Publications

  1. Wang, Z.*, Yu, H.*, Gu, Z., Shi, X., Ma, J., Shao, Q., Yao, Y., Yao, S., Xu, Y., Gu, Y., Dai, J., Liu, Q., Shi, J., Qi, R., Shen, X., Huang, W., Jin, M., Liu, W., Brook, M.#, & Chen, D.# (2024). RNA-binding proteins DND1 and NANOS3 coordinately suppress the translation of SOX4 mRNAs in processing bodies for restricting the entry of germ cell lineage. Nature Communications, paper accepted

 

 

  1. Yu, H., Wang, Z., Ma, J., Wang, R., Yao, S., Gu, Z., Lin, K., Li, J., Young, R. S., Yu, Y., Yu, Y., Jin, M., & Chen, D. (2025). The establishment and regulation of human germ cell lineage. Stem cell research & therapy, 16(1), 139.

https://doi.org/10.1186/s13287-025-04171-2

 

  1. Lan, Y., Xia, Z., Shao, Q., Lin, P., Lu, J., Xiao, X., Zheng, M., Chen, D. #, Dou, Y.#, & Xie, Q.# (2025). Synonymous mutations promote tumorigenesis by disrupting m6A-dependent mRNA metabolism. Cell, S0092-8674(25)00095-9. Advance online publication.

https://doi.org/10.1016/j.cell.2025.01.026

 

  1. Zhou, Z., Tong, L., Chen, Y., Wang, R., Shen, Y., & Chen, D.# (2025). Dual-Selection Strategy for Generating Knock-Out Lines of Human Embryonic Stem Cells. Journal of cellular and molecular medicine, 29(2), e70259.

https://doi.org/10.1111/jcmm.70259

 

  1. Yuan, Z., Han, X., Xiao, M., Zhu, T., Xu, Y., Tang, Q., Lian, C., Wang, Z., Li, J., Wang, B., Li, C., Xiang, X., Jin, R., Liu, Y., Yu, X., Zhang, K., Li, S., Ray, M., Li, R., Gruzdev, A., Shao, S., Shao, F., Wang, H., Lian, W., Tang, Y., Chen, D., Lei, Y., Jin, X., Li, Q., Long, W., Huang, H., DeMayo, F., & Liu, J. (2024). Overexpression of ELF3 in the PTEN-deficient lung epithelium promotes lung cancer development by inhibiting ferroptosis. Cell death & disease, 15(12), 897.

https://doi.org/10.1038/s41419-024-07274-5

 

  1. Gu, Y., Chen, J., Wang, Z., Shao, Q., Li, Z., Ye, Y., Xiao, X., Xiao, Y., Liu, W., Xie, S., Tong, L., Jiang, J., Xiao, X., Yu, Y., Jin, M., Wei, Y.#, Young, R. S.#, Hou, L.#, & Chen, D.# (2024). Integrated analysis and systematic characterization of the regulatory network for human germline development. Journal of genetics and genomics, S1673-8527(24)00306-0.

https://doi.org/10.1016/j.jgg.2024.11.005

 

  1. Feng, X., Li, Z., Liu, Y., Chen, D., & Zhou, Z. (2024). CRISPR/Cas9 technology for advancements in cancer immunotherapy: from uncovering regulatory mechanisms to therapeutic applications. Experimental hematology & oncology, 13(1), 102.

https://doi.org/10.1186/s40164-024-00570-y

 

  1. Shi, X., Xi, C., Dong, B., Yan, Z., Liu, W.#, Gao, S.#, & Chen, D.# (2024). Maternal infection with SARS-CoV-2 during early pregnancy induces hypoxia at the maternal-fetal interface. Cell proliferation, e13749.

https://doi.org/10.1111/cpr.13749

 

  1. Chen, Y., Zhou, Z., Chen, Y., & Chen, D.# (2024). Reading the m6A-encoded epitranscriptomic information in development and diseases. Cell & bioscience, 14(1), 124.

https://doi.org/10.1186/s13578-024-01293-7

 

