RNA Sequence, Structure, and Function

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 Sukosd, Ebbe S. Andersen and Rune Lyngso 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