1. Ruifang Cao, Yunchao Ling, Jiayue Meng, Ao Jiang, Ruijin Luo, Qinwen He, Anan Li, Yujie Chen, Zoutao Zhang, Feng Liu#, Yixue Li#, Guoqing Zhang#. SMDB: a Spatial Multimodal Data Browser. Nucleic Acids Res 2023 Jul 5;51(W1):W553-W559.

2. Tingjun Xu, Wenxing Gao, Lixin Zhu#, Wanning Chen, Chaoqun Niu, Wenjing Yin, Liangxiao Ma, Xinyue Zhu, Yunchao Ling, Sheng Gao, Lei Liu, Na Jiao, Weiming Chen, Guoqing Zhang#, Ruixin Zhu#, Dingfeng Wu#. NAFLDkb: A Knowledge Base and Platform for Drug Development against Nonalcoholic Fatty Liver Disease. J Chem Inf Model 2023 May 11. doi: 10.1021/acs.jcim.3c00395.

3. Yimin Wang, Yunchao Ling, Jiao Gong, Xiaohan Zhao, Hanwen Zhou, Bo Xie, Haiyi Lou, Xinhao Zhuang, Li Jin, The Han100K Initiative, Shaohua Fan#, Guoqing Zhang#, Shuhua Xu#. PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform. Nucleic Acids Res 2023 Jan 6;51(D1):D1109-D1116.

4. Ling Wang, Wan Liu, Jieliang Liang, Linna Zhao, Qiang Li, Chenfen Zhou, Hui Cen, Qingbei Weng#, Guoqing Zhang#. Mining of novel secondary metabolite biosynthetic gene clusters from acid mine drainage. Sci Data 2022 Dec 9;9(1):760.

5. Dalang Yu, Junwei Zhu, Jianing Yang, Yi-Hsuan Pan, Hailong Mu, Ruifang Cao, Bixia Tang, Guangya Duan, Zi-Qian Hao, Long Dai, Guo-Ping Zhao, Ya-Ping Zhang, Wenming Zhao#, Guoqing Zhang#, Haipeng Li#. Global cold-chain related SARS-CoV-2 transmission identified by pandemic-scale phylogenomics. Zool Res 2022 Sep 18;43(5):871-874.

6. Mengyao Han, Liyun Yuan, Yuwei Huang, Guiying Wang, Changsheng Du#, Qingzhong Wang#, Guoqing Zhang#. Integrated co-expression network analysis uncovers novel tissue-specific genes in major depressive disorder and bipolar disorder. Front Psychiatry 2022 Aug 23;13:980315.

7. Feng Xu, Yifan Wang, Yunchao Ling, Chenfen Zhou, Haizhou Wang, Andrew E. Teschendorff, Yi Zhao, Haitao Zhao, Yungang He#, Guoqing Zhang#, Zhen Yang#. dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms. Genomics Proteomics Bioinformatics 2022 Jun;20(3):446-454.

8. Rong Zhou, Shengrong Zhou, Qiguang Xia, Tiejun Zhang, Guoqing Zhang#. Quantitative Data Integration Analysis Method for Cross-Studies: Obstructive Sleep Apnea as an Example. Comput Math Methods Med 2022 Jun 7;2022:1977446.

9. Yunchao Ling, Ruifang Cao, Jiaqiang Qian, Jiefu Li, Haokui Zhou, Liyun Yuan, Zhen Wang, Liangxiao Ma, Guangyong Zheng, Guoping Zhao, Zefeng Wang#, Guoqing Zhang#, Yixue Li#. An interactive viral genome evolution network analysis system enabling rapid large-scale molecular tracing of SARS-CoV-2. Sci Bull (Beijing) 2022 Apr 15;67(7):665-669.

10. Yiwei Wang*, Jiaxin Yang*, Xinhao Zhuang*, Yunchao Ling, Ruifang Cao, Qingwei Xu, Peng Wang#, Ping Xu#, Guoqing Zhang#. Linking genomic and epidemiologic information to advance the study of COVID-19. Sci Data 2022 Mar 30;9(1):121.

11. Dalang Yu, Xiao Yang, Bixia Tang, Yi-Hsuan Pan, Jianing Yang, Guangya Duan, Junwei Zhu, Zi-Qian Hao, Hailong Mu, Long Dai, Wangjie Hu, Mochen Zhang, Ying Cui, Tong Jin, Cui-Ping Li, Lina Ma, Language translation team, Xiao Su, Guoqing Zhang#, Wenming Zhao#, Haipeng Li#. Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2. Brief Bioinform 2022 Mar 10;23(2):bbab583.

