[1] Yunyun Gao, Guoxing Zhang, Shunyao Jiang, et al. 2024. Wekemo Bioincloud: A user-friendly platform for meta-omics data analyses. iMeta 3: e175. https://doi.org/10.1002/imt2.175
[2] Yunyun Gao, Kai Peng, Defeng Bai, et al. 2024. The Microbiome Protocols eBook initiative: Building a bridge to microbiome research. iMeta 3: e182. https://doi.org/10.1002/imt2.182
[3] Tianyuan Zhang, Hanzhou Li, Mian Jiang, et al. 2024. Nanopore sequencing: flourishing in its teenage years. Journal of Genetics and Genomics https://doi.org/10.1016/j.jgg.2024.09.007
[4] 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
[5] Yao Wang, Peng Yu, Yong-Xin Liu. 2024. Metagenomic Analysis for Unveiling Agricultural Microbiome. Agronomy 14: 981. https://doi.org/10.3390/agronomy14050981
[6] Chun-Lin Shi, Tong Chen, Canhui Lan, et al. 2024. iMetaOmics: Advancing human and environmental health through integrated meta-omics. iMetaOmics 1: e21. https://doi.org/10.1002/imo2.21
[7] Tong Chen, Yong-Xin Liu, Tao Chen, et al. 2024. ImageGP 2 for enhanced data visualization and reproducible analysis in biomedical research. iMeta 3: e239. https://doi.org/10.1002/imt2.239
[8] Mei Yang, Tong Chen, Yong-Xin Liu, et al. 2024. Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams. iMeta 3: e184. https://doi.org/10.1002/imt2.184
[9] 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
[10] Shanshan Xu, Hao Zhou, Boyang Xu, et al. 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
[11] Shanshan Xu, Hao Zhou, Boyang Xu, et al. 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
[12] Kai Peng, Yong-Xin Liu, Xinran Sun, et al. 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
[13] Tao Wang, Penghao Li, Xue Bai, et al. 2024. Vaginal microbiota are associated with in vitro fertilization during female infertility. iMeta 3: e185. https://doi.org/10.1002/imt2.185
[14] Ming-Hao Lv, Wen-Chong Shi, Ming-Cong Li, et al. 2024. Ms gene and Mr gene: Microbial-mediated spatiotemporal communication between plants. iMeta 3: e210. https://doi.org/10.1002/imt2.210
[15] Zhongji Pu, Chun-Lin Shi, Che Ok Jeon, et al. 2024. ChatGPT and generative AI are revolutionizing the scientific community: A Janus-faced conundrum. iMeta 3: e178. https://doi.org/https://doi.org/10.1002/imt2.178
[16] Yao Wang, Yong-Fu Tao, Hong-Ru Wang, et al. 2024. Role of soil microbes in enhancing crop heterosis. iMetaOmics 1: e20. https://doi.org/10.1002/imo2.20
[17] Xiaofang Yao, Qiumei Liu, Yongxin Liu, et al. 2024. Managing Macadamia Decline: A Review and Proposed Biological Control Strategies. Agronomy 14: 308. https://doi.org/10.3390/agronomy14020308
[18] Shi Zhong, Yu-Qing Sun, Jin-Xi Huo, et al. 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
[19] Zhiguang Qiu, Li Yuan, Chun-Ang Lian, et al. 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
[20] Mengli Wang, Penghao Sun, Xuejun Chai, et al. 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
[21] Min Fu, Yunhe Chen, Yong-Xin Liu, et al. 2024. Genotype-associated core bacteria enhance host resistance against kiwifruit bacterial canker. Horticulture Research uhae236. https://doi.org/10.1093/hr/uhae236
[22] Yong-Xin Liu, Lei Chen, Tengfei Ma, et al. 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
[23] Tao Wen, Guoqing Niu, Tong Chen, et al. 2023. The best practice for microbiome analysis using R. Protein & Cell 14: 713-725. https://doi.org/10.1093/procel/pwad024
[24] Wenjun Li, Likun Wang, Xiaofang Li, et al. 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
[25] 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
[26] Yong-Xin Liu, Chun-Lin Shi, Tengfei Ma, et al. 2023. iMeta progress and acknowledgment of reviewers in 2022. iMeta 2: e89. https://doi.org/10.1002/imt2.89
[27] Kai Peng, Yong-xin Liu, Xinran Sun, et al. 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
[28] Yuanping Zhou, Wenjiao Luo, Maoxing Li, et al. 2023. Summer Rice-Winter Potato Rotation Suppresses Various Soil-Borne Plant Fungal Pathogens. Agronomy 13: 2143. https://doi.org/10.3390/agronomy13082143
[29] Wen Luo, Yuanli Li, Ruiping Luo, et al. 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
[30] Penghao Sun, Mengli Wang, Yong-Xin Liu, et al. 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
[31] Dongdan Yuan, Lei Zheng, Yong-Xin Liu, et al. 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
[1] Yunyun Gao, Guoxing Zhang, Shunyao Jiang, et al. 2024. Wekemo Bioincloud: A user-friendly platform for meta-omics data analyses. iMeta 3: e175. https://doi.org/10.1002/imt2.175
[2] Yunyun Gao, Kai Peng, Defeng Bai, et al. 2024. The Microbiome Protocols eBook initiative: Building a bridge to microbiome research. iMeta 3: e182. https://doi.org/10.1002/imt2.182
[3] Tianyuan Zhang, Hanzhou Li, Mian Jiang, et al. 2024. Nanopore sequencing: flourishing in its teenage years. Journal of Genetics and Genomics https://doi.org/10.1016/j.jgg.2024.09.007
[4] 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
[5] Yao Wang, Peng Yu, Yong-Xin Liu. 2024. Metagenomic Analysis for Unveiling Agricultural Microbiome. Agronomy 14: 981. https://doi.org/10.3390/agronomy14050981
