Publications

  1. Ledwich, D., Wu, Y.C., Driscoll, M, and Xue, D. (2000). Methods for the study of programmed cell death in the nematode Caenorhabditis elegans. Methods in Enzymology, 322, 76-88. ( and PDF)
  2. Parrish, J., Metters, H., Chen, L., and Xue, D. (2000). Demonstration of the in vivo interaction of key cell death regulators by structure-based design of second-site suppressors. Proc. Natl. Acad. Sci. USA. 97, 11916-11921. ( and PDF)
  3. Parrish, J., Li, L., Klotz, K., Ledwich, D., Wang, X.D., and Xue, D. (2001). C. elegans mitochondrial endonuclease G is important for apoptosis. Nature 412, 90-94. ( and PDF) 
  4. Xue, D., Wu, Y.C., and Shah, M.M. (2001). Programmed cell death in C. elegans -- a genetic framework. Chapter II in "Apoptosis: The Molecular Biology of Programmed Cell Death". Page 23-55. Edited by M. Jacobson & N. McCarthy. Oxford University Press. (PDF)
  5. Wang, X.C., Yang, C.L., Cai, J.J., Shi, Y.G., and Xue, D. (2002). Mechanisms of AIF-mediated apoptotic DNA degradation in Caenorhabditis elegans. Science 298, 1587-1592. ( and PDF).  (PDF) 
  6. Parrish, J. and Xue, D. (2003). Functional genomic analysis of apoptotic DNA degradation in C. elegans. Mol. Cell 11, 987-996. ( and PDF)
  7. Parrish, J., Yang, C.L., Shen, B.H., and Xue, D. (2003). CRN-1, a Caenorhabditis elegans FEN-1 homologue, cooperates with CPS-6/EndoG to promote apoptoticDNA degradation. EMBO. J. 22, 3451-3460. ( and PDF) Science SKTE Review (PDF) 
  8. Wu, Y.C. and Xue, D. (2003). Programmed cell death in C. elegans. Chapter IV in "Essentials of Apoptosis: A Guide for Basic and Clinical Research". Page 135-144. Edited by X.M. Yin & Z. Dong. The Humana Press Inc. (PDF)
  9. Wang, X.C., Wu, Y.C., Fadok, V., Lee, M.C., Gengyo-Ando, K., Cheng, L.C., Ledwich, D., Hsu, P.K., Chen, J.Y., Chou, B.K., Henson, P., Mitani, S., and Xue, D. (2003). Cell Corpse Engulfment Mediated by C. elegans Phosphatidylserine Receptor Through CED-5 and CED-12. Science 302, 1563-1566.( and PDF). Science Persepectives (PDF) and Science SKTE Review (PDF)
  10. Friedman, J. and Xue, D. (2004). To live or die by the sword: the regulation of apoptosis by the proteasome. Developmental Cell 6, 460-461. (PDF)
  11. Yang, N, Gu, L.C., Kokel, D., Han, A.D., Chen, L., Xue, D., and Shi, Y.G. (2004). Structural, Biochemical and Functional Analyses of CED-9 Recognition by the Pro-apoptotic Proteins EGL-1 and CED-4. Mol. Cell 15, 999-1006. ( and PDF)
  12. Breckenridge, D. and Xue, D. (2004). Regulation of mitochondrial membrane permeabilization by BCL-2 family proteins and caspases. Curr. Opin. Cell Biol. 16, 647-652. ( and PDF)
  13. Conradt, B. and Xue, D. (2005). Programmed cell death. WormBook, ed. The C. elegans Research Community. ( and PDF)
  14. Yan, N., Chai, J.J., Lee, E.S., Gu, L.C., Liu, Q., He, J.Q., Wu, J.W., Li, H.L., Hao, Q., Xue, D., and Shi, Y.G. (2005). Structure of the CED-4/CED-9 complex reveals insights into programmed cell death in Caenorhabditis elegans. Nature 437, 831-837. ( and PDF)
  15. Fadeel, B. and Xue, D. (2005). PS externalization: from corpse clearance to drug delivery. Cell Death Differentiation 13, 360-362. (PDF)
  16. Parrish, J., and Xue, D. (2005). Cuts can kill: the roles of apoptotic nucleases in cell death and animal development. Chromosoma 115, 89-97. (PDF)
  17. Yang, C.L., Yan, N., Parrish, J., Wang, X.C., Shi, Y.G., and Xue, D. (2006). RNA aptamers targeting the cell death inhibitor CED-9 induce cell killing in C. elegans. Journal of Biological Chemistry 281, 9137-9144. ( and PDF)
