1. ‣Refereed Publications (also listed at Google Scholar and Pubmed):

  2. 1.Li, Y.*, Wang, Y.*, Zhang, Z., Zamudio, A. V., and Zhao, J. C. (2015). Genome-wide detection of high abundance N6-methyladenosine sites by microarray. RNA.

  3. 2.Li, Y. and Zhang, Z. Computational Biology in microRNA. (2015) WIREs RNA. doi: 10.1002/wrna.1286

  4. 3.Liang, C.*, Li, Y.*, Luo J., and Zhang, Z. (Jan, 2015) A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human. Bioinformatics (Advance Access)

  5. 4.Li, Y., Zhang, Z. (November, 2014). Potential microRNA-mediated oncogenic intercellular communication revealed by pan-cancer analysis. Scientific Reports. 4(7097)

  6. 5.Li, Y., Liang, M., Zhang, Z. (September, 2014). Regression analysis of combined gene expression regulation in acute myeloid leukemia. PloS Computational Biology. 10(10): e1003908. doi:10.1371/journal.pcbi.1003908

  7. 6.Li, Y.*, Liang, C.*, Easterbrook, S., Luo, J., Zhang, Z. (September, 2014). Investigating functional implication of reinforcing feedback loops in transcriptional regulatory network. Molecular BioSystem 1-11. doi:10.1039/C4MB00526K (Advance Article)

  8. 7.Wong, KC, Li, Y., Peng, C., Zhang, Z. (September, 2014).  SignalSpider: Probabilistic Pattern Discovery on Multiple Normalized ChIP-Seq Signal Profiles. Bioinformatics. doi:10.1093/bioinformatics/btu604 (Online Advance)

  9. 8.Li, Y.*, Liang, C.*, Wong, KC., Luo, J., Zhang, Z. (May, 2014). Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion. Bioinformatics. 30(18), 2627-2635. doi: 10.1093/bioinformatics/btu373.

  10. 9.Wong,  KC., Peng, C., Li, Y., Chan, TM. (May 2014). Herd Clustering: A synergistic approach using collective intelligence. Applied Soft Computing 23, 61-75, ISSN 1568-4946, http://dx.doi.org/10.1016/j.asoc.2014.05.034

  11. 10.Li, Y., Liang, C., Wong, KC, Jin, K., and Zhang, Z. (February, 2014) Inferring probabilistic miRNA-mRNA interaction signatures in cancers: a role-switch approach. Nucleic Acids Research, 42(9), e76. doi: 10.1093/nar/gku182

  12. 11.Wang, Y., Li, Y., Toth, J. I., Petroski, M. D., Zhang, Z., & Zhao, J. C. (January, 2014). N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nature Cell Biology, 16(2), 1-10. doi:10.1038/ncb2902

  13. 12.Li, Y., Goldenberg, A., Wong, KC., Zhang Z. (October, 2013). A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information. Bioinformatics (Oxford, England), 30(5), 621–628. doi:10.1093/bioinformatics/btt599

  14. 13.Wong, K.-C., Chan, T.-M., Peng, C., Li, Y., & Zhang, Z. (May, 2013). DNA motif elucidation using belief propagation. Nucleic Acids Research, 41(16), e153. doi:10.1093/nar/gkt574

  15. 14.Li, Y., Zhao, D. Y., Greenblatt, J. F., & Zhang, Z. (March, 2013). RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments. Nucleic Acids Research, 41(8), e94. doi:10.1093/nar/gkt142

  16. 15.Arsenault, R. J., Li, Y., Maattanen, P., Scruten, E., Doig, K., Potter, A., Griebel, P., Kusalik, A., and Napper, S. (January, 2013) Altered Toll-like receptor 9 signaling in Mycobacterium avium subsp. paratuberculosis infected bovine monocytes reveals potential therapeutic targets. Infection and immunity, 81(1), 226-237.

  17. 16.Arsenault, R. J., Li, Y., Potter, A., Griebel, P. J., Kusalik, A., and Napper, S. (November, 2012). Induction of ligand-specific PrPC signaling in human neuronal cells. Prion, 6(5), 477-488.

  18. 17.Arsenault, R. J., Li, Y., Bell, K., Doig, K., Potter, A., Griebel, P. J., Kusalik, A., and Napper, S. (June, 2012). Mycobacterium avium subsp. paratuberculosis Inhibits Interferon Gamma-Induced Signaling in Bovine Monocytes. Insights into the Cellular Mechanisms of Johne’s Disease. Infection and immunity, 80, 3039–3048.

  19. 18.Li, Y., Arsenault, R. J., Trost, B., Slind, J., Griebel, P. J., Napper, S., and Kusalik, A. (April, 2012). A Systematic Approach for Analysis of Peptide Array Kinome Data. Science Signaling, 5(220), pl2–pl2.

*=co-first author


  1. ‣Book chapters:

  2. •Zhao, D., Li, Y., Greenblatt, J., & Zhang, Z. (2014). ncRNA–Protein Interactions in Development and Disease from the Perspective of High-Throughput Studies. In A. Emili, J. Greenblatt, & S. Wodak (Eds.), Systems Analysis of Chromatin-Related Protein Complexes in Cancer (pp. 87-115). Springer New York. doi:10.1007/978-1-4614-7931-4_5