Hongde Liu

Summary

Affiliation: Southeast University
Country: China

Publications

  1. doi request reprint Quantitative analysis reveals increased histone modifications and a broad nucleosome-free region bound by histone acetylases in highly expressed genes in human CD4+ T cells
    Hongde Liu
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China Electronic address
    Genomics 101:113-9. 2013
  2. pmc Chromatin structure is distinct between coding and non-coding single nucleotide polymorphisms
    Hongde Liu
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
    BMC Mol Biol 15:22. 2014
  3. doi request reprint Histone chaperone Chz1 facilitates the disfavouring property of Spt16 to H2A.Z-containing genes in Saccharomyces cerevisiae
    Hongde Liu
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
    Biochem J 460:387-97. 2014
  4. doi request reprint Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid feature
    Xin Ma
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, People s Republic of China
    Proteins 79:1230-9. 2011
  5. pmc The patterns of histone modifications in the vicinity of transcription factor binding sites in human lymphoblastoid cell lines
    Yumin Nie
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    PLoS ONE 8:e60002. 2013
  6. pmc MicroRNA genes derived from repetitive elements and expanded by segmental duplication events in mammalian genomes
    Zhidong Yuan
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    PLoS ONE 6:e17666. 2011
  7. pmc The nucleosome regulates the usage of polyadenylation sites in the human genome
    Huan Huang
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
    BMC Genomics 14:912. 2013
  8. ncbi request reprint Nucleosome distribution near the 3' ends of genes in the human genome
    Huan Huang
    State Key Laboratory of Bioelectronics, Southeast University
    Biosci Biotechnol Biochem 77:2051-5. 2013
  9. pmc Analysis of nucleosome positioning determined by DNA helix curvature in the human genome
    Hongde Liu
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
    BMC Genomics 12:72. 2011
  10. doi request reprint Prediction of autism susceptibility genes based on association rules
    Lejun Gong
    State Key Laboratory of Bioelectronics, Department of Biological Science and Medical Engineering, Southeast University, Nanjing, People s Republic of China
    J Neurosci Res 90:1119-25. 2012

Collaborators

Detail Information

Publications16

  1. doi request reprint Quantitative analysis reveals increased histone modifications and a broad nucleosome-free region bound by histone acetylases in highly expressed genes in human CD4+ T cells
    Hongde Liu
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China Electronic address
    Genomics 101:113-9. 2013
    ..We also suggested that single nucleotide polymorphisms (SNPs) occur at a much lower frequency in highly expressed genes than in repressed genes. Our analysis quantitatively revealed details of chromatin dynamics. ..
  2. pmc Chromatin structure is distinct between coding and non-coding single nucleotide polymorphisms
    Hongde Liu
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
    BMC Mol Biol 15:22. 2014
    ..We aimed to determine if the chromatin organization is genomic locus specific around SNPs, and if newly occurring mutations are associated with SNPs...
  3. doi request reprint Histone chaperone Chz1 facilitates the disfavouring property of Spt16 to H2A.Z-containing genes in Saccharomyces cerevisiae
    Hongde Liu
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
    Biochem J 460:387-97. 2014
    ..Chz1-escorted Htz1 therefore impairs Spt16 binding at chromatin...
  4. doi request reprint Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid feature
    Xin Ma
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, People s Republic of China
    Proteins 79:1230-9. 2011
    ..8675) which represents that PRBR attains excellent performance on predicting the RNA-binding residues in proteins. The PRBR web-server implementation is freely available at http://www.cbi.seu.edu.cn/PRBR/...
  5. pmc The patterns of histone modifications in the vicinity of transcription factor binding sites in human lymphoblastoid cell lines
    Yumin Nie
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    PLoS ONE 8:e60002. 2013
    ..These findings have epigenetic implications for future analysis of regulatory elements...
  6. pmc MicroRNA genes derived from repetitive elements and expanded by segmental duplication events in mammalian genomes
    Zhidong Yuan
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    PLoS ONE 6:e17666. 2011
    ..Our study is a valuable contribution to the knowledge of evolution and function of non-coding region in genome...
  7. pmc The nucleosome regulates the usage of polyadenylation sites in the human genome
    Huan Huang
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
    BMC Genomics 14:912. 2013
    ..However, the association between nucleosome occupancy and polyadenylation site usage is still unclear...
  8. ncbi request reprint Nucleosome distribution near the 3' ends of genes in the human genome
    Huan Huang
    State Key Laboratory of Bioelectronics, Southeast University
    Biosci Biotechnol Biochem 77:2051-5. 2013
    ..Our results reveal influences on nucleosome occupancy near polyadenylation sites and constitute evidence indicating that nucleosome distribution regulates 3' end processing of protein-coding genes. ..
  9. pmc Analysis of nucleosome positioning determined by DNA helix curvature in the human genome
    Hongde Liu
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
    BMC Genomics 12:72. 2011
    ..What role does sequence-dependent positioning play? In this paper, using a curvature profile model, nucleosomes are predicted in the human genome and patterns of nucleosomes near some key sites are investigated...
  10. doi request reprint Prediction of autism susceptibility genes based on association rules
    Lejun Gong
    State Key Laboratory of Bioelectronics, Department of Biological Science and Medical Engineering, Southeast University, Nanjing, People s Republic of China
    J Neurosci Res 90:1119-25. 2012
    ..The web portal for the predicted results, which is freely available at http://biolab.hyit.edu.cn/ar, can be a valuable resource in studies of diseases related to genes...
  11. doi request reprint Nucleosome organization in sequences of alternative events in human genome
    Huan Huang
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
    Biosystems 109:214-9. 2012
    ..These results provided a new approach for better appreciation of the connection between chromatin structure and gene expression regulation...
  12. doi request reprint Role of 10-11bp periodicities of eukaryotic DNA sequence in nucleosome positioning
    Hongde Liu
    School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    Biosystems 105:295-9. 2011
    ..Our study reveals some details about the roles of DNA sequence in positioning nucleosomes...
  13. pmc Origin and evolution of a placental-specific microRNA family in the human genome
    Zhidong Yuan
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    BMC Evol Biol 10:346. 2010
    ..With the rapid development of technology, more and more miRNAs are being discovered. However, the origin and evolution of most miRNAs remain obscure. Here we report the origin and evolution dynamics of a human miRNA family...
  14. pmc Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature
    Jiansheng Wu
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P R China
    Bioinformatics 25:30-5. 2009
    ..The numbers of binding and non-binding residues in proteins are highly unbalanced, so a novel scheme is proposed to deal with the problem of imbalanced datasets by downsizing the majority class...
  15. doi request reprint Role of the repressor Oaf3p in the recruitment of transcription factors and chromatin dynamics during the oleate response
    Yakun Wan
    The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Science, Southeast University, Nanjing 210096, China
    Biochem J 449:507-17. 2013
    ..Most impressively, a highly protected nucleosome structure on the POT1 promoter during activation was observed in the OAF3 mutant cells in response to oleate induction...
  16. pmc Characteristics of nucleosome core DNA and their applications in predicting nucleosome positions
    Hongde Liu
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
    Biophys J 94:4597-604. 2008
    ..Based on predictions, nucleosome distributions near the beginning and end of open reading frames were analyzed. Results indicated that the majority of open reading frames' start and end sites were occupied by nucleosomes...