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Results: 1 to 20 of 91

1.

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
2.

PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis.

Chen B, Yun J, Kim MS, Mendell JT, Xie Y.

Genome Biol. 2014 Jan 22;15(1):R18. doi: 10.1186/gb-2014-15-1-r18.

PMID:
24451213
[PubMed - in process]
Free PMC Article
3.

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
4.

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
5.

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
6.

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
7.

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]
8.

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
9.

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
10.

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
11.

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data.

Bi Y, Davuluri RV.

BMC Bioinformatics. 2013 Aug 27;14:262. doi: 10.1186/1471-2105-14-262.

PMID:
23981227
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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
13.

QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions.

Liu B, Yi J, Sv A, Lan X, Ma Y, Huang TH, Leone G, Jin VX.

BMC Genomics. 2013;14 Suppl 8:S3. doi: 10.1186/1471-2164-14-S8-S3. Epub 2013 Dec 9.

PMID:
24564479
[PubMed - in process]
Free PMC Article
14.

Site identification in high-throughput RNA-protein interaction data.

Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, Hannon GJ, Sanford JR, Penalva LO, Smith AD.

Bioinformatics. 2012 Dec 1;28(23):3013-20. doi: 10.1093/bioinformatics/bts569. Epub 2012 Sep 28.

PMID:
23024010
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data.

Fukunaga T, Ozaki H, Terai G, Asai K, Iwasaki W, Kiryu H.

Genome Biol. 2014 Jan 21;15(1):R16. doi: 10.1186/gb-2014-15-1-r16.

PMID:
24447569
[PubMed - in process]
Free PMC Article
16.

SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction.

Yang Y, Zhao H, Wang J, Zhou Y.

Methods Mol Biol. 2014;1137:119-30. doi: 10.1007/978-1-4939-0366-5_9.

PMID:
24573478
[PubMed - in process]
17.

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]
18.

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
19.

Editorial: protein systems biology: method, regulation, and network.

Chen Q, Chen M.

Curr Protein Pept Sci. 2014;15(6):519-21.

PMID:
25135673
[PubMed - in process]
20.

Gene Ontology based housekeeping gene selection for RNA-seq normalization.

Chen CM, Lu YL, Sio CP, Wu GC, Tzou WS, Pai TW.

Methods. 2014 Jun 1;67(3):354-63. doi: 10.1016/j.ymeth.2014.01.019. Epub 2014 Feb 18.

PMID:
24561167
[PubMed - in process]

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