  18. Kokel, D., Li, Y.H., Qin, J., and Xue, D. (2006). The non-genotoxic carcinogens naphthalene and para-dichlorobenzene suppress apoptosis in C. elegans. Nature Chemical Biology 2, 338-345. ( and PDF). News in , , , , , , 
  19. Kokel, D. and Xue, D. (2006). A class of benzenoid chemicals suppresses apoptosis in C. elegans. ChemBioChem 7, 2010-2015. ( and PDF)
  20. Wang, X.C., Wang, J., Gengyo-Ando, K., Gu, L.C., Sun, C.L., Yang, C.L., Shi, Y., Kobayashi, T., Shi, Y.G., Mitani, S., Xie, X.S., and Xue, D. (2007). "C. elegans mitochondrial factor WAH-1 promotes phosphatidylserine externalization in apoptotic cells through phospholipid scramblase SCRM-1". Nature Cell Biology 9, 541-549. ( and PDF).  (PDF)
  21. Peden, E., Kimberly, E.L., Gengyo-Ando, K., Mitani, S., and Xue, D. (2007). Control of sex-specific apoptosis in C. elegans by the BarH homeodomain protein CEH-30 and the transcriptional repressor UNC-37/Groucho. Genes & Development 21, 2195-3207. ( and PDF).
  22. Darland-Ransom, M., Wang, X.C., Sun, C.L., Mapes, J., Gengyo-Ando, K., Mitani, S. and Xue, D. (2008). Role of C. elegans TAT-1 protein in maintaining plasma membrane phosphatidylserine asymmetry. Science 320, 528-531. ( and PDF). Science Perspectives (PDF)
  23. Breckenridge, D., Kang, B.H., Kokel, D., Mitani, S., Staehelin, A.L., and Xue, D. (2008). Caenorhabditis elegans drp-1 and fis-2 regulate distinct cell death execution pathways downstream of ced-3 and independent of ced-9. Mol. Cell 31 586-597. ( and PDF) Developmental Cell Preview (PDF)
  24. Peden, E., Killian, D., and Xue, D. (2008). Cell death specification in C. elegans. Cell Cycle 7, 2479-2484. ( and PDF)
  25. Killian, D., Harvey, E., Johnson, P., Otori, M., Mitani, S., and Xue, D. (2008). SKR-1, a homolog of Skp1 and a member of the SCFSEL-10 complex,regulates sex-determination and LIN-12/Notch signaling in C. elegans. Developmental Biology 322, 322-331. ( and PDF)
  26. Geng, X., Shi, Y., Nakagawa, A., Yoshina, S., Mitani, S., Shi, Y., and Xue, D. (2008). Inhibition of CED-3 zymogen activation and apoptosis in Caenorhabditis elegans by a caspase homolog CSP-3. Nature Structural & Molecular Biology 15, 1094-1101. ( and PDF). Research Focus in Trends in Biological Sciences (PDF)
  27. Hsiao, Y.Y., Nakagawa, A., Shi, Z., Mitani, S., Xue, D. and Yuan, H. S. (2009). Crystal structure of CRN-4: implications for domain function in apoptotic DNA degradation. Mol. Cell. Biol. 29, 448-457. ( and PDF)
  28. Breckenridge, D., Kang, B.H., and Xue, D. (2009). Bcl-2 proteins EGL-1 and CED-9 do not regulate mitochondrial fission or fusion in Caenorhabditis elegans. Current Biology 19, 768-773. ( and PDF)
  29. Geng, X., Zhou, Q.H., Kage-Nakadai, E., Shi, Y., Yan, N., Mitani, S., and Xue, D. (2009). Caenorhabditis elegans caspase homolog CSP-2 inhibits CED-3 autoactivation and apoptosis in germ cells. Cell Death & Differentiation 16, 1385-1394. ( and PDF)
  30. Fadeel, B. and Xue, D. (2009). The ins and outs of phospholipid asymmetry in the plasma membrane: roles in health and disease. Critical Reviews In Biochemistry & Molecular Biology 44: 264¨C277. ( and PDF)
  31. Lai, H.J., Lo, S.Z., Kage-Nakadai, E., Mitani, S., and Xue, D. (2009). The roles and acting mechanism of Caenorhabditis elegans DNase II genes in apoptotic DNA degradation and development. PLoS One 4, e7348. ( and PDF)
