RNA Bioinformatics (Paperback, Softcover Repri)

Part I - RNA Secondary and Tertiary Structures 1. Free Energy Minimization to Predict RNA Secondary Structures and Computational RNA Design Alexander Churkin, Lina Weinbrand, and Danny Barash 2. RNA Secondary Structure Prediction from Multi-aligned Sequences Michiaki Hamada 3. A Simple Protocol for the Inference of RNA Global Pairwise Alignments Eugenio Mattei, Manuela Helmer Citterich, and Fabrizio Ferre 4. De Novo Secondary Structure Motif Discovery Using RNAProfile Federico Zambelli and Giulio Pavesi 5. Drawing and Editing the Secondary Structure(s) of RNA Yann Ponty and Fabrice Leclerc 6. Modeling and Predicting RNA Three-dimensional Structures Jerome Waldispuhl and Vladimir Reinharz 7. Fast Prediction of RNA-RNA Interaction Using Heuristic Algorithm Soheila Montaseri Part II - Analysis of high-throughput RNA sequencing data 8. Quality Control of RNA-Seq Experiments Xing Li, Asha Nair, Shengqin Wang, and Liguo Wang 9. Accurate Mapping of RNA-seq data Kin Fai Au 10. Quantifying Entire Transcriptomes by Aligned RNA-Seq Data Raffaele A. Calogero and Francesca Zolezzi 11. Transcriptome Assembly and Alternative Splicing Analysis Paola Bonizzoni, Gianluca Della Vedova, Graziano Pesole, Ernesto Picardi, Yuri Pirola, and Raffaella Rizzi 12. Detection of Post-transcriptional RNA Editing Events Ernesto Picardi, Anna Maria D'Erchia, Angela Gallo, and Graziano Pesole 13. Prediction of miRNA Targets Anastasis Oulas, Nestoras Karathanasis, Annita Louloupi, Georgios A. Pavlopoulos, Panayiota Poirazi, Kriton Kalantidis, and Ioannis Iliopoulos 14. Using Deep Sequencing Data for Identification of Editing Sites in Mature miRNAs Shahar Alon and Eli Eisenberg 15. NGS-Trex: An Automatic Analysis Workflow for RNA-Seq Data Ilenia Boria, Lara Boatti, Igor Saggese, and Flavio Mignone 16. e-DNA Meta-barcoding: From NGS Raw Data to Taxonomic Profiling Fosso Bruno, Marzano Marinella, and Monica Santamaria 17. Deciphering Metatranscriptomic Data E. Kopylova, L. Noe, C. Da Silva, J.F. Berthelot, A. Alberti, J.M. Aury, and H. Touzet 18. RIP-Seq Data Analysis to Determine RNA-protein Associations Federico Zambelli and Giulio Pavesi Part III - Web resources for RNA data analysis 19. The ViennaRNA Web Services Andreas R. Gruber, Stephan H. Bernhart, and Ronny Lorenz 20. Exploring the RNA Editing Potential of RNA-Seq Data by ExpEdit Mattia D'Antonio, Ernesto Picardi, Tiziana Castrignano, Anna Maria D'Erchia, and Graziano Pesole 21. A Guideline for the Annotation of UTR Regulatory Elements in the UTRsite Collection Matteo Giulietti, Giorgio Grillo, Sabino Liuni, and Graziano Pesole 22. Rfam: Annotating Families of Non-coding RNA Sequences Jennifer Daub, Ruth Y. Eberhardt, John G. Tate, and Sarah W. Burge 23. ASPicDB: A Database Web Tool for A lternative Splicing Analysis Mattia D'Antonio, Tiziana Castrignano, Matteo Pallocca, Anna Maria D'Erchia, Ernesto Picardi, and Graziano Pesole 24. Analysis of Alternative Splicing Events in Custom Gene Datasets by AStalavista Sylvain Foissac and Michael Sammeth 25. Computational Design of Artificial RNA Molecules For Gene Regulation Alessandro Lagana', Dario Veneziano, Francesco Russo, Alfredo Pulvirenti, Rosalba Giugno, Carlo Maria Croce, and Alfredo Ferro