Research Interests
Bioinformatics and functional genomics
Integrative OMICs approaches for gene regulation studies
Bioinformatics tool development
Education
2011 - 2013
PhD (Bioinformatics). The University of Hong Kong
2006 - 2009
MPhil (Biology). The Chinese University of Hong Kong
2002 - 2006
BSc (Biological Science). Zhejiang University
Previous Position
2013 - 2015
Post-doctoral fellow, University of Hong Kong
Research Grants
- Computational identification of aberrant regulatory functions of enhancer RNAs in Chinese non-small-cell lung carcinoma (NSCLC) patients. AstraZeneca Oncology Research Program. Principal investigator. HK$ 200,000. 2017/10-2019/09.
- Transcriptomic analysis on ovarian maturation in the Chinese mitten crab Eriocheir sinensis. Direct Grant for Research, The Chinese University of Hong Kong (4053187). Principal investigator. HK$ 29,162. 2017/03-2018/02.
- Evolutionary analysis on crustacean transcription factors and their functions. National Natural Science Foundation of China (41606143). Principal investigator. RMB 190,000. 2017/01-2019/12.
- Transcriptomic analysis on transcriptional regulations in crustaceans. Direct Grant for Research, The Chinese University of Hong Kong (4053150). Principal investigator. HK$ 150,000. 2016/03-2017/02.
- Prediction of determining factors and underlying networks for cell conversion by integrating ChIP-seq/chip and transcriptome data. Small Project Fund, University of Hong Kong (201409176183). Principal investigator. HK$ 21,128. 2015/03-2016/02.
- Understanding the evolutionary ecology of brachyuran crabs: a transcriptomic approach. General Research Fund, Hong Kong. Co-investigator. HK$ 970,000. 2018/01-2020/12.
- Transcriptomic study on an animal model of shrimp tropomyosin hypersensitivity. Direct Grant for Research, The Chinese University of Hong Kong. Co-investigator. HK$ 33,030. 2016/01-2017/01.
- Systems biology approach to understand gene regulatory network of lung cancer pathogenesis. National Natural Science Foundation of China (91229105). Co-investigator. RMB 900,000. 2013/01-2015/12.
Selected Publications
- Qin, J.*, Hu, Y., Ma, K.Y., Jiang, X., Ho, C.H., Tsang, L.M., Yi, L. and Chu, K.H.* (2017) CrusTF: a comprehensive resource of transcriptomes for evolutionary and functional studies of crustacean transcription factors. BMC Genomics, 18(1):908. [* co-corresponding authors]
- Hu, Y., Li, C., Meng, K., Qin, J., and Yang, X. (2017). Group sparse optimization via ℓp,q regularization. Journal of Machine Learning Research, 18, 1-53. (Authors in alphabetical order)
- Yan, B., Guan, D., Wang, C., Wang, J., He, B., Qin, J., Boheler, K.R., Lu, A., Zhang, G., and Zhu, H. (2017). An integrative method to decode regulatory logics in gene transcription. Nature Communications 8, 1044.
- Xiao, Z.J., Liu, J., Wang, S.Q., Zhu, Y., Gao, X.Y., Tin, V.P., Qin, J., Wang, J.W., and Wong, M.P. (2017). NFATc2 enhances tumor-initiating phenotypes through the NFATc2/SOX2/ALDH axis in lung adenocarcinoma. eLife 6, e26733.
- Tang, J., Shen, Y., Chen, G., Wan, Q., Wang, K., Zhang, J., Qin, J., Liu, G., Zuo, S., Tao, B., Yu, Y., Wang, J., Lazarus, M., and Yu. Y. (2017). Activation of E-prostanoid 3 receptor in macrophages facilitates cardiac healing after myocardial infarction. Nature Communications 8, 14656.
- Wang, P.*, Qin, J.*, Qin, Y., Zhu, Y., Wang, L.Y., Li, M.J., Zhang, M.Q. and Wang, J. (2015) ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks. Nucleic Acids Research, 43, W264-269. [* equal contribution]
- Guan, D., Shao, J., Zhao, Z., Wang, P., Qin, J., Deng, Y., Boheler, K.R., Wang, J., and Yan, B. (2014). PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data. Nucleic Acids Research 42, W130-136. [Cover story]
- Qin, J.*, Hu, Y.*, Xu, F., Yalamanchili, H.K., and Wang, J. (2014). Inferring gene regulatory networks by integrating ChIP-seq/chip and transcriptome data via LASSO-type regularization methods. Methods 67, 294-303. [* equal contribution]
- Qin, J., Li, M.J., Wang, P., Wong, N.S., Wong, M.P., Xia, Z., Tsao, G.S., Zhang, M.Q., and Wang, J. (2013). ProteoMirExpress: inferring microRNA and protein-centered regulatory networks from high-throughput proteomic and mRNA expression data. Molecular & Cellular Proteomics 12, 3379-3387.
- Qin, J., Li, M.J., Wang, P., Zhang, M.Q., and Wang, J. (2011). ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. Nucleic Acids Research 39, W430-436. [Recommended by F1000Prime]
Tools and Databases
Integrating multiple OMICs data to construct gene regulatory networks
Inferring microRNA and protein-centered regulatory networks from high-throughput proteomic and mRNA expression data
A comprehensive resource for evolutionary and functional studies of crustacean transcription factors
Inferring gene regulatory networks by integrating ChIP-seq/chip and transcriptome data via LASSO-type regularization methods
Group sparse optimization
An integrative method to decode regulatory logics in gene transcription
Post-translational hierarchical gene regulatory networks
Constructing epigenetic regulatory network from high throughput gene expression data for humans
Gapped alignment based network inference with time-series transcriptomic data
Awards
2017 2nd Winning Proposal in AstraZeneca Oncology Research Program.
2010 University Postgraduate Fellowship from the University of Hong Kong.