上海同济大学 生命科学与技术学院 刘琦（副教授）导师简介

Bio Sketch：

Qi Liu is an Associate Professor at the Department of Bioinformatics, College of Life Science and Technology, Tongji University (2009.9 - ). He received his Ph.D. degree in 2008 as a joint student from Zhejiang University and University of Georgia (UGA), U.S. (Ph.D. thesis supervised by Prof. Xiuzi Ye and Prof. Ying Xu ).Before that, he completed his Master degree majoring in computer science in Zhejiang University in 2005 (Master thesis supervised by Prof. Chun Chen),and B.S. degree majoring in computer science in Hefei University of Technology in 2002(With close interaction with Prof. Xuegang Hu and Prof. Xindong Wu) .In 2008 - 2009, he was a Postdoc Associate at the Department of Computer Science in Hong Kong University of Science and Technology (HKUST), supervised by Prof. Qiang Yang. In 2006 - 2008, he was a visiting student in the lab of Prof. Ying Xu in University of Georgia, and started his bioinformatics career from then.

He has been actively in charged of and participated in several national and mainland projects including: U.S. NSF, Hong Kong RGC and China 863, China NSF etc. He has published more than 40 significant papers in Briefings in Bioinformatics,Plos one,Journal of Computational Chemistry,Journal of Chemical Information and Modeling, NAR, Bioinformatics, BMC bioinformatics etc, and developed several computational platforms and tools for bioinformatics analysis.

His former research interesting mainly focused on the developing of fancy machine learning models to solve biological problems, especially for the small RNA secondary structure modeling. After joining the bioinformatics group in Tongji, he began to devote on in-silico siRNA design and developing various computational methodologies and tools for in-silico drug target prediction and drug virtual screen.

Select papers in the area of Bioinformatics:

2012

1. 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, in press, J. Chem. Inf. Model. 2012. (Top Journal in Computational Chemistry Community).  

2.Mohammad Shabbir Hasan, Qi Liu, Han Wang, John Fazekas, Bernard Chen, Dongsheng Che, GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences, Bioinformation 8(4): 203-205 , 2012.

3.Tianlei Xu, Ruixin Zhu, Qi Liu# and Zhiwei Cao#, Quantitatively Integrating Molecular Structure and Bioactivity Profile Evidence into Drug-Target Relationship Analysis, BMC Bioinformatics, in press, 2012.

4. 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, in press, 2012.(Top Journal in Bioinformatics Community). 

5. Qi Liu, Han Zhou, Juan Cui, Zhiwei Cao and Ying Xu, Reconsideration of In-silico siRNA Design Based on Feature Selection: A Cross-platform Data Integration Perspective, Plos one, in press, 2012.

6. Jun Gao , Dongsheng Che, Vincent W. Zheng, Ruixin Zhu, Qi Liu#，Integrated QSAR study for inhibitors of Hedgehog Signal Pathway against multiple cell lines：a collaborative filtering method，BMC Bioinformatics, in press, 2012

2011

1. Qi Liu, Han Zhou, Lin Liu, Xi Chen, Ruixin Zhu and Zhiwei Cao, Multi-target QSAR Modelling in the Analysis and Design of HIV-HCV Co-Inhibitors An In-silico Study, BMC Bioinformatics, 2011 12:294.

2. Gao Jun, Zhu Ruixin Liu, Qi Liu #, Cao Zhiwei#, Petri Net based Metabolic Network Parameters Fitting with GPU Acceleration, Chin. J. Chem., 2011, 29(9),1805-1810.

3. Zhu Ruixin, Wang Fei, Liu Qi#, Kang Tingguo#, Quantitative Structure-Activity Relationship of IOPY/ISPY Analogues as HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors, ACTA CHIMICA SINICA, Vol,69,2011, No.15,1731-1736.

4. Ruixin Zhu #, Qi Liu #, Jian Tang, Huiliang and Zhiwei Cao, Investigations on Inhibitors of Hedgehog Signal Pathway: A QSAR Study, Int. J. Mol. Sci., 12, 3018-3033, 2011.

5. Chao Ma, Hong Kang, Qi Liu, Ruixin Zhu, Zhiwei Cao, Insight into potential toxicity mechanisms of melamine: an in silico study, Toxicology, 2011, Volume 283, Issues 2-3, 96-100.

6. Tianli Dai, Qi Liu, Jun Gao, Zhiwei Cao, Ruixin Zhu, A New Protein-Ligand Binding Sites Prediction Method by integrating Sequence Conservation of Protein, BMC Bioinformatics, 12 Suppl 14,2011.

7. Dongsheng Che, Shabbir Hasan, Han Wang, John Fazekas, Jinling Huang, and Qi Liu, EGID: an ensemble algorithm for improved genomic island detection in genomic sequences, Bioinformation, 7(6),313-314. 2011.

8. Shenzhen, Huangqi, Kanghong, Liu Qi, Zhiwei Cao, Ruixin Zhu, A new fingerprint of chemical compounds and its application for virtual drug screens,ACTA CHIMICA SINICA, 69(16),1845-1850,2011.

