Curriculum Vitae of Dr. Hong-Yu Zhang
Professor in Computational Biology/Systems Biology
College of Informatics, Huazhong Agricultural University
Shizishan Street 1#, Wuhan 430070, Hubei, P. R. China
E-mail: zhy630@mail.hzau.edu.cn / Tel.: 0086-27-87285085
Research area: Bioinformatics/Planetary biology
Research interests:
l Systems evolution
l Evolutionary medicine
l Planetary health
Education & academic appointments
07/2014-present |
Dean, Professor in Computational Biology/Systems Biology, College of Informatics, Huazhong Agricultural University, Wuhan, China |
02/2009-06/2014 |
Professor in Computational Biology/Systems Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China |
07/2000-01/2009 |
Professor in Computational Biology/Systems Biology, School of Life Sciences, Shandong University of Technology, Zibo, China |
02/1997-06/2000 |
Lecturer (up to 11/1998) and Professor in Biophysics, Department of Biology, Shandong Normal University, Jinan, China |
08/1992-01/1997 |
Ph.D. in Biophysics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China |
09/1988-07/1992 |
Bachelor in Biochemistry, Department of Biology, Shandong University, Jinan, China |
Ongoing third-party funding
11/2021 |
Hubei Provincial Science and Technology Project (2021DFA014): “Building of Hubei Key Laboratory of Agricultural Bioinformatics” (800,000 RMB Yuan for 2 years) |
01/2021 |
Hubei Provincial Science and Technology Project (2020DFA007): “Building of Hubei Key Laboratory of Agricultural Bioinformatics” (800,000 RMB Yuan for 2 years) |
01/2019 |
National Natural Science Foundation of China (NSFC) grant (31870837): “Systems biology study on the role of phosphates in facilitating the origin of metabolic networks” (590,000 RMB Yuan for 4 years) |
12/2018 |
Hubei Provincial Science and Technology Project (2018BFC359): “Building of Hubei Key Laboratory of Agricultural Bioinformatics” (700,000 RMB Yuan for 2 years) |
01/2018 |
Special Projects for Technological Innovation in Hubei (2018ABA107): Systems genetics-based drug discovery for combating Japanese Encephalitis Virus (2,000,000 RMB Yuan for 3 years) |
06/2017 |
National Key Research & Development Project of China (2017YFD0200506): “Target discovery for agricultural biomedicine and molecular design for green drugs” (300,000 RMB Yuan for 4 years) |
05/2017 |
Enterprise entrusted project: “New generation drug discovery technology” (8,000,000 RMB Yuan for 5 years) |
01/2017 |
National Natural Science Foundation of China (NSFC) grant (31670779): “Ancestor reconstruction and evolutionary mechanism studies on bZIP transcriptional factor superfamily” (600,000 RMB Yuan for 4 years) |
External recognition & duties
i. Professional memberships
2022 Vice director of Digital Agriculture Branch, China Computer Federation (CCF)
2022 Member of IEC/SEG12
2018 Chairman of Hubei Society of Bioinformatics
2017 Council member of Systems Biology Division, The Chinese Society of Biochemistry
and Molecular Biology
2016 Council member of Functional Genomic Informatics and Systems Biology Division,
Chinese Society for Cell Biology
2016 Council member of Chinese Society of Space Research
ii. Honors & distinctions
2021 Outstanding expert of Hubei province, China.
2018 3551 Optics Valley talent, Wuhan, Hubei, China
2018 Third-Class Teaching Achievement Award, Hubei, China
2013 Manager of the Funds for Creative Research Groups, Hubei, China
2012 Chutian Scholar Distinguished Professor, Hubei, China
2012 High-End Talent of Hubei Province, China
2011 Second-Class Prize for Natural Science Research, Ministry of Education, China
2009 ScienceDirect Top 25 paper
2008 Shandong Provincial Funds for Distinguished Young Scientists
2008 Faculty of 1000 Biology
2005 Young Investigator Prize in Chemistry, Chinese Chemical Society
2005 ESI Top 1% paper, Thomson Scientific
1999 Servier Young Investigator Prize, Chinese Pharmacological Society
iii. Peer-review & editorial duties
I am involved in the Editorial Board of Metabolites, Frontiers in Genetics, Frontiers in Bioscience-Landmark, Protein & Peptide Letters, Current Computer-Aided Drug Design, Current Bioinformatics and Current Chinese Science. I have served as a reviewer for 70+ international journals, such as Nat. Biotechnol., J. Am. Chem. Soc., Genome Biol., Trends Pharmacol. Sci., Med. Res. Rev., Antioxid. Redox Signal., Bioinformatics, PLoS Comput. Biol., Chem.-Eur. J., J. Biol. Chem., J. Med. Chem..
Five selected & project-relevant publications
(* for corresponding author, # for co-first author)
Author of 200+ SCI-listed publications (total sum of citations: >10000, h-index: 50)
1. Quan Y.#, Wang Z.-Y.#, Chu X.-Y., Zhang H.-Y.* (2018) Evolutionary and genetic features of drug targets. Med. Res. Rev. 38: 1536-1549.
2. Xie T.#, Yang Q.-Y.#, Wang X.-T., McLysaght A.*, Zhang H.-Y.* (2016) Spatial colocalization of human ohnolog pairs acts to maintain dosage-balance. Mol. Biol. Evol. 33: 2368-2375.
3. Wang Z.-Y., Zhang H.-Y.* (2013) Rational drug repositioning by medical genetics. Nat. Biotechnol. 31: 1080-1082.
4. Wang M.#, Jiang Y.-Y.#, Kim K. M., Qu G., Ji H.-F., Mittenthal J. E., Zhang H.-Y.*, Caetano-Anollés G.* (2011) A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation. Mol. Biol. Evol. 28: 567-582.
5. Ji H.-F., Kong D.-X., Shen L., Chen L.-L., Ma B.-G., Zhang H.-Y.* (2007) Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery. Genome Biol. 8: R176.
Mentoring of students, and teaching duties
I have extensive (20+ years) experience in student mentoring. Tens of master and Ph.D. students have already graduated under my supervision. Currently, I am actively involved in both under- and post-graduate teaching at the Huazhong Agricultural University (Wuhan, China).
Paper list (*corresponding author)
1. Hui Li, Ya-Wen Xue, Yuan Quan*, Hong-Yu Zhang. Reducing virus infection risk in space environments through nutrient supplementation. Genes, 2022, 13: 1536.
2. Xuan Xu, Hui Wang, David A. Bennett, Qing-Ye Zhang, Gang Wang, Hong-Yu Zhang*. Systems genetic identification of mitochondrion-associated Alzheimer's disease genes and implications for disease risk prediction. Biomedicines, 2022, 10: 1782.
3. Xin-Yi Chu, Yuan-Yuan Xu, Xin-Yu Tong, Gang Wang, Hong-Yu Zhang*. The legend of ATP: from origin of life to precision medicine. Metabolites, 2022, 12: 461.
4. Xin-Yi Chu, Gang Wang, Hong-Yu Zhang*. ATP as an anti-aging agent-beyond energy reservoir. Drug Discov. Today, 2021, 26: 2783-2785.
5. Yao Ruan, Xiao-Hui Chen, Feng Jiang, Yan-Guang Liu, Xiao-Long Liang, Bo-Min Lv, Hong-Yu Zhang, Qing-Ye Zhang*. Agent clustering strategy based on metabolic flux distribution and transcriptome expression for novel drug development. Biomedicines, 2021, 9: 1640.
6. Shu-Hui Xie, Hui Li, Jing-Jing Jiang, Yuan Quan*, Hong-Yu Zhang. Multi-omics interpretation of anti-aging mechanisms for ω-3 fatty acids. Genes, 2021, 12: 1691.
7. Xuan Xu, Qing-Ye Zhang*, Xin-Yi Chu, Yuan Quan, Bo-Min Lv, Hong-Yu Zhang*. Facilitating antiviral drug discovery using genetic and evolutionary knowledge. Viruses, 2021, 13: 2117.
8. Xuehai Hu, Bo Yang, Jie Li, Xuesong Bai, Shilin Li, Honglan Liu, Hongyu Zhang, Fanxin Zeng*. Individualized prediction of acute pancreatitis recurrence using a nomogram. Pancreas, 2021, 50: 873-878.
