Zhiming Dai

Summary

Publications

  1. pmc Insights into distinct regulatory modes of nucleosome positioning
    Zhiming Dai
    Electronic Department, Sun Yat Sen University, Guangzhou, China
    BMC Genomics 10:602. 2009
  2. pmc Nuclear colocalization of transcription factor target genes strengthens coregulation in yeast
    Zhiming Dai
    Department of Electronics, School of Information Science and Technology, Sun Yat Sen University, Guangzhou 510006, China
    Nucleic Acids Res 40:27-36. 2012
  3. doi request reprint Antisense transcription is coupled to nucleosome occupancy in sense promoters
    Zhiming Dai
    Department of Electronics, School of Information Science and Technology, Sun Yat Sen University, Guangzhou 510006, China
    Bioinformatics 28:2719-23. 2012
  4. pmc Gene expression divergence is coupled to evolution of DNA structure in coding regions
    Zhiming Dai
    School of Information Science and Technology, Sun Yat Sen University, Guangzhou, China
    PLoS Comput Biol 7:e1002275. 2011
  5. doi request reprint Genome-wide DNA sequence polymorphisms facilitate nucleosome positioning in yeast
    Zhiming Dai
    Department of Electronic, School of Information Science and Technology, Sun Yat Sen University, Guangzhou 510006, China
    Bioinformatics 27:1758-64. 2011
  6. pmc Robustness of transcriptional regulatory program influences gene expression variability
    Zhiming Dai
    Electronic Department, Sun Yat Sen University, Guangzhou, PR China
    BMC Genomics 10:573. 2009
  7. pmc Genome-wide analysis of interactions between ATP-dependent chromatin remodeling and histone modifications
    Zhiming Dai
    Electronic Department, Sun Yat Sen University, Guangzhou, PR China
    BMC Genomics 10:304. 2009
  8. pmc Two distinct modes of nucleosome modulation associated with different degrees of dependence of nucleosome positioning on the underlying DNA sequence
    Zhiming Dai
    Electronic Department, Sun Yat Sen University, Guangzhou, PR China
    BMC Genomics 10:15. 2009
  9. pmc Transcriptional interaction-assisted identification of dynamic nucleosome positioning
    Zhiming Dai
    Electronic Department, Sun Yat Sen University, Guangzhou, 510275, PR China
    BMC Bioinformatics 10:S31. 2009
  10. pmc Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in Saccharomyces cerevisiae
    Yangyang Deng
    School of Information Science and Technology, Sun Yat Sen University, 135 West Xin gang Road, Guangzhou, PR China
    BMC Genomics 11:550. 2010

