研究方向
（1）分子遗传
（2）基因工程
（3）分子育种

主要研究领域：
       园艺作物分子标记遗传图谱构建、基因精细定位、基因克隆、遗传转化，分子标记辅助育种，培育符合市场需求的新品种。
       曾获教育部骨干教师，创新团队方向负责人。获教育部技术发明一等奖1项，上海市科技进步二、三等奖各1项，上海市优秀博士论文奖，上海市育才奖。分别获中国第七届、第八届花卉博览会草花类金、银、铜和优秀奖，申请专利20多项（其中已获得授权专利15项）。培育出适应温室栽培的单性结实黄瓜新品种10个，矮牵牛新品种10个，长春花新品种3个，均获得新品种审定证书，其中2个黄瓜品种获得农业部品种保权。在全国10多个省市推广种植，推广面积30多万亩次。近年发表论文80余篇，其中SCI论文30多篇（The Plant Journal; J Exp Bot; Genetics; Thoer Appl Genet; Frontiers in Plant Science ;Mol Breeding;等）。

主要论文： 

1. Zhu W, Huang L, Chen L, Yang J, Wu J, Qu M, Yao D, Guo C, Lian H, He H, Pan J,  Cai R* A High-Density Genetic Map for Cucumber (Cucumis Sativus L.) Based on Specific Length Amplified Fragment (SLAF) Sequencing and QTL Analysis of Fruit Traits in Cucumber. Frontiers in Plant Science, 2016, 7(569)
2. Yunli Wang, Jingltao Nie, Huiming Chen, Chunli Guo, Jian Pan, Huanle He, Junsong Pan, Run Cai*. Identification and mapping of Tril, a homeodomain-leucine zipper gene involved in multicellular trichome initiation in Cucumis sativus. Theoretical and Applied Genetics, 2015: 1-12
3. Nie J, Wang Y, He H, Guo C, Zhu W, Pan J, Li D, Lian H, Pan J, Cai R*. Loss-of-Function Mutations in CsMLO1 Confer Durable Powdery Mildew Resistance in Cucumber (Cucumis sativus L.). Frontiers in plant science, 2015, 6
4. Junlong Zhao, Junsong Pan, Yuan Guan, Weiwei Zhang, Beibei Bie, Yunli Wang,Huanle He,Hongli Lian, Run Cai* Identification and characterization of Micro-trichome, a homeodomain- leucine zipper gene involved in multicellular trichome development in Cucumis sativus. Journal of Integrative Plant Biology, DOI: 10.1111/jipb.12345
5. JunLong Zhao, Jun-Song Pan, Yuan Guan, Wei-Wei Zhang, Bei-Bei Bie, Yun-Li Wang, Huan-Le He, Hong-Li Lian and Run Cai*, Transcriptome profiling of trichome-less reveals genes associated with multicellular trichome development in Cucumis sativus, Mol Genet Genomics, 2015, DOI 10.1007/s00438-015-1057-z
6. Jun-Long Zhao, Jun-Song Pan, Yuan Guan, Jing-Tao Nie, Jun-Jun Yang, Mei-Ling Qu, Huan-Le He, Run Cai*. Transcriptome analysis in Cucumis sativus identifies genes involved in multicellular trichome development. Genomics, 2015, 105, 296–303
7. Xuqin Yang, Weiwei Zhang, Huanle He, Jingtao Nie, Beibei Bie, Junlong Zhao, Guoliang Ren, Yue Li, Dabing Zhang, Junsong Pan, Run Cai*. Tuberculate fruit gene Tu encodes a C2H2 zinc finger protein that  is required for the warty fruit phenotype in cucumber (Cucumis sativus L.). The Plant Journal, 2014. 78(6):1034–1046
8. Xuqin Yang, Weiwei Zhang, Yue Li, Huanle He, Beibei Bie, Guoliang Ren, Junlong Zhao, Yunli Wang, Jingtao Nie, Junsong Pan, Run Cai*. High-resolution mapping of the dull fruit skin gene D in cucumber (Cucumis sativus L.). Mol Breeding, 2014, 33:15–22
9. Xuqin Yang · Yue Li · Weiwei Zhang · Huanle He · Junsong Pan · Run Cai*. Fine mapping of the uniform immature fruit color gene u in cucumber (Cucumis sativus L.). Euphytica, 2014, 196:341–348
10. Zheng Li, Shu Wang, Qianyi Tao, Junsong Pan, Longting Si, Zhenhui Gong, Run Cai*. A putative positive feedback regulation mechanism in CsACS2 expression suggests a modified model for sex determination in cucumber (Cucumis sativus L.). J Exp Bot, 2012, 63: 4475-4484
11. Wei-Wei Zhang, Jun-Song Pan, Huan-Le He, Chi Zhang, Zheng Li, Jun-Long Zhao , Xiao-Jun Yuan , Li-Huang Zhu, San-Wen Huang, Run Cai*. Construction of a high density integrated genetic map for cucumber (Cucumis sativus L.). Theor Appl Genet (2012) 124:249–259
12. Li-Hua Yuan, Jun-Song Pan, Gang Wang, Jun Zhu, Wei-Wei Zhang, Zheng Li, Huan-Le He, Zhong-Nan Yang, Run Cai*, Li-Huang Zhu. The cucumber lateral suppressor gene (CLS) is functionally associated with axillary meristem initiation. Plant Mol Biol Rep, 2010, 28: 421-429
13. Zhang Weiwei, He Huanle, Guan Yuan, Du Hui, Yuan Lihua, Li Zheng, Yao Danqing, Pan Junsong, Cai Run*. Identificating and mapping of molecular markers linked to the tuberculate fruit gene in the cucumber (Cucumis sativus L.). Theor Appl Genet, 2010, 120: 645-654
14. Li Zheng, Huang Sanwen, Liu Shiqiang, Pan Junsong, Zhang Zhonghua, Tao Qianyi, Shi Qiuxiang, Jia Zhiqi, Zhang, Weiwei, Chen Huiming, Si Longting, Zhu Lihuang, Cai Run*. Molecular Isolation of the M Gene Suggests That a Conserved-Residue Conversing Induces the Formation of Bisexual Flowers in Cucumber Plants. Genetics, 2009, 182: 1381-1385
15. Li Z, Pan J S, Guan Y, Tao Q Y, He H L, Si L T, Cai R*. Development and fine mapping of three co-dominant SCAR markers linked to the M/m gene in the cucumber plant (Cucumis sativus L.). Theor Appl Genet. 2008, 117: 1253-1250
16. Yuan X J, Li X Z, Pan J S, Wang G, Jiang S, Li X H, Deng S L, He H L , Si M X, Lai L, Wu A Z, Zhu L H, Cai R*. Genetic linkage map construction and location of QTLs for fruit-related traits in cucumber. Plant Breeding. 2008, 127: 180-188