My Bibliography

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Bai Z, Zhang D, Gao Y, Tao B, Zhang D, Bao S, Enninful A, Wang Y, Li H, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu ML, Fan R. Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues. Cell. 2024 Nov 14;187(23):6760-6779.e24. doi: 10.1016/j.cell.2024.09.001. Epub 2024 Sep 30. PubMed PMID: 39353436; PubMed Central PMCID: PMC11568911.

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Zhang N, Tang W, Torres L, Wang X, Ajaj Y, Zhu L, Luan Y, Zhou H, Wang Y, Zhang D, Kurbatov V, Khan SA, Kumar P, Hidalgo A, Wu D, Lu J. Cell surface RNAs control neutrophil recruitment. Cell. 2024 Feb 15;187(4):846-860.e17. doi: 10.1016/j.cell.2023.12.033. Epub 2024 Jan 22. PubMed PMID: 38262409; PubMed Central PMCID: PMC10922858.

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Zhang D, Tian J, Wang Y, Lu J. Evitar: designing anti-viral RNA therapies against future RNA viruses. Bioinformatics. 2022 Apr 28;38(9):2437-2443. doi: 10.1093/bioinformatics/btac144. PubMed PMID: 35294970; PubMed Central PMCID: PMC9048652.

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Kanoria S, Rennie WA, Carmack CS, Lu J, Ding Y. N (6)-methyladenosine enhances post-transcriptional gene regulation by microRNAs. Bioinform Adv. 2022;2(1):vbab046. doi: 10.1093/bioadv/vbab046. eCollection 2022. PubMed PMID: 35098135; PubMed Central PMCID: PMC8792947.

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Wang N, Zheng J, Chen Z, Liu Y, Dura B, Kwak M, Xavier-Ferrucio J, Lu YC, Zhang M, Roden C, Cheng J, Krause DS, Ding Y, Fan R, Lu J. Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation. Nat Commun. 2019 Jan 9;10(1):95. doi: 10.1038/s41467-018-07981-6. PubMed PMID: 30626865; PubMed Central PMCID: PMC6327095.

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Roden C, Gaillard J, Kanoria S, Rennie W, Barish S, Cheng J, Pan W, Liu J, Cotsapas C, Ding Y, Lu J. Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation. Genome Res. 2017 Mar;27(3):374-384. doi: 10.1101/gr.208900.116. Epub 2017 Jan 13. PubMed PMID: 28087842; PubMed Central PMCID: PMC5340965.

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Rennie W, Kanoria S, Liu C, Mallick B, Long D, Wolenc A, Carmack CS, Lu J, Ding Y. STarMirDB: A database of microRNA binding sites. RNA Biol. 2016 Jun 2;13(6):554-60. doi: 10.1080/15476286.2016.1182279. PubMed PMID: 27144897; PubMed Central PMCID: PMC4962797.

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Cheng J, Roden CA, Pan W, Zhu S, Baccei A, Pan X, Jiang T, Kluger Y, Weissman SM, Guo S, Flavell RA, Ding Y, Lu J. A Molecular Chipper technology for CRISPR sgRNA library generation and functional mapping of noncoding regions. Nat Commun. 2016 Mar 30;7:11178. doi: 10.1038/ncomms11178. PubMed PMID: 27025950; PubMed Central PMCID: PMC4820989.

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Kanoria S, Rennie W, Liu C, Carmack CS, Lu J, Ding Y. STarMir Tools for Prediction of microRNA Binding Sites. Methods Mol Biol. 2016;1490:73-82. doi: 10.1007/978-1-4939-6433-8_6. PubMed PMID: 27665594; PubMed Central PMCID: PMC5353976.

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Wang J, Rennie W, Liu C, Carmack CS, Prévost K, Caron MP, Massé E, Ding Y, Wade JT. Identification of bacterial sRNA regulatory targets using ribosome profiling. Nucleic Acids Res. 2015 Dec 2;43(21):10308-20. doi: 10.1093/nar/gkv1158. Epub 2015 Nov 5. PubMed PMID: 26546513; PubMed Central PMCID: PMC4666370.

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Levina E, Ji H, Chen M, Baig M, Oliver D, Ohouo P, Lim CU, Schools G, Carmack S, Ding Y, Broude EV, Roninson IB, Buttyan R, Shtutman M. Identification of novel genes that regulate androgen receptor signaling and growth of androgen-deprived prostate cancer cells. Oncotarget. 2015 May 30;6(15):13088-104. doi: 10.18632/oncotarget.3743. PubMed PMID: 26036626; PubMed Central PMCID: PMC4537001.

