Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Results: 1 to 20 of 97

1.

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
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.

Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis.

Moore MJ, Zhang C, Gantman EC, Mele A, Darnell JC, Darnell RB.

Nat Protoc. 2014 Feb;9(2):263-93. doi: 10.1038/nprot.2014.012. Epub 2014 Jan 9.

PMID:
24407355
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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
6.

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]
7.

HITS-CLIP (CLIP-Seq) for mouse Piwi proteins.

Vourekas A, Mourelatos Z.

Methods Mol Biol. 2014;1093:73-95. doi: 10.1007/978-1-62703-694-8_7.

PMID:
24178558
[PubMed - indexed for MEDLINE]
8.

Transcriptome-wide analysis of protein-RNA interactions using high-throughput sequencing.

Milek M, Wyler E, Landthaler M.

Semin Cell Dev Biol. 2012 Apr;23(2):206-12. doi: 10.1016/j.semcdb.2011.12.001. Epub 2011 Dec 27. Review.

PMID:
22212136
[PubMed - indexed for MEDLINE]
9.

CLIP-based prediction of mammalian microRNA binding sites.

Liu C, Mallick B, Long D, Rennie WA, Wolenc A, Carmack CS, Ding Y.

Nucleic Acids Res. 2013 Aug;41(14):e138. doi: 10.1093/nar/gkt435. Epub 2013 May 22.

PMID:
23703212
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Identifying Argonaute binding sites in Caenorhabditis elegans using iCLIP.

Broughton JP, Pasquinelli AE.

Methods. 2013 Sep 15;63(2):119-25. doi: 10.1016/j.ymeth.2013.03.033. Epub 2013 Apr 10.

PMID:
23583680
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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]
12.

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
13.

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]
14.

CPSS: a computational platform for the analysis of small RNA deep sequencing data.

Zhang Y, Xu B, Yang Y, Ban R, Zhang H, Jiang X, Cooke HJ, Xue Y, Shi Q.

Bioinformatics. 2012 Jul 15;28(14):1925-7. doi: 10.1093/bioinformatics/bts282. Epub 2012 May 9.

PMID:
22576177
[PubMed - indexed for MEDLINE]
Free Article
15.

iMir: an integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq.

Giurato G, De Filippo MR, Rinaldi A, Hashim A, Nassa G, Ravo M, Rizzo F, Tarallo R, Weisz A.

BMC Bioinformatics. 2013 Dec 13;14:362. doi: 10.1186/1471-2105-14-362.

PMID:
24330401
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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
17.

A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets.

Khorshid M, Hausser J, Zavolan M, van Nimwegen E.

Nat Methods. 2013 Mar;10(3):253-5. doi: 10.1038/nmeth.2341. Epub 2013 Jan 20.

PMID:
23334102
[PubMed - indexed for MEDLINE]
18.

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
19.

Genome-wide identification of miRNA targets by PAR-CLIP.

Hafner M, Lianoglou S, Tuschl T, Betel D.

Methods. 2012 Oct;58(2):94-105. doi: 10.1016/j.ymeth.2012.08.006. Epub 2012 Aug 19.

PMID:
22926237
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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

Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Write to the Help Desk