RNA Bioinformatics

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

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