Research outputs

  1. 2020
  2. Machine learning uncovers cell identity regulator by histone code

    Xia, B., Zhao, D., Wang, G., Zhang, M., Lv, J., Tomoiaga, A. S., Li, Y., Wang, X., Meng, S., Cooke, J. P., Cao, Q., Zhang, L. & Chen, K., Jun 1 2020, In : Nature Communications. 11, 1, 2696.

    Research output: Contribution to journalArticle

  3. TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription

    Wang, G., Meng, Q., Xia, B., Zhang, S., Lv, J., Zhao, D., Li, Y., Wang, X., Zhang, L., Cooke, J. P., Cao, Q. & Chen, K., Apr 2 2020, In : Genome Biology. 21, 1, 84.

    Research output: Contribution to journalArticle

  4. BMI1 is directly regulated by androgen receptor to promote castration-resistance in prostate cancer

    Zhu, S., Zhao, D., Li, C., Li, Q., Jiang, W., Liu, Q., Wang, R., Fazli, L., Li, Y., Zhang, L., Yi, Y., Meng, Q., Wang, W., Wang, G., Zhang, M., Zu, X., Zhao, W., Deng, T., Yu, J., Dong, X. & 2 othersChen, K. & Cao, Q., Jan 2020, In : Oncogene. 39, 1, p. 17-29 13 p.

    Research output: Contribution to journalArticle

  5. 2019
  6. Nuclear S-nitrosylation defines an optimal zone for inducing pluripotency

    Chanda, P. K., Meng, S., Lee, J., Leung, H. E., Chen, K. & Cooke, J. P., Sep 24 2019, In : Circulation. 140, 13, p. 1081-1099 19 p.

    Research output: Contribution to journalArticle

  7. Polycomb group proteins EZH2 and EED directly regulate androgen receptor in advanced prostate cancer

    Liu, Q., Wang, G., Li, Q., Jiang, W., Kim, J. S., Wang, R., Zhu, S., Wang, X., Yan, L., Yi, Y., Zhang, L., Meng, Q., Li, C., Zhao, D., Qiao, Y., Li, Y., Gursel, D. B., Chinnaiyan, A. M., Chen, K. & Cao, Q., Jul 15 2019, In : International Journal of Cancer. 145, 2, p. 415-426 12 p.

    Research output: Contribution to journalArticle

  8. AIBP-mediated cholesterol efflux instructs hematopoietic stem and progenitor cell fate

    Gu, Q., Yang, X., Lv, J., Zhang, J., Xia, B., Kim, J. D., Wang, R., Xiong, F., Meng, S., Clements, T. P., Tandon, B., Wagner, D. S., Diaz, M. F., Wenzel, P. L., Miller, Y. I., Traver, D., Cooke, J. P., Li, W., Zon, L. I., Chen, K. & 2 othersBai, Y. & Fang, L., Mar 8 2019, In : Science. p. eaav1749

    Research output: Contribution to journalArticle

  9. Roles of the HOXA10 gene during castrate-resistant prostate cancer progression

    Long, Z., Li, Y., Gan, Y., Zhao, D., Wang, G., Xie, N., Lovnicki, J. M., Fazli, L., Cao, Q., Chen, K. & Dong, X., Mar 1 2019, In : Endocrine-Related Cancer. 26, 3, p. 279-292 14 p.

    Research output: Contribution to journalArticle

  10. 2018
  11. Dna2 nuclease deficiency results in large and complex DNA insertions at chromosomal breaks

    Yu, Y., Pham, N., Xia, B., Papusha, A., Wang, G., Yan, Z., Peng, G., Chen, K. & Ira, G., Dec 13 2018, In : Nature. 564, 7735, p. 287-290 4 p.

    Research output: Contribution to journalArticle

  12. TBX20 Regulates Angiogenesis Through the Prokineticin 2-Prokineticin Receptor 1 Pathway

    Meng, S., Gu, Q., Yang, X., Lv, J., Owusu, I., Matrone, G., Chen, K., Cooke, J. P. & Fang, L., Aug 28 2018, In : Circulation. 138, 9, p. 913-928 16 p.

