职称

副教授

学位

博士

电话

邮箱

ypfang@mail.hzau.edu.cn

政治面貌

中共党员

工作单位

华中农业大学信息学院

研究方向

数据挖掘、机器学习、生物信息学和人工智能

教育经历

2005.9 - 2010.7，四川大学，化学生物学，博士

2001.9 - 2005.7，华中师范大学，学士

主要职历

2014.7 - 至今， 华中农业大学信息学院，副教授

2013.9 - 2014.6 华中农业大学理学院，副教授

2011.7 - 2013.7 美国堪萨斯大学 博士后

2010.10 - 2011.7 美国俄克拉荷马 博士后

科研成果

先后主持国家自然科学基金项目1项、省部级基金项目2项、校级基金项目3项，横向项目1项，参与国家重点研发计划1项，国家自然科学基金项目3项，教改项目2项，获软件著作权1项，参编专著1部，十三五规划教材1部。在Nucleic Acids Research、 Molecular Plant ，Briefings in Bioinformatics、Bioinformatics、BMC Genomics等期刊上发表学术论文30多篇，SCI引用400多次。担任《Briefings in Bioinformatics》、 《BMC Bioinformatics》、 《Scientific Reports》等期刊审稿人。

近期发表论文：

1. Zhenji Wang, Minghao Liu, Fuming Lai, Qiangqiang Fu, Liang Xie, Yaping Fang, Qiangwei Zhou, Guoliang Li. AraENCODE: A comprehensive epigenomic database of Arabidopsis thaliana. Mol Plant. 2023, 16(7):1113-1116. S1674-2052(23)00171-5.

2. 刘峰，吴文杰，刘小磊，王欣然，方亚平，李国亮，杜小勇. 计算机视觉与深度学习在猪只识别中的研究进展，2023,42(3): 47-56

3. Zhenfei Sun, Yunlong Wang, Zhaojian Song, Hui Zhang, Yuanda Wang, Kunpeng Liu, Min Ma, Pan Wang, Yaping Fang, Detian Cai, Guoliang Li, Yuda Fang. DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplication. J Adv Res. 2022(42)41-53.

4. Yunlong Wang, Yaqi Liu, Qian Xu, Yao Xu, Kai Cao, Nan Deng, Ruimin Wang, Xueying Zhang, Ruiqin Zheng, Guoliang Li*,  Yaping Fang*. TAD boundary and strength prediction by integrating sequence and epigenetic profile information. Briefings in Bioinformatics, 2021;22(5), Doi:10.1093/bib/bbab139  

5. Ting Zhang, Pengpeng Guan, WenYe Liu, Guang Zhao, Yaping Fang, Hui Fu, Jian-Fang Gui, Guoliang Li, Jing-Xia Liu. Copper stress induces zebrafish central neural system myelin defects via WNT/NOTCH-hoxb5b signaling and pou3f1/fam168a/fam168b DNA methylation. BBA - Gene Regulatory Mechanisms. 2020; 1863(10):194612 Doi:10.1016/j.bbagrm.2020.194612  

6. Wei, X., Zhang, Y., Huang, Y. and Fang, Y., "Predicting drug–disease associations by network embedding and biomedical data integration", Data Technologies and Applications, 2019(53):217-229. Doi:10.1108/DTA-01-2019-0004.  

7. Changzhi Zhao, Yunlong Wang, Xiongwei Nie, Xiaosong Han, Hailong Liu, Guanglei Li, Gaojuan Yang, Jinxue Ruan, Yunlong Ma, Xinyun Li, Huijun Cheng, Shuhong Zhao, Yaping Fang*, Shengsong Xie*. Evaluation of the effects of sequence length and microsatellite instability on sgRNA activity and specificity. Int J Biol Sci 2019; 15(12):2641-2653  

8. Hui Zhang, Ruiqin Zheng, Yunlong Wang, Yu Zhang, Ping Hong, Yaping Fang, Guoliang Li, Yuda Fang. The effects of Arabidopsis genome duplication on the chromatin organization and transcriptional regulation. Nucleic Acids Research, 2019 DOI: 10.1093/nar/gkz511  

