1. Concepts and Introduction to RNA Bioinformatics
Jan Gorodkin, Ivo L. Hofacker and Walter L. Ruzzo
2. The Principles of RNA Structure Architecture
Christian Zwieb
3. The Determination of RNA Folding Nearest Neighbor Parameters
Mirela Andronescu, Anne Condon, Douglas H. Turner, and David H. Mathews
4. Energy Directed RNA Structure Prediction
Ivo L. Hofacker
5. Introduction to Stochastic Context Free Grammars
Robert Giegerich
6. An Introduction to RNA Databases
Marc P. Hoeppner, Lars E. Barquist, and Paul P. Gardner
7. Energy-based RNA Consensus Secondary Structure Prediction in Multiple Sequence
Alignments
Stefan Washietl and Stephan H. Bernhart and Manolis Kellis
8. SCFGs in RNA Secondary Structure Prediction: A Hands-on Approach
Zsuzsanna S]uk]osd, Ebbe S. Andersen and Rune Lyngsø
9. Annotating Functional RNAs in Genomes using Infernal
Eric P. Nawrocki
10. Class-specific Prediction of ncRNAs
Peter F. Stadler
11. Abstract Shape Analysis of RNA
Stefan Janssen and Robert Giegerich
12. Introduction to RNA Secondary Structure Comparison
Stefanie Schirmer, Yann Ponty, and Robert Giegerich
13. RNA Structural Alignments, Part I: Sankoff Based Approaches for Structural Alignments
Jakob Hull Havgaard and Jan Gorodkin
14. RNA Structural Alignments, Part II: Non-Sankoff Approaches for Structural Alignments
Kiyoshi Asai and Michiaki Hamada
15. De novo Discovery of Structured ncRNA Motifs in Genomic Sequences
Walter L. Ruzzo and Jan Gorodkin
16. Phylogeny and Evolution of RNA Structure
Tanja Gesell and Peter Schuster
17. The Art of Editing RNA Structural Alignments
Ebbe Sloth Andersen
18. Automated Modeling of RNA 3D Structure
Kristian Rother, Magdalena Rother, Pawel Skiba, Janusz M. Bujnicki
19. Computational Prediction of RNA-RNA Interactions
Rolf Backofen
20. Computational Prediction of microRNA Genes
Jana Hertel, David Langenberger, and Peter F. Stadler
21. MicroRNA Target Finding by Comparative Genomics
Robin C. Friedman and Christopher B. Burge
22. Bioinformatics of siRNA Design
Hakim Tafer
23. RNA-protein Interactions: An Overview
Angela Re, Tejal Joshi, Eleonora Kulberkyte, Quaid Morris and Christopher T Workman