12. Ningning Liu, Na Jiao, Jingcong Tan, Ziliang Wang, Dingfeng Wu, Anjun Wang, Jie Chen, Liwen Tao, Chenfen Zhou, Wenjie Fang, Lo Hong Cheong, Weihua Pan, Wanqing Liao, Zisis Kozlakidis, Christopher Heeschen, Geromy G. Moore, Lixin Zhu#, Xingdong Chen#, Guoqing Zhang#, Ruixin Zhu#, Hui Wang#. Multi-kingdom microbiota analyses identify bacterial-fungal interactions and biomarkers of colorectal cancer across cohorts. Nat Microbiol 2022 Feb;7(2):238-250.

13. Lu Zhao*, Wanning Chen*, Yongsheng Ge, Xin Lv, Ying Wang, Han Yu, Yi Liu, Dingfeng Wu, Na Jiao, Yuanqi Wu, Daqing Lv, Guoqing Zhang, Fuzhong Xue, Xiaohong Xu, Zhongtao Gai#, Ruixin Zhu#, Lei Zhang#, Guoping Zhao. Putative Familial Transmissible Bacteria of Various Body Niches Link with Home Environment and Children's Immune Health. Microbiol Spectr 2021 Dec 22;9(3):e0087221.

14. Hui Dong, Qiang Tan, Yuanyuan Xu, Yongqiang Zhu, Yaxian Yao, Yuezhu Wang, Chong Li, Hong Li, Guoqing Zhang, Yan Xiong, Meihua Ruan, Jiadong Zhao, Weirong Jin, Lungen Lu, Shun Lu#. Convergent alteration of lung tissue microbiota and tumor cells in lung cancer. iScience 2021 Dec 16;25(1):103638.

15. Meng Hao, Weilin Pu, Yi Li, Shaoqing Wen, Chang Sun, Yanyun Ma, Hongxiang Zheng, Xingdong Chen, Jingze Tan, Guoqing Zhang, Menghan Zhang, Shuhua Xu, Yi Wang, Hui Li, Jiucun Wang, Li Jin. The HuaBiao project: whole-exome sequencing of 5000 Han Chinese individuals. J Genet Genomics 2021 Nov 20;48(11):1032-1035

16. Yanzhi Ge, Chenfen Zhou, Xiujuan Xiao, Zhijiang Jin, Li Zhou, Zuxiang Chen, Fucun Liu, Qiang Yuan, Guoqing Zhang#, Letian Shan#, Peijian Tong#. A Novel Mutation of the KLK6 Gene in a Family With Knee Osteoarthritis. Front Genet 2021 Nov 11;12:784176.

17. Lu Zhang, Ruifang Cao, Tiantian Mao, Yuan Wang, Daqing Lv, Liangfu Yang, Yuanyuan Tang, Mengdi Zhou, Yunchao Ling, Guoqing Zhang#, Tianyi Qiu#, Zhiwei Cao#. SAS: A Platform of Spike Antigenicity for SARS-CoV-2. Front Cell Dev Biol 2021 Sep 20;9:713188.

18. CNCB-NGDC Members and Partners. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Res 2021 Jan 8;49(D1):D18-D28.

19. Wendi Huang, Yunchao Ling, Sirui Zhang, Qiguang Xia, Ruifang Cao, Xiaojuan Fan, Zhaoyuan Fang, Zefeng Wang#, Guoqing Zhang#. TransCirc: an interactive database for translatable circular RNAs based on multi-omics evidence. Nucleic Acids Res 2021 Jan 8;49(D1):D236-D242.

20. Ying Wang, Ning Li, Junjie Yang, Dongmei Zhao, Bin Chen, Guoqing Zhang, Shuo Chen, Ruifang Cao, Han Yu, Changying Zhao, Lu Zhao, Yongsheng Ge, Yi Liu, Lehai Zhang, Wei Hu, Lei Zhang, Zhongtao Gai. Probiotics and fructo-oligosaccharide intervention modulate the microbiota-gut brain axis to improve autism spectrum reducing also the hyper-serotonergic state and the dopamine metabolism disorder. Pharmacol Res 2020 Jul;157:104784.

