第一及通讯作者文章：
[1] 表观及多组学数据分析算法开发：
1. Chen R., Chen J.*, Shi L.*, He J.*, iceDP: identifying inter-chromatin engagement via density peaks clustering algorithm. Brief in Bioinformatics, 2026. （开发染色质间互作检测新算法）
2. 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.（开发单细胞组学定量转座元件新工具）
3. He J., Fu X., Zhang M., He F., Li W., Abdul M., Zhou J., Sun L., Chang C., Li Y., Liu H., Wu K., Babrinde I., Zhuang Q., Loh Y-H., Chen J., Esteban M., Hutchins A.P., Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells. Nature Communications, 2019. （开发表观组学定量转座元件算法）
[2] 发育谱系表观遗传调控机制解析：
4. 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. （阐明转座元件调控内胚层形成机制）
5. Liu J.#, Gao M.#, He J.#, Wu K., Lin S., Jin L., Chen Y., Liu H., Xu S., Lin Y., Zhao Y., Wu G., Zhang X., Luo G., Pei D., Wang J., Bao X., Chen J., The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity. Nature, 2021.（发现RNA m6A修饰调控转座元件和着床前胚胎发育新功能）
6. Yu S.#, Zhou C.#, Cao S.#, He J.#, Cai B., Wu K., Qin Y., Huang X., Xiao L., Ye J., Xu S., Xie W., Kuang J., Chu S., Guo J., Liu H., Pang W., Guo L., Zeng M., Wang X., Luo R., Li C., Zhao G., Wang B., Wu L., Chen J., Liu J.*, Pei D.*, BMP4 Resets Mouse Epiblast Stem Cells to Naïve Pluripotency through Zbtb7a/b-mediated Chromatin Remodeling. Nature Cell Biology, 2020. （BMP4信号分子调控着床阶段胚胎发育分子机制）
7. 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. （BMP4信号分子调控着床阶段胚胎发育细胞机制）
[3] 疾病谱系表观遗传调控机制解析：
8. 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.（阐明RNA m6A修饰调控抗肿瘤免疫机制）
9. 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. （组蛋白甲基转移酶PHF8通过转座元件调控抗肿瘤免疫机制）
10. 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., … , Huang X., Zhou P*., Jiang Q*., Huang Z*., Bei JX*., Wei L*., Bian XW*., 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. （新冠肺炎单细胞研究中国联盟，限于篇幅未列出所有作者)
11. Sun J.#, Zhuang Z.#, Zhen J.#, Li K.#, Wong R.#, Liu D.#, Huang J.#, He J.#, Zhu A.#, Zhao J.#, Li X.#, Xi Y.#, Chen R., Alshukairi A., Chen Z., Zhang Z., Chen C., Huang X., Li F., Lai X., Chen D., Wen L., Zhuo J., Zhang Y., Wang Y., Huang S., Dai J., Shi Y., Zheng K., Leidinger M., Chen J., Li Y., Zhong N., Meyerholz D., Jr. Paul B. *, Perlman S.*, Zhao J.*, Generation of a Broadly Useful Model for COVID-19 Pathogenesis, Vaccination, and Treatment. Cell, 2020. （构建新冠肺炎动物模型）
12. 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. （阐明新冠病人巨噬细胞诱导T细胞耗竭机制）
13. He J.#, Cai S.#, Feng H.#, Cai B.#, Lin L.#, Mai Y., Fan Y., Zhu A., Huang H., Shi J., Li D., Wei Y., Li Yu., Zhao Y., Pan Y., Liu H., Mo X., He X., Cao S., Hu F., Zhao J., Wang J., Zhong N., Chen X.*, Deng X.*, Chen J.*, Single-cell analysis reveals bronchoalveolar epithelial dysfunction in COVID-19 patients. Protein & Cell, 2020. （新冠肺炎粘液分泌导致的急性呼吸窘迫机制）
参与文章：
14. Shi L., Xiao Z., Zhou X., Babarinde I., Fu X., Ma G., Huang G., Sun L., He J., Strunnikov A., Hutchins A.P., Genome Biology, 2026.
15. Zhu A#., Chen Z#., Yan Q#., Jiang M#., Liu X#., Li Z#., Li N#., Tang C#., Jian W#., He J., Chen L., Cheng J., Chen C., Tang T., Xu Z., Hu Q., Li F., Wang Y., Sun J., Zhuang Z., Wen L., Zhuo J., Liu D., Zhang Y., Huang X., Li S., Zeng Q., Chen F., Zhou L., Liu D., Zhong C., Chen Y., Li S., Liang K., Zhong N., Zhang X., Chen J., Chen X*., Xu Y*., Zhong N*., Zhao J*., Zhao J*., Robust mucosal SARS-CoV-2-specific T cells effectively combat COVID-19 and establish polyfunctional resident memory in patient lungs. Nature Immunology, 2025.
16. Li S#., Hao J#., Hong G., Dong H., Liu H., Jin L., Zhang Z., Wu H., Hu M., Huang R., Luo G., He J., Chen J*., Wu K*., METTL3 inhibits primed-to-naive transition of pluripotent stem cells through m(6)A-YTHDF2-pluripotency/Gstp1 mRNA degradation axis. Cell Regeneration, 2025.
