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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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Energetic characteristics of hybridization between a structured target and
a microRNA  |
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Shtutman, M.,
Maliyekkel, A.,
Shao, Y.,
Carmack, C.S.,
Baig, M.,
Warholic, N.,
Cole, K.,
Broude, E.V.,
Harkins, T.T.,
Ding, Y., and
Roninson, I.B..
(2010) Function-based gene identification using enzymatically generated normalized shRNA library and massive parallel sequencing.
Proc Natl. Acad Sci. U. S. A. 107(16):7377-7382.
[ Abstract ]
[ PDF file ]
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Ding, Y..
(2010) RNA secondary structure prediction and gene regulation by small RNAs. In:
Frontiers in Computational and System Biology, eds. Jianfeng Feng, Wenjiang Fu and Feng Zhu Sun. Springer (in press).
[ PDF file ]
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Yu, J.Y.,
Reynolds, S.H.,
Hatfield, S.D.,
Shcherbata, H.R.,
Fischer, K.A.,
Ward, E.J.,
Long, D.,
Ding, Y., and
Ruohola-Baker, H..
(2009) Dicer-1-dependent Dacapo suppression acts downstream of Insulin receptor in regulating cell division of Drosophila germline stem cells.
Development. 136, 1497-1507.
[ Abstract ]
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Keck, K.,
Volper, E.M.,
Spengler, R.M.,
Long, D.D.,
Chan, C.Y.,
Ding, Y., and
McCaffrey, A.P.
(2009) Rational design leads to more potent RNA interference against hepatitis B virus:
factors effecting silencing efficiency.
Mol Ther. 17(3):538-47
[ Abstract ]
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Chan, C.Y., Carmack, C.S., Long, D.,
Maliyekkel, A., Shao, Y., Roninson, I., and Ding, Y.
(2009) A structural interpretation of the effects of GC-content on
efficiency of RNA interference.
The Seventh Asia Pacific Bioinformatics
Conference (APBC 2009).
BMC Bioinformatics 2009, 10(Suppl 1):S33
[ Abstract ]
[ PDF file ]
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Hammel, M., Long, D., Zhang, L., Lee, A.,
Carmack, C.S., Han, M., Ding, Y., and Ambros, V. 240
(2008) mirWIP: microRNA target prediction based on microRNA-containing
ribonucleoprotein-enriched transcripts.
Nature Methods 5, 813-819
[ Abstract ]
[ PDF file ]
[ Faculty of 1000 Biology Recommended ]
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Chan, C.Y. and Ding, Y.
(2008) Boltzmann ensemble features of RNA secondary structures:
a comparative analysis of biological RNA sequences and random shuffles.
J Math Biol 56, 93-105.
[ Abstract ]
[ PDF file ]
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Long, D., Chan, C.Y., and Ding, Y.
(2008) Analysis of microRNA-target interactions by a target structure
based hybridization model.
Pacific Symposium on Biocomputing 13, 64-74.
[ Abstract ]
[ PDF file ]
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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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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, 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. (2006) Clustering
of RNA secondary structures with application to messenger RNAs.
J. Mol. Biol. 359, 554-571.
[ Abstract ]
[ PDF file ]
[ Related review article by Mathews, D.H. ]
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Ding, Y. (2006) Statistical and Bayesian approaches to
RNA secondary structure prediction.
RNA 12, 323-331.
[ Abstract ]
[ PDF file ]
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Chan, C.Y., Lawrence, C.E., and Ding, Y. (2005) Structure
clustering features on the Sfold Web server.
Bioinformatics 21, 3926-3928.
[ 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. and Lawrence, C.E. (2005) Rational design of siRNAs with the Sfold software.
In RNA Interference: from Basic Science to Drug Development, ed. Krishnarao Appasani, Cambridge University Press. [ PDF file ]
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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 ]
[ Article ]
[ Faculty of 1000 Biology Must Read ]
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Ding, Y. (2002) Rational statistical design of antisense oligonucleotides for
high throughput functional genomics and drug target validation. Statistica Sinica 12, 273-296.
[ Abstract ]
[ PDF file ]
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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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Ding, Y. and Lawrence, C.E. (1999) A Bayesian statistical algorithm for RNA secondary structure prediction.
Computer & Chemistry 23, 387-400.
[ Abstract ]
[ PDF file ]
[
Comments in a review by Zuker (2000) Curr Opin Struct Biol.
10, 303-310. ]
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