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Results: 1 to 20 of 89

1.

PARma: identification of microRNA target sites in AGO-PAR-CLIP data.

Erhard F, Dölken L, Jaskiewicz L, Zimmer R.

Genome Biol. 2013 Jul 29;14(7):R79. doi: 10.1186/gb-2013-14-7-r79.

PMID:
23895117
[PubMed - in process]
Free PMC Article
2.

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
3.

RIP-chip enrichment analysis.

Erhard F, Dölken L, Zimmer R.

Bioinformatics. 2013 Jan 1;29(1):77-83. doi: 10.1093/bioinformatics/bts631. Epub 2012 Oct 26.

PMID:
23104891
[PubMed - indexed for MEDLINE]
Free Article
4.

MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action.

Wen J, Parker BJ, Jacobsen A, Krogh A.

RNA. 2011 May;17(5):820-34. doi: 10.1261/rna.2387911. Epub 2011 Mar 9.

PMID:
21389147
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

TargetSpy: a supervised machine learning approach for microRNA target prediction.

Sturm M, Hackenberg M, Langenberger D, Frishman D.

BMC Bioinformatics. 2010 May 28;11:292. doi: 10.1186/1471-2105-11-292.

PMID:
20509939
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data.

Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH.

Nucleic Acids Res. 2011 Jan;39(Database issue):D202-9. doi: 10.1093/nar/gkq1056. Epub 2010 Oct 30.

PMID:
21037263
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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
8.

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
9.

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
[PubMed - indexed for MEDLINE]
10.

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
11.

miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature.

Naeem H, Küffner R, Csaba G, Zimmer R.

BMC Bioinformatics. 2010 Mar 16;11:135. doi: 10.1186/1471-2105-11-135.

PMID:
20233441
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs.

Shirdel EA, Xie W, Mak TW, Jurisica I.

PLoS One. 2011 Feb 25;6(2):e17429. doi: 10.1371/journal.pone.0017429.

PMID:
21364759
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments.

Li Y, Zhao DY, Greenblatt JF, Zhang Z.

Nucleic Acids Res. 2013 Apr;41(8):e94. doi: 10.1093/nar/gkt142. Epub 2013 Feb 28.

PMID:
23455476
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

miRBase: annotating high confidence microRNAs using deep sequencing data.

Kozomara A, Griffiths-Jones S.

Nucleic Acids Res. 2014 Jan;42(Database issue):D68-73. doi: 10.1093/nar/gkt1181. Epub 2013 Nov 25.

PMID:
24275495
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

microPIR: an integrated database of microRNA target sites within human promoter sequences.

Piriyapongsa J, Bootchai C, Ngamphiw C, Tongsima S.

PLoS One. 2012;7(3):e33888. doi: 10.1371/journal.pone.0033888. Epub 2012 Mar 16.

PMID:
22439011
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

The miRNA-targetome of KSHV and EBV in human B-cells.

Malterer G, Dölken L, Haas J.

RNA Biol. 2011 Jan-Feb;8(1):30-4. Epub 2011 Jan 1.

PMID:
21301209
[PubMed - indexed for MEDLINE]
Free Article
17.

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
18.

Dispom: a discriminative de-novo motif discovery tool based on the jstacs library.

Grau J, Keilwagen J, Gohr A, Paponov IA, Posch S, Seifert M, Strickert M, Grosse I.

J Bioinform Comput Biol. 2013 Feb;11(1):1340006. doi: 10.1142/S0219720013400064. Epub 2013 Jan 21.

PMID:
23427988
[PubMed - indexed for MEDLINE]
19.

dCLIP: a computational approach for comparative CLIP-seq analyses.

Wang T, Xie Y, Xiao G.

Genome Biol. 2014 Jan 7;15(1):R11. doi: 10.1186/gb-2014-15-1-r11.

PMID:
24398258
[PubMed - in process]
Free PMC Article
20.

ProCope--protein complex prediction and evaluation.

Krumsiek J, Friedel CC, Zimmer R.

Bioinformatics. 2008 Sep 15;24(18):2115-6. doi: 10.1093/bioinformatics/btn376. Epub 2008 Jul 17.

PMID:
18635566
[PubMed - indexed for MEDLINE]
Free Article

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