  1. Su, Y., Yu, Z., Jin, S., Ai, Z., Yuan, R., Chen, X., Xue, Z., Guo, Y., Chen, D., Liang, H., Liu, Z., & Liu, W. (2024). Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data. Nature communications, 15(1), 3972.

https://doi.org/10.1038/s41467-024-48117-3

 

  1. Wang, R., Wang, Z., Tong, L., Wang, R., Yao, S., Chen, D.#, & Hu, H.# (2024). Microfluidic Mechanoporation: Current Progress and Applications in Stem Cells.Biosensors,14(5), 256.

https://doi.org/10.3390/bios14050256

 

 

  1. Zhang, J., Tong, L., Liu, Y., Li, X., Wang, J., Lin, R., Zhou, Z., Chen, Y., Chen, Y., Liu, Y., & Chen, D.# (2023). The regulatory role of m6A modification in the maintenance and differentiation of embryonic stem cells.Genes & diseases,11(5), 101199.

https://doi.org/10.1016/j.gendis.2023.101199

 

  1. Wang, X., Song, C., Ye, Y., Gu, Y., Li, X., Chen, P., Leng, D., Xiao, J., Wu, H., Xie, S., Liu, W., Zhao, Q., Chen, D., Chen, X., Wu, Q., Chen, G., & Zhang, W. (2023). BRD9-mediated control of the TGF-β/Activin/Nodal pathway regulates self-renewal and differentiation of human embryonic stem cells and progression of cancer cells.Nucleic acids research,51(21), 11634–11651.

https://doi.org/10.1093/nar/gkad907

 

  1. Li, Z., Xu, H., Li, J., Xu, X., Wang, J., Wu, D., Zhang, J., Liu, J., Xue, Z., Zhan, G., Tan, B. C. P., Chen, D., Chan, Y. S., Ng, H. H., Liu, W., Hsu, C. H., Zhang, D., Shen, Y., & Liang, H. (2023). Selective binding of retrotransposons by ZFP352 facilitates the timely dissolution of totipotency network.Nature communications,14(1), 3646.

https://doi.org/10.1038/s41467-023-39344-1

 

  1. Ai, Z., Xiang, X., Xiang, Y., Szczerbinska, I., Qian, Y., Xu, X., Ma, C., Su, Y., Gao, B., Shen, H., Bin Ramli, M. N., Chen, D., Liu, Y., Hao, J. J., Ng, H. H., Zhang, D., Chan, Y. S., Liu, W., & Liang, H. (2022). Krüppel-like factor 5 rewires NANOG regulatory network to activate human naive pluripotency specific LTR7Ys and promote naive pluripotency.Cell reports,40(8), 111240.

https://doi.org/10.1016/j.celrep.2022.111240

 

  1. Watanabe, M., Buth, J.E., Haney, J.R., Vishlaghi, N., Turcios, F., Elahi, L.S., Gu, W., Pearson, C.A., Kurdian, A,, Baliaouri, N.V., Collier, A.J., Miranda, O.A., Dunn, N., Chen, D., Sabri, S., Torre-Ubieta, L., Clark, A.T., Plath, K., Christofk, H.R., Kornblum, H.I., Gandal, M.J., & Novitch, B.G. (2022). TGFβ superfamily signaling regulates the state of human stem cell pluripotency and capacity to create well-structured telencephalic organoids.Stem cell reports,17(10), 2220–2238.

https://doi.org/10.1016/j.stemcr.2022.08.013

 

  1. Jin, S., Xue, Z., Zhang, J., Wang, Z., Zhang, J., Chen, D.#, Liu, W.#, & Lin, J.# (2021). Identification of SRSF3 target mRNAs using inducible TRIBE.Biochemical and biophysical research communications,578, 21–27.

https://doi.org/10.1016/j.bbrc.2021.09.019

 

  1. Hancock, G. V., Liu, W., Peretz, L., Chen, D., Gell, J. J., Collier, A. J., Zamudio, J. R., Plath, K., & Clark, A. T. (2021). Divergent roles for KLF4 and TFCP2L1 in naive ground state pluripotency and human primordial germ cell development.Stem cell research,55, 102493.

