Publications

  • Journal Papers
  • Authored Books

Publications (* indicates co-first authors,# indicates corresponding authors)

Research articles:

  • Huang M, Wang Y, Yang M, Yan J, Yang H, Zhuang W, Xu Y, Koeffler HP, Lin DC, Chen X#. (2019) dbInDel: a database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq. Bioinformatics. pii: btz770.
  • Gao X*, Nowak-Imialek M*, Chen X*, Chen D, Herrmann D, Ruan D, Chen ACH, Eckersley-Maslin MA, Ahmad S, Lee YL, Kobayashi T, Ryan D, Zhong J, Zhu J, Wu J, Lan G, Petkov S, Yang J, Antunes L, Campos LS, Fu B, Wang S, Yong Y, Wang X, Xue SG, Ge L, Liu Z, Huang Y, Nie T, Li P, Wu D, Pei D, Zhang Y, Lu L, Yang F, Kimber SJ, Reik W, Zou X, Shang Z, Lai L, Surani A, Tam PPL, Ahmed A, Yeung WSB, Teichmann SA, Niemann H, Liu P. (2019) Establishment of porcine and human expanded potential stem cells. Nat Cell Biol. 21, 687-699.
  • Henriksson, J.*, Chen, X.*, Gomes, T., Ullah, U., and Meyer, K.B. (2019). Genome-wide CRISPR screens in T helper cells reveal pervasive cross-talk between activation and differentiation. Cell 176, 1–15.
  • Zhang, W.*, Chronis, C.*, Chen, X.*, Zhang, H., Spalinskas, R., Pardo, M., Chen, L., Wu, G., Zhu, Z., Yu, Y., et al. (2019). The BAF and PRC2 Complex Subunits Dpf2 and Eed Antagonistically Converge on Tbx3 to Control ESC Differentiation. Cell Stem Cell 24, 138–152.e8.
  • Chen, X., Miragaia, R.J., Natarajan, K.N., and Teichmann, S.A. (2018). A rapid and robust method for single cell chromatin accessibility profiling. Nat. Commun. 9, 5345.
  • Jia, G.*, Preussner, J.*, Chen, X.*, Guenther, S., Yuan, X., Yekelchyk, M., Kuenne, C., Looso, M., Zhou, Y., Teichmann, S., et al. (2018). Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement. Nat. Commun. 9, 4877.
  • Hagai, T., Chen, X., Miragaia, R.J., Rostom, R., Gomes, T., Kunowska, N., Henriksson, J., Park, J.-E., Proserpio, V., Donati, G., et al. (2018). Gene expression variability across cells and species shapes innate immunity. Nature 563, 197–202.
  • Pramanik, J., Chen, X., Kar, G., Henriksson, J., Gomes, T., Park, J.-E., Natarajan, K., Meyer, K.B., Miao, Z., McKenzie, A.N.J., et al. (2018). Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation. Genome Med. 10, 76.
  • Chen, X., Ji, Z., Webber, A., and Sharrocks, A.D. (2016). Genome-wide binding studies reveal DNA binding specificity mechanisms and functional interplay amongst Forkhead transcription factors. Nucleic Acids Res. 44, 1566–1578.
  • Yu, Y., Tsang, J.C.H., Wang, C., Clare, S., Wang, J., Chen, X., Brandt, C., Kane, L., Campos, L.S., Lu, L., et al. (2016). Single-cell RNA-seq identifies a PD-1hi ILC progenitor and defines its development pathway. Nature 539, 102–106.
  • Aguilar-Martinez, E., Chen, X., Webber, A., Paul Mould, A., Seifert, A., Hay, R.T., and Sharrocks, A.D. (2015). Screen for multi-SUMO–binding proteins reveals a multi-SIM–binding mechanism for recruitment of the transcriptional regulator ZMYM2 to chromatin. Proc. Natl. Acad. Sci. U. S. A. 112, E4854–E4863.
  • Wiseman, E.F., Chen, X., Han, N., Webber, A., Ji, Z., Sharrocks, A.D., and Ang, Y.S. (2015). Deregulation of the FOXM1 target gene network and its coregulatory partners in oesophageal adenocarcinoma. Mol. Cancer 14, 69.
  • Chen, X., Müller, G.A., Quaas, M., Fischer, M., Han, N., Stutchbury, B., Sharrocks, A.D., and Engeland, K. (2013). The forkhead transcription factor FOXM1 controls cell cycle-dependent gene expression through an atypical chromatin binding mechanism. Mol. Cell. Biol. 33, 227–236.

Comments and reviews:

  • Chen, X., Teichmann, S.A., and Meyer, K.B. (2018). From Tissues to Cell Types and Back: Single-Cell Gene Expression Analysis of Tissue Architecture. Annu. Rev. Biomed. Data Sci. 1, 29-51.
  • Chen, X., Love, J.C., Navin, N.E., Pachter, L., Stubbington, M.J.T., Svensson, V., Sweedler, J.V., and Teichmann, S.A. (2016). Single-cell analysis at the threshold. Nat. Biotechnol. 34, 1111–1118.
  • Vieira Braga, F.A.*, Teichmann, S.A., and Chen, X.* (2016). Genetics and immunity in the era of single-cell genomics. Hum. Mol. Genet. 25, R141–R148.

Book chapters:

  • Kunowska, N.*, Chen, X*. (2019). ChIPmentation for Low-Input Profiling of In Vivo Protein-DNA Interactions. Methods Mol Biol. 1979: 269-282.

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