[1] Tianyuan Zhang, Mian Jiang, Hanzhou Li, Yunyun Gao, Salsabeel Yousuf, Kaimin Yu, Xinxin Yi, Jun Wang, Lulu Yang, Yong-Xin Liu. 2025. Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio. Genomics, Proteomics & Bioinformatics qzaf075. https://doi.org/10.1093/gpbjnl/qzaf075
[2] Defeng Bai, Tong Chen, Jiani Xun, Chuang Ma, Hao Luo, Haifei Yang, Chen Cao, Xiaofeng Cao, Jianzhou Cui, Yuan-Ping Deng, Zhaochao Deng, Wenxin Dong, Wenxue Dong, Juan Du, Qunkai Fang, Wei Fang, Yue Fang, Fangtian Fu, Min Fu, Yi-Tian Fu, He Gao, Jingping Ge, Qinglong Gong, Lunda Gu, Peng Guo, Yuhao Guo, Tang Hai, Hao Liu, Jieqiang He, Zi-Yang He, Huiyu Hou, Can Huang, Shuai Ji, ChangHai Jiang, Gui-Lai Jiang, Lingjuan Jiang, Ling N. Jin, Yuhe Kan, Da Kang, Jin Kou, Ka-Lung Lam, Changchao Li, Chong Li, Fuyi Li, Liwei Li, Miao Li, Xin Li, Ye Li, Zheng-Tao Li, Jing Liang, Yongxin Lin, Changzhen Liu, Danni Liu, Fengqin Liu, Jia Liu, Tianrui Liu, Tingting Liu, Xinyuan Liu, Yaqun Liu, Bangyan Liu, Minghao Liu, Wenbo Lou, Yaning Luan, Yuanyuan Luo, Hujie Lv, Tengfei Ma, Zongjiong Mai, Jiayuan Mo, Dongze Niu, Zhuo Pan, Heyuan Qi, Zhanyao Shi, Chunjiao Song, Fuxiang Sun, Yan Sun, Sihui Tian, Xiulin Wan, Guoliang Wang, Hongyang Wang, Hongyu Wang, Huanhuan Wang, Jing Wang, Jun Wang, Kang Wang, Leli Wang, Shao-kun Wang, Xinlong Wang, Yao Wang, Zufei Xiao, Huichun Xing, Yifan Xu, Shu-yan Yan, Li Yang, Song Yang, Yuanming Yang, Xiaofang Yao, Salsabeel Yousuf, Hao Yu, Yu Lei, Zhengrong Yuan, Meiyin Zeng, Chunfang Zhang, Chunge Zhang, Huimin Zhang, Jing Zhang, Na Zhang, Tianyuan Zhang, Yi-Bo Zhang, Yupeng Zhang, Zheng Zhang, Mingda Zhou, Yuanping Zhou, Chengshuai Zhu, Lin Zhu, Yue Zhu, Zhihao Zhu, Hongqin Zou, Anna Zuo, Wenxuan Dong, Tao Wen, Shifu Chen, Guoliang Li, Yunyun Gao, Yong-Xin Liu. 2025. EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research. iMeta 4: e70001. https://doi.org/10.1002/imt2.70001
[3] Defeng Bai, Chuang Ma, Jiani Xun, Hao Luo, Haifei Yang, Hujie Lyu, Zhihao Zhu, Anran Gai, Salsabeel Yousuf, Kai Peng, Shanshan Xu, Yunyun Gao, Yao Wang, Yong-Xin Liu. 2025. MicrobiomeStatPlots: Microbiome statistics plotting gallery for meta-omics and bioinformatics. iMeta 4: e70002. https://doi.org/10.1002/imt2.70002
[4] Kai Peng, Yunyun Gao, Changan Li, Qiaojun Wang, Yi Yin, Muhammad Fazal Hameed, Edward Feil, Sheng Chen, Zhiqiang Wang, Yong-Xin Liu, Ruichao Li. 2025. Benchmarking of analysis tools and pipeline development for nanopore long-read metagenomics. Science Bulletin 70: 1591-1595. https://doi.org/10.1016/j.scib.2025.03.044
[5] Yunyun Gao, Hao Luo, Hujie Lyu, Haifei Yang, Salsabeel Yousuf, Shi Huang, Yong-Xin Liu. 2025. Benchmarking short-read metagenomics tools for removing host contamination. GigaScience 14: https://doi.org/10.1093/gigascience/giaf004
[6] Tao Wen, Yong-Xin Liu, Lanlan Liu, Guoqing Niu, Zhexu Ding, Xinyang Teng, Jie Ma, Ying Liu, Shengdie Yang, Penghao Xie, Tianjiao Zhang, Lei Wang, Zhanyuan Lu, Qirong Shen, Jun Yuan. 2025. ggClusterNet 2: An R package for microbial co-occurrence networks and associated indicator correlation patterns. iMeta 4: e70041. https://doi.org/10.1002/imt2.70041
[7] Yujia Wu, Lyu Hujie, Deng Xuliang, Liu Yong-Xin, He Ying, Mingming Xu. 2025. Correlation between oral microbiota and dry socket at different time periods on tooth extraction. Journal of Oral Microbiology 17: 2485210. https://doi.org/10.1080/20002297.2025.2485210
[8] Yanli Li, Wenjun Zhao, Bingyan Jiang, Xiao-Chun Huang, Jie Liu, Junyuan Huang, Bang Hu, Yong-Xin Liu, Bing Du, Pan Li. 2025. Effects of inactivated bacillus sp. DU-106 on high-fat diet-induced obesity and the gut–liver axis. International Journal of Food Science and Technology vvaf028. https://doi.org/10.1093/ijfood/vvaf028
[9] Salsabeel Yousuf, Yao Wang, Peng Yu, Yong-Xin Liu. 2025. 'Metagenomic Analysis for Unveiling Agricultural Microbiome—2nd Edition', Agronomy.
