfalterer, Brian Gaschen, Chienchi Lo, Bette Korber 17. Molecular Network Analysis of Diseases and Drugs in KEGGMinoru Kanehisa