GCER

Yan Zhang, Professor, Doctor of Philosophy in science, System Biology room in Harbin Medical University Bioinformatics Department, who graduated with the degree of Bachelor of Clinical Medicine in 1992 and then in 2003 earned Master's degree in science in Functional Biology in the Graduate School of Science and Technology in Niigata University, Japan., and has been awarded the degree in the Doctor of Philosophy in science of Biosphere Science, Graduate School of Science and Technology in Niigata University, Japan on March 23, 2006. Studying abroad in Japan, she has published three papers on Zoological Science as the first author. Due to her research results, she was invited by the Japanese "Biophysics" magazine to write a review paper about hemoglobin synergies in early September 2006. Since May 2006, she has served as director of Department of Systems Biology in Harbin Medical University, and engaged in research in the field of computational biology. Her research focus areas are in the computational epigenetics in which she has achieved outstanding success. Her research results have been published in more than 20 papers in SCT, EI and core journals, including four papers published on 《Nucleic Acids Research》(SCI-IF 7.836) . She is currently the chair of a national natural Fund project and four provincial departmental level issues. She also participates a 973 pre-project as key personnel. One of her two master graduates has received honors of the Outstanding Master's Graduates of Heilongjiang Province.

Papers:
1. Su J.*, Yan H.*, Wei Y., Liu H., Wang F., Wu Q., and Zhang, Y.(2013) CpG_MPs:identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. Nucleic Acids Res.,1;41(1):e4.
2. Xiao, X., Li, Z., Liu, H., Su, J., Wang, F., Wu, F., Wu, X., Liu, H., Wu, Q., Zhang, Y., (2013)Genome-wide identification of Polycomb target genes in human embryonic stem cells. Gene, 518:425-430.
3. Lv, J, Liu, H, Qi, Huang, Z., Su J., Liu, Q., Zhang Y. and Wu, Q., (2013) Long non-coding RNA Identification over mouse brain development by integrative modeling of chromatin and genomic features. Nucleic Acids Res. (In press)
4. Huang, D.,Su J.*, Liu, H, Liu H., B, Yan, H., Wang, F., Wu Q., and Zhang Y., Genome-wide evolutionary analysis of DNA methylation patterns associated with sequence features and orthologs from invertebrates to vertebrates. Genomics (Under Review)
5. 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.
6. 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.
7. 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.
8. Liu H, Su J, Liu H, Lv J, Li B, Qiao H, Zhang Y*: Prioritizing Cancer-related Genes with Aberrant Methylation Based on Weighted Protein-protein Interaction Network. BMC Systems Biology 2011, accepted.
9. 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.
10. 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.
11. 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.
12. 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(12):e14219.
13. 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(2):159-167.
14. 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.
15. 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). vol. 5. Tianjin; 2009: 33-36.
16. 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: P001.
17. Zhang Y, Kobayashi K, Kitazawa K, Imai K, Kobayashi M: Contribution of cooperativity and the Bohr effect to efficient oxygen transport by hemoglobins from five mammalian species. Zoolog Sci 2006, 23(1):49-55.
18.Zhang Y, Kobayashi M: Oxygen transport efficiency and effectiveness of Bohr shift in fetal and maternal blood of five mammalian species. Zoolog Sci 2004, 21(12):1307.
19.Zhang Y, Kobayashi K, Sasagawa K, Imai K, Kobayashi M: Significance of affinity and cooperativity in oxygen binding to hemoglobin of horse fetal and maternal blood. Zoolog Sci 2003, 20(9):1087-1093.
20.Zhang Y, Miki M, Sasagawa K, Kobayashi M, Imai K: The cooperativity of human fetal and adult hemoglobins is optimized: a consideration based on the effectiveness of the Bohr shift. Zoolog Sci 2003, 20(1):23-28.

Ph.D. Lecture. Graduate from the mathematics department of Harbin Institute of Technology.

Research Interest
1. Computational methods for processing and analyzing high-throughput sequencing data about DNA methylation (BS-seq), chromatin modifications (Chip-seq) and gene expression(RNA-seq).
2. Epigenetics dynamics during embryonic stem cell differentiation and cancer development.