[6] Chun-Lin Shi, Tong Chen, Canhui Lan, et al. 2024. iMetaOmics: Advancing human and environmental health through integrated meta-omics. iMetaOmics 1: e21. https://doi.org/10.1002/imo2.21
[7] Tong Chen, Yong-Xin Liu, Tao Chen, et al. 2024. ImageGP 2 for enhanced data visualization and reproducible analysis in biomedical research. iMeta 3: e239. https://doi.org/10.1002/imt2.239
[8] Mei Yang, Tong Chen, Yong-Xin Liu, et al. 2024. Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams. iMeta 3: e184. https://doi.org/10.1002/imt2.184
[9] 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
[10] Shanshan Xu, Hao Zhou, Boyang Xu, et al. 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
[11] Shanshan Xu, Hao Zhou, Boyang Xu, et al. 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
[12] Kai Peng, Yong-Xin Liu, Xinran Sun, et al. 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
[13] Tao Wang, Penghao Li, Xue Bai, et al. 2024. Vaginal microbiota are associated with in vitro fertilization during female infertility. iMeta 3: e185. https://doi.org/10.1002/imt2.185
[14] Ming-Hao Lv, Wen-Chong Shi, Ming-Cong Li, et al. 2024. Ms gene and Mr gene: Microbial-mediated spatiotemporal communication between plants. iMeta 3: e210. https://doi.org/10.1002/imt2.210
[15] Zhongji Pu, Chun-Lin Shi, Che Ok Jeon, et al. 2024. ChatGPT and generative AI are revolutionizing the scientific community: A Janus-faced conundrum. iMeta 3: e178. https://doi.org/https://doi.org/10.1002/imt2.178
[16] Yao Wang, Yong-Fu Tao, Hong-Ru Wang, et al. 2024. Role of soil microbes in enhancing crop heterosis. iMetaOmics 1: e20. https://doi.org/10.1002/imo2.20
[17] Xiaofang Yao, Qiumei Liu, Yongxin Liu, et al. 2024. Managing Macadamia Decline: A Review and Proposed Biological Control Strategies. Agronomy 14: 308. https://doi.org/10.3390/agronomy14020308
[18] Shi Zhong, Yu-Qing Sun, Jin-Xi Huo, et al. 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
[19] Zhiguang Qiu, Li Yuan, Chun-Ang Lian, et al. 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
[20] Mengli Wang, Penghao Sun, Xuejun Chai, et al. 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
[21] Min Fu, Yunhe Chen, Yong-Xin Liu, et al. 2024. Genotype-associated core bacteria enhance host resistance against kiwifruit bacterial canker. Horticulture Research uhae236. https://doi.org/10.1093/hr/uhae236
[22] Yong-Xin Liu, Lei Chen, Tengfei Ma, et al. 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
[23] Tao Wen, Guoqing Niu, Tong Chen, et al. 2023. The best practice for microbiome analysis using R. Protein & Cell 14: 713-725. https://doi.org/10.1093/procel/pwad024
[24] Wenjun Li, Likun Wang, Xiaofang Li, et al. 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
[25] 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
[26] Yong-Xin Liu, Chun-Lin Shi, Tengfei Ma, et al. 2023. iMeta progress and acknowledgment of reviewers in 2022. iMeta 2: e89. https://doi.org/10.1002/imt2.89
[27] Kai Peng, Yong-xin Liu, Xinran Sun, et al. 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
[28] Yuanping Zhou, Wenjiao Luo, Maoxing Li, et al. 2023. Summer Rice-Winter Potato Rotation Suppresses Various Soil-Borne Plant Fungal Pathogens. Agronomy 13: 2143. https://doi.org/10.3390/agronomy13082143
[29] Wen Luo, Yuanli Li, Ruiping Luo, et al. 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
[30] Penghao Sun, Mengli Wang, Yong-Xin Liu, et al. 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
[31] Dongdan Yuan, Lei Zheng, Yong-Xin Liu, et al. 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
[32] Sunde Xu, Yong-Xin Liu, Tomislav Cernava, et al. 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
[33] Yong-Xin Liu, Tong Chen, Danyi Li, et al. 2022. iMeta: Integrated meta-omics for biology and environments. iMeta 1: e15. https://doi.org/10.1002/imt2.15
[34] 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
[35] Tao Wen, Penghao Xie, Shengdie Yang, et al. 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
[36] Jiao Xi, Zanbo Ding, Tengqi Xu, et al. 2022. Maize rotation combined with Streptomyces rochei D74 to eliminate Orobanche cumana seed bank in the farmland. Agronomy 12: 3129. https://doi.org/10.3390/agronomy12123129
[37] Xin Zheng, Likun Wang, Linhao You, et al. 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
[38] Jiao Xi, Beilei Lei, Yong-Xin Liu, et al. 2022. Microbial community roles and chemical mechanisms in the parasitic development of Orobanche cumana. iMeta 1: e31. https://doi.org/10.1002/imt2.31
[39] Leli Wang, Qihang Liu, Yuwei Chen, et al. 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
[40] Jun Xu, Jie-Ni Zhang, Bo-Hui Sun, et al. 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
[41] 崔亚俊, 翟志文, 王超, et al. 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
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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)
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