[10] Jingying Zhang, Bing Wang, Haoran Xu, Weidong Liu, Jingwei Yu, Qiuxia Wang, Hong Yu, Jin-Wei Wei, Rui Dai, Jinghang Zhou, Yuhang He, Di Zou, Jinhua Yang, Xinwei Ban, Qingliang Hu, Xiangbing Meng, Yong-Xin Liu, Binglei Wang, Bin Hu, Mingyu Wang, Peiyong Xin, Jinfang Chu, Changsheng Li, Ruben Garrido-Oter, Peng Yu, Aalt Dirk Jan van Dijk, Lemeng Dong, Harro Bouwmeester, Song Gao, Ancheng Huang, Chengcai Chu, Jiayang Li, Yang Bai. 2025. Root microbiota regulates tiller number in rice. Cell 188: 3152-3166. https://doi.org/10.1016/j.cell.2025.03.033
[11] Penghao Sun, Mengli Wang, Xuejun Chai, Yong-Xin Liu, Luqi Li, Wei Zheng, Shulin Chen, Xiaoyan Zhu, Shanting Zhao. 2025. Disruption of tryptophan metabolism by high-fat diet-triggered maternal immune activation promotes social behavioral deficits in male mice. Nature Communications 16: 2105. https://doi.org/10.1038/s41467-025-57414-4
[12] Yunyun Gao, Guoxing Zhang, Shunyao Jiang, Yong-Xin Liu. 2024. Wekemo Bioincloud: A user-friendly platform for meta-omics data analyses. iMeta 3: e175. https://doi.org/10.1002/imt2.175
[13] Yunyun Gao, Kai Peng, Defeng Bai, Xiao-Ye Bai, Yujing Bi, Anqi Chen, Baodong Chen, Feng Chen, Juan Chen, Lei Chen, Tong Chen, Wei Chen, Xu Cheng, Yanfen Cheng, Jie Cui, Jingjing Dai, Junbiao Dai, Zhaolai Dai, Ye Deng, Yi-Zhen Deng, Wei Ding, Zhencheng Fang, Wei Fu, Hanbing Gao, Shaohua Gu, Xue Guo, Xuguang Guo, Dongfei Han, Lele He, Yatao He, Hui-Yu Hou, Baolei Jia, Gengjie Jia, Shuo Jiao, Wei Jin, Feng Ju, Zhicheng Ju, Siyuan Kong, Canhui Lan, Bing Li, Da Li, Diyan Li, Jingdi Li, Meng Li, Qi Li, Qiang Li, Wen-Jun Li, Xiaofang Li, Xuemeng Li, Yahui Li, You-Gui Li, Zhibin Liang, Ning Ling, Fufeng Liu, Qing Liu, Shuang-Jiang Liu, Hongye Lu, Qi Lu, Guangwen Luo, Hao Luo, Yuheng Luo, Hujie Lyu, Chuang Ma, Liyuan Ma, Tengfei Ma, Jinfeng Ni, Ziqin Pang, Xiaojing Qiang, Yuan Qin, Qingyue Qu, Chao Ran, Shuqiang Ren, Haitao Shang, Luyang Song, Linyang Sun, Weimin Sun, Liping Tang, Jian Tian, Kai Wang, Mengzhi Wang, Ming-Ke Wang, Tao Wang, Xiao-Yan Wang, Yao Wang, Yiwen Wang, Youshan Wang, Hailei Wei, Hong Wei, Zhong Wei, Tao Wen, Jiqiu Wu, Linhuan Wu, Linkun Wu, Jiao Xi, Bo Xie, Guofang Xu, Jun Xu, Shanshan Xu, Qing Xue, Liping Yan, Haifei Yang, Jun Yang, Junbo Yang, Ruifu Yang, Yalin Yang, Ying-Jie Yang, Xiaofang Yao, Yanpo Yao, Salsabeel Yousuf, Ke Yu, Zhengrong Yuan, Zhilin Yuan, Dong Zhang, Tianyuan Zhang, Weipeng Zhang, Yunzeng Zhang, Zhaonan Zhang, Zhen Zhang, Zhi-Feng Zhang, Shengguo Zhao, Wei Zhao, Maosheng Zheng, Ziqiang Zheng, Xin Zhou, Yuanping Zhou, Zhigang Zhou, Mo Zhu, Yong-Guan Zhu, Haiyan Chu, Yang Bai, Yong-Xin Liu. 2024. The Microbiome Protocols eBook initiative: Building a bridge to microbiome research. iMeta 3: e182. https://doi.org/10.1002/imt2.182
[14] Tianyuan Zhang, Hanzhou Li, Mian Jiang, Huiyu Hou, Yunyun Gao, Yali Li, Fuhao Wang, Jun Wang, Kai Peng, Yong-Xin Liu. 2024. Nanopore sequencing: flourishing in its teenage years. Journal of Genetics and Genomics https://doi.org/10.1016/j.jgg.2024.09.007
[15] Chun-Lin Shi, Yong-Xin Liu. 2024. Dynamic control of lipid provisioning in plant-fungal symbiosis. Molecular Plant 367-367. https://doi.org/10.1016/j.molp.2024.02.009
[16] Yao Wang, Peng Yu, Yong-Xin Liu. 2024. Metagenomic Analysis for Unveiling Agricultural Microbiome. Agronomy 14: 981. https://doi.org/10.3390/agronomy14050981
[17] Chun-Lin Shi, Tong Chen, Canhui Lan, Ren-You Gan, Jun Yu, Fangqing Zhao, Yong-Xin Liu. 2024. iMetaOmics: Advancing human and environmental health through integrated meta-omics. iMetaOmics 1: e21. https://doi.org/10.1002/imo2.21
