Shapiro BA - Search Results

1

A Suite of Therapeutically-Inspired Nucleic Acid Logic Systems for Conditional Generation of Single-Stranded and Double-Stranded Oligonucleotides.

Zakrevsky P, Bindewald E, Humbertson H, Viard M, Dorjsuren N, Shapiro BA. Zakrevsky P, et al. Among authors: shapiro ba. Nanomaterials (Basel). 2019 Apr 15;9(4):615. doi: 10.3390/nano9040615. Nanomaterials (Basel). 2019. PMID: 30991728 Free PMC article.

2

Structural polymorphism of the HIV-1 leader region explored by computational methods.

Kasprzak W, Bindewald E, Shapiro BA. Kasprzak W, et al. Among authors: shapiro ba. Nucleic Acids Res. 2005 Dec 20;33(22):7151-63. doi: 10.1093/nar/gki1015. Print 2005. Nucleic Acids Res. 2005. PMID: 16371347 Free PMC article.

3

RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers.

Bindewald E, Shapiro BA. Bindewald E, et al. Among authors: shapiro ba. RNA. 2006 Mar;12(3):342-52. doi: 10.1261/rna.2164906. RNA. 2006. PMID: 16495232 Free PMC article.

4

CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments.

Bindewald E, Schneider TD, Shapiro BA. Bindewald E, et al. Among authors: shapiro ba. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W405-11. doi: 10.1093/nar/gkl269. Nucleic Acids Res. 2006. PMID: 16845037 Free PMC article.

5

Bridging the gap in RNA structure prediction.

Shapiro BA, Yingling YG, Kasprzak W, Bindewald E. Shapiro BA, et al. Curr Opin Struct Biol. 2007 Apr;17(2):157-65. doi: 10.1016/j.sbi.2007.03.001. Epub 2007 Mar 23. Curr Opin Struct Biol. 2007. PMID: 17383172 Review.

6

RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign.

Bindewald E, Hayes R, Yingling YG, Kasprzak W, Shapiro BA. Bindewald E, et al. Among authors: shapiro ba. Nucleic Acids Res. 2008 Jan;36(Database issue):D392-7. doi: 10.1093/nar/gkm842. Epub 2007 Oct 18. Nucleic Acids Res. 2008. PMID: 17947325 Free PMC article.

7

Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler.

Bindewald E, Grunewald C, Boyle B, O'Connor M, Shapiro BA. Bindewald E, et al. Among authors: shapiro ba. J Mol Graph Model. 2008 Oct;27(3):299-308. doi: 10.1016/j.jmgm.2008.05.004. Epub 2008 May 24. J Mol Graph Model. 2008. PMID: 18838281 Free PMC article.

8

Protocols for the in silico design of RNA nanostructures.

Shapiro BA, Bindewald E, Kasprzak W, Yingling Y. Shapiro BA, et al. Methods Mol Biol. 2008;474:93-115. doi: 10.1007/978-1-59745-480-3_7. Methods Mol Biol. 2008. PMID: 19031063 Review.

9

Role of 3'UTRs in the translation of mRNAs regulated by oncogenic eIF4E--a computational inference.

Santhanam AN, Bindewald E, Rajasekhar VK, Larsson O, Sonenberg N, Colburn NH, Shapiro BA. Santhanam AN, et al. Among authors: shapiro ba. PLoS One. 2009;4(3):e4868. doi: 10.1371/journal.pone.0004868. Epub 2009 Mar 17. PLoS One. 2009. PMID: 19290046 Free PMC article.

10

CyloFold: secondary structure prediction including pseudoknots.

Bindewald E, Kluth T, Shapiro BA. Bindewald E, et al. Among authors: shapiro ba. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W368-72. doi: 10.1093/nar/gkq432. Epub 2010 May 25. Nucleic Acids Res. 2010. PMID: 20501603 Free PMC article.

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