Hong Yu Zhang

Summary

Affiliation: Huazhong Agricultural University
Country: China

Publications

  1. pmc Chemical basis of metabolic network organization
    Qiang Zhu
    National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
    PLoS Comput Biol 7:e1002214. 2011
  2. pmc The impact of oxygen on metabolic evolution: a chemoinformatic investigation
    Ying Ying Jiang
    National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
    PLoS Comput Biol 8:e1002426. 2012
  3. doi request reprint Structural phylogenomics uncovers the early and concurrent origins of cysteine biosynthesis and iron-sulfur proteins
    Hong Yu Zhang
    National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
    J Biomol Struct Dyn 30:542-5. 2012
  4. pmc DIGA--a database of improved gene annotation for phytopathogens
    Na Gao
    Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China
    BMC Genomics 11:54. 2010
  5. doi request reprint Evolutionary inspirations for drug discovery
    Hong Yu Zhang
    National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P R China
    Trends Pharmacol Sci 31:443-8. 2010
  6. ncbi request reprint Exploring the biologically relevant chemical space for drug discovery
    Zhi Luo Deng
    State Key Laboratory of Agricultural Microbiology, Center for Bioinformatics, College of Life Science and Technology, and National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
    J Chem Inf Model 53:2820-8. 2013
  7. pmc Dissecting the chromatin interactome of microRNA genes
    Dijun Chen
    Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P R China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P R China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben IPK, Corrensstrasse 3, D 06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
    Nucleic Acids Res 42:3028-43. 2014
  8. doi request reprint Identification of transcription factors for drug-associated gene modules and biomedical implications
    Min Xiong
    National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P R China
    Bioinformatics 30:305-9. 2014
  9. doi request reprint Oxidative DNA damage is important to the evolution of antibiotic resistance: evidence of mutation bias and its medicinal implications
    Zhong Yi Wang
    National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P R China
    J Biomol Struct Dyn 31:729-33. 2013
  10. doi request reprint Historical variation of structural novelty in a natural product library
    De Xin Kong
    State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, P R China
    Chem Biodivers 8:1968-77. 2011