  32. Nakagawa, A.*, Shi, Y.*, Kage-Nakadai, E., Mitani, S., and Xue, D. (2010). Caspase-Dependent Conversion of Dicer Ribonuclease into a Death-Promoting Deoxyribonuclease. Science 328, 327-334. *Equal contributions ( and PDF). Research Article featured on the  of Science and Science Perspectives, Developmental Cell Preview, Highlights in Nature Structural and Molecular Biology, Nature Reviews Molecular Cell Biology, Disease Models and Mechanisms, and Faculty of 1000
  33. Wang, X.C., Li W., Zhao, D.F., Liu, B., Shi, Y., Chen, B.H., Yang, H.W., Guo, P.F., Geng, X., Shang, Z.H., Peden, E., Kage-Nakadai, E., Mitani, S., and Xue, D. (2010). C. elegans transthyretin-like protein TTR-52 mediates recognition of apoptotic cells by the CED-1 phagocyte receptor. Nature Cell Biology 12, 655-664. ( and PDF) Nature Cell Biology News and Views
  34. Mapes, J., Chen, J.T., Yu, J.S., and Xue, D. (2010). Somatic sex determination in C. elegans is modulated by SUP-26 repression of tra-2 translation. Proc. Natl. Acad. Sci. USA 107:18022-18027. ( and PDF)
  35. Harry, B. and Xue, D. (2010). C. elegans and apoptosis. Chapter 34 in "Apoptosis: Physiology and Pathology". In press. Edited by D.R. Green & J.C. Reed. Cambridge University Press.
  36. Harry, B., Nakagawa, A., and Xue, D. (2010). Dicing Up Chromosomes: the Unexpected Role of Dicer in Apoptosis. Cell Cycle 9, 4772 - 4773. (PDF)
  37. Zhou, Q.H., Li, H.M., and Xue, D. (2011). Elimination of Paternal mitochondria through the lysosomal degradation pathway in C. elegans. Cell Research 21, 1662-1669. ( and )
  38. Lin, J.L., Nakagawa, A., Lin, C.L., Hsiao, Y.Y., Yang, W.Z., Wang, Y.T., Doudeva, L.G., Skeen-Gaar, R.R., Xue, D., and Yuan, H.S. (2012). Structural insights into apoptotic DNA degradation by CED-3 Protease Suppressor-6 (CPS-6) from Caenorhabditis elegans. Journal of Biological Chemistry 287:7110-7120 ( and ).
  39. Mapes, J., Chen, Y.Z., Kim, A., Mitani, S., Kang, B.H., and Xue, D. (2012). CED-1, CED-7, and TTR-52 act in a pathway to regulate exoplasmic phosphatidylserine expression on apoptotic and phagocytic cells. Current Biology 22, 1267-1275. ( and PDF). Faculty of 1000
  40. Geng, X., Harry, B.L., Zhou, Q.H., Skeen-Gaar, R.B., Ge, X., Lee, E.S., Mitani, S., and Xue, D. (2012). Hepatitis B Virus X protein targets the Bcl-2 protein CED-9 to induce intracellular Ca2+ increase and cell death in C. elegans. Proc. Natl. Acad. Sci. USA 109: 18465-18470. ( and PDF)
  41. Geng, X., Huang, C.H., Qin, Y., McComb, J., Yuan, Q., Harry, B.L., Palmer, A., Xia, N.S., and Xue, D. (2012). Hepatitis B virus X protein targets Bcl-2 proteins to increase cytosolic Ca2+, required for virus replication and cell death induction. Proc. Natl. Acad. Sci. USA 109, 18471-18476. ( and PDF)
  42. Morton, LA, Yang H, Saludes JP, Fiorini Z, Beninson L, Chapman ER, Fleshner M, Xue D, Yin H (2013). MARCKS-ED Peptide as a Curvature and Lipid Sensor. ACS Chemical Biology 8: 218-225. ( and PDF)
  43. Chen, Y.Z., Mapes, J., Lee, E.S. and Xue, D. (2013). Caspase-mediated activation of Caenorhabditis elegans CED-8 promotes apoptosis and PS externalization. Nature Communications 4:2726 doi: 10.1038/ncomms3726. ( and PDF)
  44. Ge, X., Zhao, X., Nakagawa, A., Gong, X., Skeen-Gaar, R., Shi, Y., Gong, H.P., Wang, X.Q., and Xue, D. (2013). A novel mechanism underlies caspase-dependent conversion of the dicer ribonuclease into a deoxyribonuclease during apoptosis. Cell Research 24: 218-232 ( and PDF).
