曹沁教授 - 生物醫學學院

曹沁教授

研究助理教授

39436805

qcao@cuhk.edu.hk

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

Publons

ORCID

個人簡介

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 been a (co-)first or (co-)corresponding author of papers in international journals, including Nature Genetics, Nature Machine Intelligence, Genome Biology, and Briefings in Bioinformatics.

研究興趣

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

著作選錄

1. Chen W*, Miao C*, Zhang Z, Fung CSH, Wang R, Chen Y, Qian Y, Cheng L, Yip KY#, Tsui SKW#, and Cao Q#. (2024) Commonly used software tools produce conflicting and overly-optimistic AUPRC values. Genome Biology 25(1), 118.

2. Wang L*, Xiong Q*, Saelim N, Wang L, Nong W, Wan ATY, Shi M, Liu X, Cao Q, Hui JHL, Sookrung N, Leung TF, Tungtrongchitr A, and Tsui SKW. (2022) Genome assembly and annotation of Periplaneta americana reveal a comprehensive cockroach allergen profile. Allergy 78(4): 1088-1103.

3. Hong C*, Cao Q*#, Zhang Z, Tsui SKW, and Yip KY#. (2022) Reusability report: Capturing properties of biological objects and their relationships using graph neural networks. Nature Machine Intelligence 4: 222-226.

4. 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 nodes metastasis in gastric cancer. International Journal of Cancer 151(8): 1367-1381.

5. Cao Q*, Zhang Z*, Fu AX, Wu Q, Lee TL, Lo E, Cheng ASL, Cheng C, Leung D, and Yip KY. (2020) A unified framework for integrative study of heterogeneous gene regulatory mechanisms. Nature Machine Intelligence 2(8): 447-456.

6. Ho EYK*, Cao Q*, Gu M, Chan RWL, Wu Q, Gerstein M, and Yip KY. (2020) Shaping the nebulous enhancer in the era of high-throughput assays and genome editing. Briefings in Bioinformatics 21(3): 836-850.

7. 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 KK, Sethi A, Gürsoy G, Schoenberg MR, Rozowsky J, Warrell J, Emani P, Yang YT, Galeev T, Kong X, Liu S, Li X, Krishnan J, Feng Y, Rivera-Mulia JC, Adrian J, Broach JR, 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 RJ, Snyder M, Gilbert DM, Yip K, Cheng C, Yue F#, Liu XS#, White KP#, and Gerstein M#. (2020) An integrative ENCODE resource for cancer genomics. Nature Communications 11(1): 1-11.

8. Jiang Q*, Ang JYJ*, Lee AY, Cao Q, Li KY, Yip KY, and Leung DCY. (2020) G9a plays distinct roles in maintaining DNA methylation, retrotransposon silencing and chromatin looping. Cell Reports 33(4): 108315.

9. Cao Q, Anyansi C, Hu X, Xu L, Xiong L, Tang W, Mok MTS, Cheng C, Fan X, Gerstein M, Cheng ASL, and Yip KY. (2017) Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines. Nature Genetics 49: 1428-1436.

10. Cao Q, and Yip KY. (2016) A survey of the computational methods for enhancers and enhancer-target predictions. Computational biology and bioinformatics: Gene regulation 3-27.

(*:co-first authors; #:co-corresponding authors)

研究資助

NSFC Young Scientists Fund [PI 1-Jan-22– 31-Dec-24]. “Refining computational predictions of multiscale 3D genome structures in a large number of cancer samples” (HK$ 322,476).
Co-PI of 3 CRF; Co-I of 1 TRS