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hqzhu_at_pku.edu.cn
Vice dean of Dept of BME at PKU |
Education:
Ph.D. in computational fluid dynamics, Peking University, 2000;
M.S. in fluid dynamics, Peking University, 1997;
B.S. in engineering mechanics, Huazhong University of Science and Technology, 1992.
Research interests:
Research in the Zhu lab is currently centered at developing bioinformatics methods and tools for basic biomedicine studies. Recently methodology development includes gene finding algorithms for prokaryotes and eukaryotes, gene calling and sequence assembly in metagenomic shotgun reads. The lab also focuses on the regulatory mechanisms studies based on genome sequence and chip data analysis, comparative genomics, molecular evolution, and protein molecular dynamic simulation.
Academic Work experiences:
Since 2003, Peking University;
2007-2008, Visiting researcher of the University of Helsinki, Finland;
2001-2002, Postdoc. Peking University
Selected publications:
1． Xu CM, Zhu HQ*, Qiu P*. Aging progression of human gut microbiota. BMC Microbiology, 2019, 19: 236.
2． Fang ZC, Tan J, Wu SF, Li M, Xu CM, Xie ZJ, Zhu HQ*. PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning. GigaScience, 2019, 8(6): giz066. (IF: 7.267)
3． Jiang XQ, Li X, Yang LS, Liu CH, Wang Q, Chi WL, Zhu HQ*. How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes. Genomics, Proteomics & Bioinformatics, 2019, 17(1): 91-105. (5年IF: 6.615）
4． Wang Z, Xu CM, Liu YX, Wang XQ, Zhang L, Li M, Zhu SW, Xie ZJ, Wang PH, Duan LP, Zhu HQ*. Characteristic dysbiosis of gut microbiota of Chinese patients with diarrhea-predominant irritable bowel syndrome by an insight into the pan-microbiome. Chin Med J, 2019, 132(8): 889- 904. (5年IF: 1.196）
5． Zhang L, Liu YX, Wang Z, Wang XQ, Zhang JJ, Jiang RH, Wang XQ, Zhu SW, Wang K, Liu ZJ, Zhu HQ, Duan LP*. Clinical and fecal microbiota responses to probiotic or antidepressant in diarrhea-predominant irritable bowel syndrome patients with depression comorbidity: a pilot study. Chin Med J, 2019, 132(3): 346-351. (5年IF: 1.196）
6． Yu JF, Qu A, Tang,HC, Wang FH, Wang CL, Wang HM, Wang JH, Zhu HQ. A novel numerical model for protein sequences analysis based on spherical coordinates and multiple physicochemical properties of amino acids. Biopolymers, 2019, 110(11): e23282.（5年IF: 2.003）
7． Guo YG, Zhu HQ*, Wang Q*. Piezoelectric Effects in Surface-Engineered Two-Dimensional Group III Nitrides. ACS Applied Materials & Interfaces, 2019, 11(1): 1033-1039.
8． Yang C, Yang LS, Zhou M, Xie HL, Zhang CJ, Wang M DM, Zhu HQ*. LncADeep: An ab initio lncRNA identification and functional annotation tool based on deep learning. Bioinformatics, 2018, 34(22): 3825-3834.
9． Miao YY (Miao, Yuan-Yi), Xu CM, Xia M, Zhu HQ, Chen YQ*. Relationship between Gut Microbiota and Phosphorus Metabolism in Hemodialysis Patients: A Preliminary Exploration. Chin Med J, 2018, 131(23): 2792-2799.
10. Zhai P, Yang LS, Guo X, Wang Z, Guo JT, Wang XQ, Zhu HQ*. MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics. BMC Bioinformatics, 2017, 18: 434.
11. Yixuan Liu, Lu Zhang, Xiaoqi Wang, Zhe Wang, Jingjing Zhang, Ronghuan Jiang, Xiangqun Wang, Kun Wang, Zuojing Liu, Zhiwei Xia, Zhijie Xu,Yong Nie, Xianglin Lv, Xiaolei Wu, Huaiqiu Zhu*, Liping Duan*. Similar fecal microbiota signatures in patients with diarrhea-predominant irritable bowel syndrome and patients with depression. Clin. Gastroenterol. H., 2016, 14(11):1602-1611.
12． Feifei He, Yang Li, Yuhang Tang, Jian Ma*, Huaiqiu Zhu*. Identifying micro-inversions using high-throughput sequencing reads. BMC Genomics, 2016, 17 (Suppl 1): 4.
13．Binbin Lai, Fumeng Wang, Xiaoqi Wang, Lipng Duan, Huaiqiu Zhu*. InteMAP: Integrated metagenomic assembly pipeline for NGS short reads. BMC Bioinformatics, 2015, 16: 244.
