Shi, Yi

Ph.D.
Associate Professor

Bio-X Institutes
School of Life Science and Biotechnology
Shanghai Jiaotong University
Email:
yishi[at]sjtu.edu.cn

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.


Experience
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

B.Eng,
CS, Zhejiang University 2000-2004


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

2022:

Zehua Guo+, Liangjie Liu+, Mofan Feng+, Kai Su, Runqiu Chi, Keyi Li, Qing Lu, Xianbin Su, Lintai Da, Song Cao, Mingxuan Zhang, Luming Meng, Dan Cao, Jiayi Wang, Guang He* and Yi Shi*, 3D genome assisted protein-protein interaction prediction, Future Generation Computer Systems, 137: 87-96, 2022.

Xianbin Su+*, Shihao Bai+, Gangcai Xie+, Yi Shi+, Linan Zhao, Guoliang Yang, Futong Tian, Kun-Yan He, Lan Wang, Xiaolin Li, Qi Long*, Ze-Guang Han*, Accurate tumor clonal structures require single-cell analysis, Annals of the New York Academy of Sciences, doi:10.1111/nyas.14897, 2022.

Xiangfei Xue, Lifang Ma, Xiao Zhang, Xin Xu, Susu Guo, Yikun Wang, Shiyu Qiu, Jiangtao Cui, Wanxin Guo, Yongchun Yu, Fenyong Sun*, Yi Shi* and Jiayi Wang*, Tumour cells are sensitised to ferroptosis via RB1CC1-mediated transcriptional reprogramming, Clinical and Translational Medicine, Volume12, Issue2, 2022.

Peng Li*, Jianhui Shang*, Yi Shi*, A simple linear time algorithm to solve the MIST problem on interval graphs. Theoretical Computer Science, 930: 77-85, 2022.

2021:

Xueyin Shang+*, Yi Shi+*, Dandan He, Qing Luo, Chuan-Huai Deng, Yu-Lan Qu, Na Wang and Zeguang Han*, ARID1A deficiency weakens BRG1-RAD21 interaction that jeopardizes chromatin compactness and drives liver cancer cell metastasis. Cell Death & Disease, 12, 990, 2021.

Luming Meng, Chenxi. Wang, Yi Shi, and Q. Luo, Si-C is a method for inferring super-resolution intact genome structure from single-cell Hi-C data, Nature Communication, 12:4369, 2021.

Mengna Lin, Honglin Xu, Yi Shi* and Lin-Tai Da*, Antigenic peptide loading into major histocompatibility complex class I is driven by the substrate N-terminus, CCS Chemistry, 0:ja, March, 2021.

Zehua Guo+, Kai Su+, Liangjie Liu+, Xianbin Su+, Mofan Feng+, Song Cao+, Mingxuan Zhang+, Runqiu Chi, Luming Meng, Guang He* and Yi Shi*, Improving Protein-protein Interaction Prediction by Incorporating 3D Genome Information, Bioinformatics Research and Applications (Springer Lecture Notes in Computer Science, ISBRA 2021), 13064, 2021.

Na Wu, Fan Yuan, Siran Yue, Fengyan Jiang, Decheng Ren, Liangjie Liu, Yan Bi, Zhenming Guo, Lei Ji, Ke Han, Xiao Yang, Mofan Feng, Kai Su, Fengping Yang, Xi Wu, Qing Lu, Xingwang Li, Ruirui Wang, Baocheng Liu, Shenglong Le, Yi Shi* and Guang He*, Effect of exercise and diet intervention in NAFLD and NASH via GAB2 methylation, Cell & Bioscience, 11:189, 2021.

Xianbin Su+*, Linan Zhao+, Yi Shi+, Rui Zhang, Qi Long, Shihao Bai, Qing Luo, Yingxin Lin, Xin Zou, Shila Ghazanfar, Kun Tao, Guoliang Yang, Lan Wang, Kun-Yan He, Xiaofang Cui, Jian He, Jiao-Xiang Wu, Bo Han, Bin Yan, Biao Deng, Na Wang, Xiaolin Li, Pengyi Yang, Shangwei Hou, Jielin Sun, Jean Y. H. Yang, Jinhong Chen* and Ze-Guang Han*, Clonal Evolution in Liver Cancer at Single-cell and Single-variant Resolution, Journal of Hematology & Oncology, 14:22, 2021.

Tingting Liu+, Jing Han+, Rongrong Zhang+, Zihan Tang, Gang Yi, Wen Gong, Liyan Wan, Qiongyi Hu, Jialin Teng, Honglei Liu, Xiaobing Cheng, Junna Ye, Yutong Su, Yue Sun, Yi Shi, Jianxin Gu, Shifang Ren, Chengde Yang and Hui Shi*, Characteristics of purified anti-beta2GPI IgG N-glycosylation associate with thrombotic, obstetric and catastrophic antiphospholipid syndrome, Rheumatology, keab416:00:1-12, 2021.

