工作经历
2008.07-2010.08: 浙江大学，生命科学学院，生物信息学，科研助理，合作导师：陈铭教授
2015.05-2016.09: [德国]波茨坦大学，生物信息学，博士后，导师：Prof. Kerstin Kaufmann
2016.10-2019.09: [德国]洪堡大学，生物信息学，博士后，导师：Prof. Kerstin Kaufmann
2019.10-: 南京大学，副教授/博导
荣誉奖励
学术任职
中国生物信息学学会（筹）多组学与整合生物学专业委员会 委员
江苏省生物医学工程学会生物信息学专业委员会 委员
浙江省生物信息学会人工智能专委会 委员
江苏省植物学会青年工作委员会 委员
代表性成果
1.Zhang Y, Ming W, Yu B, Wang L, Lu K, Xu L, Ni Y, Deng R*, Chen D*. Robust integration and annotation of single-cell and spatial omics data using interpretable gene programs. Cell Genom. 2025. doi: 10.1016/j.xgen.2025.101105.
2.Hawar A, Chen W, Zhu T, Wang X, Liu J, Xiong S, Ito T, Chen D*, Sun B*. The histone acetyltransferase GCN5 regulates floral meristem activity and flower development in Arabidopsis. Plant Cell. 2025;37(6):koaf135. doi: 10.1093/plcell/koaf135.
3.Zhou X, Fan HY, Feng XY, Ruan Z, Yuan J, Han Q, He Z, You Y, Chao H, Chen M, Shao ZQ*, Xue JY*, Chen D*.PGCP: A comprehensive database of plant genomes for comparative phylogenomics. Plant Biotechnol J. 2025;23(7):2928-2930. doi: 10.1111/pbi.70110.
4.Cao G, Chao H, Zheng W, Lan Y, Lu K, Wang Y, Chen M, Zhang H*, Chen D*. scPlantLLM: A Foundation Model for Exploring Single-cell Expression Atlases in Plants. Genomics Proteomics Bioinformatics. 2025;23(3):qzaf024. doi: 10.1093/gpbjnl/qzaf024.
5.Zhang Y, Yu B, Ming W, Zhou X, Wang J, Chen D*. SpaTopic: A statistical learning framework for exploring tumor spatial architecture from spatially resolved transcriptomic data. Sci Adv. 2024;10(39):eadp4942.
6.Zhu T, Xia C, Yu R, Zhou X, Xu X, Wang L, Zong Z, Yang J, Liu Y, Ming L, You Y, Chen D*, Xie W*. Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits. Nat Commun. 2024;15(1):6562.
7.He Z, Luo Y, Zhou X, Zhu T, Lan Y, Chen D*. scPlantDB: a comprehensive database for exploring cell types and markers of plant cell atlases. Nucleic Acids Res. 2024;52(D1):D1629-D1638.
8.Zhang S, Fang W, Zhou S, Zhu D, Chen R, Gao X, Li Z, Fu Y, Zhang Y, Yang F, Zhao J, Wu H, Wang P, Shen Y, Shen S, Xu G, Wang L, Yan C*, Zou X*, Chen D*, Lv Y*. Single cell transcriptomic analyses implicate an immunosuppressive tumor microenvironment in pancreatic cancer liver metastasis. Nat Commun. 2023;14(1):5123.
9.Qu J, Yang F, Zhu T, Wang Y, Fang W, Ding Y, Zhao X, Qi X, Xie Q, Chen M, Xu Q, Xie Y*, Sun Y*, Chen D*. A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys. Nat Commun. 2022; 13(1):4069. Featured Article.
Fu LY, Zhu T, Zhou X, Yu R, He Z, Zhang P, Wu Z, Chen M, Kaufmann K*, Chen D*. ChIP-Hub provides an integrative platform for exploring plant regulome. Nat Commun. 2022; 13(1):3413. Featured Article.
