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Items: 11

1.

mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances.

Lai WC, Kayedkhordeh M, Cornell EV, Farah E, Bellaousov S, Rietmeijer R, Salsi E, Mathews DH, Ermolenko DN.

Nat Commun. 2018 Oct 18;9(1):4328. doi: 10.1038/s41467-018-06792-z.

2.

Accelerated RNA secondary structure design using preselected sequences for helices and loops.

Bellaousov S, Kayedkhordeh M, Peterson RJ, Mathews DH.

RNA. 2018 Nov;24(11):1555-1567. doi: 10.1261/rna.066324.118. Epub 2018 Aug 10.

PMID:
30097542
3.

Transcriptional Regulation on Aneuploid Chromosomes in Divers Candida albicans Mutants.

Tucker C, Bhattacharya S, Wakabayashi H, Bellaousov S, Kravets A, Welle SL, Myers J, Hayes JJ, Bulger M, Rustchenko E.

Sci Rep. 2018 Jan 26;8(1):1630. doi: 10.1038/s41598-018-20106-9.

4.

Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA.

Gamache ER, Doh JH, Ritz J, Laederach A, Bellaousov S, Mathews DH, Curcio MJ.

Viruses. 2017 Apr 26;9(5). pii: E93. doi: 10.3390/v9050093.

5.

RNA Secondary Structure Determination by NMR.

Chen JL, Bellaousov S, Turner DH.

Methods Mol Biol. 2016;1490:177-86. doi: 10.1007/978-1-4939-6433-8_11.

PMID:
27665599
6.

Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints.

Chen JL, Bellaousov S, Tubbs JD, Kennedy SD, Lopez MJ, Mathews DH, Turner DH.

Biochemistry. 2015 Nov 17;54(45):6769-82. doi: 10.1021/acs.biochem.5b00833. Epub 2015 Nov 3.

7.

RNAstructure: Web servers for RNA secondary structure prediction and analysis.

Bellaousov S, Reuter JS, Seetin MG, Mathews DH.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W471-4. doi: 10.1093/nar/gkt290. Epub 2013 Apr 24.

8.

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.

Hajdin CE, Bellaousov S, Huggins W, Leonard CW, Mathews DH, Weeks KM.

Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5498-503. doi: 10.1073/pnas.1219988110. Epub 2013 Mar 15.

9.

Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure.

Shen M, Bellaousov S, Hiller M, de La Grange P, Creamer TP, Malina O, Sperling R, Mathews DH, Stoilov P, Stamm S.

Nucleic Acids Res. 2013 Apr 1;41(6):3819-32. doi: 10.1093/nar/gkt063. Epub 2013 Feb 7.

10.

Sharing and archiving nucleic acid structure mapping data.

Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P, Das R, Davis-Neulander L, Duncan CD, Halvorsen M, Knight R, Leontis NB, Mathews DH, Ritz J, Stombaugh J, Weeks KM, Zirbel CL, Laederach A.

RNA. 2011 Jul;17(7):1204-12. doi: 10.1261/rna.2753211. Epub 2011 May 24.

11.

ProbKnot: fast prediction of RNA secondary structure including pseudoknots.

Bellaousov S, Mathews DH.

RNA. 2010 Oct;16(10):1870-80. doi: 10.1261/rna.2125310. Epub 2010 Aug 10.

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