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 Glöckler, Paul Perco, and Arno Lukas
5. Statistical Analysis Principles for Omics Data
Daniela Dunkler, Fátima Sánchez-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
Fátima Sánchez-Cabo, Johannes Rainer, Ana Dopazo, Zlatko Trajanoski, and Hubert Hackl
14. Bioinformatics for RNomics
Kristin Reiche, Katharina Schutt, Kerstin Ullmann, Friedemann Horn, and Jörg Hackermüller
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 Mühlberger, 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 and Craig 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
