Machine learning, Bioinformatics

2006 - 2012, Ph.D. in Machine learning, Department of Computer Science and Engineering, The Chinese University of Hong Kong

2002 - 2006, B.Sc. in Applied mathematics, School of Mathematical Sciences, Peking University

Our lab is devoted to not only developing machine learning theories and algorithms but also applications in computational health.
- New deep learning theories and algorithms for creative intelligence
- Applications in big data analysis on biological system

- Donglei Zhang*, Shikui Tu*, Michael Stubna, Wei-Sheng Wu, Wei-Che Huang, Zhiping Weng, Heng-Chi Lee (2018). The rules for piRNA targeting reveal resistance of endogenous genes to piRNA silencing in C. elegans. Science, 359, 587-592, 2 February 2018 (*co-first author)
- Enzhi Shen, Hao Chen, Ahmet R. Ozturk, Shikui Tu, Masaki Shirayama, Wen Tang, Yue-He Ding, Si-Yuan Dai, Zhiping Weng, and Craig C. Mello (2018). Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline. Cell 172(5), 937–951.e18, 22 February 2018
- Wen Tang, Meetu Seth, Shikui Tu, En-Zhi Shen, Qian Li, Masaki Shirayama, Zhiping Weng, and Craig C. Mello (2018). A Sex Chromosome piRNA Promotes Robust Dosage Compensation and Sex Determination in C. elegans. Developmental Cell, pii: S1534-5807(18)30060-1, 15 February 2018
- Meetu Seth, Masaki Shirayama, Wen Tang, En-Zhi Shen, Shikui Tu, Heng-Chi Lee, Zhiping Weng, and Craig C. Mello, (2018), The Coding Regions of Germline mRNAs Confer Sensitivity to Argonaute Regulation in C. elegans. Cell Reports 22, 2254–2264, 15 February 2018
- Swapnil S. Parhad, Shikui Tu, Zhiping Weng, and William E. Theurkauf. (2017). Adaptive Evolution Leads to Cross-Species Incompatibility in the piRNA Transposon Silencing Machinery. Developmental Cell 43, 60–70.e5, October 9, 2017
- Weijian Long, Shikui Tu, and Lei Xu (2017), “A Comparative Study on Lagrange Ying-Yang Alternation Method in Gaussian Mixture-Based Clustering,” in Intelligent Data Engineering and Automated Learning – IDEAL 2017, pp. 489–499, 2017
- Yajing Chen, Shikui Tu, Lei Xu (2017). The Prognostic Role of Genes with Skewed Expression Distribution in Lung Adenocarcinoma. In: Sun Y., Lu H., Zhang L., Yang J., Huang H. (eds) Intelligence Science and Big Data Engineering (IScIDE 2017). Lecture Notes in Computer Science, vol 10559. Springer, Cham
- Yajing Chen, Shikui Tu, Lei Xu (2017). Survival-Expression Map and Essential Forms of Survival-Expression Relations for Genes. In: Sun Y., Lu H., Zhang L., Yang J., Huang H. (eds) Intelligence Science and Big Data Engineering (IScIDE 2017). Lecture Notes in Computer Science, vol 10559. Springer, Cham
- Jin-Xiong Lv, Shikui Tu, Lei Xu (2017). A Comparative Study of Joint-SNVs Analysis Methods and Detection of Susceptibility Genes for Gastric Cancer in Korean Population. In: Sun Y., Lu H., Zhang L., Yang J., Huang H. (eds) Intelligence Science and Big Data Engineering (IScIDE 2017). Lecture Notes in Computer Science, vol 10559. Springer, Cham
- Wen Zhang, Xiang Yue, Feng Liu, Yanlin Chen, Shikui Tu, and Xining Zhang, “A unified frame of predicting side effects of drugs by using linear neighborhood similarity,” BMC Systems Biology, vol. 11, no. 6, p. 101, Dec. 2017.
- Longqiang Luo, Dingfang Li, Wen Zhang, Shikui Tu, Xiaopeng Zhu, Gang Tian. Accurate Prediction of Transposon-Derived piRNAs by Integrating Various Sequential and Physicochemical Features. PLoS ONE 11(4): e0153268, 2016
- Wen Zhang, Yanlin Chen, Shikui Tu, Feng Liu and Qianlong Qu. Drug side effect prediction through linear neighborhoods and multiple data source integration. 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shenzhen, 2016, pp. 427-434.
- Wen Tang, Shikui Tu, Heng-Chi Lee, Zhiping Weng, Craig C. Mello. The RNase PARN-1 Trims piRNA 3´ Ends to Promote Transcriptome Surveillance in C. elegans. Cell, 164, 974-984, February 2016
- Ming Gao, Travis C Thomson, T Michael Creed, Shikui Tu, Sudan N Loganathan, Christina A Jackson, Patrick McCluskey, Yanyan Lin, Scott E Collier, Zhiping Weng, Paul Lasko, Melanie D Ohi, Alexey L Arkov*. Glycolytic enzymes localize to ribonucleoprotein granules in Drosophila germ cells, bind Tudor and protect from transposable elements. EMBO report, 16 (3), 379-386, 2015
- Shikui Tu, Monica Z Wu, Jie Wang, Asher D Cutter, Zhiping Weng, Julie M Claycomb. Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes. Nucleic Acids Research, 43 (1): 208-224, 2014