    Research output: Contribution to journalArticle

  13. Ssd1 and Gcn2 suppress global translation efficiency in replicatively aged yeast while their activation extends lifespan

    Hu, Z., Xia, B., Postnikoff, S. D. L., Shen, Z. J., Tomoiaga, A. S., Harkness, T. A., Seol, J. H., Li, W., Chen, K. & Tyler, J. K., Aug 17 2018, In : eLife. 7, e35551.

    Research output: Contribution to journalArticle

  14. Homeobox oncogene activation by pan-cancer DNA hypermethylation

    Su, J., Huang, Y. H., Cui, X., Wang, X., Zhang, X., Lei, Y., Xu, J., Lin, X., Chen, K., Lv, J., Goodell, M. A. & Li, W., Aug 10 2018, In : Genome Biology. 19, 1, 108.

    Research output: Contribution to journalArticle

  15. OX40 Costimulation Inhibits Foxp3 Expression and Treg Induction via BATF3-Dependent and Independent Mechanisms

    Zhang, X., Xiao, X., Lan, P., Li, J., Dou, Y., Chen, W., Ishii, N., Chen, S., Xia, B., Chen, K., Taparowsky, E. & Li, X. C., Jul 17 2018, In : Cell Reports. 24, 3, p. 607-618 12 p.

    Research output: Contribution to journalArticle

  16. HP1ɣ promotes lung adenocarcinoma by downregulating the transcription-repressive regulators NCOR2 and ZBTB7A

    Alam, H., Li, N., Dhar, S. S., Wu, S. J., Lv, J., Chen, K., Flores, E. R., Baseler, L. & Lee, M. G., Jul 15 2018, In : Cancer Research. 78, 14, p. 3834-3848 15 p.

    Research output: Contribution to journalArticle

  17. MLL4 Is Required to Maintain Broad H3K4me3 Peaks and Super-Enhancers at Tumor Suppressor Genes

    Dhar, S. S., Zhao, D., Lin, T., Gu, B., Pal, K., Wu, S. J., Alam, H., Lv, J., Yun, K., Gopalakrishnan, V., Flores, E. R., Northcott, P. A., Rajaram, V., Li, W., Shilatifard, A., Sillitoe, R. V., Chen, K. & Lee, M. G., Jun 7 2018, In : Molecular Cell. 70, 5, p. 825-841.e6

    Research output: Contribution to journalArticle

  18. 3′ UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk

    Park, H. J., Ji, P., Kim, S., Xia, Z., Rodriguez, B., Li, L., Su, J., Chen, K., Masamha, C. P., Baillat, D., Fontes-Garfias, C. R., Shyu, A. B., Neilson, J. R., Wagner, E. J. & Li, W., Jun 1 2018, In : Nature Genetics. 50, 6, p. 783-789 7 p.

    Research output: Contribution to journalArticle

  19. PAF-Myc-Controlled Cell Stemness Is Required for Intestinal Regeneration and Tumorigenesis

    Kim, M. J., Xia, B., Suh, H. N., Lee, S. H., Jun, S., Lien, E. M., Zhang, J., Chen, K. & Park, J. I., Mar 12 2018, In : Developmental Cell. 44, 5, p. 582-596.e4

    Research output: Contribution to journalArticle

  20. BMI1 regulates androgen receptor in prostate cancer independently of the polycomb repressive complex 1

    Zhu, S., Zhao, D., Yan, L., Jiang, W., Kim, J. S., Gu, B., Liu, Q., Wang, R., Xia, B., Zhao, J. C., Song, G., Mi, W., Wang, R. F., Shi, X., Lam, H. M., Dong, X., Yu, J., Chen, K. & Cao, Q., Feb 5 2018, In : Nature Communications. 9, 1, 500.

    Research output: Contribution to journalArticle

  21. 2017
  22. Lmo2 (LIM-Domain-Only 2) Modulates Sphk1 (Sphingosine Kinase) and Promotes Endothelial Cell Migration

    Matrone, G., Meng, S., Gu, Q., Lv, J., Fang, L., Chen, K. & Cooke, J. P., Oct 1 2017, In : Arteriosclerosis, thrombosis, and vascular biology. 37, 10, p. 1860-1868 9 p.

    Research output: Contribution to journalArticle

  23. Sparse conserved under-methylated CpGs are associated with high-order chromatin structure

    Lin, X., Su, J., Chen, K., Rodriguez, B. & Li, W., Aug 31 2017, In : Genome Biology. 18, 1, 163.

