Dr. Ye Zhiqiang
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叶志强 Zhi-Qiang Ye
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Assoc. Prof. (2011 ~ )
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Ph. D. Peking University
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| Email: yezq at pku.edu.cn |
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Tel: +86-755-26033196
Google Scholar: https://scholar.google.com/citations?user=qq5hIhgAAAAJ
ORCID: https://orcid.org/0000-0002-8822-6148
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Education & Work Experience
| 2011/05 - present | School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School | |
| Associate Professor | ||
| 2007/08 – 2011/04 | Shanghai Center for Bioinformation Technology | |
| Associate Investigator (2009/01 – 2011/04)
Staff Scientist (2007/08 – 2008/12) |
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| 2007/11 – 2010/10 | Key Lab of Systems Biology, SIBS, CAS | |
| Postdoctoral fellow | ||
| 2001/09 – 2007/07 | College of Life Sciences, Peking University | |
| Ph.D in Bioinformatics | ||
| 1997/09 - 2001/07 | College of Life Sciences, Peking University | |
| Bachelor's degree in Physiology and Biophysics | ||
Grants
| 2015/01 - 2018/12 | NSFC, General Program, "Methodological Study of Predicting Functional Impact of Non-synonymous SNVs on Proteins (31471243, project leader)" |
| 2015/01 - 2016/12 | Shenzhen General Program for Basic Research, “New target discovery and drug design based on the structure prediction of WD40 repeat proteins (JCYJ20140509093817689, key participant)” |
| 2015/01 - 2016/06 | Nanshan Innovative Organization Establishing Program, “Nanshan Key Lab for Computational Biology (KC2014ZDZJ0026A, project vice leader)” |
| 2010/01 - 2011/12 | MOST 863 project, "Development and Completion of the Technical System for Pharmacogenomic Studies (2009AA022710)" (project vice leader) |
| 2009/12 - 2010.10 | China Postdoctoral Science Foundation (20090460669) |
| 2009/01 - 2011/12 | NSFC, Natural Science for Youth Foundation, "Disease association prediction and analysis of single amino acid polymorphisms (30800641, project leader)" |
Awards
| 2017/02 | High-level Talent in Nanshan District (Level B) （南山区B类领航人才） |
| 2015/05 | Shenzhen Local-level Talent (深圳市地方级领军人才) |
| 2011/08 | Shenzhen Reserve Talent (深圳市后备级人才) |
| 2009/08 | Sanofi-aventis-SIBS Scholarship, "Mining Synergic SNPs from HapMap" |
Presentation
| 2017/08 | The 11th International Conference on Computational Systems Biology (ISB 2017) (Shenzhen Kylin Villa, a presentation on human WD40 PPI network) |
| 2016/05 | Genome Informatics Forum in Tangshan City (North China University of Science and Technology, a presentation on human WD40 family) |
| 2015/08 | South China Bioinformatics Symposium for Young Scholars (Harbin Institute of Technology Shenzhen, a presentation on WDSP database) |
| 2008/05 | China Bioinformatics Symposium for Doctoral Students (FudanUniversity, a presentation on nsSNP) |
Research Interests
1. Mining genomic variants (CNV, SNP) with regard to their disease association based on public and in-house data
2. Studying the relationship of sequence, structure, and function of proteins
3. Developing pipeline for bioinformatics analysis aiming to answer specific biological questions
Publication
1. Xiong Y, Zhou JB, An K, Ye ZQ*, Wu YD*, Incorporating structural features to improve the prediction and understanding of pathogenic amino acid substitutions (AASs). Frontiers in Bioscience-Landmark, 2021, 26(12):1422-1433. https://doi.org/10.52586/5036
2. Li B, Hou C, Ju X, Feng Y, Ye ZQ, Xiao Y, Gu M, Fu C, Wei C*, You C*, Gain of Spontaneous clpX Mutations Boosting Motility via Adaption to Environments in Escherichia coli. Frontiers in Bioengineering and Biotechnology, 2021, 9:772397. https://doi.org/10.3389/fbioe.2021.772397
3. An K, Zhou JB, Xiong Y, Han W, Wang T, Ye ZQ*, Wu YD*, Computational Studies of the Structural Basis of Human RPS19 Mutations Associated With Diamond-Blackfan Anemia. Frontiers in Genetics, 2021, 12: 650897. https://doi.org/10.3389/fgene.2021.650897
4. Zhou JB, Xiong Y, An K, Ye ZQ*, Wu YD*, IDRMutPred: predicting disease-associated nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions. Bioinformatics, 2020, 36(20):4977-4983. https://doi.org/10.1093/bioinformatics/btaa618
5. Ma J#, An K#, Zhou JB, Wu NS, Wang Y, Ye ZQ*, Wu YD*, WDSPdb: an updated resource for WD40 proteins. Bioinformatics, 2019, 35(22):4824-4826.(* Co-corresponding author)
6. Zou XD, An K, Wu YD*, Ye ZQ*, PPI network analyses of human WD40 protein family systematically reveal their tendency to assemble complexes and facilitate the complex predictions. BMC Systems Biology, 2018, 12(Supp1 4):41. (* Co-corresponding author)
7. Hu XJ#, Li T#, Wang Y, Xiong Y, Wu XH, Zhang DL, Ye ZQ*, Wu YD*, Prokaryotic and Highly-Repetitive WD40 Proteins: A Systematic Study. Scientific reports, 2017, 7(1): 10585. (* Co-corresponding author)
8. Zou XD, Hu XJ, Ma J, Li T, Ye ZQ*, Wu YD, Genome-wide Analysis of WD40 Protein Family in Human. Scientific reports, 2016, 6: 39262. (* Corresponding author)
9. Wang Y, Hu XJ, Zou XD, Wu XH, Ye ZQ*, Wu YD*, WDSPdb: A Database for WD40-repeat Proteins. Nucleic Acids Res, 2015. 43(Database Issue) D339-344. (* Co-corresponding author)
10. Chen JY, Peng Z, Zhang R, Yang XZ, Tan BC, Fang H, Liu CJ, Shi M, Ye ZQ, Zhang YE, Deng M, Zhang X, Li CY, RNA editome in rhesus macaque shaped by purifying selection. PLoS Genet, 2014. 10(4) e1004274.
