Publications

Publications

  • Wang, Z., Xu, W., and Liu, Y. Systematic and Integrative Analysis of Gene Expression to Identify Feature Genes Underlying Human Diseases. Transcriptomics and Gene Regulation, 161-185, 2016.
  • Tripathi, S., Waxham, M.N., Cheung, M., and Liu, Y. Lessons in protein design from combined evolution and conformational dynamics. Scientific Reports, 5, 14259, 2015.
  • Wang, Z., Xu, W., and Liu, Y. Integrating full spectrum of sequence features into predicting functional microRNA-mRNA interactions. Bioinformatics, 31(21), 3529-3536, 2015.
  • Xu, W. and Liu, Y. mHealthApps: A Repository and Database of Mobile Health Apps. JMIR mHealth uHealth (2015), 3(1):e28.
  • Wang, Z., Xu, W., Zhu, H., and Liu, Y. A Bayesian framework to improve microRNA target prediction by incorporating external knowledge, Cancer Informatics (2014), Suppl. 7: 19-25.
  • Xu, W., Wang, Z., and Liu, Y. The characterization of microRNA-mediated gene regulation as impacted by both target site location and seed match type. PLoS One (2014), 9(9): e108260.
  • Wang Z., Qiu, P., Xu, W., and Liu, Y. Spectral feature selection and its application in high dimensional gene expression studies. Proceedings of 2014 ACM conference on Bioinformatics, Computational Biology and Health Informatics (ACM BCB’14) , 314-320.
  • Xu, W., San Lucas, F., Wang, Z., and Liu, Y. MicroRNA target prediction based on analysis of coding sequences and untranslated regions. BMC Bioinformatics (2014), 15:S4.
  • Wang, Z., San Lucas, F., Qiu, P., and Liu, Y. Improving the sensitivity of sample clustering by leveraging gene co-expression networks in variable selection. BMC Bioinformatics (2014), 15(1):153.
  • Wang, Q., Zhang, P., Hoffman, L., Tripathi, S., Homouz, D., Liu, Y., Waxham, N., and Cheung, M. Protein recognition and selection through conformational and mutually induced fit. Proc Natl Acad Sci USA (2013), 110(51): 20545–20550.
  • Wang, Z., Xu, W., San Lucas, A. and Liu, Y. Incorporating prior knowledge into gene network study. Bioinformatics (2013), 29: 2633-40.
  • Zage, P., Sirisaengtaksin, S., Liu, Y., Gireud, M., Brown, B., Palla, S., Richards, K., Hughes, D., and Bean, A. UBE4B levels are associated with altered clinical outcomes in neuroblastoma patients and with neuroblastoma cell proliferation, EGFR trafficking, and sensitivity to EGFR inhibitors. Cancer (2013), 119: 915-23.
  • Redell, J., Moore, A., Grill, R., Zhao, J., Johnson, D., Liu, Y. and Dash, P. Analysis of Functional Pathways Altered Following Mild Traumatic Brain Injury. Journal of Neurotrauma (2013), 30:752-764.
  • Tan, Y. and Liu, Y. Evaluation of statistical methods for identifying genes differentially expressed among multiple groups, Bioinformation (2011), 7: 400-404.
  • Kim, I., Liu, Y. and Zhao, H. Sparsity priors for protein-protein interaction predictions. In: Bayesian Modeling in Bioinformatics (Dey, D., Ghosh S., and Mallick, B., eds.), Chapman & Hall, 255-270, 2010.
  • Liu, Y., Kim, I., and Zhao, H. Protein interaction predictions from diverse sources. In: New Developments in Biostatistics and Bioinformatics (Fan, J., Lin, X., Liu, J., eds.), Higher Education Press & World Scientific, 159-175, 2009.
  • Redell J., Liu, Y., and Dash, P. Traumatic Brain Injury Alters Expression of Hippocampal MicroRNAs: Potential Regulators of Multiple Pathophysiological Processes. Journal of Neuroscience Research (2008), 87:1435-1448.
  • Liu, Y., Kim, I., and Zhao, H. Protein interaction predictions from diverse sources. Drug Discovery Today (2008), 13: 409-416.
  • Kim, I., Liu, Y., and Zhao, H. Bayesian methods for predicting interacting protein pairs using domain information. Biometrics (2007), 63: 824-833.
  • Liu, Y., Sun, N., Liu, J., Chen, L., McIntosh, M., Zheng, L., and Zhao, H. Identifying stage-specific genes by combining information from two different types of oligonucleotide arrays. Methods of Microarray Data Analysis V (2007), 59-75.
  • Liu, Y., Liu, N., and Zhao, H.  Inferring protein-protein interactions through high-throughput interaction data from diverse organisms. Bioinformatics (2005), 21: 3279-3285.
  • Liu, Y., and Zhao, H. A computational approach for ordering signal transduction pathway components from genomics and proteomics data. BMC Bioinformatics (2004), 5, 158.
  • Zhang, Z., Harrison, P., Liu Y., and Gerstein, M. Millions of years of evolution preserved: a comprehensive catalogue of over 8000 pseudogenes in the human genome. Genome Research (2003), 13:2541-2558.