Qin's Lab

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

2015 - 2018

Research assistant professor, The Chinese University of Hong Kong

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

Cheung, F.K.M. and Qin J.* (2021). The Methods and Tools for Molecular Network Construction. In: Wolkenhauer, Olaf (ed.), Systems Medicine: Integrative, Qualitative and Computational Approaches. vol. 1, pp. 14–28. Oxford. [* corresponding author]
Hu, X., Hu, Y., Wu, F., Leung, R.W.T. and Qin J.* (2020) Integration of single-cell multi-omics for gene regulatory network inference. Comput Struct Biotechnol J, 18, 1925-1938. [* corresponding author]
Wang, S.Q., Liu, J., Qin, J., Zhu, Y., Tin, V.P., Yam, J.W.P., Wong, M.P. and Xiao, Z.J. (2020) CAMK2A supported tumor initiating cells of lung adenocarcinoma by upregulating SOX2 through EZH2 phosphorylation. Cell Death Dis, 11, 410.
Li, B., Zhu, C., Dong, L., Qin, J., Xiang, W., Davidson, A.J., Feng, S., Wang, Y., Shen, X., Weng, C. et al. (2020) ADAM10 mediates ectopic proximal tubule development and renal fibrosis through Notch signalling. J Pathol.
Nong, W., Chai, Z.Y.H., Jiang, X., Qin, J., Ma, K.Y., Chan, K.M., Chan, T.F., Chow, B.K.C., Kwan, H.S., Wong, C.K.C. et al. (2020) A crustacean annotated transcriptome (CAT) database. BMC Genomics, 21, 32.
Tak Leung, R.W., Jiang, X., Chu, K.H. and Qin, J.* (2019) ENPD - A Database of Eukaryotic Nucleic Acid Binding Proteins: Linking Gene Regulations to Proteins. Nucleic Acids Res, 47, D322-D329. [* corresponding author]
Chu, K.H., Wai, C.Y.Y., Leung, N.Y.H., Qin, J. and Leung, P.S.C. (2019) IgE signaling repression by a designer DNA vaccine to modulate shrimp hypersensitivity. Allergy, 74, 196-196.
Ma, K.Y., Qin, J., Lin, C.W., Chan, T.Y., Ng, P.K.L., Chu, K.H. and Tsang, L.M. (2019) Phylogenomic analyses of brachyuran crabs support early divergence of primary freshwater crabs. Molecular Phylogenetics and Evolution, 135, 62-66.
Zhang, J.T., Qin, H., Man Cheung, F.K., Su, J., Zhang, D.D., Liu, S.Y., Li, X.F., Qin, J., Lin, J.T., Jiang, B.Y. et al. (2019) Plasma extracellular vesicle microRNAs for pulmonary ground-glass nodules. J Extracell Vesicles, 8, 1663666.
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 author]
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]