[18] Tong Chen, Yong-Xin Liu, Tao Chen, Mei Yang, Siqing Fan, Minglei Shi, Buqing Wei, Huijiao Lv, Wandi Cao, Chongming Wang, Jianzhou Cui, Jiwen Zhao, Yilai Han, Jiao Xi, Ziqiang Zheng, Luqi Huang. 2024. ImageGP 2 for enhanced data visualization and reproducible analysis in biomedical research. iMeta 3: e239. https://doi.org/10.1002/imt2.239
[19] Mei Yang, Tong Chen, Yong-Xin Liu, Luqi Huang. 2024. Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams. iMeta 3: e184. https://doi.org/10.1002/imt2.184
[20] Yuanping Zhou, Yong-Xin Liu, Xuemeng Li. 2024. USEARCH 12: Open-source software for sequencing analysis in bioinformatics and microbiome. iMeta 3: e236. https://doi.org/10.1002/imt2.236
[21] Shanshan Xu, Hao Zhou, Boyang Xu, Wuyang Liu, Weiqi Hu, Qinxiang Xu, Jiong Hong, Yongxin Liu, Xingjiang Li. 2024. Environmental microbiota and its influence on microbial succession and metabolic profiles in baijiu fermentation across three distinct-age workshops. LWT 201: 116262. https://doi.org/10.1016/j.lwt.2024.116262
[22] Shanshan Xu, Hao Zhou, Boyang Xu, Wuyang Liu, Weiqi Hu, Qinxiang Xu, Jiong Hong, Yongxin Liu, Xingjiang Li. 2024. Deciphering layer formation in Red Heart Qu: A comprehensive study of metabolite profile and microbial community influenced by raw materials and environmental factors. Food Chemistry 451: 139377. https://doi.org/10.1016/j.foodchem.2024.139377
[23] Kai Peng, Yong-Xin Liu, Xinran Sun, Qiaojun Wang, Luyang Song, Zhiqiang Wang, Ruichao Li. 2024. Large-scale bacterial genomic and metagenomic analysis reveals Pseudomonas aeruginosa as potential ancestral source of tigecycline resistance gene cluster tmexCD-toprJ. Microbiological Research 285: 127747. https://doi.org/10.1016/j.micres.2024.127747
[24] Tao Wang, Penghao Li, Xue Bai, Shilin Tian, Maosen Yang, Dong Leng, Hua Kui, Sujuan Zhang, Xiaomiao Yan, Qu Zheng, Pulin Luo, Changming He, Yan Jia, Zhoulin Wu, Huimin Qiu, Jing Li, Feng Wan, Muhammad A. Ali, Rurong Mao, Yong-Xin Liu, Diyan Li. 2024. Vaginal microbiota are associated with in vitro fertilization during female infertility. iMeta 3: e185. https://doi.org/10.1002/imt2.185
[25] Ming-Hao Lv, Wen-Chong Shi, Ming-Cong Li, Bo Zhou, Yong-Xin Liu, Zheng Gao. 2024. Ms gene and Mr gene: Microbial-mediated spatiotemporal communication between plants. iMeta 3: e210. https://doi.org/10.1002/imt2.210
[26] Zhongji Pu, Chun-Lin Shi, Che Ok Jeon, Jingyuan Fu, Shuang-Jiang Liu, Canhui Lan, Yanlai Yao, Yong-Xin Liu, Baolei Jia. 2024. ChatGPT and generative AI are revolutionizing the scientific community: A Janus-faced conundrum. iMeta 3: e178. https://doi.org/10.1002/imt2.178
[27] Yao Wang, Yong-Fu Tao, Hong-Ru Wang, Guo-Hua Du, Qian-Si Chen, Yong-Xin Liu, Hong Lu. 2024. Role of soil microbes in enhancing crop heterosis. iMetaOmics 1: e20. https://doi.org/10.1002/imo2.20
[28] Xiaofang Yao, Qiumei Liu, Yongxin Liu, Dejun Li. 2024. Managing Macadamia Decline: A Review and Proposed Biological Control Strategies. Agronomy 14: 308. https://doi.org/10.3390/agronomy14020308
[29] Shi Zhong, Yu-Qing Sun, Jin-Xi Huo, Wen-Yi Xu, Ya-Nan Yang, Jun-Bo Yang, Wei-Jie Wu, Yong-Xin Liu, Chong-Ming Wu, You-Gui Li. 2024. The gut microbiota-aromatic hydrocarbon receptor (AhR) axis mediates the anticolitic effect of polyphenol-rich extracts from Sanghuangporus. iMeta 3: e180. https://doi.org/10.1002/imt2.180
[30] Zhiguang Qiu, Li Yuan, Chun-Ang Lian, Bin Lin, Jie Chen, Rong Mu, Xuejiao Qiao, Liyu Zhang, Zheng Xu, Lu Fan, Yunzeng Zhang, Shanquan Wang, Junyi Li, Huiluo Cao, Bing Li, Baowei Chen, Chi Song, Yongxin Liu, Lili Shi, Yonghong Tian, Jinren Ni, Tong Zhang, Jizhong Zhou, Wei-Qin Zhuang, Ke Yu. 2024. BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis. Nature Communications 15: 2179. https://doi.org/10.1038/s41467-024-46539-7
