1、 团队致力于药用植物基因资源的发掘与利用研究，以次生代谢产物的生物合成与调控为研究核心，以药用模式植物或真菌为研究对象，综合利用多种组学技术和分子生物学技术，建立相关基因资源的发掘、筛选和鉴定技术平台。解析次生代谢产物的生物合成途径，通过合成生物学技术合成重要的天然药物；揭示遗传信息调控次生代谢产物的时空分布和环境应答的分子机制，通过分子育种提高药用植物的药用价值。

2、 团队是国内外最早开展药用植物/真菌基因组学研究的团队之一，对灵芝、丹参、青蒿和长春花等多种模式药用植物/真菌进行了基因组学和转录组学研究。团队完成染色体水平灵芝基因组测序和分析，文章发表在《Nature Communications》。期刊编辑部以特别图片（Featured Image）形式进行了推介，认为该论文表明灵芝对于研究传统菌类中药的次生代谢途径及其调控是一个有价值的模式系统。论文被Nature China网站选为中国最佳研究，《今日美国》（USA TODAY）以“揭秘中国‘仙草’基因组”为题报道了该研究成果。

3、 团队创立“本草基因组学”，出版“十三五”规划教材《本草基因组学》，目前已有北京协和医学院、上海中医药大学、武汉理工大学、天津中医药大学、湖北中医药大学和成都中医药大学等多所高等院校相继开设了“本草基因组学”课程，推动了前沿组学技术在药用植物基因组和基因研究中的应用。

1、国家科技基础性工作专项，2014FY130400，长白山区药用植物资源考察与DNA 条形码数据采集，项目负责人

2、国家自然基金面上项目，81573704，灵芝萜类合酶的产物多样性及其形成机制研究，项目负责人

3、国家自然基金面上项目，81273485，灵芝三萜的生物合成途径解析及其异源生物合成研究，项目负责人

4、国家自然基金面上项目，30873459，通过关键酶的鉴定和途径重建阐明西洋参达玛烷型皂甙的合成途径，项目负责人

在Nature Communications、Science增刊、New Phytologist、中国科学等国内外杂志发表论文80余篇，其中第一作者或通讯作者论文30余篇，最高影响因子12.1，以副主编出版“十三五”规划教材《本草基因组学》一部，以第一作者出版《生物信息学中的计算机技术》、《基因开关》、《信号转导与人类疾病》、《信号转导与调控的生物化学》等4部译著，以第一发明人获得6项发明专利授权。

代表性论著：

1.      ShilinChen*, #, Jiang Xu#, Chang Liu#, Yingjie Zhu, D R. Nelson, Shiguo Zhou,Chunfang Li, Lizhi Wang, Xu Guo, Yongzhen Sun, Hongmei Luo, Ying Li, JingyuanSong, B Henrissat, A Levasseur, Jun Qian, Jiangqin Li, Xiang Luo, Linchun Shi,Liu He, Li Xiang, Xiaolan Xu, Yunyun Niu, Qiushi Li, Mira V. Han, Haixia Yan,Jin Zhang, Haimei Chen, Aiping Lv, Zhen Wang, Mingzhu Liu, David C. Schwartzand Chao Sun*. Genome sequence of the model medicinal mushroom Ganodermalucidum. Nature Communications, 3,e913, 2012

2.      SunSijie#, Li Ying#, Chu Lihua, Kuang Xiejun, Song Jingyuan, Sun Chao*. Full-length sequencing of ginkgo transcriptomes for anin-depth understanding of flavonoid and terpenoid trilactone biosynthesis.Gene, https://doi.org/10.1016/j.gene,2020

3.      Gao Ting, Xu Zhichao, SongXiaojun, Huang, Kai, Li Ying, Wei Jianhe, Zhu Xunzhi, Ren Hongwei, Sun Chao*. Hybrid Sequencing ofFull-Length cDNA Transcripts of the Medicinal Plant Scutellaria baicalensis.International Journal of Molecular Sciences, 20(18): e4426, 2019

4.       KuangXuejun, Sun Sijie, Wei Jianhe, Li Ying*, Sun Chao*. Iso-Seq analysis of the Taxus cuspidata transcriptome reveals the complexity of Taxol biosynthesis. BMC Plant Biology,19(1): e210, 2019

5.       LiangTongTong, Zou Liqiu, Sun Sijie, Kuang Xiejun, Wei Jianhe, Wang Lizhi, Li Ying*,Sun Chao*. Hybrid sequencing of theGynostemma pentaphyllum transcriptome provides new insights into gypenosidebiosynthesis. BMC Genomics, 20(1): e632, 2019

