1. Advanced Design of Structural RNAs Using RNARedPrint
Yann Ponty, Stefan Hammer, Hua-Ting Yao, and Sebastian Will
2. Modeling and Predicting RNA Three-Dimensional Structures
Vladimir Reinharz, Roman Sarrazin-Gendron, and Jérôme Waldispühl
3. Motif Discovery from CLIP Experiments
Marco Pietrosanto, Gabriele Ausiello, and Manuela Helmer-Citterich
4. Profiling of RNA Structure at Single-Nucleotide Resolution Using nextPARS
Uciel Chorostecki, Jesse R. Willis, Ester Saus, and Toni Gabaldon
5. RNA Framework for Assaying the Structure of RNAs by High-Throughput Sequencing
Tycho Marinus and Danny Incarnato
6. Using RNentropy to Detect Significant Variation in Gene Expression across Multiple RNA-Seq or Single Cell RNA-Seq Samples Federico Zambelli and Giulio Pavesi
7. Statistical Modeling of High Dimensional Counts
Michael I. Love
8. QuickIsoSeq for Isoform Quantification in Large-Scale RNA Sequencing
Ramya Gamini, Reiko Nakashima, Wen He, Ying Huang, Ying Zhang, and Shanrong Zhao
9. Summarizing RNA-Seq Data or Differentially Expressed Genes Using Gene Set, Network or Pathway Analysis
Enrica Calura and Paolo Martini
10. Computational Analysis of circRNA Expression Data
Giulio Ferrero, Nicola Licheri, Michele De Bortoli, Raffaele A Calogero, Marco Beccuti, and Francesca Cordero
11. Differential Expression Analysis of Long Non-Coding RNAs
Qian Li and Xuefeng Wang
12. Micro-RNA Quantification, Target Gene Identification, and Pathway Analysis
Gabriele Sales and Enrica Calura
13. In Silico Analysis of MicroRNA Sequencing Data
Ernesto Aparicio-Puerta, Bastian Fromm, Michael Hackenberg, and Marc K. Halushka
14. RNA Editing Detection in HPC Infrastructures
Claudio Lo Giudice, Luigi Mansi, Tiziano Flati, Silvia Gioiosa, Giovanni Chillemi, Pietro Libro, Tiziana Castrignanò, Graziano Pesole, and Ernesto Picardi
15. Identification of Genes Post-Transcriptionally Regulated from RNA-Seq: The Case Study of Liver Hepatocellular Carcinoma
Stefano de Pretis, Mattia Furlan, and Mattia Pelizzola
16. Computational Analysis of Single Cell RNA-Seq Data
Luca Alessandrì, Francesca Cordero, Marco Beccuti, Maddalena Arigoni, and Raffaele A. Calogero
17. Normalization of Single-Cell RNA-Seq Data
Davide Risso