9. Min-Hui Cao, Bao-He Tang, Yao Ruan, Xiao-Long Liang, Xin-Yi Chu, Zhan-Min Liang, Qing-Ye Zhang*, Hong-Yu Zhang. Development of specific and selective bactericide by introducing exogenous metabolite of pathogenic bacteria. Eur. J. Med. Chem., 2021, 225: 113808.
10. Yuan Quan, Hong-Yu Zhang*. Chemical genetic validation of GWAS-derived disease loci. Curr. Bioinform., 2021, 16: 789-798.
11. Xin-Yi Chu, Si-Ming Chen, Ke-Wei Zhao, Tian Tian, Jun Gao, Hong-Yu Zhang*. Plausibility of early life in a relatively wide temperature range: clues from simulated metabolic network expansion. Life, 2021, 11: 738.
12. Ze-Jia Cui, Min Gao, Yuan Quan, Bo-Min Lv, Xin-Yu Tong, Teng-Fei Dai, Xiong-Hui Zhou*, Hong-Yu Zhang*. Systems pharmacology-based precision therapy and drug combination discovery for breast cancer. Cancers, 2021, 13: 3586.
13. Bo-Min Lv, Yuan Quan, Hong-Yu Zhang*. Causal inference in microbiome medicine: principles and applications. Trends Microbiol., 2021, 29: 736-746.
14. Xin-Yi Chu, Hong-Yu Zhang*. Protein homochirality may be derived from primitive peptide synthesis by RNA. Astrobiology, 2021, 21: 628-635.
15. Qin Liu, Jie Li, Lin Xu, Jiasi Wang, Zhaoping Zeng, Jiangping Fu, Xuan Huang, Yanpeng Chu, Jing Wang*, Hong-Yu Zhang*, Fanxin Zeng*. Individualized prediction of colorectal cancer metastasis using a radiogenomics approach. Front. Oncol., 2021, 11: 620945.
16. Xin-Yu Tong, Yuan Quan, Hong-Yu Zhang*. NUDT5 as a novel drug target and prognostic biomarker for ER-positive breast cancer. Drug Discov. Today, 2021, 26: 620-625.
17. Hui Wang, David A. Bennett, Philip L De Jager, Qing-Ye Zhang, Hong-Yu Zhang*. Genome-wide epistasis analysis for Alzheimer's disease and implications for genetic risk prediction. Alzheimers Res. Ther., 2021, 13: 55.
18. Xin-Yi Chu, Hong-Yu Zhang*. Cofactors as molecular fossils to trace the origin and evolution of proteins. ChemBioChem, 2020, 21: 3161-3168.
19. Yuan Quan*, Qing-Ye Zhang, Bo-Min Lv, Rui-Feng Xu, Hong-Yu Zhang*. Genome-wide pathogenesis interpretation using a heat diffusion-based systems genetics method and implications for gene function annotation. Mol. Genet. Genomic Med., 2020, 8: e1456.
20. Ze-Jia Cui, Wei-Tong Zhang, Qiang Zhu*, Qing-Ye Zhang*, Hong-Yu Zhang. Using a heat diffusion model to detect potential drug resistance genes of Mycobacterium tuberculosis. Protein Peptide Lett., 2020, 27: 711-717.
21. Wen-Wen Cheng, Qiang Zhu*, Hong-Yu Zhang. Identifying risk genes and interpreting pathogenesis for Parkinson’s disease by a multiomics analysis. Genes, 2020, 11: 1100.
22. Jiang Li, Xin-Yu Tong, Li-Da Zhu*, Hong-Yu Zhang. A machine learning method for drug combination prediction. Front. Genet., 2020, 11: 1000.
23. Wen-Wen Cheng, Ze-Kun Wang, Huang-Fang Shangguan, Qiang Zhu, Hong-Yu Zhang*. Are vitamins relevant to cancer risks? A Mendelian randomization investigation. Nutrition, 2020, 78: 110870.
24. Yuan Quan, Hong-Yu Zhang, Jang-Hui Xiong, Rui-Feng Xu, Min Gao*. Heat diffusion kernel algorithm-based interpretation of the disease intervention mechanism for DHA. Genes, 2020, 11: 754.
25. Zhi-Hui Luo, Meng-Wei Shi, Zhuang Yang, Hong-Yu Zhang*, Zhen-Xia Chen*. pyMeSHSim: an integrative python package for biomedical named entity recognition, normalization and comparison of MeSH terms. BMC Bioinform., 2020, 21: 252.
26. Xin-Yi Chu, Yuan Quan, Hong-Yu Zhang*. Human accelerated genome regions with great values in medical genetics and drug discovery. Drug Discov. Today, 2020, 25: 821-827.
27. Hui Wang, Jingyun Yang, Julie A. Schneider, Philip L. De Jager, David A. Bennett*, Hong-Yu Zhang*. Genome-wide interaction analysis of pathological hallmarks in Alzheimer’s disease. Neurobiol. Aging, 2020, 93: 61-68.
28. Xiao-Long Liang, Zhan-Min Liang, Shuo Wang, Xiao-Hui Chen, Yao Ruan, Qing-Ye Zhang*, Hong-Yu Zhang. An analysis of the mechanism underlying photocatalytic disinfection based on integrated metabolic networks and transcriptional data. J. Environ. Sci., 2020, 92: 28-37.
29. Xuan Liao, Qing-Ye Zhang*, Lei Xu, Hong-Yu Zhang. Potential targets of actein identified by systems chemical biology methods. ChemMedChem, 2020, 15: 473-480.
30. Xin-Yu Tong, Xuan Liao, Min Gao, Bo-Min Lv, Xiao-Hui Chen, Xin-Yi Chu*, Qing-Ye Zhang*, Hong-Yu Zhang. Identification of NUDT5 inhibitors from approved drugs. Front. Mol. Biosci., 2020, 7: 44.
31. Jiang Li, Yawen Xue, Muhammad Talal Amin, Yanbo Yang, Jiajun Yang, Wen Zhang, Wenqian Yang, Xiaohui Niu, Hong-Yu Zhang, Jing Gong*. ncRNA-eQTL: a database to systematically evaluate the effects of SNPs on non-coding RNA expression across cancer types. Nucleic Acids Res., 2020, 48: D956-D963.
32. Gang Xue, Ze-Jia Cui, Xiong-Hui Zhou, Yue-Xing Zhu, Ying Chen, Feng-Ji Liang, Da-Nian Tang, Bing-Yang Huang, Hong-Yu Zhang, Zhi-Huang Hu*, Xi-Yu Yuan*, Jianghui Xiong*. DNA methylation biomarkers predict objective responses to PD-1/PD-L1 inhibition blockade. Front. Genet., 2019, 10: 724.
33. Ting Xie*, Fu-Gui Zhang, Hong-Yu Zhang, Xiao-Tao Wang, Ji-Hong Hu, Xiao-Ming Wu. Biased gene retention during diploidization in Brassica linked to three-dimensional genome organization. Nat. Plants, 2019, 5: 822-832.
34. Qing Li, Le Xiong, Jun Gao*, Hong-Yu Zhang*. Molecular mechanisms of the protein-protein interaction-regulated binding specificity of basic-region leucine zipper transcription factors. J. Mol. Model., 2019, 25: 246.
35. Ze-Jia Cui, Xiong-Hui Zhou*, Hong-Yu Zhang*. DNA Methylation module network-based prognosis and molecular typing of cancer. Genes, 2019, 10: 571.
36. Yuan Quan, Fengji Liang, Yuexing Zhu, Ying Chen, Zi Xu, Fang Du, Ke Lv, Hailong Chen, Lina Qu, Ruifeng Xu, Hong-Yu Zhang, Jianghui Xiong*, Yinghui Li*. Integrated analysis of DNA methylation and biochemical/metabolic parameter during the long-term isolation environment. Front. Physiol., 2019, 10: 917.
37. Yuan Quan, Zhi-Hui Luo, Qing-Yong Yang, Jiang Li, Qiang Zhu, Ye-Mao Liu, Bo-Min Lv, Ze-Jia Cui, Xuan Qin, Yan-Hua Xu, Li-Da Zhu*, Hong-Yu Zhang*. Systems chemical genetics-based drug discovery: prioritizing agents targeting multiple/reliable disease- associated genes as drug candidates. Front. Genet., 2019, 10: 474.
