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Results: 1 to 20 of 96

1.

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae.

Freeberg MA, Han T, Moresco JJ, Kong A, Yang YC, Lu ZJ, Yates JR, Kim JK.

Genome Biol. 2013 Feb 14;14(2):R13. doi: 10.1186/gb-2013-14-2-r13.

PMID:
23409723
[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.

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae.

Yang Y, Umetsu J, Lu ZJ.

Sci China Life Sci. 2014 Jan;57(1):22-35. doi: 10.1007/s11427-013-4583-0. Epub 2013 Dec 26.

PMID:
24369346
[PubMed - indexed for MEDLINE]
4.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug 2;10(4):040301. [Epub ahead of print]

PMID:
23912807
[PubMed - as supplied by publisher]
5.

Differential protein occupancy profiling of the mRNA transcriptome.

Schueler M, Munschauer M, Gregersen LH, Finzel A, Loewer A, Chen W, Landthaler M, Dieterich C.

Genome Biol. 2014 Jan 13;15(1):R15. doi: 10.1186/gb-2014-15-1-r15.

PMID:
24417896
[PubMed - in process]
Free PMC Article
6.

In silico characterization and prediction of global protein-mRNA interactions in yeast.

Pancaldi V, Bähler J.

Nucleic Acids Res. 2011 Aug;39(14):5826-36. doi: 10.1093/nar/gkr160. Epub 2011 Apr 1.

PMID:
21459850
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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
8.

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
9.

Functionally related transcripts have common RNA motifs for specific RNA-binding proteins in trypanosomes.

Noé G, De Gaudenzi JG, Frasch AC.

BMC Mol Biol. 2008 Dec 8;9:107. doi: 10.1186/1471-2199-9-107.

PMID:
19063746
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Hyper conserved elements in vertebrate mRNA 3'-UTRs reveal a translational network of RNA-binding proteins controlled by HuR.

Dassi E, Zuccotti P, Leo S, Provenzani A, Assfalg M, D'Onofrio M, Riva P, Quattrone A.

Nucleic Acids Res. 2013 Mar 1;41(5):3201-16. doi: 10.1093/nar/gkt017. Epub 2013 Feb 1.

PMID:
23376935
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome.

Riordan DP, Herschlag D, Brown PO.

Nucleic Acids Res. 2011 Mar;39(4):1501-9. doi: 10.1093/nar/gkq920. Epub 2010 Oct 18.

PMID:
20959291
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system.

Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO.

PLoS Biol. 2008 Oct 28;6(10):e255. doi: 10.1371/journal.pbio.0060255.

PMID:
18959479
[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.

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]
15.

Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR.

Lebedeva S, Jens M, Theil K, Schwanhäusser B, Selbach M, Landthaler M, Rajewsky N.

Mol Cell. 2011 Aug 5;43(3):340-52. doi: 10.1016/j.molcel.2011.06.008. Epub 2011 Jun 30.

PMID:
21723171
[PubMed - indexed for MEDLINE]
Free Article
16.

Folding free energies of 5'-UTRs impact post-transcriptional regulation on a genomic scale in yeast.

Ringnér M, Krogh M.

PLoS Comput Biol. 2005 Dec;1(7):e72. Epub 2005 Dec 9.

PMID:
16355254
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networks.

Mittal N, Roy N, Babu MM, Janga SC.

Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20300-5. doi: 10.1073/pnas.0906940106. Epub 2009 Nov 16.

PMID:
19918083
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
23685613
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts.

Baltz AG, Munschauer M, Schwanhäusser B, Vasile A, Murakawa Y, Schueler M, Youngs N, Penfold-Brown D, Drew K, Milek M, Wyler E, Bonneau R, Selbach M, Dieterich C, Landthaler M.

Mol Cell. 2012 Jun 8;46(5):674-90. doi: 10.1016/j.molcel.2012.05.021.

PMID:
22681889
[PubMed - indexed for MEDLINE]
Free Article
20.

Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition.

Hafner M, Max KE, Bandaru P, Morozov P, Gerstberger S, Brown M, Molina H, Tuschl T.

RNA. 2013 May;19(5):613-26. doi: 10.1261/rna.036491.112. Epub 2013 Mar 12.

PMID:
23481595
[PubMed - indexed for MEDLINE]
Free PMC Article

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