[31] Mengli Wang, Penghao Sun, Xuejun Chai, Yong-Xin Liu, Luqi Li, Wei Zheng, Shulin Chen, Xiaoyan Zhu, Shanting Zhao. 2024. Reconstituting gut microbiota-colonocyte interactions reverses diet-induced cognitive deficits: The beneficial of eucommiae cortex polysaccharides. Theranostics 14: 4622-4642. https://doi.org/10.7150/thno.99468
[32] Min Fu, Yunhe Chen, Yong-Xin Liu, Xiaoxi Chang, Lei Zhang, Xinyi Yang, Li Li, Lixin Zhang. 2024. Genotype-associated core bacteria enhance host resistance against kiwifruit bacterial canker. Horticulture Research uhae236. https://doi.org/10.1093/hr/uhae236
[33] Yong-Xin Liu, Lei Chen, Tengfei Ma, Xiaofang Li, Maosheng Zheng, Xin Zhou, Liang Chen, Xubo Qian, Jiao Xi, Hongye Lu, Huiluo Cao, Xiaoya Ma, Bian Bian, Pengfan Zhang, Jiqiu Wu, Ren-You Gan, Baolei Jia, Linyang Sun, Zhicheng Ju, Yunyun Gao, Tao Wen, Tong Chen. 2023. EasyAmplicon: An easy-to-use, open-source, reproducible, and community-based pipeline for amplicon data analysis in microbiome research. iMeta 2: e83. https://doi.org/10.1002/imt2.83
[34] Tao Wen, Guoqing Niu, Tong Chen, Qirong Shen, Jun Yuan, Yong-Xin Liu. 2023. The best practice for microbiome analysis using R. Protein & Cell 14: 713-725. https://doi.org/10.1093/procel/pwad024
[35] Wenjun Li, Likun Wang, Xiaofang Li, Xin Zheng, Michael F. Cohen, Yong-Xin Liu. 2023. Sequence-Based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes. Genomics, Proteomics & Bioinformatics 21: 1182-1194. https://doi.org/10.1016/j.gpb.2022.08.006
[36] Yunyun Gao, Danyi Li, Yong-Xin Liu. 2023. Microbiome research outlook: past, present, and future. Protein & Cell 14: 709-712. https://doi.org/10.1093/procel/pwad031
[37] Yong-Xin Liu, Chun-Lin Shi, Tengfei Ma, Wubin Ding, Danyi Li, Tong Chen, Jingyuan Fu, Shuang-Jiang Liu. 2023. iMeta progress and acknowledgment of reviewers in 2022. iMeta 2: e89. https://doi.org/10.1002/imt2.89
[38] Kai Peng, Yong-xin Liu, Xinran Sun, Qiaojun Wang, Pengcheng Du, Yunzeng Zhang, Mianzhi Wang, Zhiqiang Wang, Ruichao Li. 2023. Long-read metagenomic sequencing reveals that high-copy small plasmids shape the highly prevalent antibiotic resistance genes in animal fecal microbiome. Science of The Total Environment 893: 164585. https://doi.org/10.1016/j.scitotenv.2023.164585
[39] Yuanping Zhou, Wenjiao Luo, Maoxing Li, Qiong Wang, Yongxin Liu, Huachun Guo. 2023. Summer Rice-Winter Potato Rotation Suppresses Various Soil-Borne Plant Fungal Pathogens. Agronomy 13: 2143. https://doi.org/10.3390/agronomy13082143
[40] Wen Luo, Yuanli Li, Ruiping Luo, Gehong Wei, Yongxin Liu, Weimin Chen. 2023. Dodder parasitism leads to the enrichment of pathogen alternaria and flavonoid metabolites in soybean root. Agronomy 13: 1571. https://doi.org/10.3390/agronomy13061571
[41] Penghao Sun, Mengli Wang, Yong-Xin Liu, Luqi Li, Xuejun Chai, Wei Zheng, Shulin Chen, Xiaoyan Zhu, Shanting Zhao. 2023. High-fat diet-disturbed gut microbiota-colonocyte interactions contribute to dysregulating peripheral tryptophan-kynurenine metabolism. Microbiome 11: 154. https://doi.org/10.1186/s40168-023-01606-x
[42] Dongdan Yuan, Lei Zheng, Yong-Xin Liu, Hongguang Cheng, Aizhong Ding, Xiaomin Wang, Qiuyang Tan, Xue Wang, Yuzi Xing, En Xie, Haoming Wu, Shanyun Wang, Guibing Zhu. 2023. Nitrifiers Cooperate to Produce Nitrous Oxide in Plateau Wetland Sediments. Environmental Science & Technology 57: 810-821. https://doi.org/10.1021/acs.est.2c06234