38. Shou-Kai Kang, Xin-Yi Chu, Tian Tian, Peng-Fei Dong, Bai-Xue Chen, Hong-Yu Zhang*. Why the c-Fos/c-Jun complex is extremely conserved: An in vitro evolution exploration by combining cDNA display and proximity ligation. FEBS Lett., 2019, 593: 1040-1049.
39. Tian Tian, Xin-Yi Chu, Yi Yang, Xuan Zhang, Ye-Mao Liu, Jun Gao, Bin-Guang Ma, Hong-Yu Zhang*. Phosphates as energy sources to expand metabolic networks. Life, 2019, 9: 43.
40. Gang Xue, Xin-Yi Chu, Hong-Yu Zhang*. Oxidative DNA damage is associated more with genome accessibility than spatial positioning in the nucleus. J. Biomol. Struct. Dyn., 2019, 37: 1857-1862.
41. Xiong-Hui Zhou, Xin-Yi Chu, Gang Xue, Jiang-Hui Xiong, Hong-Yu Zhang*. Identifying cancer prognostic modules by module network analysis. BMC Bioinform., 2019, 20: 85.
42. Min Gao, Yuan Quan*, Xiong-Hui Zhou, Hong-Yu Zhang. PheWAS-based systems genetics methods for anti-breast cancer drug discovery. Genes, 2019, 10: 154.
43. Wen-Wen Cheng, Qiang Zhu*, Hong-Yu Zhang. Mineral nutrition and the risk of chronic diseases: A mendelian randomization study. Nutrients, 2019, 11: 378.
44. Gen Li, Yuan Quan, Xiaocong Wang, Rong Liu, Lihua Bie, Jun Gao*, Hong-Yu Zhang. Trinucleotide base pair stacking free energy for understanding TF-DNA recognition and the functions of SNPs. Front. Chem., 2019, 6: 666.
45. Bo-Min Lv, Xin-Yu Tong, Yuan Quan, Meng-Yuan Liu, Qing-Ye Zhang, Yun-Feng Song, Hong-Yu Zhang*. Drug repurposing for Japanese encephalitis virus by systems biology methods. Molecules, 2018, 23: 3346.
46. Hui Wang, Gang Wang, Li-Da Zhu, Xuan Xu, Bo Diao*, Hong-Yu Zhang*. Subnetwork identification and chemical modulation for neural regeneration. A study combining network guided forest and heat diffusion model. Quant. Biol., 2018, 6: 321-333.
47. Yuan Quan, Zhong-Yi Wang, Xin-Yi Chu, Hong-Yu Zhang*. Evolutionary and genetic features of drug targets. Med. Res. Rev., 2018, 38: 1536-1549.
48. Yue Huo, Hong-Yu Zhang*. Genetic mechanisms of asthma and the implications for drug repositioning. Genes, 2018, 9: 237.
49. Yuan Quan, Meng-Yuan Liu, Ye-Mao Liu, Li-Da Zhu, Yu-Shan Wu, Zhi-Hui Luo, Xiu-Zhen Zhang, Shizhong Xu, Qing-Yong Yang*, Hong-Yu Zhang*. Facilitating anticancer combinatorial drug discovery by targeting epistatic disease genes. Molecules, 2018, 23: 736.
50. Xuan Xu, Hong-Yu Zhang*. The immunogenetics of psoriasis and implications for drug repositioning. Int. J. Mol. Sci., 2017, 18: 2650.
51. Xin-Yi Chu, Ye-Mao Liu, Hong-Yu Zhang*. Activating or inhibiting Nrf2? Trends Pharmacol. Sci., 2017, 38: 953-955.
52. Xin-Yi Chu, Ling-Han Jiang, Xiong-Hui Zhou*, Ze-Jia Cui, Hong-Yu Zhang. Evolutionary origins of cancer driver genes and implications for cancer prognosis. Genes, 2017, 8: 182.
53. Qing-Ye Zhang*, Xin-Yi Chu, Ling-Han Jiang, Meng-Yuan Liu, Zhi-Ling Mei, Hong-Yu Zhang*. Identification of non-electrophilic Nrf2 activators from approved drugs. Molecules, 2017, 22, 883.
54. Jing-Fen Tao, Jin-Zhi Zhou, Ting Xie, Xiao-Tao Wang, Qing-Yong Yang*, Hong-Yu Zhang. Influence of chromatin 3D organization on structural variations of the Arabidopsis thaliana genome. Mol. Plant, 2017, 10: 340-344.
55. Yuan Quan, Le Xiong, Jing Chen, Hong-Yu Zhang*. Genetics-directed drug discovery for combating Mycobacterium tuberculosis infection. J. Biomol. Struct. Dyn., 2017, 35: 616-621.
56. Ze-Jia Cui, Qing-Yong Yang, Hong-Yu Zhang, Qiang Zhu*, Qing-Ye Zhang*. Bioinformatics identification of drug resistance-associated gene pairs in Mycobacterium tuberculosis. Int. J. Mol. Sci., 2016, 17: 1417.
57. Ting Xie, Qing-Yong Yang, Xiao-Tao Wang, Aoife McLysaght*, Hong-Yu Zhang*. Spatial colocalization of human ohnolog pairs acts to maintain dosage-balance. Mol. Biol. Evol., 2016, 33: 2368-2375.
58. Yuan Quan, Hong-Yu Zhang*. A chemical-genetic criterion for identifying disease biomarkers. Trends Mol. Med., 2016, 22: 447-448.
59. Shou-Kai Kang, Bai-Xue Chen, Tian Tian, Xi-Shuai Jia, Xin-Yi Chu, Rong Liu, Peng-Fei Dong, Qing-Yong Yang, Hong-Yu Zhang*. ATP selection in a random peptide library consisting of prebiotic amino acids. Biochem. Biophys. Res. Commun., 2015, 466: 400-405.
60. Xiao-Tao Wang, Peng-Fei Dong, Hong-Yu Zhang, Cheng Peng*. Structural heterogeneity and functional diversity of topologically associating domains in mammalian genomes. Nucleic Acids Res., 2015, 43: 7237-7246.
61. Ting Xie, Jue-Fei Zheng, Sheng Liu, Cheng Peng, Yong-Ming Zhou, Qing-Yong Yang*, Hong-Yu Zhang. De novo plant genome assembly based on chromatin interactions: A case study of Arabidopsis thaliana. Mol. Plant, 2015, 8: 489-492.
62. Ting Xie, Liang-Yu Fu, Qing-Yong Yang, Heng Xiong, Hong-Rui Xu, Bin-Guang Ma*, Hong-Yu Zhang*. Spatial features for Escherichia coli genome organization. BMC Genomics, 2015, 16: 37.
63. Yuan Quan, Bin Li, You-Min Sun, Hong-Yu Zhang*. Elucidating pharmacological mechanisms of natural medicines by biclustering analysis of gene expression profile: A case study on curcumin and Si-Wu-Tang. Int. J. Mol. Sci., 2015, 16: 510-520.
64. Hui-Yong Sun, Ting-Jun Hou*, Hong-Yu Zhang*. Finding chemical drugs for genetic diseases. Drug Discov. Today, 2014, 19: 1836-1840.
65. Yuan Quan, Zhong-Yi Wang, Min Xiong, Zheng-Tao Xiao, Hong-Yu Zhang*. Dissecting traditional Chinese medicines by omics and bioinformatics. Nat. Prod. Commun., 2014, 9: 1391-1396.
66. Xiu-Zhen Zhang*, Ling Wang, Dong-Wu Liu, Guang-Yan Tang, Hong-Yu Zhang. Synergistic inhibitory effect of berberine and d-limonene on human gastric carcinoma cell line MGC803. J. Med. Food, 2014, 17: 955-962.
67. Bin Li, Min Xiong, Hong-Yu Zhang*. Elucidating polypharmacological mechanisms of polyphenols by gene module profile analysis. Int. J. Mol. Sci., 2014, 15: 11245-11254.
68. You-Min Sun, Zheng-Tao Xiao, Hong-Yu Zhang*. Structure-activity relationships of tanshinones in activating Nrf2. A DFT study and implications for multifunctional antioxidant discovery. Nat. Prod. Commun., 2014, 9: 453-454.
