Significant research achievements

Our lab in recent years has been dedicated to a systematic exploration and research in the field of bioinformatics and made a series of progress. By now, nearly 70 research papers were published in international famous journals, such as Nature、Science、Nature Genetics、Nature Review Genetics、Biological Psychiatry、Nucleic Acids Research. The accumulative impact factor of publications is more than 500, and the total cited times is over 10,000.

Key research achievements include:

Ø  We identified a new susceptibility locus for primary Sjögren's syndrome (pSS) at 7q11.23 in Han Chinese by a three-stage genome-wide association study collaborated with Peking Union Medical College Hospital and other affiliations(Li Y*, Zhang K*, Chen H*, …, Wang J# & Zhang F#. 2013, Nature Genetics). In this study, 1845 cases and 3777 healthy controls were analyzed and two novel genes, GTF2IRD1 and GTF2I, were reported to be associated with pSS. It is a breakthrough achieved by Chinese scientists.

Ø  We developed analysis tool of non-coding loci -- rSNPBase (Guo et al., 2014, Nucleic Acids Research) which annotated regulatory features of genome-wide SNPs. Based on this published database, we released an important update presented as rVarbase (Guo et al., 2015, Nucleic Acids Research). This update expands the database to include additional types of human variants, such as copy number variants (CNVs) and novel variants, and included additional types of regulatory features.

Ø  A series of genetic databases for mental diseases with international influence have been developed, including a systematic study ranging from genetic analysis of a single disease (ADHDgene: Zhang et al., 2012, Nucleic Acids Research), multidisciplinary analysis of a single disease (MK4MDD: Guo et al., 2012, PloS ONE) to cross-analysis of multiple diseases (BDgene: Chang et al., 2013, Biological Psychiatry). These analyses provided important information resources and analytical tools for revealing the genetic mechanisms of mental disorders.

Ø  Developed two web servers for GWAS data analysis: i-GSEA4GWAS (Zhang et al., 2010, Nucleic Acids Research) is to investigate the combined effect size of SNPs, and to identify pathway/gene sets related to disease phenotype by pathway-based analysis of GWAS data. Based on this platform, we developed updated version -- i-GSEA4GWAS v2.0（Zhang et al., 2015, Protein & Cell）by improving algorithm and integrating data from ENCODE、Ensembl and eQTLs; ICSNPathway (Identify candidate Causal SNPs and Pathways) (Zhang et al., 2011, Nucleic Acids Research) is used to identify disease’s causal SNP and related causal pathway, to facilitate the disease mechanism research.

Ø  Established network-based genetic data analysis framework to excavate disease-related network module and biological functions. This framework has already been applied to schizophrenia (Chang et al., 2015, PLoS One) and primary Sj?gren's syndrome (Fang et al., 2015, Scientific Reports).

Ø  Compared relevance of susceptibility genes among seven chronic stress related diseases including Major depression disorder, Bipolar disorder, Alzheimer’s disease by using bioinformatic network analysis method (Guo et al., 2015, Scientific Reports), and further investigated the potential mechanism of how chronic stress affects the generation and development of disease.

Ø  Uncovered shared genes between autoimmune diseases and mental/neurological disorders by genome-wide association studies. We demonstrated an SNP and two haplotypes of IL-10 significantly associated with SZ, suggesting that IL-10 might be a risk factor of SZ （Gao et al., PLoS One, 201）by performing systematic analysis of genome-wide association data and candidate-gene association data.

 

 

Publications

  1. Yang, L., Chang, S., Lu, Q., Zhang, Y., Wu, Z., Sun, X., Cao, Q., Qian, Y., Jia, T., Xu, B., Duan, Q., Li, Y., Zhang, K., Gunter, S., Lu, L., Liu, D., # Wang, J.,# and Wang, Y.# (2017) A new locus regulating MICALL2 expression was identified for association with executive inhibition in children with attention deficit hyperactivity disorder. Molecular psychiatry (in press)

  2. Wang, J., Qu, S., Wang, W., Guo, L., Zhang, K., Chang, S., & Wang, J.# (2016). A combined analysis of genome-wide expression profiling of bipolar disorder in human prefrontal cortex. J Psychiatr Res, 82, 23-29. doi: 10.1016/j.jpsychires.2016.07.016 [Q1, IF: 4.465, 5-year IF: 4.761]

    3.
  3. Fang, K., Zhang, K., & Wang, J. (2015). Network-assisted analysis of primary Sjogren's syndrome GWAS data in Han Chinese. Sci Rep, 5, 18855. doi: 10.1038/srep18855 [Q1, IF: 5.578, 5-year IF: 5.597]

