Skip to content
naulon
Get started

No retraction, correction or concern found when last checked on Nov 4, 2026.

PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data

Sabrina Krakau, Hugues Richard, Annalisa Marsico

Genome Biology · 2017

doi:10.1101/146704

Abstract

Electronic supplementary material. The online version of this article (doi:10.1186/s13059-017-1364-2) contains supplementary material, which is available to authorized users.

References 40

  1. 1.

    Darnell RB. HITS-CLIP: Panoramic views of protein–RNA regulation in living cells. Wiley Interdiscip Rev: RNA. 2010;1(2):266-86.

    Not in our library10.1002/wrna.31

  2. 2.

    Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell. 2010;141(1):129-41.

    Not in our library10.1016/j.cell.2010.03.009

  3. 3.

    König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, et al. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol. 2010;17(7):909-15.

    Not in our library10.1038/nsmb.1838

  4. 4.
    Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions · 2012
    No notice
  5. 5.

    Haberman N, Huppertz I, Attig J, König J, Wang Z, Hauer C, et al. Insights into the design and interpretation of iCLIP experiments. Genome Biol. 2017;18(1):7.

    Not in our library10.1186/s13059-016-1130-x

  6. 6.

    Sibley CR. Individual nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) to determine protein–RNA interactions In: Gaspar I, editor. RNA Detection. Methods in Molecular Biology, vol 1649. New York: Humana Press. p. 427–454.

    Not in our library10.1007/978-1-4939-7213-5_29

  7. 7.

    Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang MY, Sundararaman B, et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods. 2016;13(6):508-14.

    Not in our library10.1038/nmeth.3810

  8. 8.

    ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74.

    Not in our library10.1038/nature11247

  9. 9.
    ENCODE data at the ENCODE portal · 2015
    No notice
  10. 10.

    Friedersdorf MB, Keene JD. Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs. Genome Biol. 2014;15(1):1-16.

    Not in our library10.1186/gb-2014-15-1-r2

  11. 11.

    Reyes-Herrera PH, Speck-Hernandez CA, Sierra CA, Herrera S. BackCLIP: A tool to identify common background presence in PAR-CLIP datasets. Bioinformatics. 2015;31(22):3703-3705.

    Not in our library10.1093/bioinformatics/btv442

  12. 12.
    PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data · 2011
    No notice
  13. 13.

    Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, et al. Site identification in high-throughput RNA-protein interaction data. Bioinformatics. 2012;28(23):3013-20.

    Not in our library10.1093/bioinformatics/bts569

  14. 14.

    Shah A, Qian Y, Weyn-Vanhentenryck SM, Zhang C. CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data. Bioinformatics. 2016;33(4):566-567.

    Not in our library10.1093/bioinformatics/btw653

  15. 15.

    Uhl M, Houwaart T, Corrado G, Wright PR, Backofen R. Computational analysis of CLIP-seq data. Methods. 2017;118–119:60-72.

    Not in our library10.1016/j.ymeth.2017.02.006

  16. 16.

    Weyn-Vanhentenryck SM, Mele A, Yan Q, Sun S, Farny N, Zhang Z, et al. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Rep. 2014;6(6):1139-52.

    Not in our library10.1016/j.celrep.2014.02.005

  17. 17.

    Chen B, Yun J, Kim MS, Mendell JT, Xie Y. PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis. Genome Biol. 2014;15(1):18.

    Not in our library10.1186/gb-2014-15-1-r18

  18. 18.

    Parzen E. On estimation of a probability density function and mode. Ann Math Stat. 1962;33(3):1065-76.

    Not in our library10.1214/aoms/1177704472

  19. 19.

    Lovci MT, Ghanem D, Marr H, Arnold J, Gee S, Parra M, et al. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol. 2013;20(12):1434-42.

    Not in our library10.1038/nsmb.2699

  20. 20.

    Kassuhn W, Ohler U, Drewe P. Cseq-simulator: A data simulator for CLIP-seq experiments. Pac Symp Biocomput. 2016;21:433-44.

    Not in our library

  21. 21.
    Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements · 2013
    No notice
  22. 22.

    Bailey TL. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics. 2011;27(12):1653-9.

    Not in our library10.1093/bioinformatics/btr261

  23. 23.

    Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011;27(7):1017-18.

    Not in our library10.1093/bioinformatics/btr064

  24. 24.

    Zarnegar BJ, Flynn RA, Shen Y, Do BT, Chang HY, Khavari PA. irCLIP platform for efficient characterization of protein–RNA interactions. Nat Methods. 2016. https://doi.org/10.1038/nmeth.3840.

    Not in our library10.1038/nmeth.3840

  25. 25.
    iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions · 2010
    No notice
  26. 26.

    Hussain S, Sajini AA, Blanco S, Dietmann S, Lombard P, Sugimoto Y, et al.NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Rep. 2013. https://doi.org/10.1016/j.celrep.2013.06.029.

    Not in our library10.1016/j.celrep.2013.06.029

  27. 27.

    van Nues R, Schweikert G, de Leau E, Selega A, Langford A, Franklin R, et al.Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress. Nat Commun. 2017. https://doi.org/10.1038/s41467-017-00025-5.

    Not in our library10.1038/s41467-017-00025-5

  28. 28.

    Krueger F. Trim Galore! trim_galore_v0.4.0. 2015. Retrieved September 7, 2016 from http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/.

    Not in our library

  29. 29.

    Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17(1):10.

    Not in our library10.14806/ej.17.1.200

  30. 30.

    Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21.

    Not in our library10.1093/bioinformatics/bts635

  31. 31.
    UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy · 2017
    No notice
  32. 32.

    Rabiner LR. A tutorial on hidden Markov models and selected applications in speech recognition. Proc IEEE. 1989;77(2):257-86.

    Not in our library10.1109/5.18626

  33. 33.

    Rabiner L, Juang B. An introduction to hidden Markov models. IEEE ASSP Mag. 1986;3(1):4-16.

    Not in our library10.1109/massp.1986.1165342

  34. 34.

    Reinert K, Dadi TH, Ehrhardt M, Hauswedell H, Mehringer S, Rahn R, et al.The SeqAn C++ template library for efficient sequence analysis: a resource for programmers. J Biotechnol. 2017. https://doi.org/10.1016/j.jbiotec.2017.07.017.

    Not in our library10.1016/j.jbiotec.2017.07.017

  35. 35.

    Galassi M, Davies J, Theiler J, Gough B, Jungman G, Alken P, et al. GNU Scientific Library reference manual. 2009.

    Not in our library

  36. 36.

    Schäling B. The boost C++ libraries. 2014.

    Not in our library

  37. 37.

    Dagum L, Menon R. OpenMP: an industry standard API for shared-memory programming. IEEE Comput Sci Eng. 1998;5(1):46-55.

    Not in our library10.1109/99.660313

  38. 38.

    Krakau S. skrakau/PureCLIP: PureCLIP 1.0.2. 2017. https://doi.org/10.5281/zenodo.1013920.

    Not in our library

  39. 39.
    PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data · 2017
    No notice
  40. 40.

    Krakau S. skrakau/sim_iCLIP: sim_iCLIP 1.0.0. 2017. https://doi.org/10.5281/zenodo.1048838.

    Not in our library

Cited by papers we hold 2

Reads

Read by people on this page

None yet.

Checked or read by AI through naulon

None yet.

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.

Are you an author?

Is this your paper?

Claim it to add your note and be paid when agents cite it. Free.