Huaiqiu Zhu

Ph.D., Associate Professor

Department of Biomedical Engineering, College of Engineering, Peking University
Lab for Bioinformatics and Computational System Biology

Office Add: Mechanics Building Rm. 505

Office Tel: +86-10-6276-7261

Lab Add: (1) BME Lab (Mechanics Building Rm. 507); (2) CTB Lab (East part of Old Chemistry Building), Rm. 301-4

Lab Tel: (8610) 6275-7881;(8610) 6275-9559

Fax: +86-10-6276-7261

Email: hqzhu(at)





Ph.D. in Fluid Mechanics, Peking University

M.S. in Fluid Mechanics, Peking University

B.S. in Engineering Mechanics, Huazhong University of Science and Technology



Research Areas

Bioinformatics and Computational System Biology



Research Profile

Zhu’s lab was launched since 2005, with a thriving and diverse group of young researchers from the background of mathematics, physics, mechanics and computer science. The long-term of the lab is to understand the biological complex systems based on the level of genome, protein sequence and protein structure, and develop a variety of methods and tools in the emerging field of computational system biology and bioinformatics. During recent years, the lab has obtained continual grants and funding from China government. Currently the lab has several focuses in the field:

(1) Genome analysis and gene prediction methods and tools on microbial genomes and metagenomes;

(2) Comparative genomics and genome evolution for environmental microbes and human health-associated microbes;

(3) Network and mechanism associated with splicing and alternative splicing of exons/introns in eukaryotic genomes;

(4) Data mining in biomedicine.

The lab has developed a series of bioinformatics methods in prokaryotic gene prediction, eukaryotic gene prediction, protein second structure prediction, and protein folding analysis. Our methods have been applied in several bacterial genome sequencing projects. Our research has been cited or highlighted by the academic community, such as in journals of Nature, Nat. Methods, and Nat. Rev. Microbiol. etc.
There are many opportunities to join the group: as a student doing Ph. D. research or M. S. thesis, or as an undergraduate who wants to learn more about academic research. Please contact



Professional Honors and Awards

Supervisor Award Funding for Excellent Doctoral Dissertation of Beijing, China, 2011 – 2013.

Youth Distinguished Paper of China Biomedical Engineering Joint Annual Conference, 2007.

Peking University Founder Foundation Faculty Award, 2010.

Peking University Exxon-Mobil Foundation Faculty Award, 2009.

Peking University P & G Foundation Faculty Award, 2006.



Professional Activities

Associate Editor: Int. J. Comput. Intelligence in Bioinformatics and Systems Biology (IJCIBSB)

Association Member: China Association of Biomedical Information Technology (CABMIT)


Selected Recent Publications


1.    Meng Gao, Huaiqiu Zhu*, Xin-Qiu Yao, Zhen-Su She*. Water dynamics clue to key residues in protein folding. Biochem. Bioph. Res. Co., 2010, 392: 95-99.

2.    GAO Meng, YAO Xin-Qiu, SHE Zhen-Su, LIU Zhi-Rong*, ZHU Huai-Qiu*. Intermediate structure and slow hydration water dynamics in protein folding process. Acta Phys.-Chim. Sin., 2010, 1996-2008.

3.    Chengwei Luo, Gang-Qing Hu and Huaiqiu Zhu*, Genome reannotation of Escherichia coli CFT073 with new insights into virulence, BMC Genomics, 2009, 10: 552.

4.    Hong Kang, Xin-Qiu Yao, Zhen-Su She, Huaiqiu Zhu*. Water-protein interplay reveals the specificity of alpha-lytic protease. Biochem. Bioph. Res. Co., 2009, 385: 165-169.

5.    Gang-Qing Hu, Jiang-Tao Guo, Yong-Chu Liu, Huaiqiu Zhu*. MetaTISA: Metagenomic translation initiation site annotator for improving gene start prediction. Bioinformatics, 2009, 25(14): 1843-1845.

6.    Gang-Qing Hu, Xiaobin Zheng, Yi-Fan Yang, Philippe Ortet, Zhen-Su She, Huaiqiu Zhu*. ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes. Nucleic Acids Res., 2008, 36: D114-119.

7.    SUN Zongxiao, SANG Lingjie, JU Lining, ZHU Huaiqiu*. A new method for splice site prediction based on the sequence patterns of splicing signals and regulatory elements. Chinese Sci. Bull., 2008, 53(21): 3331-3340.

8.    HU Gang-Qing, LIU Yong-Chu, ZHENG Xiao-Bin, YANG Yi-Fan, SHE Zhen-Su, ZHU Huai-Qiu*. New solutions of translation initiation site prediction for prokaryotic genomes. Prog. Biochem. Biophys., 2008, 35(11): 1254-1262.

9.    Huaiqiu Zhu, Gang-Qing Hu, Yi-Fan Yang, Jin Wang, Zhen-Su She. MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes. BMC Bioinformatics, 2007, 8: 97.

10.    Huai-Qiu Zhu, Gang-Qing Hu, Zheng-Qing Ouyang, Jin Wang, Zhen-Su She. Accuracy improvement for identifying translation initiation sites in microbial genomes. Bioinformatics, 2004, 20(18): 3308-3317.