Dr. He was awarded “Rising-Star” by the Science and Technology Commission of Shanghai Municipality in 2008. Now Dr. He undertakes the bilingual education of “Medical Genetics” for undergraduate students. Her research works have been sponsored by the 973 Program, NSFC and Shanghai Rising-Star Program.

Identification of candidate genes for bipolar and other mental disorders. Decoding the century-old mystery of the decreasing incidence of colorectal cancer in schizophrenia patients. To investigate the molecular mechanism of prenatal malnutrition or malnutrition increases the risk of schizophrenia with the rat model.

1. Wang Y, Zhang J, Liu B, Shao L, Wei Z, Li X, Ji J, Yang F, Wang T, Liu J, Wan C, Li B, Xu Y, Feng G, He L*, He G*. Genetic polymorphisms in the SCN8A gene are associated with suicidal behavior in psychiatric disorders in the Chinese population. World J Biol Psychiatry. 2010;11(8):956-63.

2. HTR2C promoter polymorphisms are associated with risperidone efficacy in Chinese female patients.Liu BC, Zhang J, Wang L, Li XW, Wang Y, Wei ZY, Ji J, Yang FP, Wan CL, Xu YF, Feng GY, He L*, He G*. Pharmacogenomics. 2010;11(5):685-92.

3. Shi YY*, He G*, Zhang Z, Tang W, Zhang J Jr, Zhao Q, Zhang J Sr, Li XW, Xi ZR, Fang C, Zhao XZ, Feng GY, He L*. A study of rare structural variants in schizophrenia patients and normal controls from Chinese Han population. Mol Psychiatry. 2008 Oct;13(10):911-3.

4. Zhang J, Shen Y, He G*, Li X, Meng J, Guo S, Li H, Gu N, Feng G, He L*. Lack of association between three serotonin genes and suicidal behavior in Chinese psychiatric patients. Prog Neuropsychopharmacol Biol Psychiatry. 2008; 32(2): 467-71.

5. He G#, Liu X#, Qin W, Chen Q, Wang X, Yang Y, Zhou J, Xu Y, Gu N, Feng G, Sang H, Wang P, He L*. MPZL1/PZR, a novel candidate predisposing schizophrenia in Han Chinese. Mol Psychiatry. 2006; 11(8):748-51.

6. Chen Q, He G, Qin W, Chen QY, Zhao XZ, Duan SW, Liu XM, Feng GY, Xu YF, St Clair D, Li M, Wang JH, Xing YL, Shi JG, He L*. Family-based association study of synapsin II and schizophrenia. Am J Hum Genet. 2004; 75(5):873-7.

# Contributed equally to the paper * Corresponding author

Dr. Li is the deputy group leader of genetic resources center in Bio-X institutes. His research works have been sponsored by 863 Program and other joint research projects. Dr. Li participated in the research on psychiatric disorder and many other complex human genetic diseases and has published over 70 papers as first author or co-author.

Identification of candidate genes of psychiatric disorders or other complex human genetic diseases.

Ren D, Xu JH, Bi Y, Zhang Z, Zhang R, Li Y, Hu J, Guo Z, Niu W, Yang F, Li W, Xu Y, He L, Yu T, Wu J*, Li X*, Du J*, He G*. Association study between LEPR, MC4R polymorphisms and overweight/obesity in Chinese Han adolescents. Gene. 2019 Apr 15; 692:54-59.

Ma G, Huang X, Bi Y, Xu F, Niu W, Ren D, Sun Q, Guo Z, Yuan R, Yuan F, Wu X, Yang F, Wang L, Li W, He L, Yu T, Li X*, Liu J*, He G*. A Case-Control Study of ABCB1, ABCB6, and ABCG1 Polymorphisms and Schizophrenia in a Han Chinese Population. Neuropsychobiology. 2019;78(3):113-117.

Ma G, Huang X, Bi Y, Ren D, Xu F, Sun Q, Zhang R, Hu J, Niu W, Guo Z, Yuan R, Yuan F, Wu X, Cao Y, Yang F, Wang L, Li W, Yu T, He L, Liu J*, He G*, Li X*. Association study between ABCB1, ABCB6 and ABCG1 polymorphisms and major depressive disorder in the Chinese Han population. Psychiatry Res. 2018 Dec; 270:1170-1171.

Yuan R, Yuan F, Ren D, Zhu Y, Bi Y, Hu J, Guo Z, Xu F, Niu W, Wu X, Cao Y, Yang F, Wang L, Li W, Xu Y, He L, Yu T, He G*, Li X*. HTR1A and HTR2A variants may not predict venlafaxine treatment response in China Han population with major depressive disorder. Psychiatry Res. 2018 Dec; 270:1179-1180.

Ren D, Bi Y, Xu F, Niu W, Zhang R, Hu J, Guo Z, Wu X, Cao Y, Huang X, Yang F, Wang L, Li W, Xu Y, He L, Yu T*, He G*, Li X*. Common variants in GRIK4 and major depressive disorder: An association study in the Chinese Han population. Neurosci Lett. 2017 Jul 13; 653:239-243.

Bi Y, Huang X, Niu W, Chen S, Wu X, Cao Y, Zhang R, Yang F, Wang L, Li W, Xu Y, He L, Yu T, He G*, Li X*. No association between SLC6A2, SLC6A3, DRD2 polymorphisms and schizophrenia in the Han Chinese population. Psychiatry Res. 2017 Jul; 253:398-400.

Bi Y, Huang X, Niu W, Chen S, Wu X, Cao Y, Zhang R, Yang F, Wang L, Li W, Xu Y, He L, Yu T, He G, Li X*. Common variants in SLC6A2, SLC6A3, DRD2, and major depressive disorder: an association study in the Chinese Han population. Psychiatr Genet. 2017 Jun;27(3):103-104.

Li X#, Wang Q#, He K, Li Z, Chen J, Li W, Wen Z, Shen J, Qiang Y, Ji J, Feng G, He G, Lin H, Wang Y, Shi Y. Common variants in the CDH7 gene are associated with major depressive disorder in the Han Chinese population. Behav Genet. 2014 Mar;44(2):97-101.

Xing-wangLi#, Bao-cheng Liu#, Yang Wang, Qing-zhu Zhao, Qi shen, Tao Yu, Shi-qing Chen, Feng-ping Yang, Wei-dongLi, Ling-han Gao, Yi-feng Xu, Guo-yin Feng, Lin He, Guang He. Association study on the DLG4 gene and schizophrenia in the Chinese Han population. Psychiatric Genetics. Psychiatr Genet. 2013 Dec;23(6):247-50.

# Contributed equally to the paper * Corresponding author

Yi’s researches focus on computational biology and bioinformatics, especially advanced machine learning method development for complex genetic diseases. Yi was granted NSFC-Youth grant and many other national and provincial grants, such Pujiang Talent Grant and SJTU Cheng Xin Pan B, etc. He is an editor of the international journal Progress in Preventive Medicine and has been senior reviewers for may bioinformatics journals including Genome Biology, Bioinformatics, BMC Genomics, BMC Bioinformatics, etc.

Machine learning in genetic diseases, cancer genetics and epigenetics, computational 3D genome, sparse learning, clinical bio-marker discovery, neo-antigen prediction (immunotherapy)

(Up to date: http://yishi.sjtu.edu.cn)

2019:

Z. Lu+, Q. Luo+, L. Zhao, Y. Shi, N. Wang, L. Wang, 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.

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.

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)