# References

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[**De, S., and Gorospe, M. (2017). Bioinformatic tools for analysis of CLIP ribonucleoprotein data. Wiley Interdiscip. Rev. RNA 8.**](http://paperpile.com/b/3c2FI2/YsbD)

[**Erika C Urdanetabenedikt (2020). Fast and unbiased purification of RNA-protein complexes after UV cross-linking. Methods 178, 72–82.**](http://paperpile.com/b/3c2FI2/F16B)

[**Garzia, A., Meyer, C., Morozov, P., Sajek, M., and Tuschl, T. (2017). Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNA-binding proteins. Methods 118-119, 24–40.**](http://paperpile.com/b/3c2FI2/A8KI)

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[**Lee, F.C.Y., and Ule, J. (2018). Advances in CLIP Technologies for Studies of Protein-RNA Interactions. Mol. Cell 69, 354–369.**](http://paperpile.com/b/3c2FI2/jqZg)

[**McIntyre, A.B.R., Gokhale, N.S., Cerchietti, L., and Jaffrey, S.R. (2019). Limits in the detection of m6A changes using MeRIP/m6A-seq. BioRxiv.**](http://paperpile.com/b/3c2FI2/8eQz)

[**Moore, K.S., and AC’t Hoen, P. (2019). Computational approaches for the analysis of RNA–protein interactions: A primer for biologists. J. Biol. Chem.**](http://paperpile.com/b/3c2FI2/Mj9Z)

[**Schwartz, S. (2018). m1A within cytoplasmic mRNAs at single nucleotide resolution: a reconciled transcriptome-wide map. RNA 24, 1427–1436.**](http://paperpile.com/b/3c2FI2/lWgc)

[**Smith, T., Heger, A., and Sudbery, I. (2017). UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Res. 27, 491–499.**](http://paperpile.com/b/3c2FI2/s7kA)

[**Ule, J., Jensen, K., Mele, A., and Darnell, R.B. (2005). CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods 37, 376–386.**](http://paperpile.com/b/3c2FI2/XHHA)

[**Ule, J., Hwang, H.-W., and Darnell, R.B. (2018). The Future of Cross-Linking and Immunoprecipitation (CLIP). Cold Spring Harb. Perspect. Biol. 10.**](http://paperpile.com/b/3c2FI2/rPrX)

[**Wang, L.K., and Shuman, S. (2002). Mutational analysis defines the 5’-kinase and 3'-phosphatase active sites of T4 polynucleotide kinase. Nucleic Acids Res. 30, 1073–1080.**](http://paperpile.com/b/3c2FI2/IR33)[**Wheeler, E.C., Van Nostrand, E.L., and Yeo, G.W. (2018). Advances and challenges in the detection of transcriptome-wide protein-RNA interactions. Wiley Interdiscip. Rev. RNA 9.**](http://paperpile.com/b/3c2FI2/DBLj)