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Items: 1 to 20 of 221

1.

Prediction of clustered RNA-binding protein motif sites in the mammalian genome.

Zhang C, Lee KY, Swanson MS, Darnell RB.

Nucleic Acids Res. 2013 Aug;41(14):6793-807. doi: 10.1093/nar/gkt421. Epub 2013 May 18.

2.

mCarts: Genome-Wide Prediction of Clustered Sequence Motifs as Binding Sites for RNA-Binding Proteins.

Weyn-Vanhentenryck SM, Zhang C.

Methods Mol Biol. 2016;1421:215-26. doi: 10.1007/978-1-4939-3591-8_17.

PMID:
26965268
3.

rMAPS: RNA map analysis and plotting server for alternative exon regulation.

Park JW, Jung S, Rouchka EC, Tseng YT, Xing Y.

Nucleic Acids Res. 2016 Jul 8;44(W1):W333-8. doi: 10.1093/nar/gkw410. Epub 2016 May 12.

4.

RBPmap: a web server for mapping binding sites of RNA-binding proteins.

Paz I, Kosti I, Ares M Jr, Cline M, Mandel-Gutfreund Y.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W361-7. doi: 10.1093/nar/gku406. Epub 2014 May 14.

5.

Leveraging cross-link modification events in CLIP-seq for motif discovery.

Bahrami-Samani E, Penalva LO, Smith AD, Uren PJ.

Nucleic Acids Res. 2015 Jan;43(1):95-103. doi: 10.1093/nar/gku1288. Epub 2014 Dec 10.

6.

Cross-linking and immunoprecipitation of nuclear RNA-binding proteins.

Li Q, Uemura Y, Kawahara Y.

Methods Mol Biol. 2015;1262:247-63. doi: 10.1007/978-1-4939-2253-6_15.

PMID:
25555586
7.

RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins.

Kazan H, Morris Q.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W180-6. doi: 10.1093/nar/gkt463. Epub 2013 Jun 10.

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.

9.

CLIPdb: a CLIP-seq database for protein-RNA interactions.

Yang YC, Di C, Hu B, Zhou M, Liu Y, Song N, Li Y, Umetsu J, Lu ZJ.

BMC Genomics. 2015 Feb 5;16:51. doi: 10.1186/s12864-015-1273-2.

10.

Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls.

Zhang C, Frias MA, Mele A, Ruggiu M, Eom T, Marney CB, Wang H, Licatalosi DD, Fak JJ, Darnell RB.

Science. 2010 Jul 23;329(5990):439-43. doi: 10.1126/science.1191150. Epub 2010 Jun 17.

11.

Finding the target sites of RNA-binding proteins.

Li X, Kazan H, Lipshitz HD, Morris QD.

Wiley Interdiscip Rev RNA. 2014 Jan-Feb;5(1):111-30. doi: 10.1002/wrna.1201. Epub 2013 Nov 11. Review.

12.

RNA Bind-n-Seq: Measuring the Binding Affinity Landscape of RNA-Binding Proteins.

Lambert NJ, Robertson AD, Burge CB.

Methods Enzymol. 2015;558:465-93. doi: 10.1016/bs.mie.2015.02.007. Epub 2015 May 12.

PMID:
26068750
13.

Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions.

Kelley DR, Hendrickson DG, Tenen D, Rinn JL.

Genome Biol. 2014 Dec 3;15(12):537. doi: 10.1186/s13059-014-0537-5.

14.

De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function.

Han A, Stoilov P, Linares AJ, Zhou Y, Fu XD, Black DL.

PLoS Comput Biol. 2014 Jan 30;10(1):e1003442. doi: 10.1371/journal.pcbi.1003442. eCollection 2014 Jan.

15.

Nova autoregulation reveals dual functions in neuronal splicing.

Dredge BK, Stefani G, Engelhard CC, Darnell RB.

EMBO J. 2005 Apr 20;24(8):1608-20. Epub 2005 Mar 31.

16.

RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing.

Cereda M, Pozzoli U, Rot G, Juvan P, Schweitzer A, Clark T, Ule J.

Genome Biol. 2014 Jan 31;15(1):R20. doi: 10.1186/gb-2014-15-1-r20.

17.

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.

18.

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.

19.

A deep learning framework for modeling structural features of RNA-binding protein targets.

Zhang S, Zhou J, Hu H, Gong H, Chen L, Cheng C, Zeng J.

Nucleic Acids Res. 2016 Feb 29;44(4):e32. doi: 10.1093/nar/gkv1025. Epub 2015 Oct 13.

20.

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions.

Sugimoto Y, K├Ânig J, Hussain S, Zupan B, Curk T, Frye M, Ule J.

Genome Biol. 2012 Aug 3;13(8):R67. doi: 10.1186/gb-2012-13-8-r67.

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