[1]国家重点研发计划项目子课题 “海菜花属植物基因组多样性与适应性及迁地保护技术”（编号：2024YFF1307400；执行期：2024年12月-2028年12月）。主持人。

[2]植物多样性与特色经济作物全国重点实验室自主研究课题“睡莲目植物比较基因组学及生活型演化的分子机制”（编号：PDSC2023‐5；执行期：2023年12月-2025年12月）。主持人。

2025

Bei Lu, Wei Li, Yue Zhang*, Jin-Ming Chen*. 2025. Origin and evolution of the blue light receptor cryptochromes (CRY1/2) in aquatic angiosperms. Plant Physiology, 197, kiae568.

Tao Shi*, Zhi-Yan Gao, Yue Zhang, Mark D. Rausher*, Jin-Ming Chen*. 2025. A strategy of assessing gene copy number differentiation between populations using ultra-fast de novo assembly of next-generation sequencing data. Molecular Ecology Resources, 25: e14080.

Jing-Shan Yang, Jin-Ming Chen, Xiang-Yan He, Guang-Xi Wang, Spencer C.H. Barrett*, Zhi-Zhong Li*. 2025. The Monochoria genome provides insights into the molecular mechanisms underlying floral heteranthery. Journal of Genetics and Genomics, 52: 826e838.

2024

Tao Shi^#*, Zhi-Yan Gao^#, Jin-Ming Chen, Yves Van de Peer*. 2024. Dosage sensitivity shapes balanced expression and gene longevity of homoeologs after whole-genome duplications in angiosperms. The Plant Cell, 36: 4323-4337.

Zhi-Hao Qian, Wei Li, Qing-FengWang, Shi-Chu Liang, ShuangWu, Zhi-Zhong Li*, Jin-Ming Chen*. 2024. The chromosome-level genome of the submerged plant Cryptocoryne crispatula provides insights into the terrestrial-freshwater transition in Araceae. DNA Research, 31: 1-13.

John M. Nzei, Norberto Martínez-Médez, Virginia M. Mwanzia, Joseph K. Kurauka, Qing-Feng Wang, Zhi-Zhong Li*, Jin-Ming Chen*. 2024. Climatic niche evolution and niche conservatism of Nymphaea species in Africa, South America, and Australia. BMC Plant Biology, 24: 476.

2023

Jing-Shan Yang^#, Hao-Ran Xue^#, Zhi-Zhong Li, Yue Zhang, Tao Shi, Xiang-Yan He, Spencer C. H. Barrett*, Qing-Feng Wang*, Jin-Ming Chen*. 2023. Haplotype-resolved genome assembly provides insights into the evolution of S-locus supergene in distylous Nymphoides indica. New Phytologist, 240: 2058-2071.

Zhi-Hao Qian, Jun Ding, Zhi-Zhong Li* and Jin-Ming Chen*. 2023. The high-quality Pinellia pedatisecta genome reveals a key role of tandem duplication in the expansion of its agglutinin genes. Horticulture Research, 10: uhac289.

Bei Lu, Tao Shi, Jin-Ming Chen*. 2023. Chromosome-level genome assembly of watershield (Brasenia schreberi). Scientific Data, 10: 467.

Zhi-Zhong Li, Lehtonen Samuli*, Jin-Ming Chen*. 2023. The dynamic history of plastome structure across aquatic subclass Alismatidae. BMC Plant Biology, 23:125.

Zhi-Yan Gao, Xing-Yu Yang, Jin-Ming Chen*, Rausher MD*, Tao Shi*. 2023. Expression inheritance and constraints on cis- and trans-regulatory mutations underlying lotus color variation. Plant Physiology, 191: 1662-1683.

Yue Zhang, Yves Van de Peer, Bei Lu, Si-Si Zhang, Jing-Ru Che, Jin-Ming Chen*, Kathleen Marchal*, Xing-Yu Yang*. 2023. Expression divergence of expansin genes drive the heteroblasty in Ceratopteris chingii. BMC Biology, 21: 244.

2022

Zhi-Hao Qian, Jun Ding, Zhi-Zhong Li*, Jin-Ming Chen*. 2022. The chromosome‐level genome of a free‐floating aquatic weed Pistia stratiotes. Molecular Ecology Resources, 10: uhac289.

Tao Shi, Cécile Huneau, Yue Zhang, Yan Li, Jin-Ming Chen*, Jérôme Salse*, Qing-Feng Wang*. 2022. The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution. Nature Plants, 8: 764-777.