69. Dijun Chen, Liang-Yu Fu, Zhao Zhang, Guoliang Li, Hang Zhang, Li Jiang, Andrew P. Harrison, Hugh P. Shanahan, Christian Klukas, Hong-Yu Zhang, Yijun Ruan*, Ling-Ling Chen*, Ming Chen*. Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Res., 2014, 42: 3028-3043.
70. Min Xiong, Bin Li, Qiang Zhu, Yun-Xing Wang, Hong-Yu Zhang*. Identification of transcription factors for drug-associated gene modules and biomedical implications. Bioinformatics, 2014, 30: 305-309.
71. Zhong-Yi Wang, Yuan Quan, Hong-Yu Zhang*. Medical genetic inspirations for anticancer drug repurposing. Trends Pharmacol. Sci., 2014, 35: 1-3.
72. Hui-Yong Sun, Feng-Qin Ji, Liang-Yu Fu, Zhong-Yi Wang, Hong-Yu Zhang*. Structural and energetic analyses of SNPs in drug targets and implications for drug therapy. J. Chem. Inf. Model., 2013, 53: 3343-3351.
73. Zhong-Yi Wang, Hong-Yu Zhang*. Rational drug repositioning by medical genetics. Nat. Biotechnol., 2013, 31: 1080-1082.
74. Cheng Peng*, Liang-Yu Fu, Peng-Fei Dong, Zhi-Luo Deng, Jian-Xin Li, Xiao-Tao Wang, Hong-Yu Zhang*. The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling. Nucleic Acids Res., 2013, 41: e183.
75. Zhong-Yi Wang, Qiang Zhu, Hong-Yu Zhang*. Metabolite concentration as a criterion for antibacterial discovery. Current Computer-Aided Drug Design, 2013, 9: 412-416.
76. Zhong-Yi Wang, Min Xiong, Liang-Yu Fu, Hong-Yu Zhang*. Oxidative DNA damage is important to the evolution of antibiotic resistance. Evidence of mutation bias and its medicinal implications. J. Biomol. Struct. Dyn., 2013, 31: 729-733.
77. Ming-Feng Lu, Zheng-Tao Xiao*, Hong-Yu Zhang*. Where do health benefits of flavonoids come from? Insights from flavonoid targets and their evolutionary history. Biochem. Biophys. Res. Commun., 2013, 434: 701-704.
78. Qiang Xu, Ling-Ling Chen, Xiaoan Ruan, Dijun Chen, Andan Zhu, Chunli Chen, Denis Bertrand, Wen-Biao Jiao, Bao-Hai Hao, Matthew P Lyon, Jiongjiong Chen, Song Gao, Feng Xing, Hong Lan, Ji-Wei Chang, Xianhong Ge, Yang Lei, Qun Hu, Yin Miao, Lun Wang, Shixin Xiao, Manosh Kumar Biswas, Wenfang Zeng, Fei Guo, Hongbo Cao, Xiaoming Yang, Xi-Wen Xu, Yun-Jiang Cheng, Juan Xu, Ji-Hong Liu, Oscar Junhong Luo, Zhonghui Tang, Wen-Wu Guo, Hanhui Kuang, Hong-Yu Zhang, Mikeal L Roose, Niranjan Nagarajan, Xiu-Xin Deng*, Yijun Ruan*. The draft genome of sweet orange (Citrus sinensis). Nat. Genet., 2013, 45: 59-66.
79. Hong-Yu Zhang*, Tao Qin, Ying-Ying Jiang, Gustavo Caetano-Anollés*. Structural phylogenomics uncovers the early and concurrent origins of cysteine biosynthesis and iron-sulfur proteins. J. Biomol. Struct. Dyn., 2012, 30: 542-545.
80. Zhong-Yi Wang, Liang-Yu Fu, Hong-Yu Zhang*. Can medical genetics and evolutionary biology inspire drug target identification? Trends Mol. Med., 2012, 18: 69-71.
81. Kyung Mo Kim, Tao Qin, Ying-Ying Jiang, Ling-Ling Chen, Min Xiong, Derek Caetano-Anollés, Hong-Yu Zhang*, Gustavo Caetano-Anollés*. Protein domain structure uncovers the origin of aerobic metabolism and the rise of planetary oxygen. Structure, 2012, 20: 67-76.
82. Ying-Ying Jiang, De-Xin Kong, Tao Qin, Xiao Li, Gustavo Caetano-Anollés, Hong-Yu Zhang*. The impact of oxygen on metabolic evolution: a chemoinformatic investigation. PLoS Comput. Biol., 2012, 8: e1002426.
83. Min Xiong, Hong-Yu Zhang*. Finding Hsp90 inhibitors by drug repurposing: the power of chemical genetics. Drug Discov. Today, 2012, 17: 531-533.
84. Shuang-Yin Wang, Enrico Cappellini, Hong-Yu Zhang*. Why collagens best survived in fossils? Clues from amino acid thermal stability. Biochem. Biophys. Res. Commun., 2012, 422: 5-7.
85. Hong-Yu Zhang*, Tao Qin, Ying-Ying Jiang, Gustavo Caetano-Anollés*. Structural phylogenomics uncovers the early and concurrent origins of cysteine biosynthesis and iron-sulfur proteins. J. Biomol. Struct. Dyn., 2012, 30: 542-545.
86. Qiang Zhu, Tao Qin, Ying-Ying Jiang, Cong Ji, De-Xin Kong, Bin-Guang Ma, Hong-Yu Zhang*. Chemical basis of metabolic network organization. PLoS Comput. Biol., 2011, 7: e1002214.
87. Minglei Wang, Ying-Ying Jiang, Kyung Mo Kim, Ge Qu, Hong-Fang Ji, Jay E. Mittenthal, Hong-Yu Zhang*, Gustavo Caetano-Anollés*. A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation. Mol. Biol. Evol., 2011, 28: 567-582.
88. Bin-Guang Ma*, Hong-Yu Zhang*. Stoichiometry and preferential interaction: two components of the principle for protein structure organization. J. Biomol. Struct. Dyn., 2011, 28: 619-620.
89. Liang-Yu Fu, Guang-Zhong Wang, Bin-Guang Ma, Hong-Yu Zhang*. Exploring the common molecular basis for the universal DNA mutation bias: Revival of Löwdin mutation model. Biochem. Biophys. Res. Commun., 2011, 409: 367-371.
90. De-Xin Kong, Ming-Yue Guo, Zhi-Hong Xiao, Ling-Ling Chen, Hong-Yu Zhang*. Historical variation of structural novelty in natural product library. Chem. Biodivers., 2011, 8: 1968-1977.
91. Hong-Fang Ji*, Hong-Yu Zhang*. β-sheet constitution of prion proteins. Trends Biochem. Sci., 2010, 35: 129-134.
92. Hong-Yu Zhang*, Ling-Ling Chen, Xue-Juan Li, Jian Zhang. Evolutionary inspirations for drug discovery. Trends Pharmacol. Sci., 2010, 31: 443-448.
93. De-Xin Kong, Ying-Ying Jiang, Hong-Yu Zhang*. Marine natural products as sources of novel scaffolds: achievement and concern. Drug Discov. Today, 2010, 15: 884-886.
94. Na Gao, Ling-Ling Chen*, Hong-Fang Ji, Wei Wang, Ji-Wei Chang, Bei Gao, Lin Zhang, Shi-Cui Zhang, Hong-Yu Zhang*. DIGAP–a database of improved gene annotation for phytopathogens. BMC Genomics, 2010, 11: 54.
95. Ying-Ying Jiang, De-Xin Kong, Tao Qin, Hong-Yu Zhang*. How does oxygen rise drive evolution? Clues from oxygen-dependent biosynthesis of nuclear receptor ligands. Biochem. Biophys. Res. Commun., 2010, 391: 1158-1160.
96. Xiu-Zhen Zhang*, Xue-Juan Li, Hong-Yu Zhang*. Valproic acid as a promising agent to combat Alzheimer’s disease. Brain Res. Bull., 2010, 81: 3-6.
97. Xue-Juan Li, De-Xin Kong, Hong-Yu Zhang*. Chemoinformatics approaches for traditional Chinese medicine research and case application in anticancer drug discovery. Curr. Drug Discov. Technol., 2010, 7: 22-31.
