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每277.?(?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每222 (?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每287. *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.?CU 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?). ?, , CU Boulder Today, ,
  67. Li, S., Redweik, G.,?Lin, J.L., Chen, Y.N., Yuan, H.S., and Xue, D. (2024). Probing the importance of AIF interaction with endonuclease G in mitochondrial inheritance and neurodegeneration. Cell Discovery 10, 107 (Abstract and PDF).
  68. Redweik, G. and Xue, D. (2025).?Secreted autotransporter toxin produced by probiotic Escherichia coli?Nissle 1917 enhances neurodegeneration in Caenorhabditis elegans.?microPublication Biology ?.
  69. Wang, S. and Xue, D. (2025). Asymmetric partitioning of persistent paternal mitochondria during cell divisions safeguards embryo development and mitochondrial inheritance. Developmental Cell, in press.