  45. Zhao, P., Zhang, Z., Ke, H.M., Ye, Y.R. and Xue, D. (2014). Oligonucleotide-based targeted gene editing in C. elegans via the CRISPR/Cas9 system. Cell Research 24: 247-250 ( and PDF).
  46. Nakagawa, A., Sullivan, K., and Xue, D. (2014). Caspase-activated phosphoinositide binding by CNT-1 promotes apoptosis by inhibiting the AKT pathway. Nature Structural & Molecular Biology 21, 1082-1090 ( and PDF).
  47. Weaver, B.P., Zabinsky, R., Weaver, Y.M., Lee, E.S., Xue. D., and Han, M. (2014). CED-3 caspase acts with miRNAs to regulate non-apoptotic gene expression dynamics for robust development in C. elegans. eLife doi: 10.7554/eLife.04265 ( and PDF).
  48. Yang, H.W.*, Chen, Y.Z.*, Zhang, Y.*, Wang, X.H., Zhao, X., Godfroy, J.I., Liang, L., Zhang, M., Zhang, T.Y., Yuan, Q., Royal, M.A., Driscoll, M.D., Xia, N.S., Yin, H., and Xue, D. (2015). A lysine-rich motif in the phosphatidylserine receptor PSR-1 mediates recognition and removal of apoptotic cells. Nature Communications , 6: 5717 doi: 10.1038/ncomms6717. *Equal contribution. ( and PDF). 
  49. Neumann, B., Coakley, S., Giordano-Santini, R., Linton, C., Lee, E.S., Nakagawa, A., Xue, D., and Hilliard, M.A. (2015). EFF-1-mediated regenerative axonal fusion requires components of the apoptotic pathway. Nature 517, 219¨C222 ( and PDF).
  50. Sullivan, K.*, Nakagawa, A.*, Xue, D.#, and Espinosa, J.M.# (2015). Human ACAP2 is a homolog of C. elegans CNT-1 that promotes apoptosis in cancer cells. Cell Cycle 14, 1771-1778. *Equal contribution. #Co-corresponding authors. ( and PDF).
  51. Seervi, M. and Xue, D. (2015). Mitochondrial cell death pathways in Caenorhabiditis elegans. Current Topics in Developmental Biology 114, 43-65 ( and PDF).
  52. Nichols, A.A, Meelkop, E., Linton, C., Giordano-Santini, R., Sullivan, R., Donato, A., Nolan, C., Hall, D.H., Xue, D., Neumann, B., and Hilliard, M. (2016).  The Apoptotic Engulfment Machinery Regulates Axonal Degeneration in C. elegans Neurons. Cell Reports 14, 1673-1683 ( and PDF).
  53. Zhao, P., Zhang, Z., Lv, X.Y., Zhao, X., Suehiro, Y., Jiang, Y.N., Wang, X.Q., Mitani, S., Gong, H.P., and Xue, D. (2016). One-step homozygosity in precise gene editing by an improved CRISPR/Cas9 system. Cell Research 26, 633-636 ( and PDF).
  54. Lin, J.L.*, Nakagawa, A.*, Skeen-Gaar, R.R., Yang, W.Z., Zhao, P., Zhang, Z., Ge, X., Mitani, S., Xue, D.#, and Yuan, H.S.# (2016). Oxidative Stress Impairs Cell Death by Repressing the Nuclease Activity of Mitochondrial Endonuclease G. Cell Reports 16, 279¨C287. *Equal contribution. #Co-corresponding authors. ( and PDF).
  55. Zhou, Q.H.*, Li, H.M.*, Li, H.Z.*, Nakagawa, A., Harry, B., Lee, E.S., Lin, J., William, D., Mitani, S., Yuan, H., Kang, B.H.#, and Xue, D.# (2016). Mitochondrial endonuclease G mediates breakdown of paternal mitochondria following fertilization. Science 353, 394-399 ( and PDF). *Equal contribution. #Co-corresponding authors. , Nature Reviews Molecular Cell Biology, , , , , , , , , , , , , , and 
  56. Conradt, B., Wu, Y.C., and Xue, D. (2016).  Programmed Cell Death During C. elegans development.  Genetics 203, 1533-1562 ( and PDF).
