Investigators and Program Directors

Select Publications, Sfold Software and Media Coverage

• 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 10 (in press).
• 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. 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.
• 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.
• 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.
• 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.
• 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. 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.
• 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.
• Ding, Y. (2006) Statistical and Bayesian approaches to RNA secondary structure prediction. RNA 12, 323-331.
• Chan, C.Y., Lawrence, C.E. and Ding, Y. (2005) Structure clustering features on the Sfold Web server. Bioinformatics 21, 3926-3928.
• 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.
• Ding, Ye, Chan, C.Y. and Lawrence, C.E. (2005) RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA 11, 1157-1166. [Faculty of 1000 Biology Recommended]
• Ding, Ye, Chi-Yu Chan, Lawrence, C.E. (2004). Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Research 32, W135-W141
• Ding, Ye and Lawrence, C.E. (2004). Rational design of siRNAs with the Sfold software. In: RNA Interference: from Basic Science to Drug Development, ed. Krishnarao Appasani, pp. 129-138, Cambridge University Press.
• Ding, Ye and Lawrence, C.E. (2003). A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Research 31, 7280-7301 [with cover, a Faculty of 1000 Biology Must Read].
• Ding, Ye (2002). Rational statistical design of antisense oligonucleotides for high throughput functional genomic and drug target validation. Statistica Sinica 12, 273-296.
• Ding, Ye and Charles E. Lawrence (2001). Statistical prediction of single-stranded regions in RNA secondary structure with application to predicting effective antisense target sites and beyond. Nucleic Acids Research, 29, 1034-1046.
• Ding, Ye and Lawrence, C.E. (1999) A Bayesian statistical algorithm for RNA secondary structure prediction. Computers & Chemistry 23, 387-400.