Collaborators

Detail Information

Publications18

  1. pmc Insights into distinct regulatory modes of nucleosome positioning
    Zhiming Dai
    Electronic Department, Sun Yat Sen University, Guangzhou, China
    BMC Genomics 10:602. 2009
    ..Experimental evidence suggests that the genomic DNA sequence and a variety of protein factors contribute to nucleosome positioning in vivo. However, how nucleosome positioning is determined locally is still largely unknown...
  2. pmc Nuclear colocalization of transcription factor target genes strengthens coregulation in yeast
    Zhiming Dai
    Department of Electronics, School of Information Science and Technology, Sun Yat Sen University, Guangzhou 510006, China
    Nucleic Acids Res 40:27-36. 2012
    ..Our findings will have implications in understanding nuclear architecture and function...
  3. doi request reprint Antisense transcription is coupled to nucleosome occupancy in sense promoters
    Zhiming Dai
    Department of Electronics, School of Information Science and Technology, Sun Yat Sen University, Guangzhou 510006, China
    Bioinformatics 28:2719-23. 2012
    ..Individual cases have shown that antisense transcription influences sense transcription, however, genome-wide mechanisms of how antisense transcription regulates sense transcription remain to be elucidated...
  4. pmc Gene expression divergence is coupled to evolution of DNA structure in coding regions
    Zhiming Dai
    School of Information Science and Technology, Sun Yat Sen University, Guangzhou, China
    PLoS Comput Biol 7:e1002275. 2011
    ..We also found that genes with similar DNA structures are involved in the same biological process and function. These results reveal the previously unappreciated roles of DNA structure as cis-effects in gene expression...
  5. doi request reprint Genome-wide DNA sequence polymorphisms facilitate nucleosome positioning in yeast
    Zhiming Dai
    Department of Electronic, School of Information Science and Technology, Sun Yat Sen University, Guangzhou 510006, China
    Bioinformatics 27:1758-64. 2011
    ..Nucleosome positioning influences the overall rate of sequence evolution. However, its impacts on specific patterns of sequence evolution are still poorly understood...
  6. pmc Robustness of transcriptional regulatory program influences gene expression variability
    Zhiming Dai
    Electronic Department, Sun Yat Sen University, Guangzhou, PR China
    BMC Genomics 10:573. 2009
    ..Most genes are not affected when any transcription factor (TF) is knocked out, indicating that they have robust transcriptional regulatory program. Yet the mechanism underlying robust transcriptional regulatory program is less clear...
  7. pmc Genome-wide analysis of interactions between ATP-dependent chromatin remodeling and histone modifications
    Zhiming Dai
    Electronic Department, Sun Yat Sen University, Guangzhou, PR China
    BMC Genomics 10:304. 2009
    ..Although several specific interactions between these two activities have been elaborated, the global landscape remains to be elucidated...
  8. pmc Two distinct modes of nucleosome modulation associated with different degrees of dependence of nucleosome positioning on the underlying DNA sequence
    Zhiming Dai
    Electronic Department, Sun Yat Sen University, Guangzhou, PR China
    BMC Genomics 10:15. 2009
    ..Whether different determinants of nucleosome positioning have characteristic influences on nucleosome modulation also remains to be elucidated...
  9. pmc Transcriptional interaction-assisted identification of dynamic nucleosome positioning
    Zhiming Dai
    Electronic Department, Sun Yat Sen University, Guangzhou, 510275, PR China
    BMC Bioinformatics 10:S31. 2009
    ..Nucleosomes regulate DNA accessibility and therefore play a central role in transcription control. Computational methods have been developed to predict static nucleosome positions from DNA sequences, but nucleosomes are dynamic in vivo...
  10. pmc Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in Saccharomyces cerevisiae
    Yangyang Deng
    School of Information Science and Technology, Sun Yat Sen University, 135 West Xin gang Road, Guangzhou, PR China
    BMC Genomics 11:550. 2010
    ..However, the extent of the contribution of histone modifications to the coexpression of neighboring genes is unclear...
  11. pmc New insights into two distinct nucleosome distributions: comparison of cross-platform positioning datasets in the yeast genome
    Jihua Feng
    School of Information Science and Technology, Sun Yat Sen University, Guangzhou, PR China
    BMC Genomics 11:33. 2010
    ..In order to more accurately depict the genome-wide nucleosome distribution, we integrated multiple nucleosomal positioning datasets using a multi-angle analysis strategy...
  12. pmc Missing value imputation for microarray gene expression data using histone acetylation information
    Qian Xiang
    Department of Electronics and Communications Engineering, School of Information Science and Technology, Sun Yat Sen University, 135 West Xin gang Road, Guangzhou, PR China
    BMC Bioinformatics 9:252. 2008
    ..Although several methods have been suggested, their performances are not satisfactory for datasets with high missing percentages...
  13. doi request reprint Nucleosomal context of binding sites influences transcription factor binding affinity and gene regulation
    Zhiming Dai
    Electronic Department, Sun Yat Sen University, Guangzhou 510006, China
    Genomics Proteomics Bioinformatics 7:155-62. 2009
    ..This emphasizes the need to include nucleosomal context of TFBSs in modeling gene regulation...
  14. pmc Identifying the combinatorial effects of histone modifications by association rule mining in yeast
    Jiang Wang
    Department of Electronics and Communications Engineering, School of Information Science and Technology, Sun Yat Sen University, 135 West Xin gang Road, Guangzhou, P R China
    Evol Bioinform Online 6:113-31. 2010
    ..Our results demonstrate several histone modification patterns which show significant correspondence between yeast and human cells...
  15. pmc BGDB: a database of bivalent genes
    Qingyan Li
    Department of Electronics, School of Information Science and Technology, Sun Yat Sen University, Guangzhou 510006, China
    Database (Oxford) 2013:bat057. 2013
    ..The web services of BGDB database were implemented with PHP + MySQL + JavaScript, and provide diverse query functions. Database URL: http://dailab.sysu.edu.cn/bgdb/ ..
  16. pmc A de novo genome assembly algorithm for repeats and nonrepeats
    Shuaibin Lian
    School of Information Science and Technology, Sun Yat Sen University, Guangzhou High Education Mega City, No 132 Waihuan East Road, Panyu District, Guangzhou 510006, China
    Biomed Res Int 2014:736473. 2014
    ..SWA not only can detect where repeats or nonrepeats are but also can assemble them completely from NGS data, especially for assembling repeats. This is the advantage over other assemblers. ..
  17. ncbi request reprint Neighboring genes show interchromosomal colocalization after their separation
    Zhiming Dai
    Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat Sen University, Guangzhou, China
    Mol Biol Evol 31:1166-72. 2014
    ..These results suggest a mechanism by which neighboring genes could retain nuclear proximity after their separation. ..
  18. doi request reprint The pattern and evolution of looped gene bendability
    Zhiming Dai
    Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat Sen University, Guangzhou, China
    Mol Biol Evol 31:319-29. 2014
    ..These results suggest a mechanism by which DNA bendability and unstable nucleosome positioning could assist in the formation of gene loops. ..