Shuyan Li

 

Professor, Supervisor of Master Student

College of Medical Information and Engineering,

Xuzhou Medical University

Address:

209 Tongshan Road, Xuzhou, Jiangsu, China 221004

 

Email: lishuyan@xzhmu.edu.cn

 

 

 

Education

Ph.D.,Chemoinformatics,Chemical and Chemistry Engineering, Lanzhou University, 2010

Joint Ph.D., Bioinformatics, School of  Computer Science and Informatics, Indiana University Bloomington, U.S.A. 2008-2010

B.S., Computer Science, School of Information Science and Engineering, Lanzhou University, 2003

 

Training

Watson Institute of Genome Sciences, Zhejiang University

Genomics Research Class,2006

NSFC, Ministry of Education of china

Bioinformatics Summer School for Graduate Students of China,2007

  

Publications

1.     Ximing Chen, Shuyan Li, Binglin Zhang, Haili Sun, Jinxiu Wang, Wei Zhang,Wenbo Meng, Tuo Chen, Paul Dyson ,* and Guangxiu Liu. A new bacterial tRNA enhances antibiotic production in Streptomyces by circumventing inefficient wobble base-pairing. Nucleic Acids Research, 2022, 50(12), 7084-7096.

2.     Xiangyi Zan, Shuyan Li, Shixiong Wei, Liping Gao, Lanting Zhao, Xiaoxia Yan, Yan Zhao, Junnian Shi, Yuping Wang, Rong Liu, Yuanyi Zhang, Yixin Wan*, Yongning Zhou*. COL8A1 Promotes NSCLC Progression Through IFIT1/IFIT3-Mediated EGFR Activation,Frontiers in Oncology, 2022, 12, 707525.

3.     Xu Zhang, Ping Yue, Jinduo Zhang, Man Yang, Jinhua Chen, Bowen Zhang, Wei Luo, Mingyuan Wang, Zijian Da, Yanyan Lin, Wence Zhou, Lei Zhang, Kexiang Zhu, Yu Ren, Liping Yang, Shuyan Li*, Jinqiu Yuan*, Wenbo Meng**, Joseph W. Leung, and Xun Li.A novel machine learning model and a public online prediction platform for prediction of post-ERCP-cholecystitis (PEC). eClinicalMedicine, 2022, 48, 101431.

4.      Bowen Zhang, Long Cheng, Yuzhen Niu, Aming Wang, Pengyi Zhang, Tiantian Shen, Lili Xi, Dekui Zhang*, Shuyan Li*.Identification Tool for Gastric Cancer Based on Integration of 33 Clinical Available Blood Indices through Deep Learning. IEEE Access, 2022, 10, 106081-106092.

5.      Pei Li, Yuzhen Niu, Shuyan Li, Xuyu Zu, Maoyu Xiao, Liyang Yin, Jianbo Feng, Jun He, Yingying Shen*. Identification of an AXL kinase inhibitor in triple-negative breast cancer by structure-based virtual screening and bioactivity test. Chemical Biology & Drug Design, 2021, 99，222-232.

6.     Jianhong Zhao#, Jiangpeng Wu#, Jinyan Wei, Xiaolu Su, Yanjun Chai, Shuyan Li* and Zhiping Wang*. Liq_ccRCC: Identification of Clear Cell Renal Cell Carcinoma Based on the Integration of Clinical Liquid Indices. Frontiers in Oncology, 2021, 10, 605769.

7.     Jiangpeng Wu#, Yifan Yang#, Long Cheng, Jing Wu, Lili Xi, Ying Ma, Pengyi Zhang, Xiaoying Xu, Dekui Zhang* and Shuyan Li*. GCdiscrimination: identification of gastric cancer based on a milliliter of blood, Briefings in Bioinformatics, 2021, 22, 536-544.

8.     Pengyi Zhang, Jiangpeng Wu, Honglin Zhai*, Shuyan Li*. ABCModeller: An automatic data mining tool based on a consistent voting method with a user-friendly graphical interface. Briefings in Bioinformatics, 2021, 22(4), bbaa247.

