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Xuhui Deng, Na Zhang, Yuchan Li, Chengzhi Zhu, Baoyuan Qu, Hongjun Liu, Rong Li*, Yang Bai, Qirong Shen, Joana Falcao Salles. (2022). Bio-organic soil amendment promotes the suppression of Ralstonia solanacearum by inducing changes in the functionality and composition of rhizosphere bacterial communities. New Phytologist doi: 10.1111/nph.18221
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Bo Bai, Weidong Liu, Xingyu Qiu, Jie Zhang, Jingying Zhang*, Yang Bai*. (2022). The root microbiome: Community assembly and its contributions to plant fitness. Journal of Integrative Plant Biology 64 230-243 doi: 10.1111/jipb.13226
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Jing-Mei Qian & Yang Bai*. (2021). Stuck on you: Bacterial-auxin-mediated bacterial colonization of plant roots. Cell Host & Microbe 29, 1471-1473, doi:10.1016/j.chom.2021.09.014
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Zhiyao Lv#, Rui Dai#, Haoran Xu#, Yongxin 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 48, 836-843, doi:10.1016/j.jgg.2021.06.005
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Pengfan Zhang, Stjin Spaepen, Yang Bai, Stephane Hacquard, Ruben Garrido-Oter. (2021). Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities. ISME Communications 1, 73 doi:10.1038/s43705-021-00077-1
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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.doi:10.1007/s13238-020-00724-8 (Highly Cited Paper)
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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.doi:10.1038/s41596-020-00444-7
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Baoyuan Qu, Yuan Qin & Yang Bai*. (2020). From signaling to function: how strigolactones regulate plant development. Science China Life Sciences 63 1768-1770 doi:10.1007/s11427-020-1802-y
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Qin Han, Qun Ma, Yong Chen, Bing Tian, Lanxi Xu, Yang Bai*, Wenfeng Chen*, Xia Li*. (2020). Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean. The ISME Journal. doi:10.1038/s41396-020-0648-9
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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. An Arabidopsis Secondary Metabolite Directly Targets Expression of the Bacterial Type III Secretion System to Inhibit Bacterial Virulence. Cell Host & Microbe. 2020, 27: 601-613.e607. doi:10.1016/j.chom.2020.03.004
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Xiaoxuan Guo#, Xiaoning Zhang#, Yuan Qin#, Yong-Xin Liu, Jingying Zhang, Na Zhang, Kun Wu, Baoyuan Qu, Zishan He, Xin Wang, Xinjian Zhang, Stéphane Hacquard, Xiangdong Fu* & Yang Bai*. Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome. Plant Communications. 2020, 1: 100003. doi:10.1016/j.xplc.2019.100003
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Yong-Xin Liu, Yuan Qin & Yang Bai. Reductionist synthetic community approaches in root microbiome research. Current Opinion in Microbiology. 2019, 49: 97-102. doi:10.1016/j.mib.2019.10.010
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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. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology. 2019, 37: 852-857. doi:10.1038/s41587-019-0209-9
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Mathias J. E. E. E. Voges, Yang Bai, Paul Schulze-Lefert & Elizabeth S. Sattely. Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome. Proceedings of the National Academy of Sciences. 2019, 116: 12558-12565. doi:10.1073/pnas.1820691116
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Ancheng C. Huang#, Ting Jiang#, Yong-Xin Liu, Yue-Chen Bai, James Reed, Baoyuan Qu, Alain Goossens, Hans-Wilhelm Nützmann, Yang Bai*, Anne Osbourn*. A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science. 2019. doi:10.1126/science.aau6389 (Highly Cited Paper)
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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*. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nature Biotechnology. 2019. doi:10.1038/s41587-019-0104-4 (Highly Cited Paper, Hot paper)
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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*. Recently Duplicated Sesterterpene (C25) Gene Clusters in Arabidopsis thaliana Modulate Root Microbiota. Science China Life Sciences. 2019. doi:10.1007/s11427-019-9521-2
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Chunlei Zhang, Youming Zhang, Zhaojun Ding* & Yang Bai*. Contribution of Microbial Inter-kingdom Balance to Plant Health. Molecular Plant. 2019, 12: 148-149. doi:10.1016/j.molp.2019.01.016
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Kabin Xie, Liang Guo, Yang Bai, Wende Liu, Jianbing Yan & Marcel Bucher. Microbiomics and Plant Health: An Interdisciplinary and International Workshop on the Plant Microbiome. Molecular Plant. 2019, 12: 1-3. doi:10.1016/j.molp.2018.11.004
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Jun Yuan, Jun Zhao, Tao Wen, Mengli Zhao, Rong Li, Pim Goossens, Qiwei Huang, Yang Bai, Jorge M. Vivanco, George A. Kowalchuk, Roeland L. Berendsen & Qirong Shen. Root exudates drive the soil-borne legacy of aboveground pathogen infection. Microbiome. 2018, 6: 156. doi:10.1186/s40168-018-0537-x