[43] Sunde Xu, Yong-Xin Liu, Tomislav Cernava, Hongkai Wang, Yaqi Zhou, Tie Xia, Shugeng Cao, Gabriele Berg, Xing-Xing Shen, Ziyue Wen, Chunshun Li, Baoyuan Qu, Hefei Ruan, Yunrong Chai, Xueping Zhou, Zhonghua Ma, Yan Shi, Yunlong Yu, Yang Bai, Yun Chen. 2022. Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts. Nature Microbiology 7: 831-843. https://doi.org/10.1038/s41564-022-01131-x
[44] Yong-Xin Liu, Tong Chen, Danyi Li, Jingyuan Fu, Shuang-Jiang Liu. 2022. iMeta: Integrated meta-omics for biology and environments. iMeta 1: e15. https://doi.org/10.1002/imt2.15
[45] Tong Chen, Yong-Xin Liu, Luqi Huang. 2022. ImageGP: An easy-to-use data visualization web server for scientific researchers. iMeta 1: e5. https://doi.org/10.1002/imt2.5
[46] Tao Wen, Penghao Xie, Shengdie Yang, Guoqing Niu, Xiaoyu Liu, Zhexu Ding, Chao Xue, Yong-Xin Liu, Qirong Shen, Jun Yuan. 2022. ggClusterNet: An R package for microbiome network analysis and modularity-based multiple network layouts. iMeta 1: e32. https://doi.org/10.1002/imt2.32
[47] Rong-min Zhang, Jian Sun, Ruan-yang Sun, Min-ge Wang, Chao-yue Cui, Liang-xing Fang, Mei-na Liao, Xiao-qing Lu, Yong-xin Liu, Xiao-Ping Liao, Ya-Hong Liu. 2022. Erratum for Zhang et al., “Source Tracking and Global Distribution of the Tigecycline-Nonsusceptible Tet(X)”. Microbiology Spectrum 10: e01131-01122. https://doi.org/10.1128/spectrum.01131-22
[48] Xin Zheng, Likun Wang, Linhao You, Yong-Xin Liu, Michael Cohen, Siyu Tian, Wenjun Li, Xiaofang Li. 2022. Dietary licorice enhances in vivo cadmium detoxification and modulates gut microbial metabolism in mice. iMeta 1: e7. https://doi.org/10.1002/imt2.7
[49] Jiao Xi, Beilei Lei, Yong-Xin Liu, Zanbo Ding, Jiaxi Liu, Tengqi Xu, Lijun Hou, Siqi Han, Xun Qian, Yongqing Ma, Quanhong Xue, Jinming Gao, Jie Gu, James M. Tiedje, Yanbing Lin. 2022. Microbial community roles and chemical mechanisms in the parasitic development of Orobanche cumana. iMeta 1: e31. https://doi.org/10.1002/imt2.31
[50] Leli Wang, Qihang Liu, Yuwei Chen, Xinlei Zheng, Chuni Wang, Yining Qi, Yachao Dong, Yue Xiao, Cang Chen, Taohong Chen, Qiuyun Huang, Zongzhao Zhai, Cimin Long, Huansheng Yang, Jianzhong Li, Lei Wang, Gaihua Zhang, Peng Liao, Yong-Xin Liu, Peng Huang, Jialu Huang, Qiye Wang, Huanhuan Chu, Jia Yin, Yulong Yin. 2022. Antioxidant potential of Pediococcus pentosaceus strains from the sow milk bacterial collection in weaned piglets. Microbiome 10: 83. https://doi.org/10.1186/s40168-022-01278-z
[51] Jun Xu, Jie-Ni Zhang, Bo-Hui Sun, Qing Liu, Juan Ma, Qian Zhang, Yong-Xin Liu, Ning Chen, Feng Chen. 2022. The role of genotype and diet in shaping gut microbiome in a genetic vitamin A deficient mouse model. Journal of Genetics and Genomics 49: 155-164. https://doi.org/10.1016/j.jgg.2021.08.015
[52] 崔亚俊, 翟志文, 王超, 刘永鑫, 陈园园, 袁怀波, 严建兵, 白洋. 2022. 不同遗传背景自交系玉米根系微生物组差异比较. 合肥工业大学学报(自然科学版) 45: 687-693. https://doi.org/10.3969/j.issn.1003-5060.2022.05.019
1. Yong-Xin Liu#*, Yuan Qin#, Tong Chen#, Meiping Lu, Xubo Qian, Xiaoxuan Guo & Yang Bai*. (2021). A practical guide to amplicon and metagenomic analysis of microbiome data. Protein & Cell 12, 315-330, https://doi.org/10.1007/s13238-020-00724-8 (IF = 15.328, Highly Cited)
2. Yong-Xin Liu, Yuan Qin & Yang Bai*. (2019). Reductionist synthetic community approaches in root microbiome research. Current Opinion in Microbiology 49, 97-102, https://doi.org/10.1016/j.mib.2019.10.010 (IF = 7.584)
3. Wenjun Li#, Likun Wang#, Xiaofang Li*, Xin Zheng, Michael F. Cohen, Yong-Xin Liu*. 2022. Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functioning CopA in Environmental Microbiomes. Genomics Proteomics Bioinformatics https://doi.org/10.1016/j.gpb.2022.08.006 (IF = 6.409)