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Guo Y, Liu J, Elfenbein SJ, Ma Y, Zhong M, Qiu C, Ding Y, Lu J. Characterization of the mammalian miRNA turnover landscape. Nucleic Acids Res. 2015 Feb 27;43(4):2326-41. doi: 10.1093/nar/gkv057. Epub 2015 Feb 4. PubMed PMID: 25653157; PubMed Central PMCID: PMC4344502.

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Liu C, Rennie WA, Carmack CS, Kanoria S, Cheng J, Lu J, Ding Y. Effects of genetic variations on microRNA: target interactions. Nucleic Acids Res. 2014 Sep;42(15):9543-52. doi: 10.1093/nar/gku675. Epub 2014 Jul 31. PubMed PMID: 25081214; PubMed Central PMCID: PMC4150780.

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Rennie W, Liu C, Carmack CS, Wolenc A, Kanoria S, Lu J, Long D, Ding Y. STarMir: a web server for prediction of microRNA binding sites. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W114-8. doi: 10.1093/nar/gku376. Epub 2014 May 6. PubMed PMID: 24803672; PubMed Central PMCID: PMC4086099.

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Liu C, Rennie WA, Mallick B, Kanoria S, Long D, Wolenc A, Carmack CS, Ding Y. MicroRNA binding sites in C. elegans 3' UTRs. RNA Biol. 2014;11(6):693-701. doi: 10.4161/rna.28868. Epub 2014 Apr 25. PubMed PMID: 24827614; PubMed Central PMCID: PMC4156501.

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Cheng J, Guo S, Chen S, Mastriano SJ, Liu C, D'Alessio AC, Hysolli E, Guo Y, Yao H, Megyola CM, Li D, Liu J, Pan W, Roden CA, Zhou XL, Heydari K, Chen J, Park IH, Ding Y, Zhang Y, Lu J. An extensive network of TET2-targeting MicroRNAs regulates malignant hematopoiesis. Cell Rep. 2013 Oct 31;5(2):471-81. doi: 10.1016/j.celrep.2013.08.050. Epub 2013 Oct 10. PubMed PMID: 24120864; PubMed Central PMCID: PMC3834864.

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Kallen AN, Zhou XB, Xu J, Qiao C, Ma J, Yan L, Lu L, Liu C, Yi JS, Zhang H, Min W, Bennett AM, Gregory RI, Ding Y, Huang Y. The imprinted H19 lncRNA antagonizes let-7 microRNAs. Mol Cell. 2013 Oct 10;52(1):101-12. doi: 10.1016/j.molcel.2013.08.027. Epub 2013 Sep 19. PubMed PMID: 24055342; PubMed Central PMCID: PMC3843377.

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Liu C, Mallick B, Long D, Rennie WA, Wolenc A, Carmack CS, Ding Y. CLIP-based prediction of mammalian microRNA binding sites. Nucleic Acids Res. 2013 Aug;41(14):e138. doi: 10.1093/nar/gkt435. Epub 2013 May 22. PubMed PMID: 23703212; PubMed Central PMCID: PMC3737542.

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Cosgrove MS, Ding Y, Rennie WA, Lane MJ, Hanes SD. The Bin3 RNA methyltransferase targets 7SK RNA to control transcription and translation. Wiley Interdiscip Rev RNA. 2012 Sep-Oct;3(5):633-47. doi: 10.1002/wrna.1123. Epub 2012 Jun 27. Review. PubMed PMID: 22740346; PubMed Central PMCID: PMC3629726.

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Kluiver J, Gibcus JH, Hettinga C, Adema A, Richter MK, Halsema N, Slezak-Prochazka I, Ding Y, Kroesen BJ, van den Berg A. Rapid generation of microRNA sponges for microRNA inhibition. PLoS One. 2012;7(1):e29275. doi: 10.1371/journal.pone.0029275. Epub 2012 Jan 6. PubMed PMID: 22238599; PubMed Central PMCID: PMC3253070.

