Education Training:
Ph.D., Joint Degree between Zhejiang University and University of Georgia, U.S., Bioinformatics, 2008
Postdoctoral Associate, HongKong University of Science and Technology, Computer Science, 2009

  Research Interests:

1. Precision medicine and drug informatics

2. RNAi and gene editing analysis, siRNA and sgRNA in-silico design

3. Clinical data analysis and related disease mechanism study

Research Description:

1. My research aims at using various statistical learning and machine learning techniques to address the bioinformatics and chemo-informatics problems. Please refer to our lab page: http://bm2.tongji.edu.cn/

2. Key Word: Machine Learning, Bioinformatics, Chemo-informatics, Drug design, Data integration, Precision Medicine, Gene editing

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.