    Research output: Contribution to journalArticle

  24. Developing Spindlin1 small-molecule inhibitors by using protein microarrays

    Bae, N., Viviano, M., Su, X., Lv, J., Cheng, D., Sagum, C., Castellano, S., Bai, X., Johnson, C., Khalil, M. I., Shen, J., Chen, K., Li, H., Sbardella, G. & Bedford, M. T., Jul 1 2017, In : Nature Chemical Biology. 13, 7, p. 750-756 7 p.

    Research output: Contribution to journalArticle

  25. Steroid receptor coactivator-1 can regulate osteoblastogenesis independently of estrogen

    Watters, R. J., Hartmaier, R. J., Osmanbeyoglu, H. U., Gillihan, R. M., Rae, J. M., Liao, L., Chen, K., Li, W., Lu, X. & Oesterreich, S., Jun 15 2017, In : Molecular and cellular endocrinology. 448, p. 21-27 7 p.

    Research output: Contribution to journalArticle

  26. Discovery of novel determinants of endothelial lineage using chimeric heterokaryons

    Wong, J., Matrone, G., Tian, X., Tomoiaga, S. A., Au, K. F., Meng, S., Yamazoe, S., Sieveking, D., Chen, K., Burns, D. M., Chen, J. K., Blau, H. M. & Cooke, J. P., Mar 21 2017, In : eLife. 6, e23588.

    Research output: Contribution to journalArticle

  27. RPA binds histone H3-H4 and functions in DNA replication-coupled nucleosome assembly

    Liu, S., Xu, Z., Leng, H., Zheng, P., Yang, J., Chen, K., Feng, J. & Li, Q., Jan 27 2017, In : Science (New York, N.Y.). 355, 6323, p. 415-420 6 p.

    Research output: Contribution to journalArticle

  28. 2016
  29. LIM domain only 2 regulates endothelial proliferation, angiogenesis, and tissue regeneration

    Meng, S., Matrone, G., Lv, J., Chen, K., Wong, J. W. T. & Cooke, J. P., Oct 6 2016, In : Journal of the American Heart Association. 5, 10, e004117.

    Research output: Contribution to journalArticle

  30. Broad H3K4me3 as A Novel Epigenetic Signature for Normal Development and Disease

    Lv, J. & Chen, K., Oct 1 2016, In : Genomics, Proteomics and Bioinformatics. 14, 5, p. 262-264 3 p.

    Research output: Contribution to journalEditorial

  31. A feedback loop comprising PRMT7 and miR-24-2 interplays with Oct4, Nanog, Klf4 and c-Myc to regulate stemness

    Lee, S. H., Chen, T. Y., Dhar, S. S., Gu, B., Chen, K., Kim, Y. Z., Li, W. & Lee, M. G., Sep 12 2016, In : Nucleic acids research. 44, 22, p. 10603-10618 16 p.

    Research output: Contribution to journalArticle

  32. ZMYND8 Reads the Dual Histone Mark H3K4me1-H3K14ac to Antagonize the Expression of Metastasis-Linked Genes

    Li, N., Li, Y., Lv, J., Zheng, X., Wen, H., Shen, H., Zhu, G., Chen, T. Y., Dhar, S. S., Kan, P. Y., Wang, Z., Shiekhattar, R., Shi, X., Lan, F., Chen, K., Li, W., Li, H. & Lee, G. M., Jul 28 2016, In : Molecular Cell. 63, 3, p. 470-484 15 p.

    Research output: Contribution to journalArticle

  33. An essential role for UTX in resolution and activation of bivalent promoters

    Dhar, S. S., Lee, S. H., Chen, K., Zhu, G., Oh, W. K., Allton, K., Gafni, O., Kim, Y. Z., Tomoiga, A. S., Barton, M. C., Hanna, J. H., Wang, Z., Li, W. & Lee, M. G., May 5 2016, In : Nucleic acids research. 44, 8, p. 3659-3674 16 p.

    Research output: Contribution to journalArticle

  34. The overlooked fact: Fundamental need for spike-in control for virtually all genome-wide analyses

    Chen, K., Hu, Z., Xi, Z., Zhao, D., Li, W. & Tyler, J. K., Jan 1 2016, In : Molecular and Cellular Biology. 36, 5, p. 662-667 6 p.