9. Han Wang, John Fazekas, Matthew Booth, Qi Liu# and Dongsheng Che#, An Integrative Approach for Genomic Island Prediction in Prokaryotic Genomes, Bioinformatics Research and Applications, Lecture Notes in Computer Science, 2011, Volume 6674/2011, 404-415 (ISBRA 2011).

10. Huang Qi, Kang Hong, Duanfeng Zhang, Sheng, Zhen, Liu Qi, Ruixin Zhu, Cao Zhiwei, Comparison of Ligand-, Target Structure-, and Protein-Ligand Interaction Fingerprint-base Virtual Screening Methods, ACTA CHIMICA SINICA,2011,69(5),515-522.

2010

1. Sheng Zhen, Kong Hong, Dai Tianli, Liu Qi#, Zhu Ruixin#, Complementary study of structure features and gene profile features for chemical compounds, ACTA CHIMICA SINICA,2010, 68(23),2395-2400.

2. Liu Qi, Che Dongsheng, Huang Qi, Cao Zhiwei , Zhu Ruixin, Multi-target QSAR Study in the Analysis and Design of HIV-1 Inhibitors, Chin. J. Chem. 1587-1592, 2010.

3. Qi Liu, Juan Cui, Qiang Yang and Ying Xu, In-silico prediction of blood-secretory human proteins using a ranking algorithm, BMC Bioinformatics, 11:250, 2010. (Manifold ranking framework for bloody secreted protein prediction )

4. Qi Liu, Qian Xu, Wencheng Zhen, Hong Xue, ZhiWei Cao, Qiang Yang, Multi-task learning for cross-platform siRNA efficacy prediction, an in-silico study. BMC Bioinformatics, 11:181, 2010. (Multi-task learning framework for siRNA efficacy prediction)

5. Hao Ye, Li Ye, Hong Kang, Duanfeng Zhang, Lin Tao, Kailin Tang, Xueping Liu, Ruixin Zhu, Qi Liu, Y. Z. Chen, Yixue Li and Zhiwei Cao, HIT: linking herbal active ingredients to targets, Nucleic Acids Research. 2010, 1-5.

6. Xiaolian Xu, Jing Sun, Qi Liu, Xiaojing Wang, Tianlei Xu, Ruixin Zhu, Di Wu and Z. W. Cao, Evaluation of the spatial epitope prediction tools based on the independent testing dataset of protein antigens, Chinese Science Bulletin, 55(18), 1810-1815, 2010.

2009

1. Qi Liu, Jinling Huang, Huiqing Liu, Ping Wan, Xiuzi Ye, Ying Xu, Analyses of Domains and Domain Fusions in Human Proto-Oncogenes, BMC Bioinformatics, 2009, 10:88. (Taxdom)

2008

1. Qi Liu,Yin Zhang,Ying Xu, Xiuzi Ye, Fuzzy kernel clustering of RNA secondary structure ensemble using a novel similarity metric. Journal of Biomolecular Structure and Dynamics, 25(6):685-696, 2008. (RNAsscc: software upon request)

2. Qi Liu, Yu Yang, Chun Chen, Jiajun Bu,Ying Zhang, Xiuzi Ye, RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure. BMC Bioinformatics, 9:176, 2008.  (RNACompress: software upon request)

3. 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.(Top Journal in Computational Chemistry Community) (RNACluster)

4. Juan Cui, Qi Liu, David Puett, Ying Xu, Computational prediction of human proteins that can be secreted into the bloodstream, Bioinformatics, 24(20),2370-2375,2008. (Computational Webserver for bloody secreted protein prediction)

5. Qi Liu, Ying Zhang, Mingyi Wang, Rongdong Yu and Xiuzi Ye, Progress of normalization methods for high-density oligonucleotide microarray data, Journal of Zhejiang University (Engineering Science), 2008,42(9),1653-1660.

2007

1. Qi Liu, Yin Zhang and Xiuzi Ye, Computing similarity between RNA secondary structures based on singular value decomposition, Journal of Zhejiang University (Engineering Science),2007(4),1249-1254.

2006

1. Qi Liu,Yin Zhang, Xiuzi Ye, A Hopfield Neural Network based algorithm for RNA secondary structure prediction, The International Multi-Symposiums on Computer and Computational Science IMSCCS|06,2006,10-16.

Select papers in the area of Machine Learning:

2011

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), In press, 2011. (Top Journal in Machine Learning Community)

2010

1. 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. (Top Conference in Machine Learning Community)

2. 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. (Top Conference in Machine Learning Community)

2008

1. Qi Liu, Yin Zhang, Xiuzi Ye, Rongdong Yu, A Discrete Hopfield Neural Network based MIS finding algorithm for stems selecting and its application in RNA secondary structure prediction, Chinese Journal of Computers, 2008(1), 51-58.

2006

1. Qi Liu, Jiajun Bu, Chun Chen, An application of the key words recommendation based on Apriori algorithm in the theme-oriented personalized search, Pattern Recognition and Artificial Intelligence,2006(2),186-190.

Patent：Before I devote into bioinformatics, I am a pure computer guy. I have already obtained 6 china utility model patents to apply computer-aided intelligence control and data mining algorithm for down feather equipment control and down feather detection.