11. Li YY, Chang X, Yu WB, Li H, Ye ZQ, Yu H, Liu BH, Zhang Y, Zhang SL, Ye BC, Li YX, Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains. BMC Genomics, 2013. 14(1) 523.
12. Zhang SJ, Liu CJ, Shi M, Kong L, Chen JY, Zhou WZ, Zhu X, Yu P, Wang J, Yang X, Hou N, Ye ZQ, Zhang R, Xiao R, Zhang X, Li CY, RhesusBase: a knowledgebase for the monkey research community. Nucleic Acids Res, 2013. 41(Database issue) D892-905.
13. Yang J, Li YY, Li YX*, and Ye ZQ*, Partition dataset according to amino acid type improves the prediction of deleterious non-synonymous SNPs. Biochem Biophys Res Commun, 2012. 419(1): p.99-103. (*Corresponding author)
14. Yu H, Liu BH, Ye ZQ, Li C, Li YX, and Li YY, Link-based Quantitative Methods to Identify Differentially Coexpressed Genes and Gene Pairs. BMC Bioinformatics, 2011. 12(1): p.315.
15. Ye ZQ, Niu S, Yu Y, Liu BH, Yu H, Li RX, Xiao HS, Zeng R, Li YX, Wu JR, and Li YY, Analyses of copy number variation of GK rat CNV reveal new putative type 2 diabetes susceptibility loci. PLoS One, 2010. 5(11): p. e14077.
16. Huang T#, Wang P#, Ye ZQ#, Xu H, He Z, Feng KY, Hu L, Cui W, Wang K, Dong X, Xie L, Kong X, Cai YD, and Li YX, Prediction of deleterious non-synonymous SNPs based on protein interaction network and hybrid properties. PLoS One, 2010. 5(7): p. e11900. (#Joint first author)
17. Shen L, Gao G, Zhang Y, Zhang H, Ye ZQ, Huang S, Huang J, and Kang J, A single amino acid substitution confers enhanced methylation activity of mammalian Dnmt3b on chromatin DNA. Nucleic Acids Res, 2010. 38(18): p. 6054-6064.
18. Du C, Liu C, Kang J, Zhao G, Ye ZQ, Huang S, Li Z, Wu Z, and Pei G, MicroRNA miR-326 regulates TH-17 differentiation and is associated with the pathogenesis of multiple sclerosis. Nat Immunol, 2009. 10(12): p. 1252-9.
19. Ye ZQ, Zhao SQ, Gao G, Liu XQ, Langlois RE, Lu H, and Wei L, Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP). Bioinformatics, 2007. 23(12): p. 1444-50.
20. Li CY#, Yu Q#, Ye ZQ#, Sun Y, He Q, Li XM, Zhang W, Luo J, Gu X, Zheng X, and Wei L, A nonsynonymous SNP in human cytosolic sialidase in a small Asian population results in reduced enzyme activity: potential link with severe adverse reactions to oseltamivir. Cell Res, 2007. 17(4): p. 357-62. (#Joint first author)
21. Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei L, and Gao G, CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res, 2007. 35(Web Server issue): p. W345-9.
22. Zhou M, Xu H, Wei X, Ye ZQ, Wei L, Gong W, Wang Y, and Zhu Z, Identification of a glyphosate-resistant mutant of rice 5-enolpyruvylshikimate 3-phosphate synthase using a directed evolution strategy. Plant Physiol, 2006. 140(1): p. 184-95.
Book chapter
Chinese translation of "Clustering methods and statistics", Chapter 16 of "Understanding Bioinformatics"
Patent
CN1858247A A method for predicting the safety of Tamiflu administration. 一种预测达菲类药物用药安全性的方法 (3rd author)