曹沁教授 – 生物醫學學院

曹沁教授

Research Assistant Professor

39436805

qcao@cuhk.edu.hk

522A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, CUHK

Publons

ORCID

Biography

Prof. CAO Qin (曹沁) completed her B.Eng. in Computer Science and Technology from Wuhan University, and her Ph.D. in Computer Science and Engineering (CSE) from The Chinese University of Hong Kong (CUHK). She then continued her postdoctoral research at School of Biomedical Sciences (SBS) and CSE in CUHK for three years and became a Research Assistant Professor in 2020. Her research areas are Bioinformatics and Computational Biology. Prof. Cao has received awards including Young Scholars Thesis Award from CUHK, Young Scientist Award 2nd Runner-up from Hong Kong Institution of Science and Top-10 paper in 2016-17 at RECOMB/ISCB Regulatory Systems Genomics. She has published papers in international journals including Nature Genetics, Nature Machine Intelligence, Nature Communications, Cell Reports, Briefings in Bioinformatics and BMC Genomics.

Research Interests

Reconstruction of gene regulatory networks.
Analysis of multi-omics data and 3D genome structures.
Development of bioinformatics algorithms, pipelines and tools.

Selected Publications

Chen, W.#, Miao, C.#, Zhang, Z., Fung, C.S.H., Wang, R., Chen, Y., Qian, Y., Cheng, L., Yip, K. Y.*, Tsui, S.K.W.* & Cao, Q.* (2024). Commonly used software tools produce conflicting and overly-optimistic AUPRC values. Genome Biology, 25(1), 118.
Wang, L., Xiong, Q., Saelim, N., Wang, L., Nong, W., Wan, A.T.Y., Shi, M., Liu, X., Cao, Q., Hui, J.H.L., Sookrung, N., Leung, T.F., Tungtrongchitr, A., & Tsui, S.K.W. (2022). Genome assembly and annotation of Periplaneta americana reveal a comprehensive cockroach allergen profile. Allergy, doi: 10.1111/all.15531.
Qian, Y.#, Zhai, E.#, Chen, S.#, Liu, Y., Ma, Y., Chen, J., Liu, J., Qin, C., Cao, Q.*, Chen, J.*, and Cai, S.* (2022). Single-cell RNA-seq dissecting heterogeneity of tumor cells and comprehensive dynamics in tumor microenvironment during lymph node metastasis in gastric cancer. International Journal of Cancer 151(8), 1367-1381.
Hong, C.#, Cao, Q.#*, Zhang, Z., Tsui, S. K., & Yip, K. Y.* (2022). Reusability report: Capturing properties of biological objects and their relationships using graph neural networks. Nature Machine Intelligence, 4, 222-226.
Jiang, Q.#, Ang, J. Y.#, Lee, A. Y., Cao, Q., Li, K. Y., Yip, K. Y., & Leung, D. C. (2020). G9a Plays Distinct Roles in Maintaining DNA Methylation, Retrotransposon Silencing, and Chromatin Looping. Cell Reports, 33(4), 108315.
Cao, Q.#, Zhang, Z.#, Fu, A.X., Wu, Q., Lee, T.L., Lo, E., Cheng, A.S.L., Cheng, C., Leung, D., & Yip, K.Y. (2020). A unified framework for integrative study of heterogeneous gene regulatory mechanisms. Nature Machine Intelligence, 2(8), 447-456.
Ho, E.Y.K.#, Cao, Q.#, Gu, M., Chan, R.W.L, Wu, Q., Gerstein, M., & Yip, K.Y. (2020). Shaping the nebulous enhancer in the era of high-throughput assays and genome editing. Briefings in Bioinformatics, 21(3), 836-850.
Zhang, J. #, Lee, D. #, Dhiman, V. #, Jiang, P. #, Xu, J., McGillivray, P., Yang, H., Liu, J., Meyerson, W., Clarke, D., Gu, M., Li, S., Lou, S., Xu, J., Lochovsky, L., Ung, M., Ma, L., Yu, S., Cao, Q., Harmanci, A., Yan, K.K., Sethi, A., Gürsoy, G., Schoenberg, M.R., Rozowsky, J., Warrell, J., Emani, P., Yang, Y.T., Galeev, T., Kong, X., Liu, S., Li, X., Krishnan, J., Feng, Y., Rivera-Mulia, J.C., Adrian, J., Broach, J.R., Bolt, M., Moran, J., Fitzgerald, D., Dileep, V., Liu, T., Mei, S., Sasaki, T., Trevilla-Garcia, C., Wang, S., Wang, Y., Zang, C., Wang, D., Klein, R.J., Snyder, M., Gilbert, D.M., Yip, K., Cheng, C., Yue, F.*, Liu, X.S.*, White, K.P.*, & Gerstein, M.* (2020). An integrative ENCODE resource for cancer genomics. Nature Communications, 11(1), 1-11.
Cao, Q., Anyansi, C., Hu, X., Xu, L., Xiong, L., Tang, W., Mok, M.T.S., Cheng, C., Fan, X., Gerstein, M., Cheng, A.S.L., & Yip, K.Y. (2017). Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines. Nature Genetics, 49, 1428-1436.
Cao, Q., & Yip, K.Y. (2016). A survey on computational methods for enhancer and enhancer target predictions. Computational biology and bioinformatics: Gene regulation, 3-27.

#Co-first author
*Co-corresponding author

Grants

NSFC Youth Program [PI 1-Jan-22– 31-Dec-24]. “Refining computational predictions of multiscale 3D genome structures in a large number of cancer samples” (HK$ 288,950).