PUBLICATIONS
Yong-Xin Liu#*, Yuan Qin#, Tong Chen#, Meiping Lu, Xubo Qian, Xiaoxuan Guo, Yang Bai*. (2020). A practical guide to amplicon and metagenomic analysis of microbiome data. Protein Cell 41 1-16 doi: 10.1007/s13238-020-00724-8
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
胡雅丽#, 戴睿#, 刘永鑫, 张婧赢, 胡斌, 储成才, 袁怀波*, 白洋*. (2020). 水稻典型品种日本晴和IR24根系微生物组的解析. 遗传 42 506-518 doi: 10.16288/j.yczz.20-070
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 doi: 10.1016/j.chom.2020.03.004
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*. (2020). Host-associated quantitative abundance profiling reveals the microbial load variation of root microbiome. Plant Communications 1 100003 doi: 10.1016/j.xplc.2019.100003
Yong-Xin Liu, Yuan Qin, Yang Bai*. (2019). Reductionist synthetic community approaches in root microbiome research. Current Opinion in Microbiology 49 97-102 doi: 10.1016/j.mib.2019.10.010
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 doi: 10.16288/j.yczz.19-222
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 doi: 10.1038/s41587-019-0209-9
Mathias J. E. E. E. Voges, Yang Bai, Paul Schulze-Lefert, Elizabeth S. Sattely*. (2019). Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome. Proceedings of the National Academy of Sciences of the United States of America 116 12558-12565 doi: 10.1073/pnas.1820691116
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 doi: 10.1126/science.aau6389
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 doi: 10.1038/s41587-019-0104-4
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 doi: 10.1007/s11427-019-9521-2
Chunlei Zhang, Youming Zhang, Zhaojun Ding*, Yang Bai*. (2019). Contribution of microbial inter-kingdom balance to plant health. Molecular Plant 12 148-149 doi: 10.1016/j.molp.2019.01.016
Kabin Xie*, Liang Guo, Yang Bai, Wende Liu, Jianbing Yan, Marcel Bucher*. (2019). Microbiomics and plant health: an interdisciplinary and international workshop on the plant microbiome. Molecular Plant 12 1-3 doi: 10.1016/j.molp.2018.11.004
王超, 白洋*. (2019). 玉米可利用气生根进行高效生物固氮. 中国科学生命科学 49 89-90 doi: 10.1360/N052018-00215
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*. (2018). Root exudates drive the soil-borne legacy of aboveground pathogen infection. Microbiome 6 156 doi: 10.1186/s40168-018-0537-x
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. (2018). Core microbiomes for sustainable agroecosystems. Nature Plants 4 247-257 doi: 10.1038/s41477-018-0139-4
Kunkun Fan, Pamela Weisenhorn, Jack A Gilbert, Yu Shi, Yang Bai, Haiyan Chu*. (2018). 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 121 185-192 doi: 10.1016/j.soilbio.2018.03.017
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 doi: 10.1007/s11427-018-9284-4
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 doi: 10.1105/tpc.17.00809
Alexander Sczyrba#*, Peter Hofmann#, Peter Belmann#, David Koslicki, Stefan Janssen, Johannes Dr？ge, Ivan Gregor, Stephan Majda, Jessika Fiedler, Eik Dahms, Andreas Bremges, Adrian Fritz, Ruben Garrido-Oter, Tue Sparholt J？rgensen, Nicole Shapiro, Philip D. Blood, Alexey Gurevich, Yang Bai, Dmitrij Turaev, Matthew Z. DeMaere, Rayan Chikhi, Niranjan Nagarajan, Christopher Quince, Fernando Meyer, Monika Balvo？iūt？, Lars Hestbjerg Hansen, S？ren J. S？rensen, 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 G？ker, Nikos C. Kyrpides, Tanja Woyke, Julia A. Vorholt, Paul Schulze-Lefert, Edward M. Rubin, Aaron E. Darling, Thomas Rattei, Alice C. McHardy*. (2017). Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software. Nature Methods 14 1063 doi: 10.1038/nmeth.4458
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*. (2017). Taxonomic structure and functional association of foxtail millet root microbiome. GigaScience 6 1-12 doi: 10.1093/gigascience/gix089
白洋*, 钱景美, 周俭民, 钱韦*. (2017). 农作物微生物组：跨越转化临界点的现代生物技术. 中国科学院院刊 32 260-265 doi: 10.16418/j.issn.1000-3045.2017.03.006
Shujuan Tian#, Jingjing Wu#, Fen Li, Jianwei Zou, Yuwen Liu, Bing Zhou, Yang Bai, Meng-Xiang Sun*. (2016). 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 6 35641 doi: 10.1038/srep35641
Daniel B. Müller, Christine Vogel, Yang Bai, Julia A. Vorholt*. (2016). The plant microbiota: systems-level insights and perspectives. Annual Review of Genetics 50 211-234 doi: 10.1146/annurev-genet-120215-034952
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*. (2015). Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528 364-369 doi: 10.1038/nature16192
Christos Zamioudis, Jolanda Korteland, Johan A. Van Pelt, Muri？l van Hamersveld, Nina Dombrowski, Yang Bai, Johannes Hanson, Marcel C. Van Verk, Hong-Qing Ling, Paul Schulze-Lefert, Corné M. J. Pieterse*. (2015). 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 84 309-322 doi: 10.1111/tpj.12995
Yang Bai#, Prasad Vaddepalli#, Lynette Fulton#, Hemal Bhasin#, Martin Hülskamp, Kay Schneitz*. (2013). ANGUSTIFOLIA is a central component of tissue morphogenesis mediated by the atypical receptor-like kinase STRUBBELIG. BMC Plant Biology 13 16 doi: 10.1186/1471-2229-13-16
Yang Bai#, Stefanie Falk#, Arp Schnittger#, Marc J. Jakoby, Martin Hülskamp*. (2010). Tissue layer specific regulation of leaf length and width in Arabidopsis as revealed by the cell autonomous action of ANGUSTIFOLIA. The Plant Journal 61 191-199 doi: 10.1111/j.1365-313X.2009.04050.x
