Wang Y, Li Y, Yue M, Wang J, Kumar S, Wechsler-Reya RJ, Zhang Z, Ogawa Y, Kellis M, Duester G, Zhao JC. (2018) "N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications" Nature Neuroscience (Advanced Access)
Kreimer, A., Zeng, H., Edwards, M. D., Guo, Y., Tian, K., Shin, S., Welch, R., Wainberg, M., Mohan, R., Sinnott-Armstrong, N. A., Li, Y., Eraslan, G., AMIN, T. B., Goke, J., Mueller, N. S., Kellis, M., Kundaje, A., Beer, M. A., Keles, S., Gifford, D. K. and Yosef, N. (2017), Predicting gene expression in massively parallel reporter assays: a comparative study. Human Mutation. doi:10.1002/humu.23197
Li, Y. & Kellis, M. (2016). Joint Bayesian inference of risk variants and tissue-specific epigenomic enrichments across multiple complex human diseases. Nucleic Acids Research. http://doi.org/10.1093/nar/gkw627
Olsen, J. B., Wong, L., Deimling, S., Miles, A., Guo, H., Li, Y., Zhang, Z., Greenblatt, J., Emili, A., Tropepe., V. (2016). G9a and ZNF644 Physically Associate to Suppress Progenitor Gene Expression during Neurogenesis. Stem Cell Reports, 7(3), 454–470. http://doi.org/10.1016/j.stemcr.2016.06.012
Paul, J.*, Toosi, B.*, Vizeacoumar, F.*, Bhanumathy, K., Li, Y., Gerger, C., Zawily, A., Freywald, T., Anderson, D., Mousseau, D., Kanthan, R., Zhang, Z., Vizeacoumar, F., & Freywald, A. (2016). Targeting synthetic lethality between the SRC kinase and the EPHB6 receptor may benefit cancer treatment. Oncotarget. http://doi.org/10.1093/nar/gkw627
Zhao, D.Y., Gish, G.*, Braunschweig, U.*, Li, Y., Ni, Z., Schmitges, F.W., Zhong, G., Liu, K., Li, W., Moffat, J., Vedadi, M., Min, J., Pawson, T., Blencowe, B., and Greenblatt, J. (2016). SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination. Nature 529(7584), pp.48-53.
Wong, K. C., Li, Y., & Peng, C. A Comparison Study for DNA Motif Modeling on Protein Binding Microarray. IEEE/ACM Transactions on Computational Biology and Bioinformatics. doi:10.1109/TCBB.2015.2443782.(In press)
Wong, K. C., Peng, C., & Li, Y. Probabilistic Inference on Multiple Normalized Signal Profiles from Next Generation Sequencing: Transcription Factor Binding Sites. IEEE/ACM Transactions on Computational Biology and Bioinformatics. doi:10.1109/TCBB.2015.2424421. (In press)
Wong, K. C., Li, Y., & Peng, C. (2015). Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells. Bioinformatics, btv555 (Advanced Online).
Wong, K. C., Li Y., Peng, C., Moses, A. M., & Zhang, Z. (2015). Computational learning on specificity-determining residue-nucleotide interactions. Nucleic acids research, gkv1134 (Advanced Online).
Li Y*, Wang Y*, Zhang Z, Zamudio AV, Zhao JC. Genome-wide detection of high abundance N6-methyladenosine sites by microarray. RNA. 2015. (Advanced Online)
Li Y and Zhang Z. Computational Biology in microRNA. WIREs RNA. 2015. doi: 10.1002/wrna.1286
Liang C*, Li Y*, Luo J, Zhang Z. A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human. Bioinformatics. 2015. (Advance Online)
Li Y and Zhang Z. Potential microRNA-mediated oncogenic intercellular communication revealed by pan-cancer analysis. Scientific Report 2014;4:7097.
Li Y, Liang M, Zhang Z. Regression Analysis of Combined Gene Expression Regulation in Acute Myeloid Leukemia. PLoS Computational Biology. 2014;10(10):e1003908.
Li Y*, Liang C*, Easterbrook S, Luo J, Zhang Z. Investigating functional implication of reinforcing feedback loops in transcriptional regulatory network. Molecular BioSystem. 2014;10(12):3238-3248.
Wong K-C, Peng C, Li Y, Chan T-M. Herd Clustering: A synergistic data clustering approach using collective intelligence. Applied Soft Computing. 2014;23:61-75.
Wong, KC, Li, Y., Peng, C., Zhang, Z. SignalSpider: Probabilistic Pattern Discovery on Multiple Normalized ChIP-Seq Signal Profiles. Bioinformatics 2014;31(1):17-24.
Li Y*, Liang C*, Wong K-C, Luo J, Zhang Z. Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion. Bioinformatics. 2014;30(18):2627–2635.
Li Y, Liang C, Wong K-C, Jin K, Zhang Z. Inferring probabilistic miRNA-mRNA interaction in cancers: a role-switch approach. Nucleic Acids Research. 2014;42(9):e76.
Li Y, Goldenberg A, Wong K-C, Zhang Z. A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information. Bioinformatics. 2014;30(5):621–628.
Wang Y, Li Y, Toth JI, Petroski MD, Zhang Z, Zhao JC. N(6)-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nature Cell Biology. 2014;16(2):1-10.
Wong K-C, Chan T-M, Peng C, Li Y, Zhang Z. DNA motif elucidation using belief propagation. Nucleic Acids Research. 2013;41(16):e153.
Li Y, Zhao DY, Greenblatt JF, Zhang Z. RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments. Nucleic Acids Research. 2013;41(8):e94–e94.
Arsenault RJ, Li Y, Potter A, Griebel PJ, Kusalik A, Napper S. Induction of ligand-specific PrP (C) signaling in human neuronal cells. Prion. 2012;6(5):477-488.
Arsenault RJ, Li Y, Bell, K., Doig, K., Potter, A., Griebel, P. J., Kusalik, A., and Napper, S. Mycobacterium avium subsp. paratuberculosis Inhibits Interferon Gamma-Induced Signaling in Bovine Monocytes. Insights into the Cellular Mechanisms of Johne's Disease. Infect Immunity 2012.
Arsenault RJ, Li Y, Maattanen, P., Scruten, E., Doig, K., Potter, A., Griebel, P., Kusalik, A., and Napper, S. Altered Toll-like receptor 9 signaling in Mycobacterium avium subsp. paratuberculosis-infected bovine monocytes reveals potential therapeutic targets. Infect Immunity. 2012;81(1):226-237.
Li Y, Arsenault RJ, Trost, B., Slind, J., Griebel, P. J., Napper, S., Kusalik, A. A Systematic Approach for Analysis of Peptide Array Kinome Data. Science Signaling. 2012;5(220):pl2-pl2.
(*=joint author)
Book chapters:
Wong, K. C., Li, Y., & Zhang, Z. (2015). Unsupervised Learning in Genome Informatics. arXiv preprint arXiv:1508.00459.
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.