9. Ruimin Wang, Yunlong Wang, Xueying Zhang, Yaliang Zhang, Xiaoyong Du, Yaping Fang*, Guoliang Li*. Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data, BMC Genomics, 2019，20:296 DOI: 10.1186/s12864-019-5535-2

10. Shengsong Xie†, Qin Zhu†, Wubin Qu†, Zhong Xu, Xiangdong Liu, Xinyun Li, Shijun Li, Wubin Ma, Yiliang Miao, Lisheng Zhang, Xiaoyong Du, Wuzi Dong, Haiwei Li, Changzhi Zhao, Yunlong Wang, Yaping Fang* and Shuhong Zhao*. sRNAPrimerDB: A comprehensive primer design and search web service for small non-coding RNAs. Bioinformatics, 2019;35(9):1566-1572  

11. Zhang Cheng, Ni Pan, Ahmad Hafiz Ishfaq, Gemingguli M, Baizilaitibei A, Gulibaheti D, Fang Yaping, Wang Haiyang, Asif Akhtar Rasool, Xiao Changyi, Chen Jianhai, Ma Yunlong, Liu Xiangdong, Du Xiaoyong*, Zhao Shuhong. Detecting the Population Structure and Scanning for Signatures of Selection in Horses ( Equus caballus ) From Whole-Genome Sequencing Data. Evolutionary bioinformatics, 2018, 14: 117693431877510.

12. Liuyang Cai, Huidan Chang, Yaping Fang, and Guoliang Li. A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions. Sci Rep. 2016(6):36572  

13. Yaping Fang*, Yunlong Wang, Qin Zhu, JIa Wang, Guoliang Li*. In silico identification of enhancers on the basis of a combination of transcription factor binding motif occurrences. Sci Rep. 2016(6):32476    

14. Haibo Cui, Xiaomei Wei, Yu Huang, Bin Hu, Yaping Fang, Jia Wang. Using multiple linear regression and physicochemical changes of amino acid mutations to predict antigenic variants of influenza A/H3N2 viruses. Biomed Mater Eng. 2014, 24(6):3729-3735

15. Le Zhan, Hui-Xin Liu, Yaping Fang, Bo Kong, Yuqi He, Xiao-bo Zhong, Jianwen Fang, Yu-Jui Yvonne Wan, Grace L. Guo*. Genome-Wide Binding and Transcriptome Analysis of Human Farnesoid X Receptor in Primary Human Hepatocytes. PLoS ONE, 2014, 9(9):e105930  

16. Yaping Fang, Shan Gao, David Tai, C Russell Middaugh and Jianwen Fang*. Identification of properties important to protein aggregation using feature selection. BMC Bioinformatics, 2013, 14:314 （Highly Accessed）

17. Yuqi He, Lei Gong, Yaping Fang, Qi Zhan, Huixin Liu, Yanliu Lu, Grace L. Guo, Lois Lehman-McKeeman, Jianwen Fang, and Yu-Jui Yvonne Wan*. The role of retinoic acid in hepatic lipid homeostasis defined by genomic binding and transcriptome profiling., BMC Genomics, 2013,28;14(1):575  

18. Hui-Xin Liu, Yaping Fang, Ying Hu, Frank J Gonzalez, Jianwen Fang and Yu-Jui Yvonne Wan*. PPARβ Regulates Liver Regeneration by Modulating E2f Signaling. PLoS ONE, 2013, 8(6): e65644  

19. Shu-Lin Wang, Yaping Fang, and Jianwen Fang*. Diagnostic Prediction of Complex Diseases Using Phase-Only Correlation Based on Virtual Sample Template, BMC Bioinformatics, 2013, 14(S8):S11  