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Shtutman M, Baig M, Levina E, Hurteau G, Lim CU, Broude E, Nikiforov M, Harkins TT, Carmack CS, Ding Y, Wieland F, Buttyan R, Roninson IB. Tumor-specific silencing of COPZ2 gene encoding coatomer protein complex subunit ζ 2 renders tumor cells dependent on its paralogous gene COPZ1. Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12449-54. doi: 10.1073/pnas.1103842108. Epub 2011 Jul 11. PubMed PMID: 21746916; PubMed Central PMCID: PMC3145676.

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Shtutman M, Maliyekkel A, Shao Y, Carmack CS, Baig M, Warholic N, Cole K, Broude EV, Harkins TT, Ding Y, Roninson IB. Function-based gene identification using enzymatically generated normalized shRNA library and massive parallel sequencing. Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7377-82. doi: 10.1073/pnas.1003055107. Epub 2010 Apr 5. PubMed PMID: 20368428; PubMed Central PMCID: PMC2867740.

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Yu JY, Reynolds SH, Hatfield SD, Shcherbata HR, Fischer KA, Ward EJ, Long D, Ding Y, Ruohola-Baker H. Dicer-1-dependent Dacapo suppression acts downstream of Insulin receptor in regulating cell division of Drosophila germline stem cells. Development. 2009 May;136(9):1497-507. doi: 10.1242/dev.025999. Epub 2009 Mar 31. PubMed PMID: 19336466; PubMed Central PMCID: PMC2674257.

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Keck K, Volper EM, Spengler RM, Long DD, Chan CY, Ding Y, McCaffrey AP. Rational design leads to more potent RNA interference against hepatitis B virus: factors effecting silencing efficiency. Mol Ther. 2009 Mar;17(3):538-47. doi: 10.1038/mt.2008.273. Epub 2008 Dec 16. PubMed PMID: 19088704; PubMed Central PMCID: PMC2770508.

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Chan CY, Carmack CS, Long DD, Maliyekkel A, Shao Y, Roninson IB, Ding Y. A structural interpretation of the effect of GC-content on efficiency of RNA interference. BMC Bioinformatics. 2009 Jan 30;10 Suppl 1(Suppl 1):S33. doi: 10.1186/1471-2105-10-S1-S33. PubMed PMID: 19208134; PubMed Central PMCID: PMC2648742.

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Ding Y. RNA secondary structure prediction and gene regulation by small RNAs. In: Feng J, Fu W, Sun F, editors. Frontiers in Computational and System Biology London: Springer; 2009. p.19-37. 410p.

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Hammell M, Long D, Zhang L, Lee A, Carmack CS, Han M, Ding Y, Ambros V. mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nat Methods. 2008 Sep;5(9):813-9. doi: 10.1038/nmeth.1247. PubMed PMID: 19160516; PubMed Central PMCID: PMC3092588.

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Long D, Chan CY, Ding Y. Analysis of microRNA-target interactions by a target structure based hybridization model. Pac Symp Biocomput. 2008;:64-74. PubMed PMID: 18232104.

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Chan CY, Ding Y. Boltzmann ensemble features of RNA secondary structures: a comparative analysis of biological RNA sequences and random shuffles. J Math Biol. 2008 Jan;56(1-2):93-105. doi: 10.1007/s00285-007-0129-z. Epub 2007 Oct 2. PubMed PMID: 17909813.

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Shao Y, Wu S, Chan CY, Klapper JR, Schneider E, Ding Y. A structural analysis of in vitro catalytic activities of hammerhead ribozymes. BMC Bioinformatics. 2007 Nov 30;8:469. doi: 10.1186/1471-2105-8-469. PubMed PMID: 18053134; PubMed Central PMCID: PMC2238771.

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Shao Y, Chan CY, Maliyekkel A, Lawrence CE, Roninson IB, Ding Y. Effect of target secondary structure on RNAi efficiency. RNA. 2007 Oct;13(10):1631-40. doi: 10.1261/rna.546207. Epub 2007 Aug 7. PubMed PMID: 17684233; PubMed Central PMCID: PMC1986803.

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Long D, Lee R, Williams P, Chan CY, Ambros V, Ding Y. Potent effect of target structure on microRNA function. Nat Struct Mol Biol. 2007 Apr;14(4):287-94. doi: 10.1038/nsmb1226. Epub 2007 Apr 1. PubMed PMID: 17401373.

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Shao Y, Wu Y, Chan CY, McDonough K, Ding Y. Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation. Nucleic Acids Res. 2006;34(19):5660-9. doi: 10.1093/nar/gkl715. Epub 2006 Oct 11. PubMed PMID: 17038332; PubMed Central PMCID: PMC1636493.