- Zhao Zhang, Jie Wang, Nadine Schultz, Fan Zhang, Swapnil S Parhad, Shikui Tu, Thom Vreven, Phillip D Zamore, Zhiping Weng, William E Theurkauf. The HP1 Homolog Rhino Anchors a Nuclear Complex that Suppresses piRNA Precursor Splicing. Cell 157(6):1353-1363, 2014
- Shikui Tu, and Lei Xu. Learning binary factor analysis with automatic model selection. Neurocomputing 134:149-158, 2014
- Lei Shi, Zhi-Yong Liu, Shikui Tu, and Lei Xu. Learning local factor analysis versus mixture of factor analyzers with automatic model selection. Neurocomputing 139:3-14, 2014
- Zaihu Pang, Shikui Tu, Xihong Wu, Lei Xu. A comparative study of RPCL and MCE based discriminative training methods for LVCSR. Neurocomputing 134:53-59, 2014
- Shikui Tu, Thoru Pederson, and Zhiping Weng. Networking development by Boolean logic. Nucleus 14:4(2), Feb 2013
- Zaihu Pang, Shikui Tu, Xihong Wu, Lei Xu. Discriminative GMM-HMM Acoustic Model Selection Using Two-Level Bayesian Ying-Yang Harmony Learning. Lecture Notes in Computer Science 7751: 719-726, 2013
- Shikui Tu and Lei Xu, A Theoretical Investigation of Several Model Selection Criteria for Dimensionality Reduction, Pattern Recognition Letters, 33(9): 1117-1126, 2012
- Shikui Tu, Runsheng Chen, Runsheng Chen, and Lei Xu. A Non-Gaussian Factor Analysis Approach to Transcription Network Component Analysis, to appear in Proceedings of 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2012), May 9-12, San Diego, California, USA
- Shikui Tu, Runsheng Chen, and Lei Xu. Transcription Network Analysis by A Sparse Binary Factor Analysis Algorithm, Journal of Integrative Bioinformatics 9 (2):198, 2012
- Shikui Tu, Runsheng Chen and Lei Xu. A binary matrix factorization algorithm for protein complex prediction, Proteome Science 9(Suppl 1):S18, 2011
- Shikui Tu and Lei Xu. Parameterizations make different model selections: Empirical findings from factor analysis. Frontiers of Electrical and Electronic Engineering in China 6(2):256-274, 2011
- Lei Shi, Shikui Tu and Lei Xu. Learning Gaussian mixture with automatic model selection: A comparative study on three Bayesian related approaches. Frontiers of Electrical and Electronic Engineering in China 6(2):215-244, 2011
- Shikui Tu and Lei Xu. An investigation of several typical model selection criteria for detecting the number of signals. Frontiers of Electrical and Electronic Engineering in China 6(2):245-255, 2011
- Zaihu Pang, Shikui Tu, Dan Su, Xihong Wu and Lei Xu. Discriminative training of GMM-HMM acoustic model by RPCL learning. Frontiers of Electrical and Electronic Engineering in China 6(2):283-290, 2011
- Lei Shi, Shikui Tu and Lei Xu. Gene clustering by structural prior based local factor analysis model under Bayesian Ying-Yang harmony learning. In Proceedings of the BIBM 2010 International on Bioinformatics and Biomedicine, Hong Kong, December 18–21, 2010, pp 696–699
- Shikui Tu, Runsheng Chen and Lei Xu. A binary matrix factorization algorithm for protein complex prediction. In Proceedings of the BIBM 2010 International Workshop on Computational Proteomics, Hong Kong, December 18–21, 2010, pp 113–118.
- Shikui Tu and Lei Xu. A study of several model selection criteria for determining the number of signals. In Proceedings of the IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP 2010), 14-19 March, 2010, Sheraton Dallas Hotel, Dallas, Texas, USA, pp. 1966-1969
- Ke Sun, Shikui Tu, David Yang Gao and Lei Xu. Canonical Dual Approach to Binary Factor Analysis. In Proceedings of the 8th International Conference on Independent Component Analysis and Signal Separation (ICA’09), Lecture Notes in Computer Science 5441 ed. by Adali, T.; Jutten, C.; Romano, J.M.T.; Barros, A.K., Springer-Verlag Berlin, Heidelberg, 2009, pp. 346-353
- Shikui Tu and Lei Xu. Theoretical Analysis and Comparison of Several Criteria on Linear Model Dimension Reduction. In Proceedings of the 8th International Conference on Independent Component Analysis and Signal Separation (ICA’09), Lecture Notes in Computer Science 5441 ed. by Adali, T.; Jutten, C.; Romano, J.M.T.; Barros, A.K., Springer-Verlag Berlin, Heidelberg, 2009, pp. 154-162
- Shikui Tu, Lei Shi and Lei Xu. A Comparative Study on Data Smoothing Regularization for Local Factor Analysis. Lecture Notes in Computer Science 5163, ed. by Kurková, Véra and Neruda, Roman and Koutník, Jan, Springer Berlin / Heidelberg, 2008, pp. 265-274