朱怀球

2020-01-03 09:55:40 28

 

朱怀球

 博士生导师

电话:010-62767261
电子信箱:hqzhu_at_pku.edu.c

1992年本科毕业于华中理工大学(现华中科技大学)力学系工程力学专业;

1997年硕士毕业于北大力学系流体力学专业;

2000年博士毕业于北大力学系流体力学专业。

 

担任职务:

北京大学定量生物学中心教授;

北京大学工学院生物医学工程系教授、工学院副院长。

 

研究方向:

生物信息学,计算系统生物学

 

研究兴趣:

目前主要研究兴趣包括基于大数据的生物医学数据分析、基于下一代测序(NGS)技术的高通量基因组生物信息学方法和技术、环境与人体微生物组学、生物进化以及生物分子动力学分析等问题。主持发展的微生物基因组分析与基因预测系列方法达到国际领先水平,并被应用于美国St. Louis华盛顿大学、英国Sanger研究所和法国原子能委员会(CEA Cadarche)等多项国际微生物基因组测序计划。近年来,致力于发展基于下一代测序(NGS)技术的基因组生物信息学方法和技术,在微生物宏基因组学分析、人类基因组结构变异检测与疾病关联分析等方面的研究,完成了一系列原创性的工作。与美国Georgia Institute of Technology生物医学工程系相关实验室保持良好的合作关系。发表各类论文110余篇,其中SCI论文50余篇,研究结果已在Nucleic Acids Res.、Bioinformatics、BMC Bioinformatics、BMC Genomics、Nat. Machine Intelligence等学术期刊发表,多篇论文被BioMed Central评为“高访问率论文”,并多次被Cell、Nature、Nat. Methods、Nat. Rev. Microbiol.等正面引用或专门报道,H-index值达到13。

  

工作经历:

2001-02年北大湍流与复杂系统国家重点实验室博士后,开始转入生物信息学的交叉学科研究;

2003年1月留校任教;

2006年加入北大工学院生物医学工程系;

2007.9-2008.8期间赫尔辛基大学芬兰基因组中心访问学者。

 

代表性论文:

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.

 

学术兼职:

《Int. J. Comput. Intelligence in Bioinformatics and Systems Biology (IJCIBSB)》副主编,中国医药生物技术协会生物医学信息技术分会委员。