Papers
1.Yang L#, Peng T#, Zhu Y#, Zhai X, Huang B, Zhou H, Tao D, Li L, Zhang T, Cao Y, Chen J, Liang D*, He J*, Zhang M*. High-throughput functional characterization of enhancers in totipotent-like cells. Nature Communications, 2026.
2.Huang R#, Han Z#, Liufu Z#, Quan X, Li D, Dong H, Hong G, Chen R, Zhang M, Peng G, Pei D, Chen J*, He J*. IAPEz retrotransposons regulate the first lineage segregation in mouse pre-implantation development. Nucleic Acids Research, 2026.
3.Chen P#, Yang X#, Chen R#, Li H#, Ma J, Chang J, Hong G, Liu W, Quan X, Yin B, Hou L, Qiang B, Shu P*, He J*, Peng X*, Chen J*. PCGF1 is a key factor for facilitating dynamic H3K27me3 modification during early lineage specification. Science Bulletin, 2026, S2095-9273(26): 00168-4.
4.Chen R, Chen J., Shi L*, He J*. iceDP: identifying inter-chromatin engagement via density peaks clustering algorithm. Briefings in Bioinformatics, 2026.
5.Zhu A#, Zhou L#, Chen Z, Liu D, Feng H, Cai B, Chen X, Zhao J, Zhao J, Chen J, Li M*, He J*. Single-cell analysis reveals T cell dysfunction driven by macrophages and differential expression of transposable elements in severe COVID-19 patients. Heliyon, 2024.
6.Wu K#, Li S#, Hong G, Dong H, Tang T, Liu H, Jin L, Lin S, Ji J, Hu M, Chen S, Wu H, Luo G, Wu H, Kong X, Chen J, He J*, Wu H*. Targeting METTL3 as a checkpoint to enhance T cells for tumour immunotherapy. Clinical and Translational Medicine, 2024.
7.Liu Y#, Hu L#, Wu Z#, Yuan K, Hong G, Lian Z, Feng J, Li N, Li D, Wong J, Chen J, Liu M, He J*, Pang X*. Loss of PHF8 induces a viral mimicry response by activating endogenous retrotransposons. Nature Communications, 2023.
8.Liufu Z*, Liu Y, He J*. Protocol for siRNA-mediated TET1 knockdown during differentiation of human embryonic stem cells into definitive endoderm cells. STAR Protocols, 2023.
9.Wu F, Liufu Z, Liu Y, Guo L, Wu J, Cao S, Qin Y, Guo N, Fu Y, Liu H, Li Q, Shu X, Pei D, Hutchins A P, Chen J*, He J*. Species-specific rewiring of definitive endoderm developmental gene activation via endogenous retroviruses through TET1-mediated demethylation. Cell Reports, 2022.
10.Yu S#, Zhou C#, He J#, Yao Z, Huang X, Rong B, Zhu H, Wang S, Chen S, Wang X, Cai B, Zhao G, Chen Y, Xiao L, Liu H, Qin Y, Guo J, Wu H, Zhang Z, Zhang M, Zhao X, Lan F, Wang X, Chen J, Cao S*, Pei D*, Liu J*. BMP4 drives primed to naïve transition through PGC-like state. Nature Communications, 2022.
11.Ren X#, Wen W#, Fan X#, Hou W#, Su B#, Cai P#, Li J#, Liu Y#, Tang F#, Zhang F#, Yang Y#, He J#, Ma W#, He J#, Wang P, Cao Q, Chen F, Chen Y, Cheng X, Deng G, Deng X, Ding W, Feng Y, Gan R, Guo C, Guo W, He S, Jiang C, Liang J, Li Y, Lin J, Ling Y, Liu H, Liu J, Liu N, Liu S, Luo M, Ma Q, Song Q, Sun W, Wang G, Wang F, Wang Y, Wen X, Wu Q, Xu G, Xie X, Xiong X, Xing X, Xu H, Yin C, Yu D, Yu K, Yuan J, Zhang B, Zhang P, Zhang T, Zhao J, Zhao P, Zhou J, Zhou W, Zhong S, Zhong X, Zhang S, Zhu L, Zhu P, Zou B, Zou J, Zuo Z, Bai F, Huang X, Zhou P*, Jiang Q*, Huang Z*, Bei J X*, Wei L*, Bian X W*, Liu X*, Cheng T*, Li X*, Zhao P*, Wang F*, Wang H*, Su B*, Zhang Z*, Qu K*, Wang X*, Chen J*, Jin R*, Zhang Z*. COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas. Cell, 2021, 184(7): 1895-1913.e19.
12.He J., Babarinde I, Sun L, Xu S, Chen R, Shi J, Wei Y, Li Y, Ma G, Zhuang Q, Hutchins A P*, Chen J*. Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE. Nature Communications, 2021.