N. Wu, L. Liu, D. Ren, F. Yuan, Y. Bi, Z. Guo, B. Hou, L. Ji, K. Han, M. Feng, K. Su, T. Yu, X. Li, F. Yang, X. Sun, Z. Dong, S. Yu, Z. Yi, Y. Xu, L. He, S. Wu, L. Zhao, C. Changqun, Y. Shi*, G. He*, No Association Between SLC6A4 Gene Polymorphisms With Treatment Remission to Venlafaxine in Han Chinese Depressive Patients, Clinical Neuropharmacology, DOI: 10.1097/wnf.0000000000000436, Jan. 2021.

Jianhui Shang, Peng Li and Yi Shi, The Longest Cycle Problem is Polynomial on Interval Graphs, SIAM Journal on Discrete Mathematics, Jan. 2021.

Liangjie Liu, Decheng Ren, Fan Yuan, Yan Bi, Zhenming Guo, Gaini Ma, Fei Xu, , Binyin Hou, Lei Ji, Zhixuan Chen, Lin An, Naixin Zhang, Tao Yu, Xingwang Li, Fengping Yang, Xueli Sun, Zaiquan Dong, Shunying Yu, Zhenghui Yi, Yifeng Xu, Lin He, Shaochang Wu, Longyou Zhao, Changqun Cai, Guang He* and Yi Shi*, Association between SLC17A7 gene polymorphisms and venlafaxine for major depressive disorder in a Chinese Han population: a prospective pharmacogenetic case-control study, Journal of Bio-X Research, 15 September 2021.

Zhenming Guo, Mengxia Chen, Yiming Chao, Chunhai Cai, Liangjie Liu, Li Zhao, Linbo Li, Qing-Ran Bai, Yanxin Xu, Weibo Niu, Lei Shi, Yan Bi, Decheng Ren, Fan Yuan, Shuyue Shi, Qian Zeng, Ke Han, Yi Shi, Shan Bian*, and Guang He*, RGCC balances self-renewal and neuronal differentiation of neural stem cells in the developing mammalian neocortex, EMBO Reports, 22:e51781, 2021.

Lei Ji, Changfeng Che, Binyin Hou, Decheng Ren, Fan Yuan, Liangjie Liu, Yan Bi, Zhenming Guo, Fengping Yang, Xi Wu, Xingwang Li, Chuanxin Liu, Zhe Zuo, Rong Zhang, Zhenghui Yi, Yifeng Xu, Lin He, Yi Shi, Tao Yu and Guang He*. A study of negative life events driven depressive symptoms and academic engagement in Chinese college students. Scientific Reports, 11, 17160, 2021.

Fan Yuan, Binyin Hou, Lei Ji, Decheng Ren, Liangjie Liu, Yan Bi, Zhenming Guo, Gaini Ma, Fengping Yang, Zaiquan Dong, Xueli Sun,  Lin He, Tao Yu, Xi Wu, Xingwang Li, Yi Shi and Guang He, Sex-specific association of MC2R polymorphisms and the risk of major depressive disorder in Chinese Southern Han, Psychiatric Genetics, 31:1, p36-37, 2021.

Jiao-Xiang Wu+, Kun-Yan He+, Zhuang-Zhuang Zhang+, Yu-Lan Qu, Xian-Bin Su, Yi Shi, Na Wang, Lan Wang and Ze-Guang Han*, LZP is required for hepatic triacylglycerol transportation through maintaining apolipoprotein B stability, Plos Genetics, 17(2):e1009357, 2021.

2020:

Yan-Ting Wu+, Chen-Jie Zhang+, Ben Willem Mol, Andrew Kawai, Cheng Li, Lei Chen, Yu Wang, Jian-Zhong Sheng, Jian-Xia Fan, Yi Shi* and He-Feng Huang*, Early prediction of gestational diabetes mellitus in the Chinese population via advanced machine learning, Journal of Clinical Endocrinology & Metabolism (JCEM), Nov. 2020.

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, June, 2020. (webserver: deepAntigen)

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. March. 2020.

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 Repports, 10, Article number: 5702. March, 2020.

Y. Shi+*, Mingxuan Zhang+, Luming Meng+, Xianbin Su+, Xueying Shang, Zehua Guo, Qingjiao Li, Mengna Lin, Xin Zou, Qing Luo, Yaoliang Yu, Yanting Wu, Lintai Da*, Tom Weidong Cai*, Guang He*, Ze-Guang Han*, A Novel Neoantigen Discovery Approach based on Chromatin High Order Conformation, BMC Medical Genomics, Vol. 3 (S3), 2020.

2019:
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, https://doi.org/10.1002/hep.30863, 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: https://doi.org/10.1016/j.ebiom.2019.03.021, 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.

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.

2017:
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.

2016:
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.

2015:
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)

2014:
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.

2013:
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.

2012:
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)

2011:
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)

2010:
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)

2009:
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)

2008:
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)

2007:
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)

2006:
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)


Software/Webserver
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:
ISBRA
Reviewer of:
Genome Biology
Bioinformatics

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)


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