6.      陈士林,孙超, 宋经元等. 本草基因组学 (普通高等教育“十三五”规划教材). 科学出版社, 2018

7.      Zhu Yingjie#, Xu,Jiang#, Sun, Chao*, et al.Chromosome-level genome map provides insights into diverse defense mechanismsin the medicinal fungus Ganoderma sinense. Scientific Reports, 5: 11087, 2015

8.      QiushiLi, Ying Li, Jingyuan Song*, Haibin Xu, Jiang Xu, Yingjie Zhu, Xiwen Li,Huanhuan Gao, Linlin Dong, Jun Qian, Chao Sun and Shilin Chen*.High-accuracy de novo assembly and SNP detection of chloroplast genomes using aSMRT circular consensus sequencing strategy. New phytologist, 204(4),1041-1049, 2014

9.      Chao Sun#,Ying Li#, Qiong Wu, Hongmei Luo, Yongzhen Sun, Jingyuan Song, Edmund MK Lui and Shilin Chen*. De novo sequencing andanalysis of the American ginseng root transcriptome using a GS FLX Titaniumplatform to discover putative genes involved in ginsenoside biosynthesis. BMCGenomics, 11, e262, 2010

10.  Xiaoxuan Zhu, Xinyi Zeng, Chao Sun*, Shilin Chen*. Biosyntheticpathway of terpenoid indole alkaloids in Catharanthus roseus. Frontiers ofmedicine, 8(3), 285-293, 2014

11.  Yongzhen Sun, Yunyun Niu, Jing Xu, Ying Li*, Hongmei Luo, YingjieZhu, Mingzhu Liu, Qiong Wu, Jingyuan Song, Chao Sun*, ShilinChen. Discovery of WRKY transcription factors through transcriptome analysisand characterization of a novel methyl jasmonate-inducible PqWRKY1 gene from Panaxquinquefolius. Plant Cell, Tissue and Organ Culture (PCTOC), 114(2),269-277, 2013

12.  Qiong Wu, Jingyuan Song, Yongqiao Sun, Fengmei Suo, Chenji Li, HongmeiLuo, Ying Liu,Ying Li, Xiaowei Zhang, Hui Yao, Xiwen Li, Songnian Hu and ChaoSun*. Transcript profiles of Panax quinquefolius from flower, leaf and rootbring new insights into genes related to ginsenosides biosynthesis andtranscriptional regulation. Physiologia Plantarum, 138(2), 134-49, 2010

13.  Xiaohui Pang, Hongmei Luo, Chao Sun*. Assessing the potential ofcandidate DNA barcodes for identifying non-flowering seed plants. PlantBiology, 14(5), 839-844, 2012

14.  Shilin Chen*, Hongmei Luo, Ying Li, Yongzhen Sun, Qiong Wu, YunyunNiu, Jingyuan Song, Aiping Lv, Yingjie Zhu, Chao Sun*, André Steinmetz,Zhongzhi Qian. 454 EST analysis detects genes putatively involved inginsenoside biosynthesis in Panax ginseng. Plant Cell Reports, 30(9),1593-1601, 2011

15.  Hongmei Luo#, Chao Sun#, Yongzhen Sun, Qiong Wu, Ying Li, JingyuanSong, Yunyun Niu, Xianglin Cheng, Hongxi Xu, Chuyuan Li, Juyan Liu, AndréSteinmetz, Shilin Chen*. Analysis of the transcriptome of Panaxnotoginseng root uncovers putative triterpene saponin-biosynthetic genes andgenetic markers. BMC Genomics. 12(Suppl 5), S5, 2011

16.  Hongmei Luo, Chao Sun, Ying Li, Qiong Wu, Jingyuan Song, Deli Wang,Xiaocheng Jia, Rongtao Li and Shilin Chen*. Analysis of expressedsequence tags from the Huperzia serrata leaf for gene discovery in the areas ofsecondary metabolite biosynthesis and development regulation. PhysiologiaPlantarum, 139 (1), 1–12, 2010

17.  Chao Sun, Yongqiao Sun, Jingyuan Song, Chenji Li, Xiwen Li,Xiaowei Zhang, Ying Li, SongnianHu, Hongmei Luo, Yingjie Zhu, Shilin Chen*. Discovery of genes relatedto steroidal alkaloid biosynthesis in Fritillaria cirrhosa by generatingand mining a dataset of expressed sequence tags (ESTs). Journal of MedicinalPlants Research, 5(21), 5307-5314, 2011