    4.
  4. Guo, L., Du, Y., Qu, S., & Wang, J. (2015). rVarBase: an updated database for regulatory features of human variants. Nucleic Acids Res. doi: 10.1093/nar/gkv1107  [Q1, IF: 9.112, 5-year IF: 8.867]

    5.
  5. Chang, S., Wang, J., Zhang, K., & Wang, J. (2015). Pathway-based analysis for genome-wide association study data of bipolar disorder provides new insights for genetic study. Protein Cell. doi: 10.1007/s13238-015-0201-1 [Q3, IF: 3.247, 5-year IF: 3.098]

    6.
  6. Chang, S., Fang, K., Zhang, K., & Wang, J. (2015). Network-Based Analysis of Schizophrenia Genome-Wide Association Data to Detect the Joint Functional Association Signals. PLoS One, 10(7), e0133404. doi: 10.1371/journal.pone.0133404 [Q1, IF: 3.234, 5-year IF: 3.702]

    7.
  7. Guo, L. Y., Du, Y., & Wang, J. (2015). Network analysis reveals a stress-affected common gene module among seven stress-related diseases/systems which provides potential targets for mechanism research. Scientific Reports, 5. doi: Artn 12939 10.1038/Srep12939 [Q1, IF: 5.578, 5-year IF: 5.597]

    8.
  8. Zong L, Guan J, Ealy M, Zhang Q, Wang D, Wang H, …Chang S, …Wang J, …et al. (2015): Mutations in apoptosis-inducing factor cause X-linked recessive auditory neuropathy spectrum disorder. Journal of medical genetics. [Q1, IF: 6.335, 5-year IF: 5.855]

    9.
  9. Ott, J., Wang, J., & Leal, S. M. (2015). Genetic linkage analysis in the age of whole-genome sequencing. Nat Rev Genet. doi: 10.1038/nrg3908 [Q1, IF: 36.978, 5-year IF: 43.234 ]

    10.
  10. Zhang, K.L.*, Chang, S.H.*, Guo, L.Y., Wang, J. (2014) I-GSEA4GWAS v2: a web server for functional analysis of SNPs in trait-associated pathways identified from genome-wide association study. Protein & Cell. DOI 10.1007/s13238-014-0114-4 [Q3, IF: 3.247, 5-year IF: 3.098]

    11.
  11. Guo, L.Y., Du, Y.,Chang, S.H., Zhang, W.N., Wang, J. (2014). Applying differentially expressed genes from rodent models of chronic stress to researches of stress-related disease: an online database. Psychosomatic Medicine. [Q1, IF: 3.473, 5-year IF: 4.819]

    12.
  12. Li, Z.*, Chang, S., Zhang, L., Gao, L., & Wang, J. (2014). Molecular genetic studies of ADHD and its candidate genes: a review.Psychiatry Research, doi: 10.1016/j.psychres.2014.05.005 [Q2, IF: 2.467, 5-year IF: 2.947]

    13.
  13. Gao, L., Li, Z., Chang, S., & Wang, J. (2014). Association of interleukin-10 polymorphisms with schizophrenia: a meta-analysis. PLoS One, 9(3), e90407. doi: 10.1371/journal.pone.0090407 [Q1, IF: 3.234, 5-year IF: 3.702]

    14.
  14. Guo, L., Du, Y., Chang, S., Zhang, K., & Wang, J. (2014). rSNPBase: a database for curated regulatory SNPs. Nucleic Acids Res, 42 (D1): D1033-D1039. doi: 10.1093/nar/gkt1167 [Q1, IF: 9.112, 5-year IF: 8.867]

    15.
  15. Li, Y. Z., Zhang, K. L., Chen, H., Sun, F., Xu, J. J., …Wang, J. & Zhang, F., C. (2013). A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjögren’s syndrome at 7q11.23. Nature Genetics doi:10.1038/ng.2779 [Q1, IF: 29.352, 5-year IF: 32.408]

    16.
  16. Zhang, W. N., Chang, S. H., Guo, L. Y., Zhang, K. L., & Wang, J. (2013). The neural correlates of reward-related processing in major depressive disorder: A meta-analysis of functional magnetic resonance imaging studies. J Affect Disord. doi: 10.1016/j.jad.2013.06.039 [Q2, IF: 3.383, 5-year IF: 3.939]