98. Hong-Yu Zhang*, Xue-Juan Li, Na Gao, Ling-Ling Chen. Antioxidants used by Deinococcus radiodurans and implications for antioxidant drug discovery. Nat. Rev. Microbiol., 2009, 7: 476 (DOI: 10.1038/nrmicro2073-c1).
99. Xiu-Zhen Zhang, Xue-Juan Li, Hong-Yu Zhang*. Curcumin’s potential to modulate stem cell fate. Trends Pharmacol. Sci., 2009, 30: 331-332.
100. Hong-Fang Ji, Xue-Juan Li, Hong-Yu Zhang*. Natural products and drug discovery. EMBO Rep., 2009, 10: 194-200.
101. De-Xin Kong, Xue-Juan Li, Hong-Yu Zhang*. Where is the hope for drug discovery? Let history tell the future. Drug Discov. Today, 2009, 14: 115-119.
102. Xue-Juan Li, Na Gao, Hong-Yu Zhang*. Natural inspirations for antioxidant drug discovery. Drug Discov. Today, 2009, 14: 910-912.
103. Hong-Fang Ji, Lei Chen, Ying-Ying Jiang, Hong-Yu Zhang*. Evolutionary formation of new protein folds is linked to metallic cofactor recruitment. BioEssays, 2009, 31: 975-980.
104. Xiu-Zhen Zhang, Xue-Juan Li, Hong-Fang Ji, Hong-Yu Zhang*. Impact of drug discovery on stem cell biology. Biochem. Biophys. Res. Commun., 2009, 383: 275-279.
105. Ge Qu, Wei Wang, Ling-Ling Chen, Shao-Song Qian, Hong-Yu Zhang*. tRNA-dependent cysteine biosynthetic pathway represents a strategy to increase cysteine contents by preventing it from thermal degradation: thermal adaptation of methanogenic archaea ancestor. J. Biomol. Struct. Dyn., 2009, 27: 111-114.
106. Xue-Juan Li, Hong-Yu Zhang*. Potential anti-dementia agents in traditional Chinese medicine. Nat. Prod. Commun., 2009, 4: 877-886.
107. Xue-Juan Li, Hong-Yu Zhang*. Synergy in natural medicines: implications for drug discovery. Trends Pharmacol. Sci., 2008, 29: 331-332.
108. Xue-Juan Li, Hong-Yu Zhang*. Western-medicine-validated anti-tumor agents and traditional Chinese medicine. Trends Mol. Med., 2008, 14: 1-2.
109. Xue-Juan Li, Hong-Yu Zhang*. Western healers in traditional Chinese medicine. EMBO Rep., 2008, 9: 112-113.
110. Hong-Yu Zhang*. Another trick of heavy isotopes. Trends Biotechnol., 2008, 26: 118-120.
111. Hong-Fang Ji, Lei Chen, Hong-Yu Zhang*. Organic cofactors participated more frequently than transition metals in redox reactions of primitive proteins. BioEssays, 2008, 30: 766-771.
112. Liang Shen, Hong-Fang Ji*, Hong-Yu Zhang*. Why is the C-terminus of Aβ(1-42) more unfolded than that of Aβ(1-40)? Clues from hydrophobic interaction. J. Phys. Chem. B, 2008, 112: 3164-3167.
113. De-Xin Kong, Xue-Juan Li, Guang-Yan Tang, Hong-Yu Zhang*. How many traditional Chinese medicine components have been recognized by modern Western medicine? A chemoinformatic analysis and implications for finding multicomponent drugs. ChemMedChem, 2008, 3: 233-236.
114. De-Xin Kong, Xue-Juan Li, Hong-Yu Zhang*. Convergent evolution of medicines. ChemMedChem, 2008, 3: 1169-1171.
115. Bin-Guang Ma, Lei Chen, Hong-Fang Ji, Zhong-Hua Chen, Fu-Rong Yang, Ling Wang, Ge Qu, Ying-Ying Jiang, Cong Ji, Hong-Yu Zhang*. Characters of very ancient proteins. Biochem. Biophys. Res. Commun., 2008, 366: 607-611.
116. Hong-Fang Ji, Hong-Yu Zhang*. Bioinformatic identification of the most ancient copper protein architecture. J. Biomol. Struct. Dyn., 2008, 26: 197-201.
117. Hong-Fang Ji, Hong-Yu Zhang*. Multipotent natural agents to combat Alzheimer’s disease. Functional spectrum and structural features. Acta Pharmacol. Sin., 2008, 29: 143-151.
118. Liang Shen*, Hong-Fang Ji, Hong-Yu Zhang*. Photophysical and photochemical properties of anthraquinones: A DFT study. J. Mol. Struct. (Theochem), 2008, 851: 220-224.
119. Liang Shen, Hong-Yu Zhang*, Hong-Fang Ji. A thermodynamic investigation of DPPH radical-scavenging mechanisms of folates. J. Mol. Struct. (Theochem), 2008, 856: 119-123.
120. Qian Zhao, De-Xin Kong, Hong-Yu Zhang*. Excited-state pKa values of curcumin. Nat. Prod. Commun., 2008, 3: 229-232.
121. Qian Zhao, Esther Joy Bowles*, Hong-Yu Zhang*. Antioxidant activities of eleven Australian essential oils. Nat. Prod. Commun., 2008, 3: 837-842.
122. Qian Zhao, Hong-Yu Zhang*. Comparative photobleaching behavior of hypocrellin A and elsinochrome C. Nat. Prod. Commun., 2008, 3: 1701-1704.
123. Guang-Yan Tang, Xue-Juan Li, Hong-Yu Zhang*. Antidiabetic components contained in vegetables and legumes. Molecules, 2008, 13: 1189-1194.
124. Hong-Fang Ji, Hong-Yu Zhang*, Ling-Ling Chen. Why are prion diseases precluded by non-mammals? Trends Biochem. Sci., 2007, 32: 206-208.
125. Hong-Fang Ji, De-Xin Kong, Liang Shen, Ling-Ling Chen, Bin-Guang Ma, Hong-Yu Zhang*. Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery. Genome Biol., 2007, 8: R176.
126. Bin-Guang Ma*, Ling-Ling Chen, Hong-Yu Zhang*. What determines protein folding type? An investigation of intrinsic structural properties and its implications for understanding folding mechanisms. J. Mol. Biol., 2007, 370: 439-448.
127. Wen-Fang Ji, Zong-Liang Li, Liang Shen, De-Xin Kong, Hong-Yu Zhang*. Density functional theory methods as powerful tools to elucidate amino acid oxidation mechanisms. A case study on methionine model peptide. J. Phys. Chem. B, 2007, 111: 485-489.
128. Yan Zhou, Bin-Guang Ma, Hong-Yu Zhang*. Human oncogene tissue-specific expression level significantly correlates with sequence compositional features. FEBS Lett., 2007, 581: 4361-4365.
129. Guang-Zhong Wang, Ling-Ling Chen, Hong-Yu Zhang*. Neighboring-site effects of amino acid mutation. Biochem. Biophys. Res. Commun., 2007, 353: 531-534.
130. Hong-Fang Ji, Hong-Yu Zhang*. A comparative molecular dynamics study on thermostability of human and chicken prion proteins. Biochem. Biophys. Res. Commun., 2007, 359: 790-794.
131. Hong-Yu Zhang*. Exploring the evolution of standard amino-acid alphabet: when genomics meets thermodynamics. Biochem. Biophys. Res. Commun., 2007, 359: 403-405.
132. Ling-Ling Chen, Guang-Zhong Wang, Hong-Yu Zhang*. Sterol biosynthesis and prokaryotes-to-eukaryotes evolution. Biochem. Biophys. Res. Commun., 2007, 363: 885-888.
133. Hao Wu, Bin-Guang Ma, Ji-Tao Zhao, Hong-Yu Zhang*. How similar are amino acid mutations in human genetic diseases and evolution? Biochem. Biophys. Res. Commun., 2007, 362: 233-237.
134. Liang Shen, Hong-Fang Ji, Hong-Yu Zhang*. How to understand the dichotomy of antioxidants? Biochem. Biophys. Res. Commun., 2007, 362: 543-545.
135. Hong-Yu Zhang*. Can food-derived multipotent agents reduce the risk of Alzheimer's disease? Trends Food Sci. Tech., 2007, 18: 492-495.
