# References

[**Chakrabarti, A.M., Haberman, N., Praznik, A., Luscombe, N.M., and Ule, J. (2018). Data Science Issues in Studying Protein–RNA Interactions with CLIP Technologies. Annu. Rev. Biomed. Data Sci. 1, 235–261.**](http://paperpile.com/b/3c2FI2/2SQ6)

[**Chen, X., Castro, S.A., Liu, Q., Hu, W., and Zhang, S. (2019). Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions. Methods 155, 49–57.**](http://paperpile.com/b/3c2FI2/dLnN)

[**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)

[**Haberman, N., Huppertz, I., Attig, J., König, J., Wang, Z., Hauer, C., Hentze, M.W., Kulozik, A.E., Le Hir, H., Curk, T., et al. (2017). Insights into the design and interpretation of iCLIP experiments. Genome Biol. 18.**](http://paperpile.com/b/3c2FI2/2HpP)

[**König, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D.J., Luscombe, N.M., and Ule, J. (2010). iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat. Struct. Mol. Biol. 17, 909–915.**](http://paperpile.com/b/3c2FI2/mqax)

[**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)


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