个人简历

学习经历 Ph.D., University of Alberta, 2007 - 2012. M.Sc., University of Alberta, 2005 - 2007. B.Eng, Zhejiang University, 2000 - 2004. 工作经历 Associate Professor, Center for Systems Biomedicine, SJTU, 2018-present; Joint Professor, Exercise Science and Technology, SJTU, 2016-Present; Assistant Professor, Center for Systems Biomedicine, SJTU, 2014-2017; Postdoctoral Research Associate, University of Southern California, 2012-2014; Guest Lecturer, University of Alberta, CMPUT606: Algorithms in Bioinformatics; Research Assistant, University of Alberta, 2006 – 2013; Teaching Assistant, University of Alberta, 2005 – 2007; Software Engineer, Huawei Shanghai, 2004 – 2005.

研究领域

cancer 3D genome, cancer genetics and epigenetics, , cancer typing, sparse learning, clinical bio-marker discovery, neo-antigen prediction, deep sparse learning

近期论文

X. Su+*, Y. Shi+, R. Li+, Z. Lu+, X. Zou, J. Wu and Z. Han, Application of qPCR assays based on haloacids transporter gene dehp2 for discrimination of Burkholderia and Paraburkholderia, BMC Microbiology, 19:36, 2019. Q. Hu, W. Gong, J. Gu, G. Geng, T. Li, R. Tian, Z. Yang, H. Zhang, L. Shao, T. Liu, L. Wan, J. Jia, C. Yang1*, Y. Shi* and H. Shi*, Plasma microRNA Profiles as a Potential Biomarker in Differentiating Adult-Onset Still's Disease From Sepsis, Frontiers in Immunology, 9(3099), 2019. Y. Yuan+*, Y. Shi+*, X. Su, X. Zou, Q. Luo, D.D. Feng, W. Cai*, and Z. Han*, Cancer Type Prediction based on Copy Number Aberration and Chromatin 3D Structure with Convolutional Neural Networks, BMC Genomics, 19:4919, 2018. X. Zhang+, Y. Shi+, L. Song, C. Shen, Q. Cai, Z. Zhang, J. Wu, G. Fu*, W. Shen*, Identification of mutations in patients with acquired pure red cell aplasia, Acta Biochimica et Biophysica Sinica, 50(2):685-692, 2018. X. Su+, Y. Shi+, X. Zou+, Z. Lu+, G. Xie, J.Y.H. Yang, C. Wu, X. Cui, K. He, Q. Luo, Y. Qu, N. Wang, L. Wang, and Z. Han*, Single-cell RNA-Seq analysis reveals dynamic trajectories during mouse liver development, BMC Genomics, 18:946, 2017. L. Da*, Y. Shi, G. Ning, and J. Yu*, Dynamics of the excised base release in thymine DNA glycosylase during DNA repair process, Nucleic Acids Research, 46(2):568-581, 2017. Y. Yang, Y. Shi*, P. Wiklund, X. Tan, N. Wu, X. Zhang, O. Tikkanen, C. Zhang, E. Munukka and S. Cheng*, The Association between Cardiorespiratory Fitness and Gut Microbiota Composition in Premenopausal Women, Nutrients, 9:792, doi:10.3390/nu9080792, 2017. Y. Yuan+, Y. Shi+*, C. Li, J. Kim, W. Cai*, Z. Han*, and D.D. Feng, Copy Number Aberration Based Cancer Type Prediction with Convolutional Neural Networks, In Proceeding of the 13th International Symposium on Bioinformatics Research and Applications (ISBRA), 2017. P. Wiklund, T. Tormakangas, Y. Shi, N. Wu, A. Vainionpaa, M. Alen, S. Cheng*, Normal-Weight Obesity and Cardiometabolic Risk: A 7-Year Longitudinal Study in Girls from Prepuberty to Early Adulthood, Obesity (Silver Spring), doi:10.1002/oby.21838. 2017. Y. Yuan+, Y. Shi+*, C. Li, J. Kim, W. Cai, Z. Han, and D.D. Feng, DeepGene: DNN-Based Cancer Classification with Clustered Gene Filtering and Indexed Sparsity Reduction, BMC Bioinformatics, Vol 17 Suppl. 17, 2016. Y. Shi+, X. Su+, K. He, B. Wu, B. Zhang, and Z. Han*. Chromatin accessibility contributes to simultaneous mutations of cancer genes. Scientific Reports. 6:35270. 2016. H. Shin+, Y. Shi+, C. Dai, H. Tjong, K. Gong, F. Alber, and X.J. Zhou. TopDom: An Efficient and Deterministic Method for Identifying Topological Domains in Genomes. Nucleic Acids Research. doi: 10.1093/nar/gkv1505. 2015. (Co-first author). T. Huan, C. Tang, R. Li, Y. Shi, G. Lin, L. Li. MyCompoundID MS/MS Search: Metabolite Identification Using a Library of Predicted Fragment-Ion-Spectra of 383,830 Possible Human Metabolites. Analytical Chemistry. 87(20):10619-10626. 2015. W. Li, S. Kang, CC. Liu, S. Zhang, Y. Shi, Y. Liu, XJ. Zhou. High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance-based lael propagation method. Nuclear Acids Research. 42(6):e39. 2014. Y. Shi, X. Zhang, X. Liao, G. Lin, D. Schuurmans. Protein-chemical interaction prediction via kernelized sparse learning SVM. Pacific Symposium on Biocomputing (PSB 2013). 18:41-52, 2013. L. Li, R. Li, J. Zhou, A. Zuniga, A. Stanislaus, Y. Wu, T. Huan, J. Zheng, Y. Shi, D. Wishart, G. Lin. MyCompoundID: Using an Evidence-based Metabolome Library for Metabolite Identification. Analytical Chemistry (ACS). Manuscript ID: ac-2013-00099b. Volumn 85, Issue 6, Page 3401-3408. 2013. Y. Shi, B. Yuan, G. Lin, D. Schuurmans. Protein phosphorylation site prediction via feature discovery support vector machine. Tsinghua Science & Technology. (SI on Bioinformatics and Computational Biology). Volume 17, Issue 6, 638-644, 2012.