136. Da-Peng Yang, De-Xin Kong, Hong-Yu Zhang*. Multiple pharmacological effects of olive oil phenols. Food Chem., 2007, 104: 1269-1271.
137. Hong-Fang Ji, Hong-Yu Zhang*. Protein architecture chronology deduced from structures of amino acid synthases. J. Biomol. Struct. Dyn., 2007, 24: 321-323.
138. Liang Shen*, Hong-Fang Ji, Hong-Yu Zhang*. Computational note on the photosensitization mechanisms of riboflavin. J. Mol. Struct. (Theochem), 2007, 821: 171-172.
139. Liang Shen, Hong-Yu Zhang*, Hong-Fang Ji. Computational note on the SOD-like antioxidant potential of nicotine-copper(II) complexes. J. Mol. Struct. (Theochem), 2007, 817: 161-162.
140. Lei Chen, Hong-Yu Zhang*. Cancer preventive mechanisms of the green tea polyphenol (-)-epigallocatechin-3-gallate. Molecules, 2007, 12: 946-957.
141. Da-Peng Yang, Hong-Fang Ji, Guang-Yan Tang, Wei Ren, Hong-Yu Zhang*. How many drugs are catecholics. Molecules, 2007, 12: 878-884.
142. Atanu Barik, Beena Mishra, Amit Kunwar, Ramakant M. Kadam, Liang Shen, Sabari Dutta, Subhash Padhye, Ashis K. Satpati, Hong-Yu Zhang and K. Indira Priyadarsini*. Comparative study of copper(II)-curcumin complexes as superoxide dismutase mimics and free radical scavengers. Eur. J. Med. Chem., 2007, 42: 431-439.
143. Hong-Yu Zhang*, Da-Peng Yang, Guang-Yan Tang. Multipotent antioxidants: from screening to design. Drug Discov. Today, 2006, 11: 749-754.
144. Hong-Yu Zhang*. The evolution of genomes and language. EMBO Rep., 2006, 7: 748-749.
145. Hong-Yu Zhang*. Comparing genomes and languages using current knowledge-Response from the author. EMBO Rep., 2006, 7: 955.
146. Bin-Guang Ma*, Jian-Xiu Guo, Hong-Yu Zhang*. Direct correlation between proteins’ folding rates and their amino acid compositions: An ab initio folding rate prediction. Proteins, 2006, 65: 362-372.
147. Hong-Yu Zhang*. Scrapie and the origin of the Chinese “itchy”. Science, 2006, 311: 1866-1867 (Letter).
148. Hong-Yu Zhang*. Same causes, same cures. Biochem. Biophys. Res. Commun., 2006, 351: 578-581.
149. Hong-Yu Zhang*, Hong-Fang Ji. How vitamin E scavenges DPPH radicals in polar protic media. New J. Chem., 2006, 30: 503-504.
150. Hong-Fang Ji, Hong-Yu Zhang*, Liang Shen. Proton dissociation is important to understanding structure-activity relationships of gallic acid antioxidants. Bioorg. Med. Chem. Lett., 2006, 16: 4095-4098.
151. Liang Shen, Hong-Fang Ji, Hong-Yu Zhang*. A theoretical elucidation on the solvent-dependent photosensitive behaviors of C60. Photochem. Photobiol., 2006, 82: 798-800.
152. Liang Shen, Hong-Fang Ji, Hong-Yu Zhang*. A TD-DFT study on photo-physicochemical properties of hypocrellin A and its implications for elucidating the photosensitizing mechanisms of the pigment. J. Photochem. Photobiol. A: Chem., 2006, 180: 65-68.
153. Liang Shen, Hong-Fang Ji, Hong-Yu Zhang*. Anion of hypericin is crucial to understanding the photosensitive features of the pigment. Bioorg. Med. Chem. Lett., 2006, 16: 1414-1417.
154. Hong-Fang Ji, Hong-Yu Zhang*. Theoretical evaluation of flavonoids as multipotent agents to combat Alzheimer’s disease. J. Mol. Struct. (Theochem), 2006, 767: 3-9.
155. Bin-Guang Ma, Qin Song, Hong-Yu Zhang*. CvP-bias as an index to predict the life style of last common ancestor. J. Biomol. Struct. Dyn., 2006, 23: 555-558.
156. Liang Shen, Hong-Fang Ji, Hong-Yu Zhang*. Theoretical study on photophysical and photosensitive properties of aloe emodin. J. Mol. Struct. (Theochem), 2006, 758: 221-224.
157. Hong-Yu Zhang*. Similar evolution of styles in physics and painting. Phys. Essays, 2006, 19: 284-286.
158. Hong-Fang Ji, Hong-Yu Zhang*. Substituent effects on proton affinity of imidazole in Cu,Zn-Superoxide dismutase. Chin. J. Chem., 2006, 24: 822-824.
159. Hong-Fang Ji, Liang Shen, Janette Carey, Rita Grandori*, Hong-Yu Zhang*. Why WrbA is weaker than flavodoxin in binding FMN? A molecular modeling study. J. Mol. Struct. (Theochem), 2006, 764: 155-160.
160. Hong-Fang Ji, Hong-Yu Zhang*, Liang Shen. A theoretical elucidation of the radical-scavenging power of cyanidin. Nat. Prod. Commun., 2006, 1: 229-236.
161. Hong-Yu Zhang*, Da-Peng Yang, Hong-Fang Ji. Naturally occurring multipotent anti-Alzheimer’s agents. Expert Opin. Drug Discov., 2006, 1: 269-277.
162. Liang Shen, Hong-Yu Zhang*, Hong-Fang Ji. Successful application of TD-DFT in transient absorption spectra assignment. Org. Lett., 2005, 7: 243-246.
163. Hong-Yu Zhang*. One-compound-multiple-targets strategy to combat Alzheimer’s disease. FEBS Lett., 2005, 579: 5260-5264.
164. Atanu Barik, Beena Mishra, Liang Shen, Hari Mohan, R. M. Kadam, S. Dutta, Hong-Yu Zhang, K. Indira Priyadarsini*. Evaluation of a new copper–curcumin complex as superoxide dismutase mimic and its free radical reactions. Free Radic. Biol. Med., 2005, 39: 811-822.
165. Guang-Zhong Wang, Bin-Guang Ma, Yan Yang, Hong-Yu Zhang*. Unexpected amino acid composition of modern Reptilia and its implications in molecular mechanisms of dinosaur extinction. Biochem. Biophys. Res. Commun., 2005, 333: 1047-1049.
166. Hong-Fang Ji, Liang Shen, Hong-Yu Zhang*. b-Lactam antibiotics are multipotent agents to combat neurological diseases. Biochem. Biophys. Res. Commun., 2005, 333: 661-663.
167. Liang Shen, Hong-Fang Ji, Hong-Yu Zhang*. A TD-DFT study on triplet excited-state properties of curcumin and its implications in elucidating the photosensitizing mechanisms of the pigment. Chem. Phys. Lett., 2005, 409: 300-303.
168. Hong-Fang Ji, Guang-Yan Tang, Hong-Yu Zhang*. A theoretical study on the structure-activity relationships of metabolites of folates as antioxidants and its implications for rational design of antioxidants. Bioorg. Med. Chem., 2005, 13: 1031-1036.
169. Hong-Fang Ji, Hong-Yu Zhang*. A new strategy to combat Alzheimer’s disease. Combining radical-scavenging potential with metal-protein-attenuating ability in one molecule. Bioorg. Med. Chem. Lett., 2005, 15: 21-24. (Correction: Bioorg. Med. Chem. Lett., 2005, 15: 1257)
170. Hong-Fang Ji, Hong-Yu Zhang*. A CCSD estimation on O-H bond dissociation enthalpies of pyrogallol. New J. Chem., 2005, 29: 535-537.
171. Nikolaos Nenadis, Lan-Fen Wang, Maria Tsimidou*, Hong-Yu Zhang. Radical scavenging potential of phenolic compounds encountered in O. Europaea products as indicated by calculation of bond dissociation enthalpy and ionization potential values. J. Agric. Food Chem., 2005, 53: 295-299.
172. Lan-Fen Wang, Hong-Yu Zhang*. A theoretical study of the different radical-scavenging activities of catechin, quercetin and a rationally designed planar catechin. Bioorg. Chem., 2005, 33: 108-115.
