Welcome to GCER (2007-now). Our lab is focusing on combining bioinformatic idea, methodology and tools to ensemble-based epigenomic researches. Our computational epigenetic studies cover several domains, including the development and improvement of algorithms, software development, software platform construction, database development, the functional interpretation of genetic and epigenetic mechanism.

The research areas cover the following:

Paper in 2013:

      Lv J., Liu H., Huang Z., Su J., He H., Xiu Y., Zhang Y., Wu Q.*. Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features. 2013, Nucleic Acids Research, 10.1093/nar/gkt818.
      Lv J., Liu H., Wu Q.*, Zhang Y.*: High-Throughput Computational Approaches to Analyzing Histone Modification Next-Generation Sequencing Data. Computational Molecular Biology, 2012, Vol. 2, No. 1
      Liu H, Chen Y, Lv J, Liu H, Zhu R, Su J, Liu X, Zhang Y, Wu Q: Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes. (Sci Rep. 2013 Sep 3;3:2576. doi: 10.1038/srep02576.)
      Lv J, Cui W, Liu H, He H, Xiu Y, Guo J, Liu H, Liu Q, Zeng T, Chen Y, Zhang Y, Wu Q: Identification and Characterization of Long Non-Coding RNAs Related to Mouse Embryonic Brain Development from Available Transcriptomic Data. (PLoS One. 2013 Aug 14;8(8):e71152. doi: 10.1371/journal.pone.0071152)
      Wu X, Liu H, Liu H, Su J, Lv J, Cui Y, Wang F, Zhang Y*: Z curve theory-based analysis of the dynamic nature of nucleosome positioning in Saccharomyces cerevisiae. (Gene. 2013 Aug 16. pii: S0378-1119(13)01048-2. doi: 10.1016/j.gene.2013.08.018.)
      Xiao X, Li Z, Liu H, Su J, Wang F, Wu X, Liu H, Wu Q, Zhang Y*: Genome-wide identification of Polycomb target genes in human embryonic stem cells. (Gene. 2013 Apr 15;518(2):425-30. doi: 10.1016/j.gene.2012.12.022. Epub 2013 Jan 9)
      Su J, Yan H, Wei Y, Liu H, Liu H, Wang F, Lv J, Wu Q, Zhang Y*: CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. (Nucleic Acids Res. 2013 Jan 7;41(1):e4. doi: 10.1093/nar/gks829. Epub 2012 Aug 31.)

Paper in 2012:

      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.
      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. 2012 Jan;99(1):10-7. doi: 10.1016/j.ygeno.2011.10.004. Epub 2011 Oct 25.)

Paper in 2011:

      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.
      Liu H., Su J., Li J., Liu H., Lv J., Li B., Qiao H.*, Zhang Y.* Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network. (2011) (BMC Systems Biology, 2011, Epub Ahead of Print)
      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 (2011)(Mol Biol Rep. 2011 May 28. Epub ahead of print)

Paper in 2010:

      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:D149-154.
      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:e6.
      Lv J, Qiao H, Liu H, Wu X, Zhu J, Su J, Wang F, Cui Y, Zhang Y*: Discovering cooperative relationships of chromatin modifications in human T cells based on a proposed closeness measure. PLoS ONE 2010, 5:e14219.
      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 2010, 40:159-167.
      Lv J., Liu H., Xiao X., Zhu J., Su J., Wang F., Cui Y., Xue-Ting Wu and Yan Zhang (2010). Discovering Functional Regulatory Relationships of Chromatin Modifications by Bayesian Network based on proposed closeness measure. Paper presented at: 2010年第四届全国生物信息学与系统生物学学术大会会议摘要集. Oct 7, 2010 - Oct 9, 2010 (HangZhou, China).
      Liu H., Lv J., Zhu J., Zhang Y. (2010). Identification of differentially methylated regions (DMRs) by entropy. Paper presented at: 2010年第四届全国生物信息学与系统生物学学术大会会议摘要集. Oct 7, 2010 - Oct 9, 2010 (HangZhou, China).

Paper in 2009:

      Jie Lv, Yunfeng Qi, Hongbo Liu, Jiang Zhu, Jianzhong Su, Ruijie Zhang and Yan Zhang*: ChIP-seq data plays an important role in a cytosine-based DNA methylation prediction model(2009), The 6th International Conference on Fuzzy Systems and Knowledge Discovery (FSKD'09), Tianjin.
      Yunfeng Qi, Yan Zhang*, Jie Lv, Hongbo Liu, Jiang Zhu and Jianzhong Su: Deducing Causal Relationships among Different Histone Modifications, DNA Methylation and Gene Expression(2009), The 5th International Conference on Natural Computation (ICNC'09), Tian jin, Vol. 6, pp. 139-143.

Paper in 2008:

      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). pp. P001. Japan; 2008:P001.