9.     Jiangpeng Wu, Pengyi Zhang, Liting Zhang, Wenbo Meng, Junfeng Li, Chongxiang Tong, Yonghong Li, Jing Cai, Zengwei Yang, Jinhong Zhu, Meie Zhao, Huirong Huang, Xiaodong Xie*, Shuyan Li*. Rapid and accurate identification of COVID-19 infection through machine learning based on clinical available blood test results, 2020, medRxiv，DOI:10.1101/2020.04.02.20051136.

10.     Pengyi Zhang, Lipei Jia, Yafei Tian, Lili Xi, Ruizhi Duan, Ximing Chen, Jianxi Xiao, Xiaojun Yao, Jingfeng Lan, Shuyan Li*. Discovery of potential Toxoplasma gondii CDPK1 inhibitors with new scaffolds based on the combination of QSAR and scaffold-hopping method with in-vitro validation. Chem. Biol. Drug. Des. 2020,95,476-484.

11.     Ying Ma, Ning Xie, Dingxiong Xie, Litao Sun, Shuyan Li, Peiqiang Li, Yi Li, Jin Li, Zhilong Dong, Xiaodong Xie*.A novel homozygous FBXO43 mutation associated with male infertility and teratozoospermia in a consanguineous Chinese family.2019,11,909-917.

12.     Jiangpeng Wu#, Jun Bai#, Wei Wang, Lili Xi, Pengyi Zhang, Jingfeng Lan, Liansheng Zhang* and Shuyan Li*. ATBdiscrimination: An in Silico Tool for Identification of Active Tuberculosis Disease Based on Routine Blood Test and T‑SPOT.TB Detection Results. Journal of Chemical Information and Modeling, 2019, 59, 4561-4568. 

13.  Jiangpeng Wu, Xiangyi Zan, Liping Gao, Jianhong Zhao, Jing Fan, Hengxue Shi, Yixin Wan, E Yu, Shuyan Li*,Xiaodong Xie. A Machine Learning Method for Identifying Lung Cancer Based on Routine Blood Iindices: Qualitative Feasibility Study. JMIR Med. Infor., 2019, 7(3), e13476. DOI: 10.2196/13476

14.   Xue Wang, Min Li Xu, Bao Qiong Li, Hong Lin Zhai, Jin Jin Liu , Shuyan Li. Prediction of phosphorylation sites based on Krawtchouk image moments. Proteins. 2017, 85, 2231-2238.

15.    Xiaofeng Xia, Yong Li, Xiao-Qiang Yu, Junhan Lin, Shuyan Li, Qiang Li, Minsheng You. Cloning and functional identification of moricins from the diamondback moth, Plutella xylostella (L.). Insect Mol. Biol. 2017,26,564-573.

16.   Lili Xi, Jia Yao, Yuhui Wei, Xinan Wu, Xiaojun Yao, Huanxiang Liu and Shuyan Li*. In Silico Identification of Human Bile Salt Export Pump (ABCB11) Inhibitors Associated with Cholestatic Drug-Induced Liver Injury. Mol. BioSyst.,  2017, 13, 417-424

17.   Binglin Zhang, Xiukun Wu, Gaosen Zhang, Shuyan Li, Wei Zhang, Ximing Chen, Likun Sun, Baogui Zhang, Guangxiu Liu and Tuo Chen. The diversity and biogeography of the communities of Actinobacteria in the forelands of glaciers at a continental scale. Environ. Res. Lett., 2016, 11(5), 054012

18.   Yuzhen Niu, Shuyan Li, Dabo Pan, Huanxiang Liu, Xiaojun Yao, Computational study on the unbinding pathway of B-RAF inhibitors and its implication for the difference in the residence time: insight from random acceleration and steered molecular dynamics simulations. Phys. Chem. Chem. Phys., 2016,18, 5622-5629

19.   Haili Sun, Tianpeng Gao, Ximing Chen, Matthew D. Hitchings, Shuyan Li, Tao Chen, Hua Zhang, Lizhe An, Paul Dyson, Complete genome sequence of a psychotrophic Arthrobacter strain A3 (CGMCC 1.8987), a novel long-chain hydrocarbons producer. J. Biotechnol., 2016,222, 23-24