173. Hong-Fang Ji, Guang-Yan Tang, Hong-Yu Zhang*. Theoretical elucidation of DPPH radical-scavenging activity difference of antioxidant xanthones. QSAR Combin. Sci., 2005, 24: 826-830.
174. Ling Kong, Lan-Fen Wang, Hong-Yu Zhang*. Theoretical elucidation on mechanism and reactivity of bisphenol A derivatives as inhibitors and radical scavengers in methacrylate polymerization. J. Mol. Struct. (Theochem), 2005, 716: 27-31.
175. Hong-Yu Zhang*, Lan-Fen Wang. Solvent effects are important in elucidating radical-scavenging mechanisms of antioxidants. A case study on genistein. J. Biomol. Struct. Dyn., 2005, 22: 483-486.
176. Hong-Fang Ji, Hong-Yu Zhang*, Liang Shen. The role of electrostatic interaction in triggering the unraveling of stable helix 1 in normal prion protein. A molecular dynamics simulation investigation. J. Biomol. Struct. Dyn., 2005, 22: 563-570.
177. Qian Zhao, Hong-Yu Zhang*. Singlet-oxygen-generating activity of deuterated perylenequinonoid pigments. Dyes Pigments, 2005, 66: 15-17.
178. Lan-Fen Wang, Xiu-Li Wang, Hong-Yu Zhang*. A theoretical study on photobleaching mechanisms of perylenequinonoid pigments. Dyes Pigments, 2005, 67: 161-166.
179. Hong-Fang Ji, Liang Shen, Hong-Yu Zhang*. Theoretical reinvestigation of opposite electronic effects on bond lengths of thiophenols and thiophenolic radicals. J. Struct. Chem., 2005, 46: 347-351.
180. Liang Shen, Hong-Yu Zhang*, Hong-Fang Ji. A theoretical study on Cu(II)-chelating properties of curcumin and its implications for curcumin as a multipotent agent to combat Alzheimer’s disease. J. Mol. Struct. (Theochem), 2005, 757: 199-202.
181. Lan-Fen Wang, Hong-Yu Zhang*. A theoretical study on physicochemical properties of elsinochrome A in ground state. J. Mol. Struct. (Theochem), 2005, 726: 135-140.
182. Hong-Fang Ji, Liang Shen, Hong-Yu Zhang*. Low-lying free energy levels of amino acids and their implications for the origin of life. J. Mol. Struct. (Theochem), 2005, 756: 109-112.
183. Hao Wu, Yan Yang, Sheng-Juan Jiang, Ling-Ling Chen*, Hai-Xia Gao, Qing-Shan Fu, Feng Li, Bin-Guang Ma, Hong-Yu Zhang*. DCCP and DCIP: construction and analyses of databases for copper- and iron-chelating proteins. Genom. Proteom. Bioinform., 2005, 3: 52-57.
184. Hong-Yu Zhang*. Structure-activity relationships and rational design strategies for radical- scavenging antioxidants. Current Computer-Aided Drug Design, 2005, 1: 257-273.
185. Hong-Fang Ji, Hong-Yu Zhang*. A Theoretical study on Cu(II)-binding modes and antioxidant activity of mammalian normal prion protein. Chem. Res. Toxicol., 2004, 17: 471-475.
186. Hong-Yu Zhang*. On the effectiveness of EPR radical equilibration technique in estimating O-H bond dissociation enthalpies of catechols and other complex polyphenols. New J. Chem., 2004, 28: 1284-1285.
187. Ling Kong, K. Indira Priyadarsini, Hong-Yu Zhang*. A theoretical investigation on intramolecular hydrogen-atom transfer in curcumin. J. Mol. Struct. (Theochem), 2004, 684: 111-116.
188. Nikolaos Nenadis, Lan-Fen Wang, Maria Tsimidou*, Hong-Yu Zhang*. Estimation of scavenging activity of phenolic compounds using the ABTS•+ Assay. J. Agric. Food Chem., 2004, 52: 4669-4674.
189. Lan-Fen Wang, Hong-Yu Zhang*. Unexpected role of 5-OH in DPPH radical-scavenging activity of 4-thiaflavans. Revealed by theoretical calculations. Bioorg. Med. Chem. Lett., 2004, 14: 2609-2611.
190. Ling-Kong, Zhen-Ling Sun, Lan-Fen Wang, Hong-Yu Zhang*, Si-De Yao. Theoretical elucidation of nitrogen dioxide radical-scavenging activity difference of hydroxycinnamic acid derivatives. Helv. Chim. Acta, 2004, 87: 511-515.
191. Lan-Fen Wang, Hong-Yu Zhang*, Ling Kong, Zhi-Wei Chen, Jian-Guo Shi. DFT calculations indicate that 1,4-dihydropyridine is a promising lead antioxidant. Helv. Chim. Acta, 2004, 87: 1515-1521.
192. Hong-Yu Zhang*, Lan-Fen Wang. Theoretical elucidation of structure-activity relationship for coumarins to scavenge peroxyl radical. J. Mol. Struct. (Theochem), 2004, 673: 199-202.
193. Yun-Xiu Shen, Xiu-Li Wang, Wei-Zhong Liu, Hong-Yu Zhang*. An exploratory theoretical investigation on intramolecular proton transfer in a novel perylenequinonoid pigment- hypomycin A. J. Mol. Struct. (Theochem), 2004, 668: 151-155.
194. Xiu-Li Wang, Lan-Fen Wang, Hong-Yu Zhang*. A theoretical study on isomerization process of hypocrellin A in ground state. Dyes Pigments, 2004, 63: 23-28.
195. Yu Ling-Hong, Liu Geng-Tao*, Sun You-Min, Zhang Hong-Yu. Antioxidative effect of schisanhenol on human low density lipoprotein and its quantum chemical calculation. Acta Pharmacol. Sin., 2004, 25: 1038-1044.
196. Hong-Yu Zhang*, You-Min Sun, Xiu-Li Wang. Substituent effects on O-H bond dissociation enthalpies and ionization potentials of catechols: a DFT study and its implications in rational design of phenolic antioxidants and elucidation of structure-activity relationships for flavonoid antioxidants, Chem.-Eur. J., 2003, 9: 502-508.
197. Hong-Yu Zhang*. On the O-H bond dissociation enthalpy of catechol. New J. Chem., 2003, 27: 453-454.
198. Hong-Yu Zhang*, Lan-Fen Wang, You-Min Sun. Why B-ring is the active center for genistein to scavenge peroxyl radical. A DFT study. Bioorg. Med. Chem. Lett., 2003, 13: 909-911.
199. Lan-Fen Wang. Hong-Yu Zhang*. A theoretical investigation on DPPH radical-scavenging mechanism of edaravone. Bioorg. Med. Chem. Lett., 2003, 13: 3789-3792.
200. Hong-Yu Zhang*, Lan-Fen Wang. Comment on "Effects of metal ions distinguishing between one-step hydrogen- and electron-transfer mechanisms for the radical-scavenging reaction of (+)-catechin". J. Phys. Chem. A, 2003, 107: 11258-11259.
201. Mei-Zi Xing, Xi-Zhen Zhang, Zhen-Ling Sun, Hong-Yu Zhang*. Perylenequinones act as wide-spectrum fungicides by generating reactive oxygen species both in dark and in light. J. Agric. Food Chem., 2003, 51: 7722-7724.
202. Nikolaos Nenadis, Hong-Yu Zhang and Maria Tsimidou*. Structure-antioxidant activity relationship of ferulic acid derivatives: Effect of carbon side chain characteristic groups. J. Agric. Food Chem., 2003, 51: 1874-1879.
203. Hong-Yu Zhang*, Hong-Fang Ji. S-H proton dissociation enthalpies of thiophenolic cation radicals. A DFT study. J. Mol. Struct. (Theochem), 2003, 663: 167-174.
204. Hong-Yu Zhang*, You-Min Sun, Lan-Fen Wang. A DFT study on intramolecular hydrogen bonds in substituted catechols and their radicals. Chin. Chem. Lett., 2003, 14: 209-212.
205. Hong-Yu Zhang*, Lan-Fen Wang. Theoretical investigation on radical-coupling activity for indolinonic aminoxyls. Chin. Chem. Lett., 2003, 14: 437-440.
