Yaping Fang-College of Informatics

Name

Yaping Fang

Title

Associate Professor

Institute

College of Informatics, Huazhong Agricultural University

Address

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

Email

ypfang@hzau.edu.cn

Fax

86+02787288509

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 Bioinformatics、BMC Bioinformatics、BMC Genomics、Plos one、Briefings in Bioinformatics、Scientific 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
09/2013-06/2014	Associate Professor, College of Science, Huazhong Agricultural University, Wuhan, China
06/2011-09/2013	Postdoctoral researcher, Shankel Structural Biology Center , University of Kansas, Kansas, USA
10/2010-06/2011	Postdoctoral researcher, Department of Chemistry and Biochemistry, University of Oklahoma, Oklahoma, USA
07/2005-06/2010	PhD in Chemical Biology, Sichuan University, Chengdu, China
09/2001-06/2005	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