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Tracking down noncoding RNAs.
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2269-70. doi: 10.1073/pnas.0500129102. Epub 2005 Feb 9.
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RNAz 2.0: improved noncoding RNA detection.
Pac Symp Biocomput. 2010:69-79.
3
Fragments of noncoding RNA in plasma of human blood.
Ann N Y Acad Sci. 2008 Aug;1137:130-4. doi: 10.1196/annals.1448.030.
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In-line probing analysis of riboswitches.
Methods Mol Biol. 2008;419:53-67. doi: 10.1007/978-1-59745-033-1_4.
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ARTS: alignment of RNA tertiary structures.
Bioinformatics. 2005 Sep 1;21 Suppl 2:ii47-53. doi: 10.1093/bioinformatics/bti1108.
7
Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome.
FEMS Microbiol Lett. 2007 Nov;276(1):83-92. doi: 10.1111/j.1574-6968.2007.00916.x.
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Noncoding RNAs of the H/ACA family.
Cold Spring Harb Symp Quant Biol. 2006;71:395-405. doi: 10.1101/sqb.2006.71.034.
9
Fast and reliable prediction of noncoding RNAs.
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2454-9. doi: 10.1073/pnas.0409169102. Epub 2005 Jan 21.
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Diversity of endogenous small non-coding RNAs in Oryza sativa.
Genetica. 2006 Sep-Nov;128(1-3):21-31. doi: 10.1007/s10709-005-2486-0.

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Review of machine learning methods for RNA secondary structure prediction.
PLoS Comput Biol. 2021 Aug 26;17(8):e1009291. doi: 10.1371/journal.pcbi.1009291. eCollection 2021 Aug.
2
Alignment of Noncoding Ribonucleic Acids with Pseudoknots Using Context-Sensitive Hidden Markov Model.
J Med Signals Sens. 2019 Oct 24;9(4):252-258. doi: 10.4103/jmss.JMSS_11_19. eCollection 2019 Oct-Dec.
3
Development of a new sequential block finding strategy for detection of conserved sequences in riboswitches.
Bioimpacts. 2018;8(1):13-22. doi: 10.15171/bi.2018.03. Epub 2017 Aug 30.
4
MicroRNA-181c targets Bcl-2 and regulates mitochondrial morphology in myocardial cells.
J Cell Mol Med. 2015 Sep;19(9):2084-97. doi: 10.1111/jcmm.12563. Epub 2015 Apr 20.
5
Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds.
BMC Bioinformatics. 2012 Apr 12;13 Suppl 5(Suppl 5):S1. doi: 10.1186/1471-2105-13-S5-S1.
6
Disease genes and gene regulation by microRNAs.
J Cardiovasc Transl Res. 2010 Jun;3(3):169-72. doi: 10.1007/s12265-010-9186-6. Epub 2010 Apr 22.
7
Riboswitch detection using profile hidden Markov models.
BMC Bioinformatics. 2009 Oct 8;10:325. doi: 10.1186/1471-2105-10-325.
8
MicroRNAs identified in highly purified liver-derived mitochondria may play a role in apoptosis.
RNA Biol. 2009 Jan-Mar;6(1):65-72. doi: 10.4161/rna.6.1.7534. Epub 2009 Jan 1.
9
Computational methods in noncoding RNA research.
J Math Biol. 2008 Jan;56(1-2):15-49. doi: 10.1007/s00285-007-0122-6. Epub 2007 Sep 4.
10
Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.
BMC Evol Biol. 2007 Feb 8;7 Suppl 1(Suppl 1):S14. doi: 10.1186/1471-2148-7-S1-S14.

本文引用的文献

1
Fast and reliable prediction of noncoding RNAs.
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2454-9. doi: 10.1073/pnas.0409169102. Epub 2005 Jan 21.
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Rfam: annotating non-coding RNAs in complete genomes.
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4. doi: 10.1093/nar/gki081.
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How do RNA folding algorithms work?
Nat Biotechnol. 2004 Nov;22(11):1457-8. doi: 10.1038/nbt1104-1457.
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MSARI: multiple sequence alignments for statistical detection of RNA secondary structure.
Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12102-7. doi: 10.1073/pnas.0404193101. Epub 2004 Aug 10.
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Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences.
Bioinformatics. 2004 Nov 22;20(17):2911-7. doi: 10.1093/bioinformatics/bth374. Epub 2004 Jun 24.
6
Aligning multiple genomic sequences with the threaded blockset aligner.
Genome Res. 2004 Apr;14(4):708-15. doi: 10.1101/gr.1933104.
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A statistical sampling algorithm for RNA secondary structure prediction.
Nucleic Acids Res. 2003 Dec 15;31(24):7280-301. doi: 10.1093/nar/gkg938.
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ddbRNA: detection of conserved secondary structures in multiple alignments.
Bioinformatics. 2003 Sep 1;19(13):1606-11. doi: 10.1093/bioinformatics/btg229.
9
Secondary structure prediction for aligned RNA sequences.
J Mol Biol. 2002 Jun 21;319(5):1059-66. doi: 10.1016/S0022-2836(02)00308-X.
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An expanding universe of noncoding RNAs.
Science. 2002 May 17;296(5571):1260-3. doi: 10.1126/science.1072249.

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