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Target accessibility prediction and RNA duplex thermodynamics for rational siRNA design |
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Target accessibility prediction and rational design of antisense oligonucleotides and nucleic acid probes |
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Target accessibility prediction and rational design of trans-cleaving ribozymes |
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General features and output for statistical RNA folding |
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CLIP-based prediction of microRNA binding sites |
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Database of microRNA binding sites predicted by STarMir |
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Selected Publications
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Rennie, W., Kanoria, S.,Liu, C. Mallick, B. Long, D., Wolenc, A., Carmack, C.S. Lu, J. and Ding, Y. (2016) STarMirDB: a database of microRNA binding sites.
RNA Biology 13 (6), 554-560.
[ Abstract ]
[ Full text ]
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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, 11 (6), 693-701
[ Full text ]
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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 ]
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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 ]
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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 ]
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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 ]
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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 ]
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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 ]
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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 ]
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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 ]
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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 ]
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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 ]
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All Publications
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