Major research article from 2009 ：
1. Su J.*, Yan H.*, Wei Y., Liu H., Wang F., Wu Q., and Zhang, Y.(2013) CpG_MPs:identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. Nucleic Acids Res.,1;41(1):e4.
2. Su, J.*, Zhang, Y. *, Lv, J., Liu, H., Tang, X., Wang, F., Qi, Y., Feng, Y. and Li, X. (2010) CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.Nucleic Acids Res., 38, e6.
3. Lv, J.*, Liu, H.*, Su, J.*, Wang, F., Liu, H., Li, B., Xiao, X., Wu, Q., Zhang, Y.（2012） DiseaseMeth: a human disease methylation database. Nucleic Acids Res., 40 D1030-1035. (*Co-first author)
4. Su, J., Shao, X., Liu, H., Liu, S., Qiong, W. and Zhang, Y. (2012) Genome-wide dynamic changes of DNA methylation of repetitive elements in human embryonic stem cells and fetal fibroblasts. Genomics, 99(1):10-7.
5. Su, J., Qi, Y., Liu, S., Wu, X., Lv, J., Liu, H., Zhang, R. and Zhang, Y. (2012) Revealing epigenetic patterns in gene regulation through integrative analysis of epigenetic interactionnetwork. Molecular Biology Reports, 2,1701-12.
6. Liu, H.*, Su, J.*, Li, J., Lv, J., Li, B., Qiao, H. and Zhang, Y. (2011) Prioritizing cancerrelatedgenes with aberrant methylation based on a weighted protein-protein interactionnetwork. BMC systems biology, 5, 158. (*Co-first author)
7. Lv, J., Su, J., Wang, F., Qi, Y., Liu, H. and Zhang, Y., (2010) Detecting novel hypermethylated genes in breast cancer benefiting from feature selection. Comput Biol Med, 40, 159-167.
8. Zhang, Y., Liu, H., Lv, J., Xiao, X., Zhu, J., Liu, X., Su, J., Li, X., Wu, Q., Wang, F. (2011) QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic acids Res, 39, e58.
9. Zhang, Y., Lv, J., Liu, H., Zhu, J., Su, J., Wu, Q., Qi, Y., Wang, F. and Li, X. (2010) HHMD: the human histone modification database. Nucleic Acids Res, 38, D149-D154
10. Lv., J., Qiao., H., Liu., H., Xiao., X., Zhu., J., Su, J., Wang., F., Cui., Y., Wu., X. and Zhang, Y. (2010)Discovering regulatory relationships of chromatin modifications in human T cells by Bayesian network inference. PLoS ONE. 5(12): e14219.
11. Xiao, X., Li, Z., Liu, H., Su, J., Wang, F., Wu, F., Wu, X., Liu, H., Wu, Q., Zhang, Y., (2013)Genome-wide identification of Polycomb target genes in human embryonic stem cells. Gene, 518:425-430.
12. Lv, J, Liu, H, Qi, Huang, Z., Su J., Liu, Q., Zhang Y. and Wu, Q., (2013) Long non-coding RNA I dentification over mouse brain development by integrative modeling of chromatin and genomic features. Nucleic Acids Res. (In press)
13. Huang, D.,Su J.*, Liu, H, Liu H., B, Yan, H., Wang, F., Wu Q., and Zhang Y., Genome-wide evolutionary analysis of DNA methylation patterns associated with sequence features and orthologs from invertebrates to vertebrates. Genomics (Under Review) (Corresponding author)

Conferences :
1. Su, J., Li, Z., Yan, H., Liu, H., Liu, H., and Zhang Y., DNA methylation phenotypes of genes reveal regulatory mechanisms of genes expression during cellular differentiation. Epigenetics &chromatin 2013, 6(Suppl 1):80 in Havard Medical School (Poster)
2. Su, J., Yan, H., and Zhang Y., The identification and analysis of genomic DNA methylation patterns during differentiation. The 2nd Cold Spring Harbor Asia conference on Epigenetics, Chromatin & Transcription, (2012). (Poster).
3. Su, J., Li Z. and Zhang Y., DNA methylation phenotypes of genes reveal regulatory mechanisms of gene expression during cellular differentiation. The 3nd Shanghai International Conference of Epigenetics in Development and Disease, (2012). (Poster).