18.  QiongWu, Chao Sun, Hongmei Luo, Ying Li, Yunyun Niu, Yongzhen Sun, Aiping Lu,Shilin Chen*. Transcriptome analysis of Taxus cuspidata needles based on454 pyrosequencing. Planta Medica, 77(4), 394-400, 2011

19.  Expressionprofiling of the triterpene saponin biosynthesis genes FPS, SS, SE, and DS inthe medicinal plant Panax notoginseng. Yunyun Niu, Hongmei Luo, ChaoSun, Tae-Jin Yang, Linlin Dong, Linfang Huang*, Shilin Chen*. Gene,533(1), 295-303, 2014

20.  HongmeiLuo #, Yingjie Zhu #, Jingyuan Song, Lijia Xu, Chao Sun, Xin Zhang,Yanhong Xu, Liu He, Wei Sun, Haibin Xu, Bo Wang, Xian’en Li, Chuyuan Li, JuyanLiu and Shilin Chen*. Transcriptional data mining of Salvia miltiorrhiza inresponse to methyl jasmonate to examine the mechanism of bioactive compoundbiosynthesis and regulation. Physiologia Plantarum, 152, 241-255, 2014

21.  YingjieZhu#, Hongmei Luo#, Xin Zhang, Jingyuan Song, Chao Sun, Aijia Ji, JiangXu, Shilin Chen*. Abundant and Selective RNA-Editing Events in the MedicinalMushroom Ganoderma lucidum. Genetics, 196, 1047-1057, 2014

22.  ChunfangLi, Yingjie Zhu, Xu Guo, Chao Sun, Hongmei Luo, JingyuanSong, Ying Li, Lizhi Wang, Jun Qian, Shilin Chen*.Transcriptome analysis reveals ginsenosides biosynthetic genes, microRNAsand simple sequence repeats in Panax ginseng C. A. Meyer. BMCGenomics, 14, 245, 2013

23.  QiongWu, Chao Sun, Shilin Chen*. Identification and expression analysis of a 3-hydroxy-3-methylglutarylcoenzyme A reductase gene from American ginseng. Plant Omics Journal,5(4), 414-420, 2012

24.  YunyunNiu, Hongmei Luo, Chao Sun, Tae-Jin Yang, Linlin Dong, Linfang Huang*,Shilin Chen*: Expression profiling of the triterpene saponinbiosynthesis genes FPS, SS, SE, and DS in the medicinal plant Panaxnotoginseng. Gene, 533, 295-303, 2014

25.  YingLi, Hongmei Luo, Chao Sun, Jingyuan Song, Yongzhen Sun, Qiong Wu, NingWang, Hui Yao, André Steinmetz* and Shilin Chen*. EST analysis reveals putativegenes involved in glycyrrhizin biosynthesis. BMC Genomics, 11, e268,2010

26.  HongmeiLuo#, Ying Li#, Chao Sun, Qiong Wu, Jingyuan Song, Yongzhen Sun, André Steinmetz,Shilin Chen*. Comparison of 454-ESTs from Huperzia serrata and Phlegmariurus carinatusreveals putative genes involved in lycopodium alkaloid biosynthesis and developmentalregulation. BMC Plant Biology, 10, e209, 2010

27.  YongzhenSun, Hongmei Luo, Ying Li, Chao Sun, Jingyuan Song, Yunyun Niu，YingjieZhu, Liang Dong, Aiping Lv, Enzo Tramontano, Shilin Chen*. Pyrosequencing ofthe Camptotheca acuminata transcriptome reveals putative genes involvedin camptothecin biosynthesis and transport. BMC Genomics, 12, e533, 2011

28.  HongmeiLuo, Chao Sun, Jingyuan Song, Jin Lan, Ying Li, Xiwen Li, Shilin Chen*. Generationand analysis of expressed sequence tags from a cDNA library of the fruitingbody of Ganoderma lucidum. Chinese Medicine, 5, e9, 2010

29.  LiXiang, Ying Li , Yingjie Zhu, Hongmie Luo, Chunfang Li, Xiaolan Xu, Chao Sun,Jingyuan Song, Linchun Shi, Liu He, Wei sun, Shilin Chen*. Transcriptomeanalysis of the Ophiocordyceps sinensis fruiting body reveals putative genesinvolved in fruiting body development and cordycepin biosynthesis. Genomics,103(1), 154-159, 2014

30.  JiangXu, Zhichao Xu , Yingjie Zhu, Hongmei Luo, Jun Qian, Aijia Ji, Yuanlei Hu, WeiSun, Bo Wang, Jingyuan Song, Chao Sun, Shilin Chen*. Identification andevaluation of reference genes for qRT-PCR normalization in ganoderma lucidum. Current microbiology, 68, 120-126, 2014