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Ding Y, Chan CY, Lawrence CE. Clustering of RNA secondary structures with application to messenger RNAs. J Mol Biol. 2006 Jun 9;359(3):554-71. doi: 10.1016/j.jmb.2006.01.056. Epub 2006 Feb 2. PubMed PMID: 16631786.

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Ding Y. Statistical and Bayesian approaches to RNA secondary structure prediction. RNA. 2006 Mar;12(3):323-31. doi: 10.1261/rna.2274106. Review. PubMed PMID: 16495231; PubMed Central PMCID: PMC1383571.

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Chan CY, Lawrence CE, Ding Y. Structure clustering features on the Sfold Web server. Bioinformatics. 2005 Oct 15;21(20):3926-8. doi: 10.1093/bioinformatics/bti632. Epub 2005 Aug 18. PubMed PMID: 16109749.

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Ding Y, Chan CY, Lawrence CE. RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA. 2005 Aug;11(8):1157-66. doi: 10.1261/rna.2500605. PubMed PMID: 16043502; PubMed Central PMCID: PMC1370799.

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Pentecost BT, Bradley LM, Gierthy JF, Ding Y, Fasco MJ. Gene regulation in an MCF-7 cell line that naturally expresses an estrogen receptor unable to directly bind DNA. Mol Cell Endocrinol. 2005 Jun 30;238(1-2):9-25. doi: 10.1016/j.mce.2005.04.005. PubMed PMID: 15913882.

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Ding Y, Lawrence CE. Rational design of siRNAs with the Sfold software. In: Appasani K, editor. RNA Interference: from Basic Science to Drug Development Cambridge, UK: Cambridge University Press; 2005. p.129-138. 510p.

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Ding Y, Chan CY, Lawrence CE. Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W135-41. doi: 10.1093/nar/gkh449. PubMed PMID: 15215366; PubMed Central PMCID: PMC441587.

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Ding Y, Lawrence CE. A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res. 2003 Dec 15;31(24):7280-301. doi: 10.1093/nar/gkg938. PubMed PMID: 14654704; PubMed Central PMCID: PMC297010.

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Keyomarsi K, Tucker SL, Buchholz TA, Callister M, Ding Y, Hortobagyi GN, Bedrosian I, Knickerbocker C, Toyofuku W, Lowe M, Herliczek TW, Bacus SS. Cyclin E and survival in patients with breast cancer. N Engl J Med. 2002 Nov 14;347(20):1566-75. doi: 10.1056/NEJMoa021153. PubMed PMID: 12432043.

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Ding Y. Rational statistical design of antisense oligonucleotides for high throughput functional genomic and drug target validation. Statistica Sinica. 2002; 12:273-296.

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Ding Y, Lawrence CE. Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res. 2001 Mar 1;29(5):1034-46. doi: 10.1093/nar/29.5.1034. PubMed PMID: 11222752; PubMed Central PMCID: PMC29728.

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Ding Y, Lawrence CE. A bayesian statistical algorithm for RNA secondary structure prediction. Comput Chem. 1999 Jun 15;23(3-4):387-400. doi: 10.1016/s0097-8485(99)00010-8. PubMed PMID: 10404626.

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Xue X, Ding Y. Assessing heterogeneity and correlation of paired failure times with the bivariate frailty model. Stat Med. 1999 Apr 30;18(8):907-18. doi: 10.1002/(sici)1097-0258(19990430)18:8<907::aid-sim82>3.0.co;2-x. PubMed PMID: 10363330.

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McEwen BF, Ding Y, Heagle AB. Relevance of kinetochore size and microtubule-binding capacity for stable chromosome attachment during mitosis in PtK1 cells. Chromosome Res. 1998 Feb;6(2):123-32. doi: 10.1023/a:1009239013215. PubMed PMID: 9543015.

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Ding Y. On the asymptotic normality of multinomial size estimates with application to the backcalculation estimates of AIDS epidemic. Biometrika. 1996; 83:695-699.

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Ding Y, Fienberg S. Multiple sample estimation of population and census undercount in the presence of matching errors. Survey Methodology. 1996; 22:55-64.

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Ding Y. Computing back-calculation estimates of AIDS epidemic. Stat Med. 1995 Jul 30;14(14):1505-12. doi: 10.1002/sim.4780141402. PubMed PMID: 7481188.