FUNGs :
1. Investigation of functional regions mining for high-throughput DNA methylation data, National Natural Science Fundation of China：2013-2015, 270 000 Yuan (RMB)
2. Epigenetic features mining during stem cellular differentiation, National Natural Science Fundation of Heilongjiang Province: 2012-2014, 50 000 Yuan (RMB)

Fang Wang: She has been a member in college of bioinformatics science and technology of Harbin Medical University since 2004. She gained Bachelor of Science from Harbin institute of technology. She has been a member in college of bioinformatics science and technology of Harbin Medical University since 2004. From then on she engages in teaching and researching in bioinformatics field. She mainly interested in epigenetics and system biology. She assumed many courses including , , , and so on, and had the A grade of quality of teaching. She participated in many projects of scientific research. Miss Wang has a better knowledge of mathematics and mainly researches susceptible site of disease and feature distribution in different population.

Cui Ying: She works as a teacher in college of bioinformatics science and technology of Harbin Medical University now. She graduated from the mathematic department of Northeast Normal University in 2008, and gained Master's Degree. She studied Bioinformatics in Northeast Normal University for three years, and started teaching and scientific research in bioinformatics from 2008. She is a member of Prof. Zhang Yan's epigenetic group. She is expertizing in analyzing the epigenetic regulation, molecular system biology and bioinformatics in multiple species. At present she commits to undergraduate and graduate students teaching tasks, including "Medical Higher Mathematics", "An Introduction to Database Systems", "Molecular Biology Network Analysis", "Medical Multi-Factor Analysis" courses.

Hongbo Liu, Master's degree, is a teaching assistant in College of Bioinformatics Science and Technology of Harbin Medical University of China. He majored in math in college, and had a lot of interest with Computer Science since then. He received honors of the Outstanding Master's Graduates of Heilongjiang Province. Currently, he is engaged in research in the field of computational biology and his main focus is Computational Epigenetics, a discipline of studying regulation in gene expression without changes in the underlying DNA sequence of the organism, simply by data mining approaches yet. Since 2007, he has published 10 research results well known biological journals, including four papers on 《Nucleic Acids Research》(SCI IF 7.836) . He is currently the chair of a Scientific Research Fund of Heilongjiang Provincial Education Department, and also participates a national natural Fund project and four provincial departmental level issues.

Papers:
1. 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 2011, doi: 10.1093/nar/gkr1169. (Co-first author) (SCI IF 7.836)
2. 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. (Co-first author) (SCI IF 7.836)
3. 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. (Co-first author) (SCI IF 7.479)
4. 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. (SCI IF 7.479)
5. Liu H, Su J, Liu H, Lv J, Li B, Qiao H, Zhang Y: Prioritizing Cancer-related Genes with Aberrant Methylation Based on Weighted Protein-protein Interaction Network. BMC Systems Biology 2011, In Press. (SCI IF 3.565)
6. 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(12):e14219. (SCI IF 4.411)
7. 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(2):159-167. (SCI IF 1.112)
8. 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, In Press. (SCI IF 1.875)
9. 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). vol. 5. Tianjin; 2009: 33-36.
10. 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.

Yanjun Wei: He is a postgraduate student in College of Bioinformatics Science and Technology of Harbin Medical University of China for his bachelor's Degree. His majored Bioinformatics. His main focus is Epigenetics, a discipline of studying regulation in gene expression without changes in the underlying DNA sequence of the organism. At the undergraduate level, he learned some program lauguages, such as Java, Perl, R, and the technology of MySQL. And he developed the database MImprintDB (Mammal Imprinted Gene Database) as his graduation thesis, which also has been selected as the excellent theses. Now, he studies for a master's degree at the Harbin Medical University. Currently, he is focusing on the cancer methylation and miRNA expression regulation by data mining approaches.

Haidan Yan: She is a postgraduate student in College of Bioinformatics Science and Technology of Harbin Medical University of China for his Master's Degree. Her majored Bioinformatics. Her main focus is Epigenetics, a discipline of studying regulation in gene expression without changes in the underlying DNA sequence of the organism. Currently, she is focusing on the cancer epigenetics by data mining approaches.

Guofeng Zhao: He is a postgraduate student in College of Bioinformatics Science and Technology of Harbin Medical University of China for his Master's Degree. Her majored Bioinformatics. Her main focus is Epigenetics, a discipline of studying regulation in gene expression without changes in the underlying DNA sequence of the organism. Currently, she is focusing on the cancer epigenetics by data mining approaches.

