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A comprehensive comparison of general RNA-RNA interaction prediction methods.

Lai D, Meyer IM.

Nucleic Acids Res. 2016 Apr 20;44(7):e61. doi: 10.1093/nar/gkv1477. Epub 2015 Dec 15.


RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data.

Sun WJ, Li JH, Liu S, Wu J, Zhou H, Qu LH, Yang JH.

Nucleic Acids Res. 2016 Jan 4;44(D1):D259-65. doi: 10.1093/nar/gkv1036. Epub 2015 Oct 12.


A mass spectrometry-based method for comprehensive quantitative determination of post-transcriptional RNA modifications: the complete chemical structure of Schizosaccharomyces pombe ribosomal RNAs.

Taoka M, Nobe Y, Hori M, Takeuchi A, Masaki S, Yamauchi Y, Nakayama H, Takahashi N, Isobe T.

Nucleic Acids Res. 2015 Oct 15;43(18):e115. doi: 10.1093/nar/gkv560. Epub 2015 May 26.


Functions of ribosomal proteins in assembly of eukaryotic ribosomes in vivo.

de la Cruz J, Karbstein K, Woolford JL Jr.

Annu Rev Biochem. 2015;84:93-129. doi: 10.1146/annurev-biochem-060614-033917. Epub 2015 Feb 20. Review.


DEAD-box RNA helicase Dbp4 is required for small-subunit processome formation and function.

Soltanieh S, Osheim YN, Spasov K, Trahan C, Beyer AL, Dragon F.

Mol Cell Biol. 2015 Mar;35(5):816-30. doi: 10.1128/MCB.01348-14. Epub 2014 Dec 22.


Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA.

Schwartz S, Bernstein DA, Mumbach MR, Jovanovic M, Herbst RH, León-Ricardo BX, Engreitz JM, Guttman M, Satija R, Lander ES, Fink G, Regev A.

Cell. 2014 Sep 25;159(1):148-62. doi: 10.1016/j.cell.2014.08.028. Epub 2014 Sep 11.


Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells.

Carlile TM, Rojas-Duran MF, Zinshteyn B, Shin H, Bartoli KM, Gilbert WV.

Nature. 2014 Nov 6;515(7525):143-6. doi: 10.1038/nature13802. Epub 2014 Sep 5.


A cluster of methylations in the domain IV of 25S rRNA is required for ribosome stability.

Gigova A, Duggimpudi S, Pollex T, Schaefer M, Koš M.

RNA. 2014 Oct;20(10):1632-44. doi: 10.1261/rna.043398.113. Epub 2014 Aug 14.


Rapid birth-and-death evolution of imprinted snoRNAs in the Prader-Willi syndrome locus: implications for neural development in Euarchontoglires.

Zhang YJ, Yang JH, Shi QS, Zheng LL, Liu J, Zhou H, Zhang H, Qu LH.

PLoS One. 2014 Jun 19;9(6):e100329. doi: 10.1371/journal.pone.0100329. eCollection 2014.


Histidine methylation of yeast ribosomal protein Rpl3p is required for proper 60S subunit assembly.

Al-Hadid Q, Roy K, Munroe W, Dzialo MC, Chanfreau GF, Clarke SG.

Mol Cell Biol. 2014 Aug;34(15):2903-16. doi: 10.1128/MCB.01634-13. Epub 2014 May 27.


Budding yeast for budding geneticists: a primer on the Saccharomyces cerevisiae model system.

Duina AA, Miller ME, Keeney JB.

Genetics. 2014 May;197(1):33-48. doi: 10.1534/genetics.114.163188. Review.


Evidence for the biogenesis of more than 1,000 novel human microRNAs.

Friedländer MR, Lizano E, Houben AJ, Bezdan D, Báñez-Coronel M, Kudla G, Mateu-Huertas E, Kagerbauer B, González J, Chen KC, LeProust EM, Martí E, Estivill X.

Genome Biol. 2014 Apr 7;15(4):R57. doi: 10.1186/gb-2014-15-4-r57.


Insulin receptor substrate-1 associates with small nucleolar RNA which contributes to ribosome biogenesis.

Ozoe A, Sone M, Fukushima T, Kataoka N, Chida K, Asano T, Hakuno F, Takahashi S.

Front Endocrinol (Lausanne). 2014 Mar 4;5:24. doi: 10.3389/fendo.2014.00024. eCollection 2014.


Mak5 and Ebp2 act together on early pre-60S particles and their reduced functionality bypasses the requirement for the essential pre-60S factor Nsa1.

Pratte D, Singh U, Murat G, Kressler D.

PLoS One. 2013 Dec 2;8(12):e82741. doi: 10.1371/journal.pone.0082741. eCollection 2013.


Characterization of the interaction between protein Snu13p/15.5K and the Rsa1p/NUFIP factor and demonstration of its functional importance for snoRNP assembly.

Rothé B, Back R, Quinternet M, Bizarro J, Robert MC, Blaud M, Romier C, Manival X, Charpentier B, Bertrand E, Branlant C.

Nucleic Acids Res. 2014 Feb;42(3):2015-36. doi: 10.1093/nar/gkt1091. Epub 2013 Nov 13.


snOPY: a small nucleolar RNA orthological gene database.

Yoshihama M, Nakao A, Kenmochi N.

BMC Res Notes. 2013 Oct 23;6:426. doi: 10.1186/1756-0500-6-426.


MODOMICS: a database of RNA modification pathways--2013 update.

Machnicka MA, Milanowska K, Osman Oglou O, Purta E, Kurkowska M, Olchowik A, Januszewski W, Kalinowski S, Dunin-Horkawicz S, Rother KM, Helm M, Bujnicki JM, Grosjean H.

Nucleic Acids Res. 2013 Jan;41(Database issue):D262-7. doi: 10.1093/nar/gks1007. Epub 2012 Oct 30.


The architecture of eukaryotic translation.

Chu D, von der Haar T.

Nucleic Acids Res. 2012 Nov 1;40(20):10098-106. doi: 10.1093/nar/gks825. Epub 2012 Sep 10.


The methyltransferase adaptor protein Trm112 is involved in biogenesis of both ribosomal subunits.

Sardana R, Johnson AW.

Mol Biol Cell. 2012 Nov;23(21):4313-22. doi: 10.1091/mbc.E12-05-0370. Epub 2012 Sep 5.

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