3. 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; Doi:10.1093/bib/bbab139
4. 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
5. 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.
6. 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
7. 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
8. 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
9. 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
10. 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.
11. 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
12. 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
13. 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
14. 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
15. 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）
16. 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
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
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