LIU Qi

homepage Faculty Professor

Faculty

Add: 50 Chifeng Road,

Medical Building,

200092,

Shanghai, China

Tel: 021 - 65981041

Fax: 021 - 65981041

Professor

LIU Qi/ Professor

Contact Info

E-mail: qiliu@tongji.edu.cn

Address: 1239 Siping Road, Tongji University, Shanghai 200092, P.R. China

Representative Publication (less than 20 papers)：

Bioinformatics community：

[1]. Guohui Chuai, Jifang Yan et al, Qi Liu#, Deciphering relationship between microhomology and in-frame mutation occurence in human CRISPR-based gene knockout, Molecular Therapy-Nucleic Acids, 5, e323; doi:10.1038, 2016.

[2]. CRISPR-DO: A genome-wide CRISPR designer and optimizer for multiple species, Bioinformatics, Jian Ma et al, Qi Liu#, Han Xu# and X. Shirley Liu#, in press, 2016.

[3]. Ranking novel cancer driving synthetic lethal gene pairs, YH, YQC et al, QL#, Jenny Wei#, Oncotarget, in press, 2016.

[4]. In-silico meets in-vivo: towards computational CRISPR-based sgRNA design，Guo-hui Chuai, Qi-Long Wang, Qi Liu#, Trends in Biotechnology, in press, 2016.

[5]. SY, ZW, Qin Ma, Jenny Wei#, Qi Liu#, Identifying anti-cancer drug response related genes using an integrative analysis of transcriptomic and genomic variations with cell line-based drug perturbations ---- With implications for tumor samples, Oncotarget, Advance Access, 2016.

[6]. Haiping Wang, Quanquan Gu, Jia Wei, Zhiwei Cao, Qi Liu#, Mining drug-disease relationships as a complement to medical genetics-based drug repositioning: Where a recommendation system meets GWAS, Clinical Pharmacology & Therapeutics, Advance Access, 2015.

[7]. Yi Sun, Zhen Sheng, Chao Ma, Kailin Tang, Ruixin Zhu, Zhuanbin Wu, Ruling Shen, Jun Feng, Dingfeng Wu, Danyi Huang, Dandan Huang, Jian Fei#, Qi Liu#, Zhiwei Cao#, Combining genomic and network characteristics for extended capability in predicting synergistic drugs for cancer, Nature Communications, Advance Access, 2015.

[8]. WZ, LJ, KT, HP W, RX Z, WJ, ZW, Qi Liu#, When drug discovery meets web searching: learning to rank for ligand-based virtual screening, Journal of Cheminformatics, Advance Access, 2015.

[9]. HK, YZ et al, Qi Liu#, YY H#, ZW C#, Integrating Clinical Indexes into Four-Diagnostic Information Contribute to the Traditional Chinese Medicine (TCM) Syndrome Diagnosis of Chronic Hepatitis B, Scientific Reports, Advance Access, 2015.

[10]. Haoqi Sun, Haiping Wang, Ruixin Zhu, Kailin Tang, Qin Gong, Juan Cui, Zhiwei Cao, Qi Liu#, iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis, Bioinformatics, Advance Access online, 2013.

[11]. Yi Sun, Ruixin Zhu, Hao Ye, Jing Zhao, Yujia Chen, Qi Liu# and Zhiwei Cao#, Towards a bioinformatics analysis of anti-Alzheimer’s herbal medicines from a target network perspective, Briefings in Bioinformatics, May;14(3):327-43, 2013.

[12]. Qi Liu, Han Zhou, Ruixin Zhu, Ying Xu and Zhiwei Cao, Reconsideration of in-silico siRNA design from a perspective of heterogeneous data integration: problems and solutions, Briefings in Bioinformatics, 2014.

[13]. Hong Kang, Zhen Sheng, Ruixin Zhu, Qi Huang, Qi Liu# and Zhiwei Cao#, A virtual drug screen schema based on multi-view similarity integration and ranking aggregation, 26;52(3):834-43, J. Chem. Inf. Model. 2012.

[14]. Qi Liu, V. Olman, Huiqing Liu, Xiuzi Ye, Shilun Qiu, Ying Xu, RNACluster : an integrated tool for RNA secondary structure comparison and clustering, Journal of Computational Chemistry, 26(9), 1517-1526, 2008.

Machine learning community：

[1]. Xiaoxiao Shi, Qi Liu, Wei Fan, and Philip S. Yu, Transfer across Completely Different Feature Spaces via Spectral Embedding, IEEE Transactions on Knowledge and Data Engineering (TKDE), vol. 25, no. 4, pp. 906-918, 2011.

[2]. Xiaoxiao Shi, Qi Liu, Wei Fan, Philip Yu, and Ruixin Zhu, Training Data Extraction from Completely Different Feature Spaces via Spectral Transformation, IEEE International Conference on Data Mining (ICDM 2010),1049-1054, 2010.

[3]. Xiao Xiao shi, Qi Liu, Wei Fan,Qiang Yang, Philip S.Yu. Predictive Modeling with heterogeneous Sources, the 2010 SIAM International Conference on Data Mining (SDM’2010), 814-825, 2010.

General information：

Liu Qi is a tenured distinguished professor in the Department of Bioinformatics at Tongji University, as well as the Principal Investigator of the Shanghai Autonomous Intelligent Unmanned Systems Science Center. He has long been dedicated to developing AI technologies to empower omics analysis, focusing on data-driven precision medicine research and translation. His research has been published in high-impact journals including Nature Methods, Nature Machine Intelligence and Nature Computational Science et c. He has been recognized as an Innovator in Intelligent Computing by MIT Technology Review, received the WuXi AppTec Life Chemistry Research Award, the Wu Wenjun AI Natural Science Prize etc.

Research Interests：

AI for Precision Medicine

AI for Science

Omics

Agent and foundation model technology development and applications

Research Publication:

[1]. Xiaohan Chen et al, Qi Liu*, Intelligent design of sequential drug treatment targeting the tumor evolving landscape with SequenTx, Nature Machine Intelligence, Advance Access, 2026.

[2]. Zhiting Wei et al, Qi Liu*, Benchmarking algorithms for generalizable single-cell perturbation response prediction, Nature Methods, Advance Access, 2025.

[3]. Shaliu Fu et al, Qi Liu*, Benchmarking single-cell multi-modal data integrations, Nature Methods, Advance Access, 2025. （Research Highlight）

[4]. Yicheng Gao et al, Qi Liu*, Toward subtask decomposition-based learning and benchmarking for genetic perturbation outcome prediction and beyond, Nature Computational Science 2024.（Research Highlight）

[5]. Yichen Gao et al., Qi Liu*, Pan-Peptide Meta Learning for T-Cell Receptor-Antigen Binding Recognition, Nature Machine Intelligence. Advance Access, 2023. （Research Highlight）

Positions：

Position available for student who has cross-disciplinary backgrounds such as computer science, mathematics, pharmacology, molecular biology, biochemistry and physics etc.