20. Ann M. Thomas, Steve N. Hart, Guodong Li, Hong Lu, Yaping Fang, Jianwen Fang, Xiao-bo Zhong, Grace L. Guo*. Hepatocyte Nuclear Factor 4 Alpha and Farnesoid X Receptor Co-regulates Gene Transcription in Mouse Livers on a Genome-wide Scale. Pharm Res. 2013, 30(9):2188-2198

21. Ying Hu, Hui-Xin Liu, Yuqi He, Yaping Fang, Jianwen Fang, and Yu-Jui Yvonne Wan*. Transcriptome profiling and genome-wide DNA binding define the differential role of fenretinide and all-trans RA in regulating the death and survival of human Huh7 cells. Biochemical Pharmacology, 2013, 85(7):1007-1017

22. Yaping Fang and Jianwen Fang. Discrimination of soluble and aggregation-prone proteins based on sequence information, Mol. BioSyst., 2013, doi:10.1039/C3MB70033J.

23. Yaping Fang, Hui-xin Liu, Ning Zhang, Grace L. Guo, Yu-Jui Yvonne Wan, Jianwen Fang*. NURBS: A Database of Experimental and Predicted Nuclear Receptor Binding Sites of Mouse, Bioinformatics, 2013, 29(2), 295-297  

24. Yaping Fang, C. Russell Middaugh and Jianwen Fang*. In silico classification of proteins from acidic and neutral cytoplasms, PLoS ONE, 2012, 7(9): e45585.  

25. Yaping Fang, Jun Li*. Genomic law guided gene prediction in fungi and metazoans, Int. J. of Computational Biology and Drug Design (IJCBDD), 2013, 6, 157-169

26. Qi Zhan, Yaping Fang, Yuqi He, Huixin Liu, Lei Gong, Lois Lehman-McKeeman, Jianwen Fang, and Yu-Jui Yvonne Wan*. Function annotation of hepatic retinoid x receptor alpha based on genome-wide DNA binding and transcriptome profiling, PLoS ONE, 2012, 7(11): e50013.  

27. Shan Gao, Shuo Xu, Yaping Fang and Jianwen Fang*. Prediction of core cancer genes using multitask classification framework. J. Theor. Biol., 2012, 317:62-70

28. Shan Gao, Shuo Xu, Yaping Fang, Jianwen Fang*. Investigating kinase-specific phosphorylation sites using multitask learning methods, Proteome Science. 2012, 10(S1):S7.  

29. Cuicui Wang†, Yaping Fang†, Menglong Li*, Jiamin Xiao. Identification RNA-binding sites in proteins by integrating various sequence information, Amino Acids, 2011, 40, 239-48 (†Co-first author)  

30. Yunqi Li, Yaping Fang, Jianwen Fang*. Predicting residue–residue contacts using random forest models, Bioinformatics, 2011, 27, 3379-3384  

31. Yaping Fang, Daichuan Ma, Menglong Li*, Zhining Wen, Yuanbo Diao. Investigation of the proteins folding rates and their properties of Amino Acid Networks, Chemom Intell Lab Syst. 2010, 101, 123-129  

32. Lirong Liu, Yaping Fang, Menglong Li*, Cuicui Wang. Prediction of Beta-Turn in Protein Using E-SSpred and Support Vector Machine, Protein J, 2009, 28, 175–181    

33. Jiang Wu, Yuanbo Diao, Menglong Li*, Yaping Fang, Daichuan Ma. A semi-supervised learning based method: Laplacian support vector machine used in diabetes disease diagnosis, Interdiscip Sci Comput Life Sci, 2009, 1, 151-155  

34. Yaping Fang, Yanzhi Guo, Yi Feng, Menglong Li*. Predicting DNA-binding proteins: approached from Chou’s pseudo amino acid composition and other specific sequence features, Amino Acids, 2008, 34,103-109 

35. Yaping Fang, Yi Feng, Menglong Li*. Optimal QSAR analysis of the carcinogenic activity of aromatic and heteroaromatic amine, QSAR Comb Sci, 2008, 27, 543–554

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