31.  LiuHe #, Xiaolan Xu #, Ying Li, Chunfang Li, Yingjie Zhu, Haixia Yan, Zhiying Sun,Chao Sun, Jingyuan Song, Yu’an Bi, Juan Shen, Ruiyang Cheng, ZhenzhongWang, Wei Xiao*, Shilin Chen*. Transcriptome Analysis of Buds and Leaves Using454 Pyrosequencing to Discover Genes Associated with the Biosynthesis of ActiveIngredients in Lonicera japonica Thunb. PLOS One, 8(4), e62922,2013

32.  Jun Qian, Jingyuan Song, Huanhuan Gao, Yingjie Zhu, Jiang Xu, XiaohuiPang, Hui Yao, Chao Sun, Xian’en Li, Chuyuan Li, Juyan Liu, Haibin Xu*,Shilin Chen*. The Complete Chloroplast Genome Sequence of the Medicinal Plant Salviamiltiorrhiza. PLOS One, 8(2), e57607, 2013

33.  Xiaohan Lin, Jin Zhang, Ying Li, Hongmei Luo, Qiong Wu, Chao Sun,Jingyuan Song, Xiwen Li, Jianhe Wei, Aipei Lu, Zhongzhi Qian, Khan IA, ShilinChen*. Functional genomics of a living fossil tree, Ginkgo, based onnext-generation sequencing technology. Physiologia Plantarum, 143 (3),207-218, 2011

34. 王丽芝,王海英, 浦香东, 孙思杰, 魏建和, 孙超*. 基于紫芝基因组的倍半萜合酶基因的发掘与功能鉴定.中国科学:生命科学, (04): 447-454, 2018

35.孙超, 胡鸢雷, 徐江, 罗红梅, 李春芳, 宋经元, 郭红卫*, 陈士林*. 灵芝: 一种研究天然药物合成的模式真菌. 中国科学: 生命科学, 06, 447-456, 2013

36. 褚丽华,王丽芝, 陈士林, 曾欣宜, 徐江, 李滢, 孙超*. 一个紫芝多产物倍半萜合酶的功能鉴定.中国实验方剂学杂志, (12): 151-157, 2019

37.徐江，孙超，徐志超，季爱加，胡鸢雷，孙伟，王丽芝，汪波，杨培，张鑫，宋经元，陈士林*. 药用模式生物研究策略. 科学通报, 59(9), 733-742, 2014

38.邹丽秋,匡雪君, 孙超*, 陈士林*. 天然产物生物合成途径解析策略. 中国中药杂志, 41(22)：4119~4123，2016

39.匡雪君,  邹丽秋, 孙超*, 陈士林*. 天然产物合成生物学体系的优化策略. 生物技术通报, 33(1): 48-57, 2016

40.匡雪君,邹丽秋, 李滢, 孙超*, 陈士林*. 天然产物合成生物学关键技术. 中国中药杂志, 41(22)：4112~411 8，2016

41.匡雪君；王彩霞；邹丽秋；李滢；孙超*. 紫杉醇生物合成途径及合成生物学研究进展，中国中药杂志，41(22)：4144~4149, 2016

42.李滢, 匡雪君, 朱孝轩, 朱英杰, 孙超*. 长春花密码子使用偏好性分析. 中国中药杂志, 41(22)：4165~416,  2016

43.曾欣宜, 朱英杰, 李滢, 孙超*. 基于全基因组的紫芝细胞色素P450分析. 中国现代中药, 18(12)：1555~1559，2016

44.朱孝轩#, 朱英杰#, 宋经元, 孙超*, 陈士林. 基于全基因组和转录组分析的赤芝密码子使用偏好性比较研究. 药学学报, 49(9), 1340-1345, 2014

45.何柳，徐晓兰，王振中，毕宇安，萧伟*，罗红梅，孙超*. 金银花莽草酸/ 奎宁酸香豆酰转移酶（LjHCT）基因克隆与序列分析. 世界科学技术—中医药现代化, 16(2), 263-268, 2014

46.李滢, 牛云云, 宋经元, 罗红梅, 李秋实, 孙超*. 甘草酸合成生物学元件初探: 甘草法呢基焦磷酸合酶基因的克隆及序列分析. 世界科学技术-中医药现代化, 03, 355-359,2013

47.何柳，朱英杰，孙超*. 金银花中表达基因密码子偏好性分析. 世界科学技术-中医药现代化, 15(3), 360-366, 2013