Shi, Yi

Associate Professor

Bio-X Institutes
School of Life Science and Biotechnology
Shanghai Jiaotong University

Current research activities: Cancer genetics and epigenetics, cancer 3D genome, cancer typing, sparse learning, clinical bio-marker discovery, neo-antigen prediction.

"Having desire, being part of the nature; having no desire, understand the nature." - Lao Zi, 206 B.c.

Associate Professor, Shanghai Jiaotong University 2018-Present
Assistant Professor, Shanghai Jiaotong University 2014-2017
Postdocal, MCB, University of Southern California (J. Zhou, F. Alber & M. Waterman) 2012-2014

Ph.D & RA,
CS, University of Alberta (D. Schuurmans & G. Lin) 2007-2012
M.Sc & TA,
CS, University of Alberta (G. Lin)2005-2007
Software Engineer, HW Shanghai 2004-2005

CS, Zhejiang University 2000-2004

Publications (+:Co-first author, *:Co-corresponding author)


Y. Shi+* , Zehua Guo+, Xianbin Su+, Luming Meng*, Mingxuan Zhang,Jing Sun, Chao Wu, Minhua Zheng, Xueyin Shang, Xin Zou, Wangqiu Cheng, Yaoliang Yu, Yujia Cai, Chaoyi Zhang, Weidong Cai, Lintai Da*, Guang He*, Ze-Guang Han*, DeepAntigen: A Novel Method for Neoantigen Prioritization via 3D Genome and Deep Sparse Learning, Bioinformatics, Published on June 27th, 2020. (webserver: deepAntigen)

B. Hou, L. Ji, Z. Chen, L. An, N. Zhang, D. Ren, F. Yuan, L. Liu, Y. Bi, Z. Guo, G. Ma, F. Xu, F. Yang, S. Yu, Z. Yi, Y. Xu, L. He, C. Liu, B. Bai, S. Wu, L. Zhao, C. Cai, T. Yu, G. He*, Y. Shi* and X. Li*, Role of rs454214 in Personality mediated Depression and Subjective Well-being, Scientific Reports, 10, Article number: 5702. Mar. 30, 2020.

X. Su+, Q. Long+, J. Bo+, Y. Shi+, L. Zhao, Y. Lin, Q. Luo, S. Ghazanfar, C. Zhang, Q. Liu, L. Wang, K. He, J. He, X. Cui, J. Y. H. Yang, Z. Han*, G. Yang* and J. Sha*. Mutational and transcriptomic landscapes of a rare human prostate basal cell carcinoma, The Prostate, 2020:1-10, DOI: 10.1002/pros.23965. Mar. 2nd. 2020.

Z. Lu+, Q. Luo+, L. Zhao, Y. Shi, N. Wang, L. Wang and Z. Han*, The Mutational Features of Aristolochic Acid Induced Mouse and Human Liver Cancers, Hepatology,, 2019.

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. Qu, C. Deng, Q. Luo, X. Shang, J. Wu, Y. Shi, L. Wang, Z. Han, Arid1a regulates insulin sensitivity and lipid metabolism, EBioMedicine, doi:, 2019.

J.H. Lautaoja, M. Lalowski, T.A. Nissinen, J.J. Hentila, Y. Shi, O. Ritvos, S. Cheng, J.J. Hulmi, Muscle and serum metabolomes are dysregulated in colon-26 tumor-bearing mice despite amelioration of cachexia with activin receptor type 2B ligand blockade, American Journal of Physiology: Endocrinology and Metabolism, 2019 Mar 12. doi:10.1152/ajpendo.00526. 2018.

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. Qi, H. Zhou, D.M. Czajkowsky, S. Guo, Y. Li, N. Wang, Y. Shi, L. Lin, J. Wang, D. Wu, and S. Tao, Rapid Production of Virus Protein Microarray Using Protein Microarray Fabrication through Gene Synthesis (PAGES), Molecular & Cellular Proteomics, 16 (2) 288-299, 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). (PDF)

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. (PDF)

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. (PDF)

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.

Y. Shi, X. Liao, X. Zhang, G. Lin, D. Schuurmans. Sparse Learning based Linear Coherent Bi-clustering. Algorithms in Bioinformatics (WABI 2012). Lecture Notes in Bioinformatics 7534, 346-364, 2012. (PDF)

Y. Shi, M. Hasan, Z. Cai, G. Lin, and D. Schuurmans. Linear Coherent Bi-clustering via Beam Searching and Sample Set Clustering. Discrete Mathematics, Algorithms and Applications. World Scientific Publishing (DMAA). Volume 4, Issue 2, 2012. (PDF)

Y. Shi
, J. Zhou, D. S. Wishart, and G. Lin. Protein Contact Order Prediction: The Most Recent Update. Chapter 10, Algorithmic and AI Methods for Protein Bioinformatics, Wiley. ISBN: 978-1-118-34578-8. (Web-server)