20.   Shuyan Li, Jun Lu, Jiazhong Li, Ximing Chen, Xiaojun Yao and Lili Xi，HydPred: A novel method for identification of protein hydroxylation sites that reveals new insights into human inherited disease, Mol. BioSyst., 2016, 12, 490-498

21.   Hongli Liu , Xiaoli An, Shuyan Li, Yuwei Wang, Jiazhong Li, Huanxiang Liu. Interaction mechanism exploration of R-bicalutamide/S-1 with WT/W741L AR using molecular dynamics simulations, Mol. Biosyst. 2015, 11(12), 3347-54

22.   Shuyan Li, Jiazhong Li, Lulu Ning, Shaopeng Wang, Yuzhen Niu, Nengzhi Jin, Xiaojun Yao, Lili Xi. In silico identification of S-palmitoylation sites and their involvement in human inherited disease. J. Chem. Inf. Model. 2015,55(9),2015-25

23.   Ximing Chen, Binglin Zhang, Jianxi Xiao, Furong Ju, Shuyan Li, Cuiling Ren, Lizhe An, Tuo Chen, Guangxiu Liu, Paul Facey, Jonathan Gl Mullins, Paul Dyson, RfiA, a novel PAP2 domain-containing polytopic membrane protein that confers resistance to the FtsZ inhibitor PC190723. Future Microbiology,2015, 10(3):325-335

24.   Lili Xi, Shuyan Li, Xiaojun Yao, Yuhui Wei, Huanxiang Liu,Xin'an Wu. In Silico Study Combining Docking and QSAR Methods on a Series of Matrix Metalloproteinase 13 Inhibitors.Arch. Pharm. Chem. Life Sci. 2014, 347, 1-9

25.   Lili Xi, Shuyan Li, Yuhui Wei,Xin'an Wu, Huanxiang Liu, Xiaojun Yao. Recognition of protein folding kinetics pathways based on amino acid properties information derived from primary sequence. Chemometr Intel Lab, 2013, 126, 76-82

26.   Jiazhong Li, Shuyan Li, Chongliang Bai, Huanxiang Liu, Paola Gramatica, Structural requirements of 3-carboxyl-4(1H)-quinolones as potential antimalarials from 2D and 3D QSAR analysis, Journal of Molecular Graphics and Modelling,  2013, 44 (7), 266-277

27.   Jun Ma, Shuyan Li, Yide Ma. Programming Hypothesis on Life Phenomena and the Key Processes Simulation. Advanced Materials Research,2013, 647,258-263

28.   Chengqi Wang, Lili Xi, Shuyan Li, Huanxiang Liu, Xiaojun Yao, A sequence-based computational model for the prediction of the solvent accessible surface area for α-helix and β-barrel transmembrane residues. J. Comput. Chem.,2012, 33, 11-17

29.   Ying Yang, Yulin Shen, Shuyan Li, Nengzhi Jin, Huanxiang Liu, Xiaojun Yao, Molecular dynamics and free energy studies on Aurora kinase A and its mutant bound with MLN8054: insight into molecular mechanism of subtype selectivity.Mol. BioSyst., 2012, 8, 3049-60

30.   Shuyan Li, Lili Xi, Jiazhong Li, Chengqi Wang, Beilei Lei, Yulin Shen, Huanxiang Liu, Xiaojun Yao, Biao Li. In silico prediction of deleterious single amino acid polymorphisms of proteins from amino acid sequence, J. Comput. Chem.,2011, 32, 1211-1216

31.   Chengqi Wang, Shuyan Li, Lili Xi, Huanxiang Liu, Xiaojun Yao. Accurate prediction of the burial status of transmembrane residues of alpha-helix membrane protein by incorporating the structural and physicochemical features, Amino Acids, 2011, 40, 991-1002

32.   Shuyan Li, Lilia M. Iakoucheva, Sean D. Mooney and Predrag Radivojac. Loss of post-translational modification sites in disease. Pac. Symp.Biocomput., 2010, 15, 337-347.

