2025

1. Yichen Li^#, Wenxia Wang^#, Ruixin Zhu^*, Xinyue Zhu, Mingwei Sun, Yanlan Huang, Wanning Chen, Sheng Gao, Na Jiao, Xutao Lin, Jia Ke, Tao Xu, Linlin Hou^*, Ping Lan^*, Lixin Zhu^*. (2025). STAT1 mediates the pro-inflammatory role of GBP5 in colitis, Communications Biology.

2. Mengping Shen^#, Sheng Gao^#, Ruixin Zhu^*, Wei Wang, Wenxing Gao, Liwen Tao, Wanning Chen, Xinyue Zhu, Yuwei Yang, Tingjun Xu, Tingting Zhao, Na Jiao^*>, Min Zhi^*, Lixin Zhu^*. (2025) Multimodal Metagenomic Analysis Reveals Microbial InDels as Superior Biomarkers for Pediatric Crohn’s Disease, Journal of Crohn’s and Colitis. 2025, 19(4):jjaf039

3. Suqi Cao^#, Lei Liu^#, Liu Yang, Haomin Li, Ruixin Zhu, Gang Yu, Na Jiao^*, Dingfeng Wu^*. (2025). Assessing severe pneumonia risk in children via clinical prognostic model based on laboratory markers, International Immunopharmacology

4. Yuwei Yang^#, Wenxing Gao^#, Ruixin Zhu^*, Liwen Tao, Wanning Chen, Xinyue Zhu, Mengping Shen, Tingjun Xu, Tingting Zhao, Xiaobai Zhang, Lixin Zhu^*, Na Jiao^*. Systematic identificationof secondary bile acid production genes in global microbiome, mSystems, 2025: e00817-24.

2024

1. Wenxing Gao^#, Weili Lin^#, Qiang Li^#, Wanning Chen, Wenjing Yin, Xinyue Zhu, Sheng Gao, Lei Liu, Wenjie Li, Dingfeng Wu, Guoqing Zhang^*, Ruixin Zhu^*, Na Jiao^*. Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder, Nature Protocols, 2024, https://doi.org/10.1038/s41596-024-00999-9.
2. Na Jiao^*, Lixin Zhu^*, Ruixin Zhu^*. The search for authentic microbiome–disease relationships. Nature Medicine. 2024, https://doi.org/10.1038/s41591-024-02920-z
3. Xinyue Zhu^#, Pingping Xu^#, Ruixin Zhu^*, Wenxing Gao, Wenjing Yin, Ping Lan, Lixin Zhu^*, Na Jiao^*, Multi-kingdom microbial signatures in excess body weight colorectal cancer based on global metagenomic analysis, Communications Biology, 2024, 7:24, 10.1038/s42003-023-05714-0
4. Xiaoyi Li^#, Dingfeng Wu^#, Qiuyu Li, Jinglan Gu, Wenxing Gao, Xinyue Zhu, Wenjing Yin, Ruixin Zhu^*, Lixin Zhu^*, Na Jiao^*, Host-microbiota interactions contributing to the heterogeneous tumor microenvironment in colorectal cancer, Physiological Genomics. 2024,56 (2), 221-234

2023

1. Wenxing Gao^#, Xiang Gaosup>#</sup>, Lixin Zhu^*, Sheng Gao, Ruicong Sun, Zhongsheng Feng, Dingfeng Wu, Zhanju Liu^*, Ruixin Zhu^*, Na Jiao^*, Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer. Gut Microbes, 2023; https://doi.org/10.1080/19490976.2023.2245562.

2. Sheng Gao^#, Xiang Gao^#, Ruixin Zhu^*, Dingfeng Wu, Zhongsheng Feng, Na Jiao, Ruicong Sun, Wenxing Gao, Qing He^*, Zhanju Liu^*, Lixin Zhu^*. Microbial genes outperform species and SNVs as diagnostic markers for Crohn’s disease on multicohort fecal metagenomes empowered by artificial intelligence. Gut microbes, 2023, 15(1): 2221428.

3. 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^*, and Dingfeng Wu^*. NAFLDkb: A Knowledge Base and Platform for Drug Development against Nonalcoholic Fatty Liver Disease. J. Chem. Inf. Model. 2023; https://pubs.acs.org/doi/10.1021/acs.jcim.3c00395

4. Xiang Gao^#, Ruicong Sun^#, Na Jiao^#, Xiao Liang, Gengfeng Li, Han Gao, Xiaohan Wu, Muqing Yang, Chunqiu Chen, Liang Chen, Wei Wu, Zhong Li, Yingzi Cong, Ruixin Zhu^*, Tiannan Guo^*, Zhanju Liu^*, Integrative multi-omics deciphers the spatial characteristics of host-gut microbiota interactions in Crohn’s disease. Cell Reports Medicine. 2023; 4, 101050.

