Selected publications

  1. 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.
  2. Feifei He, Yang Li, Yuhang Tang, Jian Ma and Huaiqiu Zhu. Identifying micro-inversions using high-throughput sequencing reads. BMC Genomics, 2016, 17(Suppl 1): 4.
  3. Binbin Lai, Fumeng Wang, Xiaoqi Wang, Lipng Duan and Huaiqiu Zhu*. InteMAP: Integrated Metagenomic Assembly Pipeline for NGS Short Reads. BMC Bioinformatics, 2015, 16: 244. (Highly accessed article)
  4. Jiangtao Guo, Qi Wang, Xiaoqi Wang, Fumeng Wang, Jinxian Yao and Huaiqiu Zhu*. Horizontal gene transfer in an acid mine drainage microbial community. BMC Genomics, 2015, 16: 496. (Highly accessed article)
  5. Xiaoqi Wang, Qi Wang, Xiao Guo, Luying Liu, Jiangtao Guo, Jinxian Yao and Huaiqiu Zhu*. Functional genomic analysis of Hawaii marine metagenomes. Sci. Bull., 2015, 60(3): 348-355
  6. Xiaopeng Song, Xiao Hu, Shuqin Zhou, Yuanyuan Xu, Yi Zhang, Yonggui Yuan, Yijun Liu, Huaiqiu Zhu, Weiguo Liu and Jia-Hong Gao. Association of specific frequency bands of functional MRI signal oscillations with motor symptoms and depression in Parkinson's disease. Sci. Rep.-UK, 2015, 5: 16376.
  7. Xiaopeng Song, Shuqin Zhou, Yi Zhang, Yijun Liu, Huaiqiu Zhu and Jia-Hong Gao. Frequency-dependent modulation of regional synchrony in the human brain by eyes open and eyes closed resting-states. PLoS One. 2015, 10(11): e0141507.23.
  8. Jinying Peng, Zhonghai Li, Xing Wen, Wenyang Li, Hui Shi, Longshu Yang, Huaiqiu Zhu, and Hongwei Guo*. Salt-induced stabilization of EIN3/EIL1 confers salinity tolerance by deterring ROS accumulation in Arabidopsis. PLoS Genet., 2014, 10(10): e1004664.
  9. Huaiqiu Zhu*, Qi Wang. Prediction of translation initiation site in bacterial and archaeal genomes. Curr. Bioinform., 2014, 9(2): 155-165.
  10. Yongchu Liu, Jiangtao Guo, Gangqing Hu, Huaiqiu Zhu*. Gene prediction in metagenomic fragments based on the SVM algorithm. BMC Bioinformatics, 2013, 14 (S5): S12.
  11. Binbin Lai, Ruogu Ding, Yang Li, Liping Duan and Huaiqiu Zhu*. A de novo metagenomic assembly program for shotgun DNA reads. Bioinformatics, 2012, 28(11): 1455-1462.
  12. Xiaobin Zheng, Gang-Qing Hu, Zhen-Su She and Huaiqiu Zhu*. Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes. BMC Genomics, 2011, 12: 361. (Highly accessed article)
  13. Changqing Zhang , Jin Wang , Xu Hua , Jinggui Fang , Huaiqiu Zhu and Xiang Gao. A mutation degree model for the identification of transcriptional regulatory elements. BMC Bioinformatics, 2011, 12: 262.
  14. 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.
  15. 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.
  16. 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.
  17. Chengwei Luo, Gang-Qing Hu and Huaiqiu Zhu*, Genome reannotation of Escherichia coli CFT073 with new insights into virulence, BMC Genomics, 2009, 10: 552. (Highly accessed article)
  18. 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.
  19. 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.
  20. 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.
  21. ZHANG ChangQing, WANG Jin, ZHU Huaiqiu, GAO Xiang. The transcriptional regulatory mechanism of CYP72B1 and AUR3 in response to light, auxin and brassinosteroid. Prog. Biochem. Biophys., 2009, 36(9): 1215-1221.
  22. 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.
  23. 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.
  24. 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.
  25. Xin-Qiu Yao, Huaiqiu Zhu, Zhen-Su She. A dynamic Bayesian network approach to protein secondary atructure prediction. BMC Bioinformatics, 2008, 9: 49.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. Wen Xue, Jin Wang, Zhirong Shen, Huaiqiu Zhu. Enrichment of transcriptional regulatory sites in non-coding genomic region. Bioinformatics, 2004, 20(4): 569-575.