Yaping Fang

Release time:May 27, 2020Edit:Browse times:

Personal Information

Basic Information


Yaping Fang


Associate   Professor


College of Informatics, Huazhong Agricultural   University


No.1   Shizishan Street, Hongshan District, Wuhan 430070, China





Research Interest

Our main research focuses on   algorithm development and integrative mining from high-throughput data to   understand gene regulation in biology. We are using bioinformatics tools as   well as statistical methods for transcription factor, ChIP-Seq, ATAC-Seq   RNA-Seq (including lncRNA and miRNA) DNA methylation, Chromatin Interaction   Analysis with Paired-End Tag (ChIA-PET) and Hi-C, CRISPR Screen data analysis   and so on. Through integrating genome-wide transcription factor binding, 3D   genome structures, chromatin dynamics, gene expression profiles, and chemical   and functional screens, we try to model the specificity and function of   transcription factors, 3D genome structures and their functions, chromatin   regulators, RNA binding proteins, kinases, and lncRNAs in cell and disease   development, progression, drug response and resistance.

Academic activities

I have served as a reviewer   for BioinformaticsBMC   BioinformaticsBMC GenomicsPlos oneBriefings in BioinformaticsScientific Reports and for the funding branch of the NSFC   (China).


Education and research experience


06/2014-     present

Associate     Professor, College of Informatics, Huazhong Agricultural University, Wuhan,     China


Associate     Professor, College of Science, Huazhong Agricultural University, Wuhan,     China


Postdoctoral     researcher, Shankel Structural Biology Center , University of Kansas, Kansas,     USA


Postdoctoral     researcher, Department of Chemistry and Biochemistry, University of     Oklahoma, Oklahoma, USA


PhD     in Chemical Biology, Sichuan University, Chengdu, China


Bachelor     in Chemistry, Central China Normal University, Wuhan, China


Grants (Government-funded)

1.         National   Science Foundation of China, Researches on the interaction of enhancer and   promoter based on the DNA sequence and epigenomic information, RMB 200K, 01/2016   - 12/2018

2.         Fundamental   Research Funds for the Central Universities, Researches on the function of   bioactive peptides based on short open reading frames, RMB 150K, 2014.9-2016.12

3.         Fundamental   Research Funds for the Central Universities, Researches for breast cancer diagnosis   based on epigenetic and chromatin three-dimensional hierarchical structure   information, RMB 240K, 01/2019-12/2021


Representative publications*for corresponding authors, # for first authors

1. 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.

2. 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

3. 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

4. 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 DOI: 10.1186/s12864-019-5535-2

5. 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

6. 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.

7. 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

8. 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

9. 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

10. 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

11. 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

12. Le Zhan, Hui-xin Liu, Yuqi He, Yaping Fang,   Yu-Jui Yvonne Wan, Jianwen Fang and Grace L. Guo. Genome-wide binding and   transcriptome analysis of human farnesoid X receptor in the liver. FASEB   JOURNAL, 2013, 27:663

13. 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

14. 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

15. 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

16. 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

17. 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

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

19. 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

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

21. 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

22. 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.

23. 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

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

25. 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)

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

27. 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

28. 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

29. 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

30. 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

31.   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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