5. Fengtao Cai^#, Chenfen Zhou^#, Na Jiao^#, Xinling Liang, Zhiming Ye, Wei Chen, Qiongqiong Yang, Hui Peng, Ying Tang, Chaoqun Niu, Guoping Zhao, Zefeng Wang^*, Guoqing Zhang^*, Xueqing Yu^*. Systematic microbiome dysbiosis are associated with IgA nephropathy. Microbiology Spectrum. 2023, e05202-22.

6. Shaobo Zhao^#, Kun Zhu^#, Xiaoyi Li^#, Xiaohui Zhong, Yanyan Zhao, Zhicong Liu, Yi Xiao, Dengming Lai, Na Jiao^*, Qiang Shu^*. Co-expression and interaction network analysis reveals dysregulated neutrophil and T-cell activation as the core mechanism associated with septic shock[J]. Frontiers in Genetics, 2023, 14.

2022

1. Dingfeng Wu^#, Lei Liu^#, Na Jiao^#, Yida Zhang, Li Yang, Chuan Tian, Ping Lan, Lixin Zhu^*, Rohit Loomba^*, and Ruixin Zhu^*. Targeting Keystone Species Helps Restore the Dysbiosis of Butyrate-Producing Bacteria in Nonalcoholic Fatty Liver Disease. iMeta, 2022; e61. https://doi.org/10.1002/imt2.61

2. Ningning Liu^#, Na Jiao^#, Jing-Cong Tan^#, Ziliang Wang^#, Dingfeng Wu, An-Jun Wang, Jie Chen, Liwen Tao, Chenfen Zhou, Wenjie Fang, Io 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. Nature Microbiology, 2022; 7(2):238-250.

3. Sheng Gao, Yichen Li, Dingfeng Wu, Na Jiao, Li Yang, Rui Zhao, Zhifeng Xu, Wanning Chen, Xutao Lin, Sijing Cheng, Lixin Zhu^*, Ping Lan^*, Ruixin Zhu^*. IBD subtype-regulators IFNG and GBP5 identified by causal inference drive more intense innate immunity and inflammatory responses in CD than those in UC. Frontiers in Pharmacology, 2022, p.1049.

2021

1. Yuqi Wu^#, Na Jiao^#, Ruixin Zhu^*, Yida Zhang, Dingfeng Wu, An-Jun Wang, Sa Fang, Liwen Tao, Yichen Li, Sijing Cheng, Ping Lan, Chuan Tian^*, Ning-Ning Liu^*, Lixin Zhu^*. Identification of microbial markers across populations in early detection of colorectal cancer. Nature Communications, 2021; 12(1):3063

2. Na Jiao^#, Rohit Loomba^#*, Zi-Huan Yang, Dingfeng Wu, Sa Fang, Richele Bettencourt, Ping Lan, Ruixin Zhu^*, Lixin Zhu^*. Alterations in bile acid metabolizing gut microbiota and specific bile acid genes as a precision medicine to subclassify NAFLD. Physiological Genomics, 2021; 53(8):336-348.

3. Yichen Li^#, Jie Li^#, Jia Ke^#, Na Jiao^#, Lixin Zhu^#*, Lihan Shen, Lei Chen, Zhiqiang Jiang, Sijing Cheng, Yibo Huang, Yifeng Zou, Ruixin Zhu^*, and Guangjun Yan^*. Adverse Outcomes Associated with Corticosteroid Use in Critical COVID-19: A Retrospective Multicenter Cohort Study. Frontiers of Medicine, 2021; 8: 604263.

4. Jingrong Weng^#, Yichen Li^#, Jie Li^#, Lihan Shen^#, Lixin Zhu^#*, Yufan Liang, Xutao Lin, Na Jiao, Sijing Cheng, Yibo Huang, Yifeng Zou^*, Guangjun Yan^*, Ruixin Zhu^*, Ping Lan^*. Gastrointestinal sequelae in patients after discharge for COVID-19. The Lancet Gastroenterology & Hepatology. 2021, 6(5): 344-346.

5. 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. Microbiology Spectrum. 2021, 9(3): e00872-21.

Before 2021

1. Yichen Li^#, Na Jiao^#, Lixin Zhu^*, Sijing Cheng, Ruixin Zhu^*; Ping Lan^*.Non-febrile COVID-19 patients were common and often became critically ill: a retrospective multicenter cohort study. Critical Care, 2020; 24:314.

