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


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Roden, C.A., Gaillard, J., Kanoria, S. , Rennie, W., Barish, S., Cheng, J., Pan, W., Liu, J., Cotsapas, C., Ding, Y. and Lu, J. (2017) Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containint transcripts and genetic variation. GenomeRes, 27 (1) doi: 10.1101/gr.208900 [ Abstract ] [ Full text ]
Kanoria, S., Rennie, W.A, Liu, C., Carmack, C.S. Lu, J., and Ding, Y. (2016) STarMir tools for prediction of microRNA binding Sites. Methods Molecular Biology, 1490, RNA Structure Determination, Chapter 6; pp. 73-82, Douglas H. Turner and David H. Mathews (Eds), Springer [ Abstract ] [ Full text ]
Rennie, W.A, Kanoria, S., Liu, C., Mallick, B., Long, D., Wolenc, A., Carmack, C.S. and Ding, Y. (2016) STarMirDB: a database of microRNA binding Sites. RNA Biology, 13 (6), 554-560 DOI:10.1080/15476286.2016.1182279; PMID: 27144897. [ Abstract ] [ Full text ]
Cheng, J., Roden, C., Pan, W., Zhu, S., Baccei, A, Pan, X, Jiang, T., Kluger, Y., Weissman, S., Guo, S, Flavell,R., Ding, Y. and Lu, J. (2016) A Molecular Chipper Technology for CRISPR sgRNA Library Generation and Functional Mapping of Noncoding Regions. Nature Communications, DOI: 10.1038/NCOMMS11178. PMID: 27025950; PMCID: PMC482098. [ Abstract ] [ Full text ]
Wang, J., Rennie, W., Carmack, C.S., Prévost, K., Caron, M.P., Massé, E., Ding, Y. and Wade, J.T. (2015) Identification of bacterial sRNA regulatory targets using ribosome profiling. Nucleic Acids Res, 43 (21) 10308-20 doi: 10.1093/nar/gkv1158. PMID: 26546513; PMCID: PMC4666370. [ Abstract ] [ Full text ]
Levina, E., Baig, M., Chen, M., Oliver, D., Ohouo, P., Lim, C., Carmack, C.S., Ding, Y., Roninson, I., Buttyan, R. and DShututman, M., (2015) Identification of Novel Genes that Regulate Androgen Receptor Signaling and Growth of Androgen-Deprived Prostate Cancer Cells. Oncotarget, 6 (15) 13088-104 PMID: 26036626; PMCID: PMC4537001. [ Abstract ] [ Full text ]
Guo,Y., Liu, J., Elfenbein, S.J., Ma, Y., Zhong, M., Qiu, C., Ding, Y. and Lu, J. (2015). Characterization of the mammalian miRNA turnover landscape. Nucleic Acids Res, 43 (4) 2326-41 doi: 10.1093/nar/gkv057; PMID: 25653157; PMCID: PMC4344502. [ Abstract ] [ Full text ]
Liu, C., Rennie, W.A, Carmack, C.S. Kanoria, S., Cheng, J., Lu, J., and Ding, Y. (2014) Effects of genetic variations on microRNA:target interactions. Nucleic Acids Res, 42 (15) 9543-52 doi: 10.1093/nar/gku675. PMID: 25081214; PMCID: PMC4150780 [ Abstract ] [ Full text ]
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 ]
Cheng, J., Guo, S., Chen, S., Mastriano, S.J., Liu, C., D` Alessio, A.C., Hysolli E., Guo, Y., Yao, H., Megyola, C.M., Li, D., Liu, J., Pan, W., Roden, C.A., Zhou, X., Heydari, K., Chen, J, Park, I., Ding, Y., Zhang, Y., and Lu, J. (2013) An Extensive Network of TET2-Targeting MicroRNAs Regulates Malignant Hematopoiesis. Cell Reports, 5 (2):471-481.
[ Abstract ] [ Full Text ]
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 ]
Cosgrove, M.S., Ding, Y., Rennie, W.A., Lane, M.J., and Hanes, S.D.. (2012) The Bin3 RNA methyltransferase targets 7SK RNA to control transcription and translation. Wiley Interdiscip Rev RNA, 3 (5) 633-47 [ Abstract ] [ PDF file ]
Kluiver, J., Gibcus, J.H., Hettinga, C., Adema, A., Richter, M.K.S., Halsema, N., Slezak-Prochazka, I., Ding, Y., Kroesen, B., and van den Berg, A.. (2012) Rapid Generation of microRNA sponges for microRNA inhibition. PLoS One, 7 (1), e29275.
[ Abstract ] [ PDF file ]
Shtutman, M., Baig, M., Levina, E., Hurteau, G., Lim, C.U., Broude, E., Nikiforov, M., Harkins, T.T., Carmack, C., Ding, Y., Wieland, F., Buttyan, R., and Roninson, I.. (2011) Tumor-specific silencing of COPZ2 gene encoding coatomer protein complex subunit ζ2 renders tumor cells dependent on its paralogous gene COPZ1. Proc Natl. Acad Sci. U. S. A.. 100(30): 12449-54.
[ Abstract ] [ Full Text ]
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, 15, 19-37, Jianfeng Feng, Wenjiang Fu and Feng Zhu Sun (eds.), Springer.
[ 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 ] [ PDF file ]
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 ] [ PDF file ]
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 ]
Hammell, 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 ] [ PDF file ] [ 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 ] [ Full text ]
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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