21. Dingfeng Wu, Wenxing Gao, Xiaoyi Li, Chuan Tian, Na Jiao, Sa Fang, Jing Xiao, Zhifeng Xu, Lixin Zhu#, Guoqing Zhang#, Ruixin Zhu#. Dr AFC: drug repositioning through anti-fibrosis characteristic. Brief Bioinform 2021 May 20;22(3):bbaa115.

22. Hangyu Zhang, Liyun Yuan, Lulu Liu, Cong Yan, Jinming Cheng, Qihan Fu, Zhou Tong, Weiqin Jiang, Yi Zheng, Peng Zhao, Guoqing Zhang#, Weijia Fang#. Dynamic alterations of genome and transcriptome in KRAS G13D mutant CRC PDX model treated with cetuximab. BMC Cancer 2020 May 13;20(1):416.

23. Chenfen Zhou, Qingwei Xu, Sheng He, Wei Ye, Ruifang Cao, Pengyu Wang, Yunchao Ling, Xing Yan, Qingzhong Wang, Guoqing Zhang#. GTDB: an integrated resource for glycosyltransferase sequences and annotations. Database (Oxford) 2020 Jan 1;2020:baaa047.

24. Shijie C Zheng, Charles E Breeze, Stephan Beck, Danyue Dong, Tianyu Zhu, Liangxiao Ma, Wei Ye, Guoqing Zhang, Andrew E Teschendorff#. EpiDISH web server: Epigenetic Dissection of Intra-Sample-Heterogeneity with online GUI. Bioinformatics 2019 Nov 9;36(6):1950-1951.

25. National Genomics Data Center Members and Partners. Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Res 2020 Jan 8;48(D1):D24-D33.

26. Hong Sun#, Yangfan Guo, Xiaoping Lan, Jia Jia, Xiaoshu Cai, Guoqing Zhang, Jingjing Xie, Qian Liang, Yixue Li, Guangjun Yu#. PhenoModifier: a genetic modifier database for elucidating the genetic basis of human phenotypic variation. Nucleic Acids Res 2020 Jan 8;48(D1):D977-D982.

27. Yang Gao, Chao Zhang, Liyun Yuan, YunChao Ling, Xiaoji Wang, Chang Liu, Yuwen Pan, Xiaoxi Zhang, Xixian Ma, Yuchen Wang, Yan Lu, Kai Yuan, Wei Ye, Jiaqiang Qian, Huidan Chang, Ruifang Cao, Xiao Yang, Ling Ma, Yuanhu Ju, Long Dai, Yuanyuan Tang, The Han100K Initiative, Guoqing Zhang, Shuhua Xu#. PGG.Han: the Han Chinese genome database and analysis platform. Nucleic Acids Res 2020 Jan 8;48(D1):D971-D976.

28. Dalang Yu, Lili Dong, Fangqi Yan, Hailong Mu, Bixia Tang, Xiao Yang, Tao Zeng, Qing Zhou, Feng Gao, Zhonghuang Wang, Ziqian Hao, Hongen Kang, Yi Zheng, Hongwei Huang, Yuzhang Wei, Wei Pan, Yaochen Xu, Junwei Zhu, Shilei Zhao, Ciran Wang, Pengyu Wang, Long Dai, Mushan Li, Li Lan, Yiwei Wang, Hua Chen, Yixue Li, Yunxin Fu, Zhen Shao, Yiming Bao, Fangqing Zhao, Luonan Chen, Guoqing Zhang#, Wenming Zhao#, Haipeng Li#. eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses. Natl Sci Rev 2019 Oct;6(5):867-869.

29. Jie Ma, Tao Chen, Songfeng Wu, Chunyuan Yang, Mingze Bai, Kunxian Shu, Kenli Li, Guoqing Zhang, Zhong Jin, Fuchu He, Henning Hermjakob, Yunping Zhu. iProX: an integrated proteome resource. Nucleic Acids Res 2019 Jan 8;47(D1):D1211-D1217.

30. Shuang Yang, Guoqing Zhang, Wan Liu, Zhen Wang, Jifeng Zhang, Dongshan Yang, Y. Eugene Chen, Hong Sun, Yixue Li. SysFinder: A customized platform for search, comparison and assisted design of appropriate animal models based on systematic similarity. J Genet Genomics 2017 May 20;44(5):251-258.

