（1）国家自然科学基金面上项目：“药用植物铁皮石斛根部微生物组与其道地性的关联分析”、No. 81973423，2020.01-2023.12，主持，在研。

（2）国家自然科学基金面上项目：“基于RNA-Seq和iTRAQ技术解析铁皮石斛种子接菌共生萌发的分子机制”、No. 81573527，2016.01 -2019.12，主持，已结题。

（3）国家自然科学基金青年基金面上项目:“两种珍稀药用石斛种子萌发过程中的内生真菌多样性与促萌发活性”、No.30900004，2010. 01-2012.12、主持, 已结题。

（4）科技部外国文教专家项目（高端外国专家引进计划）：“珍稀濒危食 药用真菌印度块菌的资源保护及菌根化栽培”、No. G20200001498，9.0 万元， 2020.01-2021.12，主持，在研。

（5）国家重点研发计划“苦参等大宗中药材的综合利用技术研究”子课题“中药食用菌的培育与评价关键技术研究”No. 2017YFC1701902-1，2018.01-2021.12，参加骨干，已结题。

（6）国家重点基础研究发展计划（973计划）：“食用菌产量和品质形成的分子机理及调控”、No. 2014CB138300，2014.01-2018.08，参加骨干，已结题。

（7）中央公益性科研院所基本科研业务费专项：“转录组和蛋白质组学研究铁皮石斛种子接菌共生萌发的分子机制”、No. YZ12-14，2012.03-2015.03，主持，已结题。

（8）科技部国际科技合作项目：“药用真菌猪苓菌丝形成菌核机理的研究”、No. 2011DFA31260，2010.9-2013.8，参加骨干，已结题。

（9）中央级公益性科研院所基本科研业务专项:、“铁皮石斛和金釵石斛根腐病和叶斑病研究和生物防治”、No. YZ-185，2008.05-2009.12主持, 已结题。

（10）协和新星，中国医学科学院，北京协和医学院，2011年。

1. Juan Chen, Herminia De la Varga, Flora Todesco, Pauline Beacco, Elena Martino , François Le Tacon, Claude Murat*. Frequency of the two mating types in the soil under productive and non-productive trees in fve French orchards of the Périgord black truffle (Tuber melanosporum Vittad.) , Mycorrhiza, 2021,31, 361-369.

2.Juan Chen*, Jia-Mei Li, Yan-Jing Tang, Ke Ma, Bing Li, Xu Zeng, Xiao-Bin Liu,Yang Li, Zhu-Liang Yang, Wei-Nan Xu, Bao-Gui Xie, Hong-Wei Liu, Shun-Xing Guo*. Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant wild Flammulina filiformis. BMC Genomics, 2020, 21:719.

3.Xing YM#, Zhao MM#, Guo LC, Li B, Chen J*, Guo SX*. Identifcation and expressio of DoCCaMK during Sebacina sp. symbiosis of Dendrobium offcinale. Scientific Reports, 2020, 10: 9733.

4. Juan Chen*, Jia-Mei Li, Yang-Jing Tang, Yong-Mei Xing, Peng Qiao, Yang Li, Pei Gui Liu, Shun-Xing Guo*. Chinese black truffle-associated bacterial communities of Tuber indicum from different geographical regions with nitrogen fixing bioactivity. Frontiers in Microbiology, 2019, 10: 2515.

5. Jia-Mei Li, Han-Qiao Liang, Peng Qiao, Kai-Mei Su, Pei-Gui Liu, Shun-Xing Guo, Juan Chen*. Chemical composition and antioxidant activity of Tuber indicum from different geographical regions of China. Chemistry & Biodiversity, 2019, 16: e1800609.

6. Juan Chen, Si Si Liu, Annegret Kohler, Bo Yan, Hong Mei Luo, Xiao Mei Chen, Shun Xing Guo*. iTRAQ and RNA-Seq analyses provide new insights into regulation mechanism of symbiotic germination of Dendrobium officinale seeds (Orchidaceae). Journal of Proteome Research, 2017, 16: 2174−2187. 

7. Juan Chen, Xu Zeng, Yan Long Yang, Yong Mei Xing, Qi Zhang, Jia Mei Li, Ke Ma, Hong Wei Liu, Shun Xing Guo*. Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceus. Scientific Reports, 2017, 7: 10151.

8. Claude Murat#, Thibaut Payen#, Benjamin Noel, Alan Kuo, Emmanuelle Morin, Juan Chen, Annegret Kohler, Krisztinan Krizs, Raffaella Balestrini, Corinne Da Silva, Barbara Montanini, Mathieu Hainaut, Elisabetta Levati, Kerrie W. Barry, Beatrice Belfiori, Nicolas Cichocki, Alicia Clum, Rhyan B. Dockter, Laure Fauchery, Julie Guy, Mirco Iotti, Francois Le Tacon, Erika A. Lindquist, Anna Lipzen, Fabienne Malagnac, Antonietta Mello, Virginie Molinier, Shingo Miyauchi, Julie Poulain, Claudia Riccioni, Andrea Rubini, Yaron Sitrit, Richard Splivallo, Stefanie Traeger, Mei Wang, Lucia Žifčakova, Daniel Wipf, Alessandra Zambonelli, Francesco Paolocci, Minou Nowrousian, Simone Ottonello, Petr Baldrian, Joseph W. Spatafora, Bernard Henrissat, Laszlo G. Nagy, Jean-Marc Aury, Patrick Wincker, Igor V. Grigoriev, Paola Bonfante, Francis M. Martin*. Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle. Nature ecology & evolution, 2018, 2: 1956-1965.

9. Xu Zeng#, Yuanyuan Li#, Hong Ling, Juan Chen* and Shunxing Guo*. Revealing proteins associated with symbiotic germination of Gastrodia elata by proteomic analysis. Botanical Studies, 2018, 59: 8.

10. Yan-long Yang, Shasha Zhang, Ke Ma, Yuxing Xu, Qiaoqiao Tao, Yihua Chen, Juan Chen, Shunxing Guo, Jinwei Ren, Wenzhao Wang, Yong Tao, Wen-Bing Yin, Hongwei Liu*. Discovery and characterization of a new Family of diterpene Cyclases in Bacteria and Fungi. Angewandte Chemie International Edition, 2017, 56: 4749–4752.