14． Jiangtao Guo, Qi Wang, Xiaoqi Wang, Fumeng Wang, Jinxian Yao, Huaiqiu Zhu*. Horizontal gene transfer in an acid mine drainage microbial community. BMC Genomics, 2015, 16: 496.
15． Xiaoqi Wang, Qi Wang, Xiao Guo, Luying Liu, Jiangtao Guo, Jinxian Yao, Huaiqiu Zhu*. Functional genomic analysis of Hawaii marine metagenomes. Sci. Bull., 2015, 60(3): 348-355.
16．Liu, Yixuan; Zhang, Lu; Wang, Xiaoqi; Wang, Fumeng; Lv, Xianglin; Nie, Yong; Wu, Xiaolei; Zhu, Huaiqiu*; Duan, Li-ping*. Characterization of intestinal microbiome in diarrhea-predominant irritable bowel syndrome, depression patients and their comorbidity. Gastroenterology, 2015, 148(4): S119-S119.
17． Jinying Peng, Zhonghai Li, Xing Wen, Wenyang Li, Hui Shi, Longshu Yang, Huaiqiu Zhu, Hongwei Guo*. Salt-induced stabilization of EIN3/EIL1 confers salinity tolerance by deterring ROS accumulation in Arabidopsis. PLoS Genet., 2014, 10(10): e1004664.
18．Huaiqiu Zhu*, Qi Wang. Prediction of translation initiation site in bacterial and archaeal genomes. Curr. Bioinform., 2014, 9(2): 155-165.
19．Yongchu Liu, Jiangtao Guo, Gangqing Hu, Huaiqiu Zhu*. Gene prediction in metagenomic fragments based on the SVM algorithm. BMC Bioinformatics, 2013, 14 (Suppl 5): S12.
20． Binbin Lai, Ruogu Ding, Yang Li, Liping Duan, Huaiqiu Zhu*. A de novo metagenomic assembly program for shotgun DNA reads. Bioinformatics, 2012, 28(11): 1455-1462.
21．Xiaobin Zheng, Gang-Qing Hu, Zhen-Su She, Huaiqiu Zhu*. Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes. BMC Genomics, 2011, 12: 361.
22． Changqing Zhang, Jin Wang, Xu Hua, Jinggui Fang, Huaiqiu Zhu*, Xiang Gao*. A mutation degree model for the identification of transcriptional regulatory elements. BMC Bioinformatics, 2011, 12: 262.
23．WU Wen-Qi, ZHENG Xiao-Bin, LIU Yong-Chu, TANG Kai, ZHU Huai-Qiu*. Operon prediction based on an iterative self-learning algorithm. Prog. Biochem. Biophys., 2011, 38(7): 642-651.
24．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, 26(7): 1998-2006.
25．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(1): 95-99.
26． Chengwei Luo, Gang-Qing Hu, Huaiqiu Zhu*. Genome reannotation of Escherichia coli CFT073 with new insights into virulence. BMC Genomics, 2009, 10: 552.
27． 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(2): 165-169.
28． 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.
29． Gang-Qing Hu, Xiaobin Zheng, Huai-Qiu Zhu, Zhen-Su She*. Prediction of translation initiation site for microbial genomes with TriTISA. Bioinformatics, 2009, 25(1): 123-125.
30． 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.
31． 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.
32． Gang-Qing Hu, Xiaobin Zheng, Li-Ning Ju, Huaiqiu Zhu, Zhen-Su She*. Computational evaluation of TIS annotation for prokaryotic genomes. BMC Bioinformatics, 2008, 9: 160.
33． Xin-Qiu Yao, Huaiqiu Zhu, Zhen-Su She*. A dynamic Baysian network approach to protein secondary structure prediction. BMC Bioinformatics, 2008, 9: 49.
34． 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.
35．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.
36． Zhu Yang, John D. O’Brien, Xiaobin Zheng, Huai-Qiu Zhu, Zhen-Su She*. Tree and Rate Estimation by Local Evaluation of Heterochronous Nucleotide Data. Bioinformatics, 2007, 23: 169-176.
37． 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.
38．Wen Xue, Jin Wang, Zhirong Shen and Huaiqiu Zhu. Enrichment of transcriptional regulatory sites in non-coding genomic region. Bioinformatics. 2004, 20(4): 569-575.
Other Activities:
Associate editor of Int. J. Comput. Intelligence in Bioinformatics and Systems Biology (IJCIBSB)
Committee member of China Association of Biomedical Information Technology (CABMIT)