https://doi.org/10.1016/j.scr.2021.102493

 

  1. Chitiashvili, T., Dror, I., Kim, R., Hsu, F. M., Chaudhari, R., Pandolfi, E., Chen, D., Liebscher, S., Schenke-Layland, K., Plath, K., & Clark, A. (2020). Female human primordial germ cells display X-chromosome dosage compensation despite the absence of X-inactivation.Nature cell biology,22(12), 1436–1446.

https://doi.org/10.1038/s41556-020-00607-4

 

  1. Liu, X., Ouyang, J.F., Rossello, F.J., Tan, J.P., Davidson, K.C., Valdes, D.S., Schröder, J., Sun, Y.B..Y, Chen, J., Knaupp, A.S., Sun, G., Chy, H.S., Huang, Z., Pflueger, J., Firas, J., Tano, V., Buckberry, S., Paynter, J.M., Larcombe, M.R., Poppe, D., Choo, X.Y., O’Brien, C.M., Pastor, W.A., Chen, D., Leichter, A.L., Naeem, H., Tripathi, P., Das, P.P., Grubman, A., Powell, D.R., Laslett, A.L., David, L., Nilsson, S.K., Clark, A.T., Lister, R., Nefzger, C.M., Martelotto, L.G., Rackham, O.J.L., & Polo, J.M.(2020). Reprogramming roadmap reveals route to human induced trophoblast stem cells.Nature,586(7827), 101–107.

https://doi.org/10.1038/s41586-020-2734-6

 

  1. Chen, D.*, Sun, N*., Hou, L.*, Kim, R., Faith, J., Aslanyan, M., Tao, Y., Zheng, Y., Fu, J., Liu, W., Kellis, M., & Clark, A. (2019). Human Primordial Germ Cells Are Specified from Lineage-Primed Progenitors.Cell reports,29(13), 4568–4582.e5.

https://doi.org/10.1016/j.celrep.2019.11.083

 

  1. Chen, D.*, Liu, W.*, Zimmerman, J., Pastor, W., Kim, R., Hosohama, L., Ho, J., Aslanyan, M., Gell, J., Jacobsen, S., & Clark, A. (2018). The TFAP2C-regulated OCT4 naïve enhancer is involved in human germline formation. Cell reports, 25(13), 3591–3602.e5.

https://doi.org/10.1016/j.celrep.2018.12.011

 

  1. Pastor, W., Liu, W., Chen, D., Ho, J., Kim, R., Hunt, T., Lukianchikov, A., Liu, X., Polo, J., Jacobsen, S., & Clark, A. (2018). Nature cell biology,20(5), 553–564.

https://doi.org/10.1038/s41556-018-0089-0

 

  1. Chen, D. & Clark, A. (2018). Mitochondrial DNA selection in human germ cells. Nature cell biology,20(2), 118–120.

https://doi.org/10.1038/s41556-017-0029-4

 

  1. Sosa, E., Chen, D., Rojas, E., Hennebold, J., Peters, K., Wu, Z., Lam, T., Mitchell, J., Tailor, R., Meistrich, M., Orwig, K., Shetty, G., & Clark, A. (2018). Nature communications, 9(1), 5339.

https://doi.org/10.1038/s41467-018-07740-7

 

  1. Gell, J., Zhao, J., Chen, D., Hunt, T., & Clark, A. (2018). PRDM14 is expressed in germ cell tumors with constitutive overexpression altering human germline differentiation and proliferation. Stem cell research, 27, 46–56.

https://doi.org/10.1016/j.scr.2017.12.016

 

  1. Chen, D., Liu, W., Lukianchikov, A., Hancock, G., Zimmerman, J., Lowe, M., Kim, R., Galic, Z., Irie, N., Surani, A., Pastor, W., Ho, J., Jacobsen, S., & Clark, A. (2017). Germline competency of human embryonic stem cells depends on EOMESODERMIN. Biology of reproduction, 97(6), 850–861.

