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Data Mining for Systems Biology

Methods and Protocols

  • Book
  • © 2013

Overview

Editors:
  1. Hiroshi Mamitsuka

    1. , Institute for Chemical Research, Kyoto University, Kyoto, Japan

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    You can also search for this editor in PubMed   Google Scholar

  2. Charles DeLisi

    1. Dept. Biomedical Engineering, Boston University, Boston, USA

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    You can also search for this editor in PubMed   Google Scholar

  3. Minoru Kanehisa

    1. Inst. Chemical Research, Bioinformatics Center, Kyoto University, Uji, Japan

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    You can also search for this editor in PubMed   Google Scholar

  • Aids researchers in the further development of databases,mining,and visualization systems.
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 939)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xii
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  2. Dense Module Enumeration in Biological Networks

    • Koji Tsuda, Elisabeth Georgii
    Pages 1-8

  3. Discovering Interacting Domains and Motifs in Protein–Protein Interactions

    • Willy Hugo, Wing-Kin Sung, See-Kiong Ng
    Pages 9-20

  4. Global Alignment of Protein–Protein Interaction Networks

    • Misael Mongiovì, Roded Sharan
    Pages 21-34

  5. Structure Learning for Bayesian Networks as Models of Biological Networks

    • Antti Larjo, Ilya Shmulevich, Harri Lähdesmäki
    Pages 35-45

  6. Supervised Inference of Gene Regulatory Networks from Positive and Unlabeled Examples

    • Fantine Mordelet, Jean-Philippe Vert
    Pages 47-58

  7. Mining Regulatory Network Connections by Ranking Transcription Factor Target Genes Using Time Series Expression Data

    • Antti Honkela, Magnus Rattray, Neil D. Lawrence
    Pages 59-67

  8. Identifying Pathways of Coordinated Gene Expression

    • Timothy Hancock, Ichigaku Takigawa, Hiroshi Mamitsuka
    Pages 69-85

  9. Mining Frequent Subtrees in Glycan Data Using the Rings Glycan Miner Tool

    • Kiyoko Flora Aoki-Kinoshita
    Pages 87-95

  10. Chemogenomic Approaches to Infer Drug–Target Interaction Networks

    • Yoshihiro Yamanishi
    Pages 97-113

  11. 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 et al.
    Pages 115-140

  12. Analysis Strategy of Protein–Protein Interaction Networks

    • Zhenjun Hu
    Pages 141-181

  13. Data Mining in the MetaCyc Family of Pathway Databases

    • Peter D. Karp, Suzanne Paley, Tomer Altman
    Pages 183-200

  14. Gene Set/Pathway Enrichment Analysis

    • Jui-Hung Hung
    Pages 201-213

  15. Construction of Functional Linkage Gene Networks by Data Integration

    • Bolan Linghu, Eric A. Franzosa, Yu Xia
    Pages 215-232

  16. Genome-Wide Association Studies

    • Tun-Hsiang Yang, Mark Kon, Charles DeLisi
    Pages 233-251

  17. Viral Genome Analysis and Knowledge Management

    • Carla Kuiken, Hyejin Yoon, Werner Abfalterer, Brian Gaschen, Chienchi Lo, Bette Korber
    Pages 253-261

  18. Molecular Network Analysis of Diseases and Drugs in KEGG

    • Minoru Kanehisa
    Pages 263-275

  19. Back Matter

    Pages 277-279
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Keywords

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. The volume is organized around two overlapping themes, network inference and functional inference. Written in the highly successful Methods in Molecular Biologyâ„¢ 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.

Editors and Affiliations

  • , Institute for Chemical Research, Kyoto University, Kyoto, Japan

    Hiroshi Mamitsuka

  • Dept. Biomedical Engineering, Boston University, Boston, USA

    Charles DeLisi

  • Inst. Chemical Research, Bioinformatics Center, Kyoto University, Uji, Japan

    Minoru Kanehisa

Bibliographic Information

  • Book Title: Data Mining for Systems Biology

  • Book Subtitle: Methods and Protocols

  • Editors: Hiroshi Mamitsuka, Charles DeLisi, Minoru Kanehisa

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-107-3

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2013

  • Hardcover ISBN: 978-1-62703-106-6Published: 29 November 2012

  • Softcover ISBN: 978-1-4939-5912-9Published: 23 August 2016

  • eBook ISBN: 978-1-62703-107-3Published: 30 November 2012

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 279

  • Topics: Bioinformatics, Systems Biology

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