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Items: 1 to 20 of 92

1.

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP.

Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T.

Cell. 2010 Apr 2;141(1):129-41. doi: 10.1016/j.cell.2010.03.009.

2.

PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins.

Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T.

J Vis Exp. 2010 Jul 2;(41). pii: 2034. doi: 10.3791/2034.

3.

PAR-CLIP and streamlined small RNA cDNA library preparation protocol for the identification of RNA binding protein target sites.

Benhalevy D, McFarland HL, Sarshad AA, Hafner M.

Methods. 2017 Apr 15;118-119:41-49. doi: 10.1016/j.ymeth.2016.11.009. Epub 2016 Nov 18.

PMID:
27871973
4.

Transcriptome-wide Identification of RNA-binding Protein Binding Sites Using Photoactivatable-Ribonucleoside-Enhanced Crosslinking Immunoprecipitation (PAR-CLIP).

Maatz H, Kolinski M, Hubner N, Landthaler M.

Curr Protoc Mol Biol. 2017 Apr 3;118:27.6.1-27.6.19. doi: 10.1002/cpmb.35.

PMID:
28369676
5.

Identification of RNA-protein interaction networks using PAR-CLIP.

Ascano M, Hafner M, Cekan P, Gerstberger S, Tuschl T.

Wiley Interdiscip Rev RNA. 2012 Mar-Apr;3(2):159-77. doi: 10.1002/wrna.1103. Epub 2011 Dec 27. Review.

6.

Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNA-binding proteins.

Garzia A, Meyer C, Morozov P, Sajek M, Tuschl T.

Methods. 2017 Apr 15;118-119:24-40. doi: 10.1016/j.ymeth.2016.10.007. Epub 2016 Oct 17. Review.

7.

Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR.

Lebedeva S, Jens M, Theil K, Schwanhäusser B, Selbach M, Landthaler M, Rajewsky N.

Mol Cell. 2011 Aug 5;43(3):340-52. doi: 10.1016/j.molcel.2011.06.008. Epub 2011 Jun 30.

8.

In vivo and transcriptome-wide identification of RNA binding protein target sites.

Jungkamp AC, Stoeckius M, Mecenas D, Grün D, Mastrobuoni G, Kempa S, Rajewsky N.

Mol Cell. 2011 Dec 9;44(5):828-40. doi: 10.1016/j.molcel.2011.11.009.

9.

PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites.

Danan C, Manickavel S, Hafner M.

Methods Mol Biol. 2016;1358:153-73. doi: 10.1007/978-1-4939-3067-8_10.

10.

Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data.

Comoglio F, Sievers C, Paro R.

BMC Bioinformatics. 2015 Feb 1;16:32. doi: 10.1186/s12859-015-0470-y.

11.

Mapping the Transcriptome-Wide Landscape of RBP Binding Sites Using gPAR-CLIP-seq: Experimental Procedures.

Han T, Kim JK.

Methods Mol Biol. 2016;1361:77-90. doi: 10.1007/978-1-4939-3079-1_5.

PMID:
26483017
12.

Landscape and variation of RNA secondary structure across the human transcriptome.

Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY.

Nature. 2014 Jan 30;505(7485):706-9. doi: 10.1038/nature12946.

13.

PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a step-by-step protocol to the transcriptome-wide identification of binding sites of RNA-binding proteins.

Spitzer J, Hafner M, Landthaler M, Ascano M, Farazi T, Wardle G, Nusbaum J, Khorshid M, Burger L, Zavolan M, Tuschl T.

Methods Enzymol. 2014;539:113-61. doi: 10.1016/B978-0-12-420120-0.00008-6.

14.

Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation.

Graf R, Munschauer M, Mastrobuoni G, Mayr F, Heinemann U, Kempa S, Rajewsky N, Landthaler M.

RNA Biol. 2013 Jul;10(7):1146-59. doi: 10.4161/rna.25194. Epub 2013 May 29.

15.

Discovery of microRNA regulatory networks by integrating multidimensional high-throughput data.

Yang JH, Qu LH.

Adv Exp Med Biol. 2013;774:251-66. doi: 10.1007/978-94-007-5590-1_13.

PMID:
23377977
16.

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).

Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang MY, Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, Stanton R, Rigo F, Guttman M, Yeo GW.

Nat Methods. 2016 Jun;13(6):508-14. doi: 10.1038/nmeth.3810. Epub 2016 Mar 28.

17.

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae.

Freeberg MA, Han T, Moresco JJ, Kong A, Yang YC, Lu ZJ, Yates JR, Kim JK.

Genome Biol. 2013 Feb 14;14(2):R13. doi: 10.1186/gb-2013-14-2-r13.

18.

Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites.

Li YE, Xiao M, Shi B, Yang YT, Wang D, Wang F, Marcia M, Lu ZJ.

Genome Biol. 2017 Sep 8;18(1):169. doi: 10.1186/s13059-017-1298-8.

19.

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins.

Kishore S, Jaskiewicz L, Burger L, Hausser J, Khorshid M, Zavolan M.

Nat Methods. 2011 May 15;8(7):559-64. doi: 10.1038/nmeth.1608.

PMID:
21572407
20.

Transcriptome-wide identification of in vivo interactions between RNAs and RNA-binding proteins by RIP and PAR-CLIP assays.

González-Buendía E, Saldaña-Meyer R, Meier K, Recillas-Targa F.

Methods Mol Biol. 2015;1288:413-28. doi: 10.1007/978-1-4939-2474-5_24.

PMID:
25827894

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