https://doi.org/10.1093/biolre/iox138

 

  1. Clark, A. T., Gkountela, S., Chen, D., Liu, W., Sosa, E., Sukhwani, M., Hennebold, H., & Orwig, K. (2017). Primate primordial germ cells acquire transplantation potential by Carnegie stage 23. Stem cell reports,9(1), 329–341.

https://doi.org/10.1016/j.stemcr.2017.05.002

 

  1. Chen, D., Gell, J. J., Tao, Y., Sosa, E., & Clark, A. T. (2017). Modeling human infertility with pluripotent stem cells. Stem cell research, 21, 187–192.

https://doi.org/10.1016/j.scr.2017.04.005

 

 

  1. Tang, Y., Geng, Q., Chen, D., Zhao, S., Liu, X., & Wang, Z. (2017). Germline proliferation is regulated by somatic endocytic genes via JNK and BMP signaling in Drosophila. Genetics,206(1), 189–197.

https://doi.org/10.1534/genetics.116.196535

 

  1. Shan, L., Wu, C., Chen, D., Hou, L., Li, X., Wang, L., Chu, X., Hou, Y., & Wang, Z. (2017). Regulators of alternative polyadenylation operate at the transition from mitosis to meiosis. Journal of genetics and genomics, 44(2), 95–106.

https://doi.org/10.1016/j.jgg.2016.12.007

 

  1. O’Brien, C.M., Chy, H.S., Zhou, Q., Blumenfeld, S., Lambshead, J.W., Liu, X., Kie, J., Capaldo, B.D., Chung, T.L., Adams, T.E., Phan, T., Bentley, J.D., McKinstry, W.J., Oliva, K., McMurrick, P.J., Wang, Y.C., Rossello, F.J., Lindeman, G.J., Chen, D., Jarde, T., Clark, A.T., Abud, H.E., Visvader, J.E., Nefzger, C.M., Polo, J.M., Loring, J.F., & Laslett, A.L. (2017). New Monoclonal Antibodies to Defined Cell Surface Proteins on Human Pluripotent Stem Cells. Stem cells, 35(3), 626–640.

https://doi.org/10.1002/stem.2558

 

  1. Pastor, W.A.*, Chen D.*, Liu, W.*, Kim R., Sahakyan, A., Lukianchikov, A., Plath, K., Jacobsen, S.E. & Clark, A.T. (2016). Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory. Cell stem cell, 18(3), 323–329.

https://doi.org/10.1016/j.stem.2016.01.019

 

  1. Chen, D., & Clark, A. T. (2015). Human germline differentiation charts a new course. The EMBO journal, 34(8), 975–977.

https://doi.org/10.15252/embj.201591447

 

  1. Chen, D.*, Wu, C.*, Zhao, S., Geng, Q., Gao, Y., Li, X., Zhang, Y., & Wang, Z. (2014). Three RNA binding proteins form a complex to promote differentiation of germline stem cell lineage in Drosophila. PLoS genetics, 10(11), e1004797.

https://doi.org/10.1371/journal.pgen.1004797

 

 

  1. Zhao, S., Chen, D., Geng, Q., & Wang, Z. (2013). The highly conserved LAMMER/CLK2 protein kinases prevent germ cell overproliferation in Drosophila. Developmental biology, 376(2), 163–170.

https://doi.org/10.1016/j.ydbio.2013.01.023

 

  1. Liu. Z., Huang, Y., Chen, D., & Zhang, Y. Q. (2011). Drosophila Acyl-CoA synthetase long-chain family member 4 regulates axonal transport of synaptic vesicles and is required for synaptic development and transmission. The Journal of neuroscience，31(6), 2052–2063.

https://doi.org/10.1523/JNEUROSCI.3278-10.2011

 

  1. Zhang, Y., Chen, D., & Wang, Z. (2009). Analyses of mental dysfunction-related ACSl4 in Drosophila reveal its requirement for Dpp/BMP production and visual wiring in the brain. Human molecular genetics, 18(20), 3894–3905.

https://doi.org/10.1093/hmg/ddp332