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spacing spacing Software for Statistical Folding of Nucleic Acids and Studies of Regulatory RNAs


button1 button2 button3 button5 button7 button6 Wednesday July 23, 2014

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button_m3 Target accessibility prediction and RNA duplex thermodynamics for rational siRNA design
button_m1 Target accessibility prediction and rational design of antisense oligonucleotides and nucleic acid probes
button_m2 Target accessibility prediction and rational design of trans-cleaving ribozymes
button_m4 General features and output for statistical RNA folding
button_m5 CLIP-based prediction of microRNA binding sites
button_m6 Database of microRNA binding sites predicted by STarMir
(comprehensive site features and CLIP annotation)beta
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Selected Publications

Liu, C., Rennie, W.A, Mallick, B., Kanoria, S., Long, D., Wolenc, A., Carmack, C.S. and Ding, Y. (2014) MicroRNA BindingSites in C. elegans 3′ UTRs. RNA Biology, doi: 10.4161/rna.28868 [ Abstract ] [ Full text ]
Rennie, W.A., Liu, C., Carmack, C.S., Wolenc, A., Kanoria, S.,Long, D. and Ding, Y. (2014) STarMir: a web server for prediction of microRNA binding Sites. Nucleic Acids Res, doi: 10.1093/mar/gku376 [ Abstract ] [ PDF file ]
Liu, C., Mallick, B., Long, D., Rennie, W.A., Wolenc, A., Carmack, C.S., and Ding, Y. (2013) CLIP-based prediction of mammalian microRNA binding sites. Nucleic Acids Res, 41 (14), e138.
[ Abstract ] [ PDF file ]
Long, D., Lee, R., Williams, P., Chan, C.Y., Ambros, V., and Ding, Y. (2007) Potent effect of target structure on microRNA function. Nat. Struct. Mol. Biol. 14, 287-294.
[ Abstract ] [ PDF file ] [ Supplementary information ] [ Highlight by Nature 446, 587. ] [ Faculty of 1000 Biology Recommended ]
Shao, Y, Wu, S., Chan, C.Y., Klapper, J.R., Schneider, E., and Ding, Y. (2007) A structural analysis of in vitro catalytic activities of hammerhead ribozymes. BMC Biofinformatics 8, 469.
[ Abstract ] [ PDF file ]
Shao, Y., Anil, M., Chan, C.Y., Lawrence, C.E., Roninson, I., and Ding, Y. (2007) Effect of target secondary structure on RNAi efficiency. RNA 13, 1631-1640.
[ Abstract ] [ PDF file ]
Shao, Y., Wu, Y., Chan, C.Y., McDonough, K., and Ding, Y. (2006) Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation. Nucleic Acids Res. 34, 5660-5669.
[ Abstract ] [ PDF file ]
Ding, Y., Chan, C.Y. and Lawrence, C.E. (2005) RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA 11, 1157-1166.
[ Abstract ] [ PDF file ] [ Supplementary information ] [ Faculty of 1000 Biology Recommended ]
Ding, Y., Chan, C.Y. and Lawrence, C.E. (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 32 Web Server issue, W135-W141.
[ Abstract ] [ PDF file ]
Ding, Y. and Lawrence, C.E. (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res. 31, 7280-7301.
[ Cover ] [ Abstract ] [ PDF file ] [ Faculty of 1000 Biology Must Read ]
Ding, Y. and Lawrence, C.E. (2001) Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res. 29, 1034-1046.
[ Abstract ] [ PDF file ]


All Publications
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