33.   Jiazhong Li, Shuyan Li, Beilei Lei, Huanxiang Liu, Xiaojun Yao, Mancang Liu, Paola Gramatica.A new strategy to improve the predictive ability of the local lazy regression and its application to the QSAR study of melanin-concentrating hormone receptor 1 antagonists. J. Comput. Chem., 2010, 31, 973-85

34.   Lili Xi, Shuyan Li, JiaZhong Li, Huanxiang Liu, Beilei Lei, Xiaojun Yao. Global and Local Prediction of Protein Folding Rates Based on Sequence Autocorrelation Information. J. Theor. Biol. 2010, 21, 1159-68

35.   Lili Xi, Juan Du, Shuyan Li, Jiazhong Li, Huanxiang Liu, Xiaojun Yao. A Combined Molecular Modeling Study over Gelatinases and Their Potent Inhibitors.J. Comput. Chem., 2010, 31, 24-42.

36.   Shuyan Li, Lili Xi, Chengqi Wang, Jiazhong Li, Beilei Lei, Huanxiang Liu, Xiaojun Yao. A novel method for protein-ligand binding affinity prediction and the related descriptors exploration. J. Comput. Chem., 2009, 30, 900-909

37.   Xiumei Liu, Shuyan Li, Jingshu Zhang, Xingguo Chen. Flow injection-capillary electrophoresis frontal analysis method for the study of the interactions of a series of drugs with human serum albumin. J. Chromatogr. B, 2009, 877, 3144-3150

38.   Beilei Lei, Shuyan Li, Lili Xi, Jiazhong Li, Huanxiang Liu, Xiaojun Yao. Novel approaches for retention time prediction of oligonucleotides in ion-pair reversed-phase high-performance liquid chromatography. J. Chromatogr. A, 2009, 1216, 4434-4439

39.   Beilei Lei, Juan Du, Shuyan Li, Huanxiang Liu, Yueying Ren, Xiaojun Yao. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of thiazolone derivatives as hepatitis C virus NS5B polymerase allosteric inhibitors.J. Comput. Aid. Mol. Des., 2008 ,22,711-725

40.   Jiazhong Li, Beilei Lei, Huanxiang Liu, Shuyan Li, Xiaojun Yao, Mancang Liu, Paola Gramatica. QSAR study of malonyl-CoA decarboxylase inhibitors using GA-MLR and a new strategy of consensus modeling. J. Comput. Chem., 2008, 29, 2636-2647

41.   Jin Chang, Beilei Lei, Jiazhong Li, Shuyan Li, Yulin Shen, Xiaojun Yao. Accurate and Validated Quantitative Structure-Activity Relationship Model of Caspase-mediated Apoptosis-inducing Activity of Phenolic Compounds Using Density Functional Theory Calculation and Genetic Algorithm-Multiple Linear Regression. QSAR & Comb. Sci., 2008, 27, 1318 - 1325

42.   Shuyan Li, Xiaojun Yao, Huanxiang Liu, Jiazhong Li, Botao Fan. Prediction of T-cell epitopes based on least squares support vector machines and amino acid properties. Anal. Chim. Acta, 2007,584, 37-42

43.   Yueying Ren, Huanxiang Liu, Shuyan Li, Xiaojun Yao, Mancang Liu. Prediction of binding affinities to β1 isoform of human thyroid hormone receptor by genetic algorithm and projection pursuit regression. Bioorg. Med. Chem. Lett., 2007, 17, 2474-2482

 

Research interests

Application of artificial intelligence in clinical diagnosis systems

Developing models/methods for analysis of DNA or protein sequence data

Protein-ligand, Protein-protein and Protein-DNA interactions analysis and prediction

Protein post-translational modification anaylsis

Computer- aided drug design

 

Software

SeqSubPred:  a web tool for prediction of deleterious amino acid substitutions

SeqPalm: Prediction of protein S-palmitoylation sites and the corresponding loss/gain of palmitoylation sites by amino acid variations

HydPred: A novel method and web tool for identification of protein hydroxylation sites

 

Courses

1. The university information technology foundation

2. Chemoinfomatics

3. Bioinformatics