2. Sijing Cheng^#, Dingfeng Wu^#, Jie Li, Yifeng Zou, Yunle Wan, Lihan Shen, Lixin Zhu^*, Mang Shi, Linlin Hou, Tao Xu, Na Jiao, Yichen Li, Yibo Huang, Zhipeng Tang, Mingwei Xu, Shusong Jiang, Maokun Li^*, Guangjun Yan^*, Ping Lan^*, and Ruixin Zhu^*. Risk factors for the critical illness in SARS-CoV-2 infection: a multicenter retrospective cohort study. Respiratory Research, 2020; 21(1), 277. DOI: https://doi.org/10.1186/s12931-020-01492-zLu.

3. Dingfeng Wu^#, WenxingGao^#, Xiaoyi Li^#, Chuan Tian, Na Jiao, Sa Fang, Jing Xiao, Zhifeng Xu, Lixin Zhu^*, Guoqing Zhang^* and Ruixin Zhu^*. Dr AFC: Drug Repositioning Through Anti-Fibrosis Characteristic. Briefings in Bioinformatics, 2020; 22(3). DOI: https://doi.org/10.1093/bib/bbaa115.

4. Yunle Wan^#, Jie Li^#, Lihan Shen^#,Yifeng Zou^#, Linlin Hou^#, Lixin Zhu^#,*, Howard S.Faden, Zhipeng Tang, Mang Shi, Na Jiao, Yichen Li, Sijing Cheng, Yibo Huang, Dingfeng Wu, ZhifengXu, Linnuo Pan, Jun Zhu, GuangjunYan^*, Ruixin Zhu^*, and Ping Lan^*. Enteric involvement in hospitalised patients with COVID-19 outside Wuhan. The Lancet Gastroenterology & Hepatology, 2020; 5(6), 534–535. DOI: https://doi.org/10.1016/S2468-1253(20)30118-7.

5. Sheng Gao^#, Qian Zhang^#, Chuan Tian, Chun Li, Yunzheng Lin, Wenxing Gao, Dingfeng Wu, Na Jiao, Lixin Zhu, Wenzhe Li, Ruixin Zhu^*, Wei Wang^*, Yong Wang^*. The roles of Qishen granules recipes, Qingre Jiedu, Wenyang Yiqi and Huo Xue, in the treatment of heart failure. Journal of Ethnopharmacology, 2020; 249, 112372.

6. Yali Zhang^#, Liting Cai^#, Junyi Qi, Yunzheng Lin, Yancheng Dai, Na Jiao, Youlan Chen, Lie Zheng, Beibei Wang, Lixin Zhu, Zhipeng Tang^*, and Ruixin Zhu. Gut Microbiota Contributes to the Distinction Between Two Traditional Chinese Medicine Syndromes of Ulcerative Colitis. World Journal of Gastroenterology, 2020; 25(25), 3242. (IF=5.374)

7. Na Jiao, Susan S Baker^*, Adrian Chapa-Rodriguez, Wensheng Liu, Colleen A Nugent, Maria Tsompana, Lucy Mastrandrea, Michael J Buck, Robert D Baker, Robert J Genco, Ruixin Zhu^*, Lixin Zhu^*. Suppressed hepatic bile acid signalling despite elevated production of primary and secondary bile acids in NAFLD. Gut. 2018; 67(10):1881-1891

8. Na Jiao, Susan S. Baker, Colleen A. Nugent, Maria Tsompana, Liting Cai, Yong Wang, Michael J. Buck, Robert J. Genco, Robert D. Baker, Ruixin Zhu^*, Lixin Zhu^*. Gut microbiome may contribute to insulin resistance and systemic inflammation in obese rodents: a meta-analysis. Physiological Genomics. 2018; 50(4):244-254. (APSselect award https://www.physiology.org/toc/apsselect/5/4)

9. Xiaoyi Li^#, , Hong Kang, Wensheng Liu, Sarita Singhal, Na Jiao, Yong Wang, Lixin Zhu, Ruixin Zhu^*. In silico Design of Novel Proton Pump Inhibitors with Reduced Adverse Effect. Frontiers of Medicine, 2018; 13(2): 277-284. (IF=9.927)

10. Wei Xie^#*, Na Jiao^#, Cenling Ma, Sa Fang, Tommy J Phelps, Ruixin Zhu^*, Chuanlun Zhang. The response of archaeal species to seasonal variables in a subtropical aerated soil: insight into the low abundant methanogens. Applied Microbiology and Biotechnology, 2017;101(16):6505-6515.

11. Zhen Sheng^#, Yi Sun, Ruixin Zhu, Na Jiao, Kailin Tang, Zhiwei Cao^*, Chao Ma^*. Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine. PLoS ONE, 2015; 10(11): e0143742.