    Research output: Contribution to journalArticle

  35. 2015
  36. Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes

    Chen, K., Chen, Z., Wu, D., Zhang, L., Lin, X., Su, J., Rodriguez, B., Xi, Y., Xia, Z., Chen, X., Shi, X., Wang, Q. & Li, W., Sep 29 2015, In : Nature Genetics. 47, 10, p. 1149-1157 9 p.

    Research output: Contribution to journalArticle

  37. Correction: MeCP2 binds to non-CG methylated DNA as neurons mature, influencing transcription and the timing of onset for Rett syndrome (Proceedings of the National Academy of Sciences of the United States of America (2015) 112, 17 (5509-5514) DOI: 10.1073/pnas.1505909112)

    Chen, L., Chen, K., Lavery, L. A., Baker, S. A., Shaw, C. A., Li, W. & Zoghbi, H. Y., Jun 2 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 22, p. E2982

    Research output: Contribution to journalArticle

  38. MeCP2 binds to non-CG methylated DNA as neurons mature, influencing transcription and the timing of onset for Rett syndrome

    Chen, L., Chen, K., Lavery, L. A., Baker, S. A., Shaw, C. A., Li, W. & Zoghbi, H. Y., Apr 28 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 17, p. 5509-5514 6 p.

    Research output: Contribution to journalArticle

  39. 2014
  40. MACE: model based analysis of ChIP-exo

    Wang, L., Chen, J., Wang, C., Uusküla-Reimand, L., Chen, K., Medina-Rivera, A., Young, E. J., Zimmermann, M. T., Yan, H., Sun, Z., Zhang, Y., Wu, S. T., Huang, H., Wilson, M. D., Kocher, J. P. A. & Li, W., Nov 10 2014, In : Nucleic Acids Research. 42, 20, p. e156

    Research output: Contribution to journalArticle

  41. A matter of access: Nucleosome disassembly from gene promoters is the central goal of transcriptional activators

    Hu, Z., Chen, K., Li, W. & Tyler, J. K., Jun 11 2014, In : Transcription. 5, JUN, e29355.

    Research output: Contribution to journalArticle

  42. Transcriptional and genomic mayhem due to aging-induced nucleosome loss in budding yeast

    Hu, Z., Chen, K., Li, W. & Tyler, J. K., Apr 1 2014, In : Microbial Cell. 1, 4, p. 133-136 4 p.

    Research output: Contribution to journalReview article

  43. Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging

    Hu, Z., Chen, K., Xia, Z., Chavez, M., Pal, S., Seol, J. H., Chen, C. C., Li, W. & Tyler, J. K., Feb 15 2014, In : Genes and Development. 28, 4, p. 396-408 13 p.

    Research output: Contribution to journalArticle

  44. Transcriptional and genomic mayhem due to aging-induced nucleosome loss in budding yeast.

    Chen, K., 2014, In : Microbial Cell Factories.

    Research output: Contribution to journalArticle

  45. 2013
  46. Genome sequence of the date palm Phoenix dactylifera L

    Al-Mssallem, I. S., Hu, S., Zhang, X., Lin, Q., Liu, W., Tan, J., Yu, X., Liu, J., Pan, L., Zhang, T., Yin, Y., Xin, C., Wu, H., Zhang, G., Ba Abdullah, M. M., Huang, D., Fang, Y., Alnakhli, Y. O., Jia, S., Yin, A. & 23 othersAlhuzimi, E. M., Alsaihati, B. A., Al-Owayyed, S. A., Zhao, D., Zhang, S., Al-Otaibi, N. A., Sun, G., Majrashi, M. A., Li, F., Wang, J., Yun, Q., Alnassar, N. A., Wang, L., Yang, M., Al-Jelaify, R. F., Liu, K., Gao, S., Chen, K., Alkhaldi, S. R., Liu, G., Zhang, M., Guo, H. & Yu, J., Aug 26 2013, In : Nature Communications. 4, 2274.

    Research output: Contribution to journalArticle

  47. A Functional Variomics Tool for Discovering Drug-Resistance Genes and Drug Targets

    Huang, Z., Chen, K., Zhang, J., Li, Y., Wang, H., Cui, D., Tang, J., Liu, Y., Shi, X., Li, W., Liu, D., Chen, R., Sucgang, R. S. & Pan, X., Feb 15 2013, In : Cell Reports. 3, 2, p. 577-585 9 p.

