Description

Part I: Omics Bioinformatics Fundamentals

1. Omics Technologies, Data, and Bioinformatics Principles

Maria V. Schneider and Sandra Orchard

2. Data Standards for Omics Data: The Basis of Data Sharing and Reuse

Stephen A. Chervitz, Eric W. Deutsch, Dawn Field, Helen Parkinson, John Quackenbush, Phillipe Rocca-Serra, Susanna-Assunta Sansone, Christian J. Stoeckert, Jr., Chris F. Taylor, Ronald Taylor, and Catherine A. Ball

3. Omics Data Management and Annotation

Arye Harel, Irina Dalah, Shmuel Pietrokovski, Marilyn Safran, and Doron Lancet

4. Data and Knowledge Management in Cross-Omics Research Projects

Martin Wiesinger, Martin Haiduk, Marco Behr, Henrique Lopes de Abreu Madeira, Gernot Gl ckler, Paul Perco, and Arno Lukas

5. Statistical Analysis Principles for Omics Data

Daniela Dunkler, F tima S nchez-Cabo, and Georg Heinze

6. Statistical Methods and Models for Bridging Omics Data Levels

Simon Rogers

7. Analysis of Time Course Omics Datasets

Martin G. Grigorov

8. The Use and Abuse of -Omes

Sonja J. Prohaska and Peter F. Stadler

Part II: Omics Data and Analysis Tracks

9. Computational Analysis of High Throughput Sequencing Data

Steve Hoffmann

10. Analysis of Single Nucleotide Polymorphisms in Case-Control Studies

Yonghong Li, Dov Shiffman, and Rainer Oberbauer

11. Bioinformatics for Copy Number Variation Data

Melissa Warden, Roger Pique-Regi, Antonio Ortega, and Shahab Asgharzadeh

12. Processing ChIP-chip Data: From the Scanner to the Browser

Pierre Cauchy, Touati Benoukraf, and Pierre Ferrier

13. Insights Into Global Mechanisms and Disease by Gene Expression Profiling

F tima S nchez-Cabo, Johannes Rainer, Ana Dopazo, Zlatko Trajanoski, and Hubert Hackl

14. Bioinformatics for RNomics

Kristin Reiche, Katharina Schutt, Kerstin Ullmann, Friedemann Horn, and J rg Hackerm ller

15. Bioinformatics for Qualitative and Quantitative Proteomics

Chris Bielow, Clemens Gr]opl, Oliver Kohlbacher, and Knut Reinert

16. Bioinformatics for Mass Spectrometry-Based Metabolomics

David P. Enot, Bernd Haas, and Klaus M. Weinberger

Part III: Applied Omics Bioinformatics

17. Computational Analysis Workflows for Omics Data Interpretation

Irmgard M hlberger, Julia Wilflingseder, Andreas Bernthaler, Raul Fechete, Arno Lukas, and Paul Perco

18. Integration, Warehousing, and Analysis Strategies of Omics Data

Srinubabu Gedela

19. Integrating Omics Data for Signaling Pathways, Interactome Reconstruction, and Functional Analysis

Paolo Tieri, Alberto de la Fuente, Alberto Termanini, and Claudio Franceschi

20. Network Inference from Time-Dependent Omics Data

Paola Lecca, Thanh-Phuong Nguyen, Corrado Priami, and Paola Quaglia

21. Omics and Literature Mining

Vinod Kumar andCraig Volker

22. Omics-Bioinformatics in the Context of Clinical Data

Gert Mayer, Georg Heinze, Harald Mischak, Merel R. Hellemons, Hiddo J. Lambers Heerspink, Stephan J.L. Bakker, Dick de Zee.