Yue Zhang, Xing-Yu Yang, Yves Van de Peer, Jin-Ming Chen*, Kathleen Marchal*, Tao Shi*. 2022. Evolution of isoform‐level gene expression patterns across tissues during lotus species. The Plant Journal, 112: 830-846.

Zhi-Zhong Li^# , Samuli Lehtonen^#, Karina Martins, Qing-Feng Wang, Jin-Ming Chen*. 2022. Complete genus-level plastid phylogenomics of Alismataceae with revisited historical biogeography Molecular Phylogenetics and Evolution, 166: 107334.）

Zhi-Zhong Li, Samuli Lehtonen, Andrew W. Gichira, Karina Martins, Qing-Feng Wang, Jin-Ming Chen*. 2022. Plastome phylogenomics and historical biogeography of aquatic plant genus Hydrocharis (Hydrocharitaceae). BMC Plant Biology, 22(1): 1-11.

2021

Zhi-Zhong Li, Andrew W. Gichira, John K. Muchuku, Wei Li, Guang-Xi Wang*, Jin-Ming Chen*. 2021. Plastid phylogenomics and biogeography of the genus Monochoria (Pontederiaceae). Journal of Systematics and Evolution, 59(5): 1027-1039.

Hui Li, Xing-Yu Yang, Qing-Feng Wang, Jin-Ming Chen*, Tao Shi*. 2021. Distinct methylome patterns contribute to ecotypic differentiation in the growth of the storage organ of a flowering plant (sacred lotus). Molecular Ecology, 30: 2831-2845.

Hui Li^#, Xing-Yu Yang^#, Yue Zhang, Zhi-Yan Gao, Yu-Ting Liang, Jin-Ming Chen*, Tao Shi*. 2021. Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera. Scientific Data, 8: 38.

2020

Tao Shi, Razgar Seyed Rahmani, Paul F. Gugger, Mu-Hua Wang, Hui Li, Yue Zhang, Zhi-Zhong Li, Qing-Feng Wang*, Yves Van de Peer*, Kathleen Marchal*, Jin-Ming Chen*. 2020. Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants. Molecular Biology and Evolution, 37(8): 2394-2413.

Tao Shi*, Jin-Ming Chen*. 2020. A reappraisal of the phylogenetic placement of the Aquilegia whole-genome duplication. Genome Biology, 21: 295.

Zhi-Zhong Li, Samuli Lehtonen, Karina Martins, Andrew W. Gichira, Shuang Wu, Wei Li, Guang-Wan Hu, Yan Liu, Chun-Yu Zou, Qing-Feng Wang, Jin-Ming Chen*. 2020. Phylogenomics of the aquatic plant genus Ottelia (Hydrocharitaceae): Implications for historical biogeography. Molecular Phylogenetics and Evolution 152: 106939.

2019

Zhi-Zhong Li, Shuang Wu, Chun-Yu Zou, Yan Liu, Guang-Wan Hu, Samuli Lehtonen, Qing-Feng Wang*, Jin-Ming Chen*. 2019. Ottelia fengshanensis (Hydrocharitaceae), a new bisexual species of Ottelia (Hydrocharitaceae) from southwestern China. Phytokeys, 135: 1-10.

2018

Zhi-Zhong Li, Kuo Liao, Chun-Yu Zou, Yan Liu, Guang-Wan Hu, Qing-Feng Wang*, Jin-Ming Chen*. 2018. Ottelia guanyangensis (Hydrocharitaceae), a new species from southwestern China. Phytotaxa, 361(3): 294.

Ding-Xuan He^#, Andrew Wanyoike Gichira^#, Zhi-Zhong Li, Qing-Feng Wang, Jin-Ming Chen*. 2018. Intergeneric relationships within the early-diverging angiosperm family Nymphaeaceae based on chloroplast phylogenomics. International Journal of Molecular Sciences, 19: 3780.

2016

Yi-Ying Liao, Andrew Wanyoike Gichira, Qing-Feng Wang*, Jin-Ming Chen*. 2016. Molecular phylogeography of four endemic Sagittaria species (Alismataceae) in the Sino-Japanese Floristic Region of East Asia. Botanical Journal of the Linnean Society, 18: 6-20.

Jin-Ming Chen, Silke Werth, Victoria L. Sork*. 2016. Comparison of phylogeographical structures of a lichen-forming fungus and its green algal photobiont in western North America. Journal of Biogeography, 43: 932-943.

Victoria L. Sork*, Paul F. Gugger, Jin-Ming Chen, Silke Werth. 2016. Evolutionary lessons from California plant phylogeography. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 113(29): 8064-8071.