Shanshan Jia: She is a postgraduate student in College of Bioinformatics Science and Technology of Harbin Medical University of China for his Master's Degree. Her majored Bioinformatics. Her main focus is Epigenetics, a discipline of studying regulation in gene expression without changes in the underlying DNA sequence of the organism. Currently, she is focusing on the cancer epigenetics by data mining approaches.

Chunlong Zhang: He is a postgraduate student in College of Bioinformatics Science and Technology of Harbin Medical University of China for his Master's Degree. He majored Bioinformatics. He main focus is Epigenetics, a discipline of studying regulation in gene expression without changes in the underlying DNA sequence of the organism. Currently, he is focusing on the cancer epigenetics by data mining approaches and molecular interaction network.

Yihan Wang: She is a recommended exemption graduate student in College of Bioinformatics Science and Technology of Harbin Medical University of China for his Master's Degree. Her majored Bioinformatics. Her main focus is Epigenetics, a discipline of studying regulation in gene expression without changes in the underlying DNA sequence of the organism. Currently, she is focusing on the cancer epigenetics by data mining approaches.

Yanhua Wen: She is a recommende exemption graduate student in College of Bioinformatics Science and Technology of Harbin Medical University of China for his Master's Degree. Her majored Bioinformatics. Her main focus is Epigenetics, a discipline of studying regulation in gene expression without changes in the underlying DNA sequence of the organism. Currently, she is focusing on the regulatory relationships between genomic gene expression and epigenetics variation by data mining approaches.

Song Li: He is a postgraduate student in College of Bioinformatics Science and Technology of Harbin Medical University of China for his bachelor's Degree.His major is Bioinformatics and he mainly focus on Epigenomics, a discipline of studying regulation in gene expression without changes in the underlying DNA sequence of the organism. Currently, he is engaged in developing a tool for comparing methods of identifying differentially methylated regions (DMRs).

Hui Liu: She is a postgraduate student in College of Bioinformatics Science and Technology of Harbin Medical University of China for his Master's Degree. Her majored Bioinformatics. Her main focus is Epigenetics, a discipline of studying regulation in gene expression without changes in the underlying DNA sequence of the organism. Currently, she is focusing on the cancer epigenetics by data mining approaches.

Boyan Li: He is a postgraduate student in College of Bioinformatics Science and Technology of Harbin Medical University of China for his Master's Degree. Her majored Bioinformatics. Her main focus is Epigenetics, a discipline of studying regulation in gene expression without changes in the underlying DNA sequence of the organism. Currently, she is focusing on the cancer epigenetics by data mining approaches.

Xueting Wu: She is a postgraduate student in College of Bioinformatics Science and Technology of Harbin Medical University of China for his Master's Degree. Her majored Bioinformatics. Her main focus is Epigenetics, a discipline of studying regulation in gene expression without changes in the underlying DNA sequence of the organism. Currently, she is focusing on the nucleosome postitioning by data mining approaches.

Xue Xiao: She is a postgraduate student in College of Bioinformatics Science and Technology of Harbin Medical University of China for his Master's Degree. Her majored Bioinformatics. Her main focus is Epigenetics, a discipline of studying regulation in gene expression without changes in the underlying DNA sequence of the organism. Currently, she is focusing on the cancer epigenetics by data mining approaches.

Jie Lü: He has graduated from College of Bioinformatics Science and Technology in Harbin Medical University, and is a postgraduate student in College of Bioinformatics Science and Technology of Harbin Medical University of China pursuing for his Master's Degree. He majored Bioinformatics in Harbin Medical University, and had a lot of interest with Bioinformatics and data mining since then. His main focus is Bioinformatics, Epigenetics, and Systems biology currently. Now, he is focusing on cancer epigenetics, database construction and web server design.

Jiang Zhu: She is a postgraduate student in College of Bioinformatics Science and Technology of Harbin Medical University of China for his Master's Degree. She majored bioinfomatics in college, and had a lot of interest with Computer Science since then. Her main focus is Epigenetics, a discipline of studying regulation in gene expression without changes in the underlying DNA sequence of the organism, especially imprinting mechanism.

Yunfeng Qi: He is a postgraduate student in College of Bioinformatics Science and Technology of Harbin Medical University of China for his Master's Degree. He majored biology in college, and had a lot of interest with Biology Science since then. His main focus is Epigenetics, a discipline of studying regulation in gene expression without changes in the underlying DNA sequence of the organism, yet only by biological approaches currently.