206. Lan-Fen Wang, Hong-Yu Zhang*. Theoretical elucidation on different lipid-oxidation potentials of aminoxyl antioxidants. Chin. J. Chem., 2003, 21: 1669-1672.
207. Hong-Yu Zhang*, You-Min Sun, Xiu-Li Wang. Electronic effects on O-H proton dissociation energies of phenolic cation radicals. A DFT study. J. Org. Chem., 2002, 67: 2709-2712.
208. Hong-Yu Zhang*, Lan-Fen Wang. Theoretical elucidation on structure-antioxidant activity relationships for indolinonic hydroxylamines. Bioorg. Med. Chem. Lett., 2002, 12: 225-227.
209. Hong-Yu Zhang*, Lan-Fen Wang. Are allylic hydrogens in catechins more abstractable than catecholic hydrogens. J. Am. Oil Chem. Soc., 2002, 79: 943-944.
210. You-Min Sun, Hong-Yu Zhang, De-Zhan Chen, Cheng-Bu Liu*. Theoretical elucidation on the antioxidant mechanism of curcumin. A DFT study. Org. Lett., 2002, 4: 2909-2911.
211. Hong-Yu Zhang*, You-Min Sun, De-Zhan Chen. 1,4-Pyrone effects on O-H bond dissociation energies of catechols in flavonoids: A density functional theory study. Chin. Chem. Lett., 2002, 13: 531-534.
212. Hong-Yu Zhang* , Wei Liu*, Wei-Zhong Liu, Jin-Lun Xie. Photosensitization of Hypomycin B ¾ a Novel Perylenequinonoid Pigment with Only One Intramolecular Hydrogen Bond. Photochem. Photobiol., 2001, 74: 191-195.
213. Hong-Yu Zhang*, You-Min Sun, De-Zhan Chen. O-H bond dissociation energies of phenolic compounds are determined by field/inductive effect or resonance effect? A DFT study and its implication. Quant. Struct.-Act. Relat., 2001, 20: 148-152.
214. You-Min Sun, Xiu-Li Wang, Hong-Yu Zhang*, De-Zhan Chen. Theoretical elucidation of structure-activity relationship for thiazolidinone derivatives, Quant. Struct.-Act. Relat., 2001, 20: 139-142.
215. Dao-Ping Wang, De-Xin Kong, De-Zhan Chen, Hong-Yu Zhang*. Intramolecular H-bonding in the bay region of hypericin: an AM1 study. Dyes Pigments, 2001, 51: 71-77.
216. You-Min Sun, Hong-Yu Zhang*, De-Zhan Chen. Evaluation of theoretical methods used in calculating O-H bond dissociation enthalpy. Chin. J. Chem., 2001, 19: 657-661.
217. Zhang Hong-Yu*, You-Min Sun, De-Zhan Chen. Why static O-H bond parameters cannot characterize the free radical scavenging activity of phenolic antioxidants: ab initio study. Chin. Chem. Lett., 2001, 12: 75-78.
218. Hong-Yu Zhang*. Theoretical investigation on free radical scavenging activity of 6,7-dihydroxyflavone. Quant. Struct.-Act. Relat., 2000, 19: 50-53.
219. Hong-Yu Zhang*, You-Min Sun, Gui-Qiu Zhang, De-Zhan Chen. Why static molecular parameters cannot characterize the free radical scavenging activity of phenolic antioxidants. Quant. Struct.-Act. Relat., 2000, 19: 375-379.
220. Hong-Yu Zhang*, Chen De-Zhan. Theoretical analysis of the fluorescence spectrum of hypocrellin A. Dyes Pigments, 2000, 45: 81-83.
221. Hong-Yu Zhang*, Chen De-Zhan. Mechanism of intramolecular proton transfer involving hypericin. Dyes Pigments, 2000, 46: 17-21.
222. Wei Liu, Hong-Yu Zhang*, De-Zhan Chen, Zhi-Yi Zhang, Man-Hua Zhang. Theoretical study on intramolecular hydrogen transfer of amino-substituted perylenequinone. Dyes Pigments, 2000, 47: 277-284.
223. Zhang Hong-Yu*, Chen De-Zhan. Is HOMO energy level a good parameter to characterize antioxidant activity. Chin. Chem. Lett., 2000, 11: 727-730.
224. Zhang Hong-Yu*, Chen De-Zhan. Theoretical elucidation on activity differences of ten flavonoid antioxidants. Acta Biochim. Biophys. Sin., 2000, 32: 317-321.
225. Hong-Yu Zhang*. Theoretical methods used in elucidating activity differences of phenolic antioxidants. J. Am. Oil Chem. Soc., 1999, 76: 745-748.
226. Hong-Yu Zhang*. Investigation on effectiveness of HOMO to characterize antioxidant activity. J. Am. Oil Chem. Soc., 1999, 76: 1109-1110.
227. Hong-Yu Zhang*. Variance of charges in the process of isomerization of perylenequinone. J. Photochem. Photobiol. A: Chem., 1999, 126: 27-30.
228. Zhang Hong-Yu*. Theoretical elucidation of structure-activity relationship of flavonoid antioxidants. Science in China (series B), 1999, 42: 106-112.
229. Zhang Hong-Yu*, Ge Nan, Zhang Zhi-Yi. Theoretical elucidation of activity differences of five phenolic antioxidants. Acta Pharmacol. Sin., 1999, 20: 363-366.
230. Zhang Hong-Yu*. Scavenging effect of chinonin on free radicals studied with quantum chemistry. Acta Pharmacol. Sin., 1999, 20: 555-558.
231. Hong-Yu Zhang*. Selection of theoretical parameter characterizing scavenging activity of antioxidants on free radicals. J. Am. Oil Chem. Soc., 1998, 75: 1705-1709.
232. Zhang Hong-Yu, Zhang Zhi-Yi*. Theoretical study of intramolecular proton transfer of perylenequinone. Science in China (series B), 1998, 41: 85-90.
233. Zhang Hong-Yu*. Changes of dipolemoment in intramolecular proton transfer process of perylenequinone. Chin. Sci. Bull., 1998, 43: 1380-1384.
234. Zhang Hong-Yu*. Scavenging effect of perylenequinone hydroxyls on free radicals: A theoretical study. Chin. Chem. Lett., 1998, 9: 1087-1090.
235. Zhang Hong-Yu, Zhang Zhi-Yi*. Molecular mechanics study on conformation of perylenequinonoid photosensitizers. Science in China (series B), 1997, 40: 428-433.
236. Zhang Hong-Yu, Zhao Hong-Xia, Zhang Zhi-Yi*. Studying dynamic process of photosensitization by ESR method. Science in China (series C), 1997, 40: 356-362.
237. Zhang Hong-Yu, Zhang Zhi-Yi*. Determination of pKa values of perylene-quinonoid photosensitizer in excited state. Chin. Sci. Bull., 1997, 42: 2005-2009.
Book chapters
1. Zhang Hong-Yu and Zhang Zhi-Yi. Application of quantum chemistry in free radical biology. In: Fang Yun-Zhong and Zheng Rong-Liang (ed.) Theory and Application of Free Radical Biology, Scientific press, Beijing, 2002, p92-121 (in Chinese).
2. Sun You-Min, Chen De-Zhan, Zhang Hong-Yu*. Selection of theoretical parameters characterizing free radical scavenging activity of monophenolic antioxidants. In: Fang Yun-Zhong and Zheng Rong-Liang (ed.) Adv Free Radic Life Sci, Atomic energy press, Beijing, 2001, 8: 48-53 (in Chinese).
3. Zhang Hong-Yu, Zhang Zhi-Yi. The structure-activity relationship and broad prospects in applications of photosensitization of perylenequinonoid derivatives. In: Fang Yun-Zhong and Zheng Rong-Liang (ed.) Adv Free Radic Life Sci, Atomic energy press, Beijing, 1999, 7: 41-47 (in Chinese).
4. Maria Z. Tsimidou, Nikolaos Nenadis, Hong-Yu Zhang. Structure-radical scavenging activity relationships of flavonoids and phenolic acids. In: Dimitrios Boskou, Ioannis P. Gerothanassis, Panagiotis Kefalas, Eds. NATURAL ANTIOXIDANT PHENOLS. Sources, Structure-Activity Relationship, Current Trends in Analysis and Characterization, 2006: 29-67. Research Signpost, Kerala, India.