Collaborators

Detail Information

Publications20

  1. pmc Chemical basis of metabolic network organization
    Qiang Zhu
    National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
    PLoS Comput Biol 7:e1002214. 2011
    ..This finding not only provides a chemical explanation to the preferential attachment principle for metabolic network expansion, but also has important implications for metabolic network design and metabolite concentration prediction...
  2. pmc The impact of oxygen on metabolic evolution: a chemoinformatic investigation
    Ying Ying Jiang
    National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
    PLoS Comput Biol 8:e1002426. 2012
    ..These findings enhance our understanding of the molecular link between oxygen and evolution. They also show the significance of chemoinformatics in addressing basic biological questions...
  3. doi request reprint Structural phylogenomics uncovers the early and concurrent origins of cysteine biosynthesis and iron-sulfur proteins
    Hong Yu Zhang
    National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
    J Biomol Struct Dyn 30:542-5. 2012
    ..It is therefore likely that Cys did not play an important role in the make up of primordial protein molecules and that Fe-S clusters were not part of active sites at the beginning of biological history...
  4. pmc DIGA--a database of improved gene annotation for phytopathogens
    Na Gao
    Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China
    BMC Genomics 11:54. 2010
    ..However, some misannotations exist in these phytopathogen genomes. Our objective is to improve these annotations and store them in a central database DIGAP...
  5. doi request reprint Evolutionary inspirations for drug discovery
    Hong Yu Zhang
    National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P R China
    Trends Pharmacol Sci 31:443-8. 2010
    ..Polyphenols have evolved a superior ability to bind various proteins, so we also argue that they are good starting points for multi-target drugs...
  6. ncbi request reprint Exploring the biologically relevant chemical space for drug discovery
    Zhi Luo Deng
    State Key Laboratory of Agricultural Microbiology, Center for Bioinformatics, College of Life Science and Technology, and National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
    J Chem Inf Model 53:2820-8. 2013
    ..A web-server named BioRel ( http://ibi.hzau.edu.cn/biorel ) was developed to provide services including BR, BRS calculation, activity class, and pharmacokinetic property prediction. ..
  7. pmc Dissecting the chromatin interactome of microRNA genes
    Dijun Chen
    Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P R China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P R China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben IPK, Corrensstrasse 3, D 06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
    Nucleic Acids Res 42:3028-43. 2014
    ..Together, our study unveils an entirely unexplored layer of MIR regulation throughout the human genome that links the spatial coordination of MIRs to their co-expression and function. ..
  8. doi request reprint Identification of transcription factors for drug-associated gene modules and biomedical implications
    Min Xiong
    National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P R China
    Bioinformatics 30:305-9. 2014
    ..One of the major findings in systems biomedicine is that both pathogenesis of diseases and drug mode of action have a module basis. However, the transcription factors (TFs) regulating the modules remain largely unknown...
  9. doi request reprint Oxidative DNA damage is important to the evolution of antibiotic resistance: evidence of mutation bias and its medicinal implications
    Zhong Yi Wang
    National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P R China
    J Biomol Struct Dyn 31:729-33. 2013
    ..Thus, we propose that consolidating the DNA repair systems of bacteria may be a viable strategy for preventing antibiotic resistance. (1)These authors contributed equally to this work. ..
  10. doi request reprint Historical variation of structural novelty in a natural product library
    De Xin Kong
    State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, P R China
    Chem Biodivers 8:1968-77. 2011
    ....
  11. ncbi request reprint Elucidating polypharmacological mechanisms of polyphenols by gene module profile analysis
    Bin Li
    National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
    Int J Mol Sci 15:11245-54. 2014
    ..The results show that the medicinal effects of polyphenols are far beyond their well-known antioxidant activities. This method is also applicable to dissect the polypharmacology of other natural products. ..
  12. ncbi request reprint Chemoinformatics approaches for traditional Chinese medicine research and case application in anticancer drug discovery
    Xue Juan Li
    National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, PR China
    Curr Drug Discov Technol 7:22-31. 2010
    ..Recent progress on the use of chemoinformatics in TCM research will be discussed and an example of the preliminary application of chemoinformatics methods in anticancer drug design will be provided...
  13. doi request reprint Can medical genetics and evolutionary biology inspire drug target identification?
    Zhong Yi Wang
    National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P R China
    Trends Mol Med 18:69-71. 2012
    ....
  14. doi request reprint Structural and energetic analyses of SNPs in drug targets and implications for drug therapy
    Hui Yong Sun
    National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P R China
    J Chem Inf Model 53:3343-51. 2013
    ..These results have direct implications for population-based drug therapy and for chemical treatment of genetic diseases as well. ..
  15. ncbi request reprint Metabolite concentration as a criterion for antibacterial discovery
    Zhong Yi Wang
    National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
    Curr Comput Aided Drug Des 9:412-6. 2013
    ..By the new-proposed criterion, we not only identify some promising antibacterial targets but also explain some perplexing experimental observations as well. ..
  16. doi request reprint Pd(II)-catalyzed C(sp2)-H hydroxylation with R2(O)P-coordinating group
    Hong Yu Zhang
    State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P R China, and State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Lanzhou 730000, P R China
    Org Lett 15:6186-9. 2013
    ..Notably, the reaction operates under mild conditions and shows good functional group tolerance, high selectivity, and yield. ..
  17. doi request reprint Exploring the common molecular basis for the universal DNA mutation bias: revival of Löwdin mutation model
    Liang Yu Fu
    National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
    Biochem Biophys Res Commun 409:367-71. 2011
    ....
  18. pmc The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling
    Cheng Peng
    National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
    Nucleic Acids Res 41:e183. 2013
    ..This method has been executed by an automatic pipeline (AutoChrom3D) and thus can be conveniently used. ..
  19. doi request reprint The draft genome of sweet orange (Citrus sinensis)
    Qiang Xu
    Key Laboratory of Horticultural Plant Biology Ministry of Education, Huazhong Agricultural University, Wuhan, China
    Nat Genet 45:59-66. 2013
    ..This draft genome represents a valuable resource for understanding and improving many important citrus traits in the future...
  20. ncbi request reprint tRNA-dependent cysteine biosynthetic pathway represents a strategy to increase cysteine contents by preventing it from thermal degradation: thermal adaptation of methanogenic archaea ancestor
    Ge Qu
    Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China
    J Biomol Struct Dyn 27:111-4. 2009
    ....