Y. Shi
, Y. Guo, G. Lin, and D. Schuurmans. Kernel-based Gene Regulatory Network Inference. International Conference on Computational Systems Bioinformatics (CSB 2010). Stanford, California, United States. August 16-18, 2010. Pages 156-165. (PDF)

Y. Shi, M. Hasan, Z. Cai, G. Lin, and D. Schuurmans. Linear Coherent Bi-cluster Discovery via Beam Detection and Sample Set clustering. International Conference on Combinatorial Optimization and Applications (COCOA 2010). The Big Island, Hawaii, United States. December 18-20, 2010. (PDF, Supplementary)

Y. Shi
, Z. Cai, G. Lin, and D. Schuurmans. Linear Coherent Bi-cluster Discovery via Line Detection and Sample Majority Voting. International Conference on Combinatorial Optimization and Applications (COCOA 2009). Yellow Mountain, An Hui, China. June 10-12, 2009. LNCS 5573, Pages 73-84. (PDF)

Z. Cai, Y. Shi, M. Song, R. Goebel, and G. Lin. Smoothing Blemished Gene Expression Microarray Data via Missing Value Imputation. In Proceedings of the 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (IEEE EMBC 2008). Vancouver, British Columbia, Canada, August 20-24, 2008. Pages 5688-5691. (PDF)

Y. Shi, J. Zhou, D. Arndt, D. S. Wishart, and G. Lin. Protein Contact Order Prediction from Primary Sequences. BMC Bioinformatics. 9(2008), 255. (PDF)

D. S. Wishart, D. Arndt, M. Berjanskii, A. C. Guo, Y. Shi, S. Shrivastava, J. Zhou, Y. Zhu, and G. Lin. PPT-DB: The Protein Property Prediction and Testing Database. Nucleic Acids Research. 36(Database Issue)(2008), D222-D229. (PDF)

Y. Shi, Z. Cai and G. Lin. Classification Accuracy Based Microarray Missing Value Imputation. Chapter 14 in Bioinformatics Algorithms: Techniques and Applications. I. Mandoiu and A. Zelikovsky (Eds). Pages 303-328. ISBN: 978-0-470-09773-1. Wiley-Interscience, 2008. (PDF)

Z. Cai, R. Goebel, M. Salavatipour, Y. Shi, L. Xu, and G. Lin. Selecting Genes with Dissimilar Discrimination Strength for Sample Class Prediction. In Proceedings of the Fifth Asia-Pacific Bioinformatics Conference (APBC 2007). Hong Kong, Page 81-90, 2007. (PDF)

Z. Cai, L. Xu, Y. Shi, M. Salavatipour, R. Goebel, and G. Lin. Using Gene Clustering to Identify Discriminatory Genes with Higher Classification Accuracy. IEEE The 6th Symposium on Bioinformatics and Bioengineering (IEEE BIBE 2006). Washinton D.C., USA. Page 235-242, 2006. (PDF)

Y. Shi, Z. Cai, L. Xu, W. Ren, R. Goebel, G. Lin. A Model-Free Greedy Gene Selection for Microarray Sample Class Prediction. 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2006). Toronto, ON., Canada Page 406-417, 2006. (PDF)

Abstracts and Posters
D. Wishart, D. Arndt, M.Berjanskii, P. Tang, J. Zhou, Y. Shi, G. Lin. CS23D: A Web Server for Rapid Protein Structure Generation Using NMR Chemical Shifts, presented at Canada's Prion Research Conference 2008 (PrP Canada 2008). Toronto, ON., Canada, Feb. 2-6, 2008.

J. Zhou, Y. Shi, G. Lin, D. Wishart. A Protein Contact Order Prediction Method, presented at The 7th International Conference of the Canadian Proteomics Initiative (CPI2007). Ottawa, ON., Canada, Jun. 16-18, 2007.

J. Zhou, G. Lin, Y. Shi, D. Wishart. Structure Comparisons between a PrPsc Structure Model and All PDB Structures, presented at Canada's Prion Research Conference 2007 (PrP Canada 2007), Calgary, AB., Canada, Feb. 20-22, 2007.

Ph.D. Thesis
Y. Shi.
Bio-relation Discovery and Sparse Learning. (PDF)

Master Thesis
Y. Shi.
Gene Expression Microarray Missing Value Imputation and Its Effects in Downstream Data Analyses. (PDF)

deepAntigen (Neoantigen prediction for personalized cancer immunotherapy)
copredictor (Protein contact order prediction and calculation)
Microarray Project (Introduction to Microarray)

Academic Service
Editor of:
Progress in Preventive Medicine
Program Chair (PC) member of:
Reviewer of:
Genome Biology

IEEE/ACM Transactions on Computational Biology and Bioinformatics (IEEE TCBB)
Federation of European Biochemical Societies Letters (FEBS Letters)
Advances in Bioinformatics (Hindawi Publishing)
Multidisciplinary Digital Publishing Institute - Information (MDPI Information)
Nerocomputing (Elsevier Editorial System)

Matrix Reference Manual
On-line Statistics Textbook
The Consortium for Mathematics and its Applications
Research Channel