4. Jingying Zhang#, Yong-Xin Liu#, Na Zhang#, Bin Hu#, Tao Jin#, Haoran Xu, Yuan Qin, Pengxu Yan, Xiaoning Zhang, Xiaoxuan Guo, Jing Hui, Shouyun Cao, Xin Wang, Chao Wang, Hui Wang, Baoyuan Qu, Guangyi Fan, Lixing Yuan, Ruben Garrido-Oter, Chengcai Chu* & Yang Bai*. (2019). NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nature Biotechnology 37, 676-684, https://doi.org/10.1038/s41587-019-0104-4 (IF = 68.164, Highly Cited, Hot Paper, Cover Story)
5. Sunde Xu#, Yong-Xin Liu#, Tomislav Cernava#, Hongkai Wang, Shugeng Cao, Yaqi Zhou, Gabriele Berg, Tie Xia, Xing-Xing Shen, Ziyue Wen, Chunshun Li, Baoyuan Qu, Hefei Ruan, Yunrong Chai, Xueping Zhou, Zhonghua Ma, Yan Shi, Yunlong Yu, Yang Bai*, Yun Chen*. (2022). Bacteria within the fungal fruiting-body microbiome reduce fungal infections in cereal by disrupting lipid rafts. Nature Microbiology 7, 831-843, https://doi.org/10.1038/s41564-022-01131-x (IF = 30.964)
6. Jingying Zhang#, Yong-Xin Liu#, Xiaoxuan Guo, Yuan Qin, Ruben Garrido-Oter*, Paul Schulze-Lefert*, Yang Bai*. (2021). High-throughput cultivation and identification of bacteria from the plant root microbiota. Nature Protocols 16, 988-1012, https://doi.org/10.1038/s41596-020-00444-7 (IF = 17.021, Highly Cited,)
7. Yong-Xin Liu, Meng Wang & Xiu-Jie Wang*. (2014). Endogenous small RNA clusters in plants. Genomics Proteomics Bioinformatics 12, 64-71, https://doi.org/10.1016/j.gpb.2014.04.003 (IF = 6.409)
8. Xu-Bo Qian#, Tong Chen#, Yi-Ping Xu, Lei Chen, Fu-Xiang Sun, Mei-Ping Lu* & Yong-Xin Liu. (2020). A guide to human microbiome research: study design, sample collection, and bioinformatics analysis. Chinese Medical Journal, https://doi.org/10.1097/cm9.0000000000000871 (IF = 6.151)
9. Jingying Zhang#, Na Zhang#, Yong-Xin Liu#, Xiaoning Zhang, Bin Hu, Yuan Qin, Haoran Xu, Hui Wang, Xiaoxuan Guo, Jingmei Qian, Wei Wang, Pengfan Zhang, Tao Jin*, Chengcai Chu* & Yang Bai*. (2018). Root microbiota shift in rice correlates with resident time in the field and developmental stage. Science China Life Sciences 61, 613-621, https://doi.org/10.1007/s11427-018-9284-4 (IF = 10.42, Cover Story)
10. Tong Chen, Haiyan Zhang, Yu Liu, Yong-Xin Liu*, Luqi Huang* (2021). EVenn: Easy to create repeatable and editable Venn diagrams and Venn networks online. Journal of Genetics and Genomics, https://doi.org/10.1016/j.jgg.2021.07.007 (IF = 5.733)
11. Tao Wen#, Penghao Xie#, Shengdie Yang, Guoqing Niu, Xiaoyu Liu, Zhexu Ding, Chao Xue, Yong-Xin Liu*, Qirong Shen, Jun Yuan*. (2022). ggClusterNet: An R package for microbiome network analysis and modularity-based multiple network layouts. iMeta 1: e32. https://doi.org/10.1002/imt2.32
12. Tong Chen, Yong-Xin Liu*, Luqi Huang*. (2022). ImageGP: An easy-to-use data visualization web server for scientific researchers. iMeta 1: e5. https://doi.org/10.1002/imt2.5
13. Yong-Xin Liu*, Tong Chen*, Danyi Li, Jingyuan Fu*, Shuang-Jiang Liu*. (2022). iMeta: Integrated meta-omics for biology and environments. iMeta 1: e15. https://doi.org/10.1002/imt2.15
14. Xubo Qian#, Yong-Xin Liu#, Xiaohong Ye, Wenjie Zheng, Shaoxia Lv, Miaojun Mo, Jinjing Lin, Wenqin Wang, Weihan Wang, Xianning Zhang & Meiping Lu*. (2020). Gut microbiota in children with juvenile idiopathic arthritis: characteristics, biomarker identification, and usefulness in clinical prediction. BMC Genomics 21, 286, https://doi.org/10.1186/s12864-020-6703-0 (IF = 4.560)
15. Yong-Xin Liu#, Wei Chang#, Ying-peng Han, Quan Zou, Mao-zu Guo & Wen-bin Li*. (2011). In silico detection of novel microRNAs genes in soybean genome. Agricultural Sciences in China 10, 1336-1345, https://doi.org/10.1016/S1671-2927(11)60126-0 (IF = 4.384)
