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button1 button2 button3 button5 button7 button6 Thursday July 29, 2010

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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 Energetic characteristics of hybridization between a structured target and a microRNA beta
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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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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, 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. (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. ]
Ding, Y. (2006) Statistical and Bayesian approaches to RNA secondary structure prediction. RNA 12, 323-331.
[ Abstract ] [ PDF file ]
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 ]
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. 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 ]
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 ] [ Article ] [ Faculty of 1000 Biology Must Read ]
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 ]
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 ]
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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