17. Guan J#., Hong G#., Liu Z#., Zheng Y., He J., Qin D., Li H., Distinct Transcriptomic Profiles of Cultured Anterior and Posterior Populations of Human Infant Scleral Fibroblasts: Including Dopamine Receptors. Investigative Ophthalmology & Visual Science, 2025.
18. Wang F#., Li K#., Wang W., Jiang H., He J., Cai J., Ren W., Zhao Y., Song Q., He Y., Ma Y., Feng X., Liu Y., Yu J., Jitkaew S., Ma D*., Cai Z*., Sensing of endogenous retroviruses-derived RNA by ZBP1 triggers PANoptosis in DNA damage and contributes to toxic side effects of chemotherapy. Cell Death & Disease, 2024.
19. Shan Z#., Zhao Y#., Chen X#., Zhan G#., Huang J., Yang X., Xu C., Guo N., Xiong Z., Wu F., Liu Y., Liu H., Chen B., Chen B., Sun J., He J., Guo Y., Cao S., Wu K., Mao R., Wu G., Lin L., Zou X*., Wang J*., Chen J*., KMT2D deficiency leads to cellular developmental disorders and enhancer dysregulation in neural-crest-containing brain organoids. Science Bulletin, 2024.
20. Shan Y#*., Zhang Y#., Wei Y#., Zhang C., Lin H., He J., Wang J., Guo W., Li H., Chen Q., Zhou T., Xing Q., Liu Y., Chen J., Pan G., METTL3/METTL14 maintain human nucleoli integrity by mediating SUV39H1/H2 degradation. Nature Communications, 2024.
21. Jin L., He J., Feng H., Li S., Liu H., Dong H., Hu M., Huang J., Wu H., Chen J*., Qi L*., Wu K*., Transposable elements activation triggers necroptosis in mouse embryonic stem cells. Cell Death & Disease, 2023.
22. Qin Y#., Huang X#., Cai Z., Cai B., He J., Yao Y., Zhou C., Kuang J., Yang Y., Chen H., Chen Y., Ou S., Chen L., Wu F., Guo N., Yuan Y., Zhang X., Pang W., Feng Z., Yu S., Liu J., Cao S*., Pei D*., Regeneration of the human segmentation clock in somitoids in vitro. The EMBO Journal, 2022.
23. Lin R#., Zhai Z#., Kuang J#., Wu C., Yao Y., Shi R., He J., Xu S., Li P., Fan Y., Li W., Wu Z., Li X., Ming J., Guo J., Wang B., Li D., Cao S., Zhang X., Li Y., Pei D*., Liu J*., H3K27ac mediated SS18/BAFs relocation regulates JUN induced pluripotent-somatic transition. Cell & Bioscience, 2022.
24. Babarinde IA., Ma G., Li Y., Deng B., Luo Z., Liu H., Abdul MM., Ward C., Chen M., Fu X., Shi L., Duttlinger M., He J., Sun L., Li W., Zhuang Q., Tong G., Frampton J., Cazier JB., Chen J., Jauch R., Esteban MA., Hutchins AP., Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells. Nucleic Acids Research, 2021.
25. Liu Y., He J., Chen R., Liu H., Chen J., Liu Y., Wang B., Guo L., Pei D., Wang J., Liu J*., Chen J*., AP-1 activity is a major barrier of human somatic cell reprogramming. Cellular and Molecular Life Sciences, 2021.
26. Pei R#., Feng J#., Zhang Y., Sun H., Li L., Yang X., He J., Xiao S., Xiong J., Lin Y., Wen K., Zhou H., Chen J., Rong Z*., Chen X*., Host metabolism dysregulation and cell tropism identification in human airway and alveolar organoids upon SARS-CoV-2 infection. Protein & Cell, 2021.
27. Wu K#., Liu H#., Wang Y., He J., Xu S., Chen Y., Kuang J., Liu J., Guo L., Li D., Shi R., Shen L., Wang Y., Zhang X., Wang J., Pei D., Chen J., SETDB1-Mediated Cell Fate Transition between 2C-Like and Pluripotent States. Cell Reports, 2020.
28. Cao S#., Yu S#., Li D#., Ye J., Yang X., Li C., Wang X., Mai Y., Qin Y., Wu J., He J., Zhou C., Liu H., Zhao B., Shu X., Wu C., Chen R., Chan W., Pan G., Chen J., Liu J*., Pei D*., Chromatin Accessibility Dynamics during Chemical Induction of Pluripotency. Cell Stem Cell, 2018.
29. Li D#., Liu J#., Yang X#., Zhou C., Guo J., Wu C., Qin Y., Guo L., He J., Yu S., Liu H., Wang X., Wu F., Kuang J., Hutchins AP*., Chen J*., Pei D*., Chromatin Accessibility Dynamics during iPSC Reprogramming. Cell Stem Cell, 2017.
30. Zhou Z., Yang X., He J., Liu J., Wu F., Yu S., Liu Y., Lin R., Liu H., Cui Y., Zhou C., Wang X., Wu J., Cao S., Guo L., Lin L., Wang T., Peng X., Qiang B., Hutchins AP., Pei D*., Chen J*., Kdm2b Regulates Somatic Reprogramming through Variant PRC1 Complex-Dependent Function. Cell Reports, 2017.
31. Hutchins AP*., Yang Z., Li Y., He F., Fu X., Wang X., Li D., Liu K., He J., Wang Y., Chen J., Esteban MA., Pei D*., Models of global gene expression define major domains of cell type and tissue identity. Nucleic Acids Research, 2017.