    17.
  17. Chang, S. H., Gao, L., Li, Z., Zhang, W. N., Du, Y., & Wang, J. (2013). BDgene: A Genetic Database for Bipolar Disorder and Its Overlap With Schizophrenia and Major Depressive Disorder.Biol Psychiatry. doi: 10.1016/j.biopsych.2013.04.016 [Q1, IF: 10.255, 5-year IF: 10.359]

    18.
  18. Guo, L., Zhang, W., Chang, S., Zhang, L., Ott, J., & Wang, J. (2012). MK4MDD: a multi-level knowledge base and analysis platform for major depressive disorder. PLoS One, 7(10), e46335. doi: 10.1371/journal.pone.0046335 [Q1, IF: 3.234, 5-year IF: 3.702]

    19.
  19. Chang, S., Zhang, W., Gao, L., & Wang, J. (2012). Prioritization of candidate genes for attention deficit hyperactivity disorder by computational analysis of multiple data sources. Protein Cell, 3(7), 526-534. doi: 10.1007/s13238-012-2931-7 [Q3, IF: 3.247, 5-year IF: 3.098]

    20.
  20. Zhao, H., Li, M., Fang, K., Chen, W., & Wang, J. (2012). In silico insights into the symbiotic nitrogen fixation in Sinorhizobium meliloti via metabolic reconstruction. PLoS One, 7(2), e31287. doi: 10.1371/journal.pone.0031287 [Q1, IF: 3.234, 5-year IF: 3.702]

    21.
  21. Liu, M. F., Cescau, S., Mechold, U., Wang, J., Cohen, D., Danchin, A., . . . Biville, F. (2012). Identification of a novel nanoRNase in Bartonella. Microbiology, 158(Pt 4), 886-895. doi: 10.1099/mic.0.054619-0 [Q4, IF: 0.642, 5-year IF: 0.754]

    22.
  22. Zhang, L., Chang, S., Li, Z., Zhang, K., Du, Y., Ott, J., & Wang, J. (2012). ADHDgene: a genetic database for attention deficit hyperactivity disorder. Nucleic Acids Res, 40(Database issue), D1003-1009. doi: 10.1093/nar/gkr992  [Q1, IF: 9.112, 5-year IF: 8.867]

    23.
  23. Zhang, K., Chang, S., Cui, S., Guo, L., Zhang, L., & Wang, J. (2011). ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework. Nucleic Acids Res, 39(Web Server issue), W437-443. doi: 10.1093/nar/gkr391  [Q1, IF: 9.112, 5-year IF: 8.867]

    24.
  24. Zhang, K. L., Zhang, L. Y., Zhang, W. N., & Wang, J. (2011). Pathway-based analysis for genome-wide association studies of schizophrenia to provide new insight in schizophrenia study. Chinese Science Bulletin, 56(32), 3398-3402. doi: DOI 10.1007/s11434-011-4742-2 [Q2, IF: 1.579, 5-year IF: 1.519]

    25.
  25. Yang, L., Zhang, K., Dai, W., He, X., Zhao, Q., Wang, J. & Sun, Z. S. (2011). Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array. BMC Genomics, 12, 10. doi: 10.1186/1471-2164-12-10 [Q1, IF: 3.986, 5-year IF: 4.360]

    26.
  26. Fang, K., Zhao, H., Sun, C., Lam, C. M., Chang, S., Zhang, K., . . . Wang, J. (2011). Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction. BMC Syst Biol, 5, 83. doi: 10.1186/1752-0509-5-83 [Q1, IF: 2.435, 5-year IF: 2.917]

    27.
  27. Zhang, J., Mamlouk, A. M., Martinetz, T., Chang, S., Wang, J., & Hilgenfeld, R. (2011). PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome. BMC Bioinformatics, 12, 248. doi: 10.1186/1471-2105-12-248 [Q1, IF: 2.576, 5-year IF: 3.452]

    28.
  28. Ott, J., & Wang, J. (2011). Multiple phenotypes in genome-wide genetic mapping studies. Protein Cell, 2(7), 519-522. doi: 10.1007/s13238-011-1059-5 [Q3, IF: 3.247, 5-year IF: 3.098]

    29.
  29. Yan, H. Q., Chang, S. H., Tian, Z. X., Zhang, L., Sun, Y. C., Li, Y., . . . Wang, J., & Wang, Y. P. (2011). Novel AroA from Pseudomonas putida confers tobacco plant with high tolerance to glyphosate. PLoS One, 6(5), e19732. doi: 10.1371/journal.pone.0019732 [Q1, IF: 3.234, 5-year IF: 3.702]