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Hirokazu Toju, Kabir G. Peay, Masato Yamamichi, Kazuhiko Narisawa, Kei Hiruma, Ken Naito, Shinji Fukuda, Masayuki Ushio, Shinji Nakaoka, Yusuke Onoda, Kentaro Yoshida, Klaus Schlaeppi, Yang Bai, Ryo Sugiura, Yasunori Ichihashi, Kiwamu Minamisawa & E. Toby Kiers. Core microbiomes for sustainable agroecosystems. Nature Plants. 2018, 4: 247-257. doi:10.1038/s41477-018-0139-4 (Highly Cited Paper)
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Kunkun Fan, Pamela Weisenhorn, Jack A Gilbert, Yu Shi, Yang Bai & Haiyan Chu. Soil pH correlates with the co-occurrence and assemblage process of diazotrophic communities in rhizosphere and bulk soils of wheat fields. Soil Biology and Biochemistry. 2018, 121: 185-192. doi:10.1016/j.soilbio.2018.03.017 (Highly Cited Paper)
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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*. Root microbiota shift in rice correlates with resident time in the field and developmental stage. Science China Life Sciences. 2018, 61: 613-621. doi:10.1007/s11427-018-9284-4
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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. Expression of the Nitrate Transporter Gene OsNRT1.1A/OsNPF6.3 Confers High Yield and Early Maturation in Rice. The Plant Cell. 2018, 30: 638-651. doi:10.1105/tpc.17.00809 (Highly Cited Paper)
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Alexander Sczyrba, Peter Hofmann, Peter Belmann, David Koslicki, Stefan Janssen, Johannes Dröge, Ivan Gregor, Stephan Majda, Jessika Fiedler, Eik Dahms, Andreas Bremges, Adrian Fritz, Ruben Garrido-Oter, Tue Sparholt Jørgensen, Nicole Shapiro, Philip D. Blood, Alexey Gurevich, Yang Bai, Dmitrij Turaev, Matthew Z. DeMaere, Rayan Chikhi, Niranjan Nagarajan, Christopher Quince, Fernando Meyer, Monika Balvočiūtė, Lars Hestbjerg Hansen, Søren J. Sørensen, Burton K. H. Chia, Bertrand Denis, Jeff L. Froula, Zhong Wang, Robert Egan, Dongwan Don Kang, Jeffrey J. Cook, Charles Deltel, Michael Beckstette, Claire Lemaitre, Pierre Peterlongo, Guillaume Rizk, Dominique Lavenier, Yu-Wei Wu, Steven W. Singer, Chirag Jain, Marc Strous, Heiner Klingenberg, Peter Meinicke, Michael D. Barton, Thomas Lingner, Hsin-Hung Lin, Yu-Chieh Liao, Genivaldo Gueiros Z. Silva, Daniel A. Cuevas, Robert A. Edwards, Surya Saha, Vitor C. Piro, Bernhard Y. Renard, Mihai Pop, Hans-Peter Klenk, Markus Göker, Nikos C. Kyrpides, Tanja Woyke, Julia A. Vorholt, Paul Schulze-Lefert, Edward M. Rubin, Aaron E. Darling, Thomas Rattei & Alice C. McHardy. Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software. Nature Methods. 2017, 14: 1063. doi:10.1038/nmeth.4458 (Highly Cited Paper)
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Tao Jin, Yayu Wang, Yueying Huang, Jin Xu, Pengfan Zhang, Nian Wang, Xin Liu, Haiyan Chu, Guang Liu, Honggang Jiang, Yuzhen Li, Jing Xu, Karsten Kristiansen, Liang Xiao, Yunzeng Zhang, Gengyun Zhang, Guohua Du, Houbao Zhang, Hongfeng Zou, Haifeng Zhang, Zhuye Jie, Suisha Liang, Huijue Jia, Jingwang Wan, Dechun Lin, Jinying Li, Guangyi Fan, Huanming Yang, Jian Wang, Yang Bai* & Xun Xu*. Taxonomic structure and functional association of foxtail millet root microbiome. GigaScience. 2017, 6: 1-12. doi:10.1093/gigascience/gix089
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Shujuan Tian, Jingjing Wu, Fen Li, Jianwei Zou, Yuwen Liu, Bing Zhou, Yang Bai & Meng-Xiang Sun. NtKRP, a kinesin-12 protein, regulates embryo/seed size and seed germination via involving in cell cycle progression at the G2/M transition. Scientific Reports. 2016, 6: 35641. doi:10.1038/srep356412
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Daniel B. Müller, Christine Vogel, Yang Bai & Julia A. Vorholt. The Plant Microbiota: Systems-Level Insights and Perspectives. Annual Review of Genetics. 2016, 50: 211-234. doi:10.1146/annurev-genet-120215-034952
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Yang Bai#, Daniel B. Müller#, Girish Srinivas#, Ruben Garrido-Oter#, Eva Potthoff, Matthias Rott, Nina Dombrowski, Philipp C. Münch, Stijn Spaepen, Mitja Remus-Emsermann, Bruno Hüttel, Alice C. McHardy, Julia A. Vorholt* & Paul Schulze-Lefert*. Functional overlap of the Arabidopsis leaf and root microbiota. Nature. 2015, 528: 364-369. doi:10.1038/nature16192 (Highly Cited Paper)
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Christos Zamioudis, Jolanda Korteland, Johan A. Van Pelt, Muriël van Hamersveld, Nina Dombrowski, Yang Bai, Johannes Hanson, Marcel C. Van Verk, Hong-Qing Ling, Paul Schulze-Lefert & Corné M. J. Pieterse. Rhizobacterial volatiles and photosynthesis-related signals coordinate MYB72 expression in Arabidopsis roots during onset of induced systemic resistance and iron-deficiency responses. The Plant Journal. 2015, 84: 309-322. doi:10.1111/tpj.12995
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Yang Bai, Prasad Vaddepalli, Lynette Fulton, Hemal Bhasin, Martin Hülskamp & Kay Schneitz. ANGUSTIFOLIA is a central component of tissue morphogenesis mediated by the atypical receptor-like kinase STRUBBELIG. BMC Plant Biology. 2013, 13: 16. doi:10.1186/1471-2229-13-16
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Yang Bai, Stefanie Falk, Arp Schnittger, Marc J. Jakoby & Martin Hülskamp. Tissue layer specific regulation of leaf length and width in Arabidopsis as revealed by the cell autonomous action of ANGUSTIFOLIA. The Plant Journal. 2010, 61: 191-199. doi:10.1111/j.1365-313X.2009.04050.x
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