EpiDiff: a computational tool for Epigenetic Difference Quantification and Identification by Entropy
About Us


Group of Computational Epigenetic Research(GCER), is interested in the mechanisms of epigenetics in the processes of development and deseases. Our project team is focusing on combining bioinformatic idea, methodology and tools to ensemble-based epigenomic researches. The computational epigenetic studies in our lab cover several domains, including the development and improvement of algorithms, software development, software platform construction, database development and the functional interpretation of genetic and epigenetic mechanism. The research contents cover the following domains:
  • The quantification of DNR methylation difference, chromosome modification difference and gene expression difference
  • The identification of DMRs, DCMRs and DEGs
  • The prediction of CpG islands
  • The prediction of the methylation patterns of CpG islands
  • Analysis of the differential methylation patterns
  • The combinatorial relationship among histone modifications and DNA methylation in gene expression
  • The epigenetic mechanism of ES cell development
  • The recognition of genomic imprinting and their association of diseases
  • The epigenomics of cancer
  • The construction of web service and databases
  • The interpretation of the structure and function of nucleosome in genomic scale
  • DNA methylation prediction in mammals
  Publications Last updated in 12/22/2011
  • Lv J, Liu H, Su J, Wu X, Li B, Xiao X, Wang F, Wu Q, Zhang Y: DiseaseMeth: a human disease methylation database. Nucleic Acids Res 2012, doi: 10.1093/nar/gkr1169. [Abstract] [PDF]
  • Zhang Y, Liu H, Lv J, Xiao X, Zhu J, Liu X, Su J, Li X, Wu Q, Wang F, Cui Y: QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Res 2011, 39:e58. [Abstract] [PDF]
  • Zhang Y., Lv J., Liu H., Zhu J., Su J., Wu Q., Qi Y., Wang F., Li X.: HHMD: the human histone modification database. Nucleic Acids Res 2010, 38(Database issue):D149-154. [Abstract] [PDF]
  • Su J., Zhang Y., Lv J., Liu H., Tang X., Wang F., Qi Y., Feng Y., Li X.: CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes. Nucleic Acids Res 2010, 38(1):e6. [Abstract] [PDF]
  • Su J, Shao X, Liu H, Liu S, Wu Q, Zhang Y: Genome-wide dynamic changes of DNA methylation of repetitive elements in human embryonic stem cells and fetal fibroblasts. Genomics 2011, accepted. [Abstract]
  • Liu H, Su J, Li J, Lv J, Li B, Qiao H, Zhang Y: Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network. BMC Syst Biol 2011, 5:158. [Abstract]
  • Lv, J., Qiao, H., Liu, H., Wu, X., Zhu, J., Su, J., Wang, F., Cui, Y. and Zhang, Y. (2010) Discovering cooperative relationships of chromatin modifications in human T cells based on a proposed closeness measure. PLoS ONE, 5, e14219. [Abstract]
  • Su J, Qi Y, Liu S, Wu X, Lv J, Liu H, Zhang R, Zhang Y: Revealing epigenetic patterns in gene regulation through integrative analysis of epigenetic interaction network. Mol Biol Rep 2011. [Abstract]
  • Lv J., Su J., Wang F., Qi Y., Liu H., Zhang Y.: Detecting novel hypermethylated genes in Breast cancer benefiting from feature selection. Comput Biol Med 2009. [Abstract]
  • Lv J., Qi Y., Liu H., Zhu J., Su J., Zhang R., Zhang Y.: ChIP-seq data plays an important role in a cytosine-based DNA methylation prediction model. In: The 6th International Conference on Fuzzy Systems and Knowledge Discovery (FSKD'09). Tianjin; 2009. [PDF]
  • Qi Y., Zhang Y., Lv J., Liu H., Zhu J., Su J.: Deducing Causal Relationships among Different Histone Modifications, DNA Methylation and Gene Expression. In: The 5th International Conference on Natural Computation (ICNC'09). vol. 6. Tian jin; 2009: 139-143. [PDF]
  • Zhang Y., Lv J., Su J., Wang F., Cui Y.: Detection of hypermethylated genes in cancer using discriminating genomic features. In: The 2008 Annual Conference of the Japanese Society for Bioinformatics (JSBi 2008). Japan; 2008.
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College of Bioinformatics Science and Technology, Harbin Medical Unversity, 194 Xuefu Road, Harbin 150081, China

College of Bioinformatics Science and Technology, Harbin Medical Unversity, 194 Xuefu Road, Harbin 150081, China

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