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Results: 1 to 20 of 88

1.

Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs.

Friedersdorf MB, Keene JD.

Genome Biol. 2014 Jan 7;15(1):R2. doi: 10.1186/gb-2014-15-1-r2.

PMID:
24393468
[PubMed - in process]
Free PMC Article
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.

PMID:
20644507
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing.

Chou CH, Lin FM, Chou MT, Hsu SD, Chang TH, Weng SL, Shrestha S, Hsiao CC, Hung JH, Huang HD.

BMC Genomics. 2013;14 Suppl 1:S2. doi: 10.1186/1471-2164-14-S1-S2. Epub 2013 Jan 21.

PMID:
23368412
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution.

Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J.

J Vis Exp. 2011 Apr 30;(50). pii: 2638. doi: 10.3791/2638.

PMID:
21559008
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP.

Yun J, Wang T, Xiao G.

Biometrics. 2014 Jun;70(2):430-40. doi: 10.1111/biom.12147. Epub 2014 Feb 24.

PMID:
24571656
[PubMed - in process]
Free PMC Article
6.

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.

PMID:
24581442
[PubMed - in process]
7.

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data.

Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, Skalsky RL, Keene JD, Ohler U.

Genome Biol. 2011 Aug 18;12(8):R79. doi: 10.1186/gb-2011-12-8-r79.

PMID:
21851591
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

A model-based approach to identify binding sites in CLIP-Seq data.

Wang T, Chen B, Kim M, Xie Y, Xiao G.

PLoS One. 2014 Apr 8;9(4):e93248. doi: 10.1371/journal.pone.0093248. eCollection 2014.

PMID:
24714572
[PubMed - in process]
Free PMC Article
9.

Argonaute CLIP--a method to identify in vivo targets of miRNAs.

Jaskiewicz L, Bilen B, Hausser J, Zavolan M.

Methods. 2012 Oct;58(2):106-12. doi: 10.1016/j.ymeth.2012.09.006. Epub 2012 Sep 27.

PMID:
23022257
[PubMed - indexed for MEDLINE]
10.

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
[PubMed - indexed for MEDLINE]
11.

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.

PMID:
22213601
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data.

Li JH, Liu S, Zhou H, Qu LH, Yang JH.

Nucleic Acids Res. 2014 Jan;42(Database issue):D92-7. doi: 10.1093/nar/gkt1248. Epub 2013 Dec 1.

PMID:
24297251
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Systematic transcriptome wide analysis of lncRNA-miRNA interactions.

Jalali S, Bhartiya D, Lalwani MK, Sivasubbu S, Scaria V.

PLoS One. 2013;8(2):e53823. doi: 10.1371/journal.pone.0053823. Epub 2013 Feb 6.

PMID:
23405074
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Transcriptome-wide identification of RNA binding sites by CLIP-seq.

Murigneux V, Saulière J, Roest Crollius H, Le Hir H.

Methods. 2013 Sep 1;63(1):32-40. doi: 10.1016/j.ymeth.2013.03.022. Epub 2013 Mar 30.

PMID:
23545196
[PubMed - indexed for MEDLINE]
15.

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.

PMID:
23770886
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data.

Sievers C, Schlumpf T, Sawarkar R, Comoglio F, Paro R.

Nucleic Acids Res. 2012 Nov 1;40(20):e160. doi: 10.1093/nar/gks697. Epub 2012 Jul 28.

PMID:
22844102
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets.

Farazi TA, Leonhardt CS, Mukherjee N, Mihailovic A, Li S, Max KE, Meyer C, Yamaji M, Cekan P, Jacobs NC, Gerstberger S, Bognanni C, Larsson E, Ohler U, Tuschl T.

RNA. 2014 Jul;20(7):1090-102. doi: 10.1261/rna.045005.114. Epub 2014 May 23.

PMID:
24860013
[PubMed - indexed for MEDLINE]
18.

Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1.

Wang X, Juan L, Lv J, Wang K, Sanford JR, Liu Y.

BMC Genomics. 2011 Dec 23;12 Suppl 5:S8. doi: 10.1186/1471-2164-12-S5-S8. Epub 2011 Dec 23.

PMID:
22369183
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data.

Zhang C, Darnell RB.

Nat Biotechnol. 2011 Jun 1;29(7):607-14. doi: 10.1038/nbt.1873.

PMID:
21633356
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

High-resolution profiling of protein occupancy on polyadenylated RNA transcripts.

Munschauer M, Schueler M, Dieterich C, Landthaler M.

Methods. 2014 Feb;65(3):302-9. doi: 10.1016/j.ymeth.2013.09.017. Epub 2013 Oct 1.

PMID:
24096003
[PubMed - in process]
Free Article

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