16. Yong-Xin Liu, Ying-peng Han, Wei Chang, Quan Zou, Mao-zu Guo & Wen-bin Li*. (2010). Genomic analysis of microRNA promoters and their cis-acting elements in soybean. Agricultural Sciences in China 9, 1561-1570, https://doi.org/10.1016/S1671-2927(09)60252-2 (IF = 4.384)
17. Jing Li#, Yong-Xin Liu#, Ying-peng Han, Yong-guang Li, Mao-zu Guo, Wen-bin Li*. (2013). MicroRNA primary transcripts and promoter elements analysis in soybean (Glycine max L. Merril.). Journal of Integrative Agriculture 12, 1522-1529, https://doi.org/10.1016/S2095-3119(13)60500-6 (IF = 4.384)
18. 刘永鑫, 秦媛, 郭晓璇 & 白洋*. (2019). 微生物组数据分析方法与应用. 遗传 41, 845-826, https://doi.org/10.16288/j.yczz.19-222
19. Ancheng C. Huang#, Ting Jiang#, Yong-Xin Liu, Yue-Chen Bai, James Reed, Baoyuan Qu, Alain Goossens, Hans-Wilhelm Nützmann, Yang Bai* & Anne Osbourn*. (2019). A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science 364, eaau6389, https://doi.org/10.1126/science.aau6389 (IF = 63.798, Highly Cited)
20. Evan Bolyen#, Jai Ram Rideout#, Matthew R. Dillon#, Nicholas A. Bokulich#, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, Eric J. Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E. Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J. Brislawn, C. Titus Brown, Benjamin J. Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily K. Cope, Ricardo Da Silva, Christian Diener, Pieter C. Dorrestein, Gavin M. Douglas, Daniel M. Durall, Claire Duvallet, Christian F. Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M. Gauglitz, Sean M. Gibbons, Deanna L. Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin A. Huttley, Stefan Janssen, Alan K. Jarmusch, Lingjing Jiang, Benjamin D. Kaehler, Kyo Bin Kang, Christopher R. Keefe, Paul Keim, Scott T. Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan G. I. Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D. Martin, Daniel McDonald, Lauren J. McIver, Alexey V. Melnik, Jessica L. Metcalf, Sydney C. Morgan, Jamie T. Morton, Ahmad Turan Naimey, Jose A. Navas-Molina, Louis Felix Nothias, Stephanie B. Orchanian, Talima Pearson, Samuel L. Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S. Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R. Spear, Austin D. Swafford, Luke R. Thompson, Pedro J. Torres, Pauline Trinh, Anupriya Tripathi, Peter J. Turnbaugh, Sabah Ul-Hasan, Justin J. J. van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C. Weber, Charles H. D. Williamson, Amy D. Willis, Zhenjiang Zech Xu, Jesse R. Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight & J. Gregory Caporaso*. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37, 852-857, https://doi.org/10.1038/s41587-019-0209-9 (IF = 68.164)
21. Wei Wang#, Jing Yang#, Jian Zhang, Yong-Xin Liu, Caiping Tian, Baoyuan Qu, Chulei Gao, Peiyong Xin, Shujing Cheng, Wenjing Zhang, Pei Miao, Lei Li, Xiaojuan Zhang, Jinfang Chu, Jianru Zuo, Jiayang Li, Yang Bai, Xiaoguang Lei* & Jian-Min Zhou*. (2020). An Arabidopsis secondary metabolite directly targets expression of the bacterial type III secretion system to inhibit bacterial virulence. Cell Host & Microbe 27, 601-613.e607, https://doi.org/10.1016/j.chom.2020.03.004 (IF = 31.316)
22. Leli Wang, Qihang Liu, Yuwei Chen, Xinlei Zheng, Chuni Wang, Yining Qi, Yachao Dong, Yue Xiao, Cang Chen, Taohong Chen, Qiuyun Huang, Zongzhao Zhai, Cimin Long, Huansheng Yang, Jianzhong Li, Lei Wang, Gaihua Zhang, Peng Liao, Yong-Xin Liu, Peng Huang, Jialu Huang, Qiye Wang, Huanhuan Chu, Jia Yin & Yulong Yin. (2022). Antioxidant potential of Pediococcus pentosaceus strains from the sow milk bacterial collection in weaned piglets. Microbiome 10: 83, https://doi.org/s40168-022-01278-z (IF = 16.837)
