Data Mining for Systems Biology Methods and Protocols

About this book

The post-genomic revolution is witnessing the generation of petabytes of data annually, with deep implications ranging across evolutionary theory, developmental biology, agriculture, and disease processes. Data Mining for Systems Biology: Methods and Protocols, surveys and demonstrates the science and technology of converting an unprecedented data deluge to new knowledge and biological insight.

Data Mining for Systems Biology: Methods and Protocols is organized around two overlapping themes, network inference and functional inference. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and key tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, Data Mining for Systems Biology: Methods and Protocols also seeks to aid researchers in the further development of databases, mining and visualization systems that are central to the paradigm altering discoveries being made with increasing frequency.

Contents

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

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