  57. Wang, Y.*, Zhang, Y.*, Chen, L.W., Liang, Q., Yin, X.M., Miao, L., Kang, B.H.#, and Xue, D.# (2016). Kinetics and specificity of paternal mitochondrial elimination in Caenorhabditis elegans. Nature Communications 7, 12569. DOI: 10.1038/ncomms12569 ( and PDF). *Equal contribution. #Co-corresponding authors.
  58. Chen, X.D.*, Wang, Y.*, Chen, Y.Z.*, Harry, Brian, L.H., Nakagawa, A., Lee, E.S., Guo, H.Y., and Xue, D. (2016). Regulation of CED-3 caspase localization and activation by C. elegans nuclear membrane protein NPP-14. Nature Structural & Molecular Biology 23, 958-964 ( and . *Equal contribution.Smith, C.E., Soti, S., Jones, T.A., Nakagawa, A., Xue, D., and Yin, H. (2017).  Non-steroidal Anti-inflammatory Drugs Are Caspase Inhibitors. Cell Chem. Biol. 24, 281-292. ( and PDF)
  59. Kl?ditz, K., Chen, Y.Z., Xue, D., and Fadeel, B. (2017). Programmed cell clearance: From nematodes to humans. Biochemical and Biophysical Research Communications, 482: 491-497 ( and PDF).
  60. Peng, Y.*, Zhang, M.*, Zheng, L.J.*, Liang,Q.*, Li, H.Z*., Chen, J.T., Guo, H., Yoshina, S. Chen, Y.Z., Zhao, X., Wu, X.Q., Liu, B., Mitani, S., Yu, J.S., and Xue, D. (2017). Cysteine protease cathepsin B mediates radiation-induced bystander effects. Nature 547, 458-462 ( and ). *Equal contribution. , 
  61. Chen, Y.Z.*, Kloditz, K.*, Lee, E.S., Nguyen, D.P., Yuan, Q., Johnson, J., Lee-yow, Y., Hall, A., Mitani, S., Xia, N.S., Fadeel, B.#, and Xue, D.# (2019). Structure and function analysis of the C. elegans aminophospholipid translocase TAT-1. Journal of Cell Science 132: jcs227660 doi: 10.1242/jcs.227660 ( and PDF). *Equal contribution. #Co-corresponding authors.
  62. Zhang, T.Y.*, Chen, H.Y.*, Cao, J.L.*, Xiong, H.L., Mo, X.B., Li, T.L., KANG, X.Z., Zhao, J.H., Yin, B., Zhao, X., Huang, C.H., Yuan, Q.#, Xue, D.#, Xia, N.S.#, and Yuan, Y.A. (2019). Structural and functional analyses of Hepatitis B virus X protein BH3-like domain and Bcl-xL interaction. Nature Communications 10: 3192 (and ). *Equal contribution. #Co-corresponding authors
  63. Zheng, L.J., Wu, X.Q., Li, S.S., Liu, B., and Xue, D. (2019). Cathepsin B inhibitors block multiple radiation-induced side effects in C. elegans. Cell Research 29, 1042-1045 (PDF).
  64. Bhadra, J.*, Sridhar, N.*, Fajrial, A.K., Hammond, N., Xue, D.#, and Ding, X.Y.# (2023). Acoustic Streaming Enabled Moderate Swimming Exercise Reduces Neurodegeneration in C. elegans (2023). Science Advances 9, eadf5056 ( and ). *Equal contribution, #Co-corresponding authors. ¶¶Òõ¶ÌÊÓƵ Boulder Today, ,
  65. Zhang, H., Zhu, Y., Suehiro, Y., Mitani, S., and Xue, D. (2023). AMPK-FOXO-IP3R signaling pathway mediates neurological and developmental defects caused by mitochondrial DNA mutations. Proc. Natl. Acad. Sci. USA 120: e2302490120 ( and ).
  66. Zhang, H., Zhu, Y., and Xue, D. (2024). Moderate embryonic delay of paternal mitochondrial elimination impairs mating and cognition and alters behaviors of adult animals. Science Advances 10, eadp8351 ( and ).  , , ¶¶Òõ¶ÌÊÓƵ Boulder Today, ,