    30.
  30. Zhang, L. Y., Chang, S. H., & Wang, J. (2011). Synthetic biology: From the first synthetic cell to see its current situation and future development. Chinese Science Bulletin, 56(3), 229-237. doi: DOI 10.1007/s11434-010-4304-z [Q2, IF: 1.579, 5-year IF: 1.519]

    31.
  31. 房柯池，王晶. (2011) 全基因组范围代谢网络的构建和最小基因组研究 生命科学 第23卷 第9期 文章编号：1004-0374(2011)09-0000-07

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  32. 张柳燕，王晶. (2010) 合成生物学进展与应用. 生物产业技术 第19期：54-59 （ISSN号：1674-0319）

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  33. 张柳燕, 常素华, 王晶. (2010) 从首个合成细胞看合成生物学的现状与发展. 科学通报 第55 卷 第36 期：3477 ~ 3488

  34. Zhang, L. Y., Chang, S. H., & Wang, J. (2010). How to make a minimal genome for synthetic minimal cell. Protein Cell, 1(5), 427-434. doi: DOI 10.1007/s13238-010-0064-4 [Q3, IF: 3.247, 5-year IF: 3.098]

    35.
  35. Vayssier-Taussat, M., Le Rhun, D., Deng, H. K., Biville, F., Cescau, S., Danchin, A., … Wang, J., Engel, P., Saenz, H., & Dehio, C. (2010). The Trw type IV secretion system of Bartonella mediates host-specific adhesion to erythrocytes. PLoS Pathog, 6(6), e1000946. doi: 10.1371/journal.ppat.1000946 [Q1, IF: 7.562, 5-year IF: 8.364]

    36.
  36. Zhang, K., Cui, S., Chang, S., Zhang, L., & Wang, J. (2010). i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study. Nucleic Acids Res, 38(Web Server issue), W90-95. doi: 10.1093/nar/gkq324[Q1, IF: 9.112, 5-year IF: 8.867]

    37.
  37. Fellay, J., Ge, D., Shianna, K. V., Colombo, S., Ledergerber, B., Cirulli, E. T., . . . Immunology, N. C. f. H. A. V. (2009). Common genetic variation and the control of HIV-1 in humans. PLoS Genet, 5(12), e1000791. doi: 10.1371/journal.pgen.1000791 [Q1, IF: 6.661, 5-year IF: 7.481]

    38.
  38. Zhu, X., Chang, S., Fang, K., Cui, S., Liu, J., Wu, Z., . . . Wang, J. (2009). MyBASE: a database for genome polymorphism and gene function studies of Mycobacterium. BMC Microbiol, 9, 40. doi: 10.1186/1471-2180-9-40 [Q2, IF: 2.729, 5-year IF: 3.251]

    39.
  39. Nijssen, E., Cescau, S., Vayssier-Taussat, M., Wang, J., & Biville, F. (2009). Identification of mechanisms involved in iron and haem uptake in Bartonella birtlesii: in silico and in vivo approaches. Clin Microbiol Infect, 15 Suppl 2, 118-119. doi: 10.1111/j.1469-0691.2008.02193.x [Q1, IF: 5.768, 5-year IF: 5.059]

    40.
  40. He, X., Chang, S., Zhang, J., Zhao, Q., Xiang, H., Kusonmano, K., . . . Wang, J. (2008). MethyCancer: the database of human DNA methylation and cancer. Nucleic Acids Res, 36(Database issue), D836-841. doi: 10.1093/nar/gkm730 [Q1, IF: 9.112, 5-year IF: 8.867]

    41.
  41. Zhu, J., He, F., Song, S., Wang, J., & Yu, J. (2008). How many human genes can be defined as housekeeping with current expression data? BMC Genomics, 9, 172. doi: 10.1186/1471-2164-9-172 [Q1, IF: 3.986, 5-year IF: 4.360]

    42.
  42. Zhu, J., He, F., Wang, J, & Yu, J. (2008). Modeling transcriptome based on transcript-sampling data. PLoS One, 3(2), e1659. doi: 10.1371/journal.pone.0001659 [Q1, IF: 3.234, 5-year IF: 3.702]

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  52. Li, R., Ye, J., Li, S., Wang, J., Han, Y., Ye, C., . . . Wang, J. (2005). ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol, 1(4), e43. doi: 10.1371/journal.pcbi.0010043 [Q1, IF: 4.620, 5-year IF: 5.279]

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