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Items: 17

1.

DotAligner: identification and clustering of RNA structure motifs.

Smith MA, Seemann SE, Quek XC, Mattick JS.

Genome Biol. 2017 Dec 28;18(1):244. doi: 10.1186/s13059-017-1371-3.

2.

Sequence-Based Prediction of RNA-Binding Residues in Proteins.

Walia RR, El-Manzalawy Y, Honavar VG, Dobbs D.

Methods Mol Biol. 2017;1484:205-235. doi: 10.1007/978-1-4939-6406-2_15.

3.

Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins.

de Beauchene IC, de Vries SJ, Zacharias M.

Nucleic Acids Res. 2016 Jun 2;44(10):4565-80. doi: 10.1093/nar/gkw328. Epub 2016 Apr 29.

4.

Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach.

Chauvot de Beauchene I, de Vries SJ, Zacharias M.

PLoS Comput Biol. 2016 Jan 27;12(1):e1004697. doi: 10.1371/journal.pcbi.1004697. eCollection 2016 Jan.

5.

Why YRNAs? About Versatile RNAs and Their Functions.

Köhn M, Pazaitis N, Hüttelmaier S.

Biomolecules. 2013 Feb 8;3(1):143-56. doi: 10.3390/biom3010143.

6.

Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein.

Zanzoni A, Marchese D, Agostini F, Bolognesi B, Cirillo D, Botta-Orfila M, Livi CM, Rodriguez-Mulero S, Tartaglia GG.

Nucleic Acids Res. 2013 Dec;41(22):9987-98. doi: 10.1093/nar/gkt794. Epub 2013 Sep 3.

7.

Widespread purifying selection on RNA structure in mammals.

Smith MA, Gesell T, Stadler PF, Mattick JS.

Nucleic Acids Res. 2013 Sep;41(17):8220-36. doi: 10.1093/nar/gkt596. Epub 2013 Jul 11.

8.

Structure and function of the T-loop structural motif in noncoding RNAs.

Chan CW, Chetnani B, Mondragón A.

Wiley Interdiscip Rev RNA. 2013 Sep-Oct;4(5):507-22. doi: 10.1002/wrna.1175. Epub 2013 Jun 10. Review.

9.

Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs.

Li Z, Ender C, Meister G, Moore PS, Chang Y, John B.

Nucleic Acids Res. 2012 Aug;40(14):6787-99. doi: 10.1093/nar/gks307. Epub 2012 Apr 9.

10.

Several RNase T2 enzymes function in induced tRNA and rRNA turnover in the ciliate Tetrahymena.

Andersen KL, Collins K.

Mol Biol Cell. 2012 Jan;23(1):36-44. doi: 10.1091/mbc.E11-08-0689. Epub 2011 Nov 2.

11.

A coarse-grained force field for Protein-RNA docking.

Setny P, Zacharias M.

Nucleic Acids Res. 2011 Nov;39(21):9118-29. doi: 10.1093/nar/gkr636. Epub 2011 Aug 16.

12.

The midblastula transition defines the onset of Y RNA-dependent DNA replication in Xenopus laevis.

Collart C, Christov CP, Smith JC, Krude T.

Mol Cell Biol. 2011 Sep;31(18):3857-70. doi: 10.1128/MCB.05411-11. Epub 2011 Jul 26.

13.

Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes.

Jung S, Swart EC, Minx PJ, Magrini V, Mardis ER, Landweber LF, Eddy SR.

Nucleic Acids Res. 2011 Sep 1;39(17):7529-47. doi: 10.1093/nar/gkr501. Epub 2011 Jun 28.

14.

Dynamic interaction of Y RNAs with chromatin and initiation proteins during human DNA replication.

Zhang AT, Langley AR, Christov CP, Kheir E, Shafee T, Gardiner TJ, Krude T.

J Cell Sci. 2011 Jun 15;124(Pt 12):2058-69. doi: 10.1242/jcs.086561. Epub 2011 May 24.

15.

A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination.

Koldobskaya Y, Duguid EM, Shechner DM, Suslov NB, Ye J, Sidhu SS, Bartel DP, Koide S, Kossiakoff AA, Piccirilli JA.

Nat Struct Mol Biol. 2011 Jan;18(1):100-6. doi: 10.1038/nsmb.1945. Epub 2010 Dec 12.

16.

Telomerase: an RNP enzyme synthesizes DNA.

Blackburn EH, Collins K.

Cold Spring Harb Perspect Biol. 2011 May 1;3(5). pii: a003558. doi: 10.1101/cshperspect.a003558. Review.

17.

A conserved motif of vertebrate Y RNAs essential for chromosomal DNA replication.

Gardiner TJ, Christov CP, Langley AR, Krude T.

RNA. 2009 Jul;15(7):1375-85. doi: 10.1261/rna.1472009. Epub 2009 May 27.

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