31. Zhitao Yang, Suyuan Huang, Li Chen, Feng Liu, Xiaohui Cai, Yangfan Guo, Mingjie Wang, Yue Han, Demin Yu, Jiehong Jiang, Donghua Zhang, Qiming Gong, Guoqing Zhang, Zhonghua Lu, Lihua Huang, Xinxin Zhang. Characterization of Full-Length Genomes of Hepatitis B Virus Quasispecies in Sera of Patients at Different Phases of Infection. J Clin Microbiol 2015 Jul;53(7):2203-2214.

32. Guoqing Zhang, Yunsheng Zhang, Yunchao Ling, Jia Jia. Web Resources for Pharmacogenomics. Genomics, Proteomics & Bioinformatics 2015 Feb;13(1):51-54.

33. Jing Li, Jia Jia, Hong Li, Jian Yu, Han Sun, Ying He, Daqing Lv, Xiaojuan Yang, Michael O. Glocker, Liangxiao Ma, Jiabei Yang, Ling Li, Wei Li, Guoqing Zhang, Qian Liu, Yixue Li, Lu Xie. SysPTM 2.0: an updated systematic resource for post-translational modification. Database (Oxford) 2014 Apr 3;2014:bau025.

34. Jian Chen, Jia Sheng, Dijing Lv, Yang Zhong, Guoqing Zhang#, Peng Nan#. The optimization of running time for a maximum common substructure-based algorithm and its application in drug design. Comput Biol Chem 2014 Feb;48:14-20.

35. Shen Niu, Zhen Wang, Dongya Ge, Guoqing Zhang, Yixue Li. Prediction of functional phosphorylation sites by incorporating evolutionary information. Protein Cell 2012 Sep;3(9):675-690.

36. Jian Yu, Xiaobin Xing, Lingyao Zeng, Jiehuan Sun, Wei Li, Han Sun, Ying He, Jing Li, Guoqing Zhang, Chuan Wang, Yixue Li, Lu Xie. SyStemCell: A Database Populated with Multiple Levels of Experimental Data from Stem Cell Differentiation Research. PLoS One 2012;7(7):e35230.

37. Ying He, Menghuan Zhang, Yuanhu Ju, Zhonghao Yu, Daqing Lv, Han Sun, Weilan Yuan, Fei He, Jianshe Zhang, Hong Li, Jing Li, Rui Wang-Sattler, Yixue Li, Guoqing Zhang#, Lu Xie#. dbDEPC 2.0: updated database of differentially expressed proteins in human cancers. Nucleic Acids Res 2012 Jan;40(Database issue):D964-D971.

38. Tao Huang, Chuan Wang, Guoqing Zhang, Lu Xie, Yixue Li. SySAP: a system-level predictor of deleterious single amino acid polymorphisms. Protein Cell 2012 Jan;3(1):38-43.

39. Hui Dong, Yanjun Zhang, Hui Xiong, An Yan, Guohui Ding, Yangyi Chen, Liqun Xie, Jiazheng Chen, Guoqing Zhang, Pei Hao, Liming Cong, Yiyu Lu, Xiaoyan Che, Xiaoning Wang, Yixue Li, Kwok-Yung Yuen, Guoping Zhao, Weirong Jin. Detection of human novel influenza A (H1N1) viruses using multi-fluorescent real-time RT-PCR. Virus Res 2010 Jan;147(1):85-90.

40. Hui Yu, Fudong Yu, Guoqing Zhang, Xiang Shen, Yunqin Chen, Yuanyuan Li, Yixue Li. DBH2H: vertebrate head-to-head gene pairs annotated at genomic and post-genomic levels. Database (Oxford) 2009;2009:bap006.

41. Qingwei Xu, Yixiang Shi, Qiang Lu, Guoqing Zhang, Qingming Luo, Yixue Li. GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations. BMC Bioinformatics 2008;9 Suppl 1(Suppl 1):S6.

42. Pei Hao, Min Chen, Guoqing Zhang, Weizhong He, Yixue Li. Bioinformatics Research on the SARS Coronavirus (SARS_CoV) in China. Curr Pharm Des 2006;12(35):4565-4572.

43. Zhou Fang, Qingming Luo, Guoqing Zhang, Yixue Li. Biological networks to the analysis of microarray data. Progress in Natural Science 2006;16(12):1242-1251.

44. Guoqing Zhang, Zhiwei Cao, Qingming Luo, Yudong Cai, Yixue Li. Operon prediction based on SVM. Computational Biology and Chemistry 2006;30(3):233-240.