Bevilacqua PC, Ritchey LE, Su Z, Assmann SM.
Genome-Wide Analysis of RNA Secondary Structure.
Annu Rev Genet. 2016 Nov 23;50:235-266. Epub 2016 Sep 14.
Pubmed

RNA secondary structure profiling in zebrafish reveals unique regulatory features.
Kaushik K et al. BMC Genomics. (2018)

Methods. 2017 May 1;120:3-16. doi: 10.1016/j.ymeth.2017.04.009. Epub 2017 Apr 20.
In silico methods for co-transcriptional RNA secondary structure prediction and for investigating alternative RNA structure expression.
Meyer IM.

GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering. Miladi M, Sokhoyan E, Houwaart T, Heyne S, Costa F, Grüning B, Backofen R. Gigascience. 2019 Dec 1;8(12). pii: giz150. doi: 10.1093/gigascience/giz150.
Pubmed

Mapping RNA-capsid interactions and RNA secondary structure within virus particles using next-generation sequencing.
Zhou Y, Routh A.
Nucleic Acids Res. 2019 Dec 4. pii: gkz1124. doi: 10.1093/nar/gkz1124. [Epub ahead of print]

RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning.
Singh J, Hanson J, Paliwal K, Zhou Y.
Nat Commun. 2019 Nov 27;10(1):5407. doi: 10.1038/s41467-019-13395-9.
PMC full text

FLASH: ultra-fast protocol to identify RNA–protein interactions in cells Ibrahim Avsar Ilik
Tugce Aktas, Daniel Maticzka, Rolf Backofen, Asifa Akhtar
Nucleic Acids Research, gkz1141, https://doi.org/10.1093/nar/gkz1141 Published: 05 December 2019