    Research output: Contribution to journalArticle

  48. DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

    Chen, K., Xi, Y., Pan, X., Li, Z., Kaestner, K., Tyler, J., Dent, S., He, X. & Li, W., Feb 1 2013, In : Genome Research. 23, 2, p. 341-351 11 p.

    Research output: Contribution to journalArticle

  49. Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor

    Chen, K., Wilson, M. A., Hirsch, C., Watson, A., Liang, S., Lu, Y., Li, W. & Dent, S. Y. R., Feb 1 2013, In : Genome Research. 23, 2, p. 312-322 11 p.

    Research output: Contribution to journalArticle

  50. 2012
  51. Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation

    Li, Z., Gadue, P., Chen, K., Jiao, Y., Tuteja, G., Schug, J., Li, W. & Kaestner, K. H., Dec 21 2012, In : Cell. 151, 7, p. 1608-1616 9 p.

    Research output: Contribution to journalArticle

  52. Discovering Thiamine Transporters as Targets of Chloroquine Using a Novel Functional Genomics Strategy

    Huang, Z., Srinivasan, S., Zhang, J., Chen, K., Li, Y., Li, W., Quiocho, F. A. & Pan, X., Nov 1 2012, In : PLoS Genetics. 8, 11, e1003083.

    Research output: Contribution to journalArticle

  53. The Fun30 nucleosome remodeller promotes resection of DNA double-strand break ends

    Chen, X., Cui, D., Papusha, A., Zhang, X., Chu, C. D., Tang, J., Chen, K., Pan, X. & Ira, G., Sep 27 2012, In : Nature. 489, 7417, p. 576-580 5 p.

    Research output: Contribution to journalArticle

  54. Loss of the methyl lysine effector protein PHF20 impacts the expression of genes regulated by the lysine acetyltransferase MOF

    Badeaux, A. I., Yang, Y., Cardenas, K., Vemulapalli, V., Chen, K., Kusewitt, D., Richie, E., Li, W. & Bedford, M. T., Jan 2 2012, In : Journal of Biological Chemistry. 287, 1, p. 429-437 9 p.

    Research output: Contribution to journalArticle

  55. SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation

    Barber, M. F., Michishita-Kioi, E., Xi, Y., Tasselli, L., Kioi, M., Moqtaderi, Z., Tennen, R. I., Paredes, S., Young, N. L., Chen, K., Struhl, K., Garcia, B. A., Gozani1, O., Li, W. & Chua, K. F., Jan 1 2012, In : Nature. 487, 7405, p. 114-118 5 p.

    Research output: Contribution to journalArticle

  56. 2011
  57. NSD2 Links Dimethylation of Histone H3 at Lysine 36 to Oncogenic Programming

    Kuo, A. J., Cheung, P., Chen, K., Zee, B. M., Kioi, M., Lauring, J., Xi, Y., Park, B. H., Shi, X., Garcia, B. A., Li, W. & Gozani, O., Nov 18 2011, In : Molecular Cell. 44, 4, p. 609-620 12 p.

    Research output: Contribution to journalArticle

  58. Sampangine inhibits heme biosynthesis in both yeast and human

    Huang, Z., Chen, K., Xu, T., Zhang, J., Li, Y., Li, W., Agarwal, A. K., Clark, A. M., Phillips, J. D. & Pan, X., Nov 1 2011, In : Eukaryotic Cell. 10, 11, p. 1536-1544 9 p.

    Research output: Contribution to journalArticle

  59. A systematic identification of Kolobok superfamily transposons in Trichomonas vaginalis and sequence analysis on related transposases

    Meng, Q., Chen, K., Ma, L., Hu, S. & Yu, J., Feb 1 2011, In : Journal of Genetics and Genomics. 38, 2, p. 63-70 8 p.

    Research output: Contribution to journalArticle

  60. An evolutionary analysis of trypanosomatid GP63 proteases

    Ma, L., Chen, K., Meng, Q., Liu, Q., Tang, P., Hu, S. & Yu, J., Jan 1 2011, In : Parasitology Research. 109, 4, p. 1075-1084 10 p.

    Research output: Contribution to journalArticle

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