23. Wei Wang#, Bin Hu#, Dingyang Yuan, Yongqiang Liu, Ronghui Che, Yingchun Hu, Shujun Ou, Zhihua Zhang, Hongru Wang, Hua Li, Zhimin Jiang, Zhengli Zhang, Xiaokai Gao, Yahong Qiu, Xiangbing Meng, Yong-Xin Liu, Yang Bai, Yan Liang, Yi-Qin Wang, Lianhe Zhang, Legong Li, Sodmergen Sodmergen, Hai-Chun Jing, Jiayang Li & Chengcai Chu*. (2018). Expression of the nitrate transporter gene OsNRT1.1A/OsNPF6.3 confers high yield and early maturation in rice. The Plant Cell 30, 638-651, https://doi.org/10.1105/tpc.17.00809 (IF = 12.085, Highly Cited)
24. Maosheng Zheng, Nan Zhou, Shufeng Liu, Chenyuan Dang, Yong-Xin Liu, Shishi He, Yijun Zhao, Wen Liu & Xiangke Wang*. (2019). N2O and NO emission from a biological aerated filter treating coking wastewater: Main source and microbial community. Journal of Cleaner Production 213, 365-374, https://doi.org/10.1016/j.jclepro.2018.12.182 (IF = 11.072)
25. Qingwen Chen#, Ting Jiang#, Yong-Xin Liu, Haili Liu, Tao Zhao, Zhixi Liu, Xiaochao Gan, Asis Hallab, Xuemei Wang, Juan He, Yihua Ma, Fengxia Zhang, Tao Jin, M.Eric Schranz, Yong Wang, Yang Bai* & Guodong Wang*. (2019). Recently duplicated sesterterpene (C25) gene clusters in Arabidopsis thaliana modulate root microbiota. Science China Life Sciences 62, 947-958, https://doi.org/10.1007/s11427-019-9521-2 (IF = 10.42)
26. Handong Su#, Yalin Liu#, Yong‐Xin Liu, Zhenling Lv, Hongyao Li, Shaojun Xie, Zhi Gao, Junling Pang, Xiu‐Jie Wang, Jinsheng Lai & Fangpu Han*. (2016). Dynamic chromatin changes associated with de novo centromere formation in maize euchromatin. Plant Journal 1, 1-17, https://doi.org/10.1111/tpj.13305 (IF = 7.091)
27. Jiao Xi#, Beilei Lei#, Yong-Xin Liu, Zanbo Ding, Jiaxi Liu, Tengqi Xu, Lijun Hou, Siqi Han, Xun Qian, Yongqing Ma, Quanhong Xue, Jinming Gao, Jie Gu*, James M. Tiedje*, Yanbing Lin*. (2022). Microbial community roles and chemical mechanisms in the parasitic development of Orobanche cumana. iMeta 1: e31. https://doi.org/10.1002/imt2.31
28. Xin Zheng#, Likun Wang#, Linhao You, Yong-Xin Liu, Michael Cohen, Siyu Tian, Wenjun Li, Xiaofang Li. (2022). Dietary licorice enhances in vivo cadmium detoxification and modulates gut microbial metabolism in mice. iMeta 1: e7. https://doi.org/10.1002/imt2.7
29. Rong-Min Zhang, Jian Sun, Ruan-Yang Sun, Min-Ge Wang, Chao-Yue Cui, Liang-Xing Fang, Mei-Na Liao, Xiao-Qing Lu, Yong-Xin Liu, Xiao-Ping Liao, Ya-Hong Liu & Wei-Hua Chen. (2021). Source Tracking and Global Distribution of the Tigecycline Non-Susceptible tet(X). Microbiology Spectrum 9: e01164-01121. https://doi.org/10.1128/Spectrum.01164-21 (IF = 9.043)
30. Maosheng Zheng, Shishi He, Yueqi Feng, Mingyuan Wang, Yong-Xin Liu, Chenyuan Dang, Jiawen Wang*. (2021). Active ammonia-oxidizing bacteria and archaea in wastewater treatment systems. Journal of Environmental Sciences 102 273-282 https://doi.org/10.1016/j.jes.2020.09.039 (IF = 6.796)
31. Zhiyao Lv, Rui Dai, Haoran Xu, Yong‐Xin Liu, Bo Bai, Ying Meng, Haiyan Li, Xiaofeng Cao, Yang Bai, Xianwei Song, Jingying Zhang. (2021). The rice histone methylation regulates hub species of the root microbiota. Journal of Genetics and Genomics, https://doi.org/10.1016/j.jgg.2021.06.005 (IF = 5.733)
32. Jun Xu#, Jie-Ni Zhang#, Bo-Hui Sun, Qing Liu, Juan Ma, Qian Zhang, Yong-Xin Liu, Ning Chen* & Feng Chen*. (2021). The role of genotype and diet in shaping gut microbiome in a genetic Vitamin A deficient mouse model. Journal of Genetics and Genomics, https://doi.org/10.1016/j.jgg.2021.08.015 (IF = 5.733)
