Klionsky publications

ARTICLES (2015-2010)

Feng Y, Yao Z, Klionsky DJ. (2015) How to control self-digestion: transcriptional, post-transcriptional, and post-translational regulation of autophagy. Trends Cell Biol  pii: S0962-8924(15)00017-3. PubMed PMID: 25759175. PubMed Link

Bernard A, Jin M, González-Rodríguez P, Füllgrabe J, Delorme-Axford E, Backues SK, Joseph B, Klionsky DJ. (2015) Rph1/KDM4 mediates nutrient-limitation signaling that leads to the transcriptional induction of autophagy. Curr Biol 25(5):546-555. PMCID: PMC4348152. PubMed Link

Delorme-Axford E, Guimaraes RS, Reggiori F, Klionsky DJ. (2015) The yeast Saccharomyces cerevisiae: an overview of methods to study autophagy progression. Methods 75:3-12. PMCID: PMC4355233. PubMed Link

Backues SK, Orban DP, Bernard A, Singh K, Cao Y, Klionsky DJ. (2015) Atg23 and Atg27 act at the early stages of Atg9 trafficking in S. cerevisiae. Traffic 16(2):172-190. PMCID: PMC4305007. PubMed Link

Gatica D, Chiong M, Lavandero S, Klionsky DJ. (2015) Molecular mechanisms of autophagy in the cardiovascular system. Circ Res 16(3):456-467. PMCID: PMC4313620. PubMed Link

Ochaba J, Lukacsovich T, Csikos G, Zheng S, Margulis J, Salazar L, Mao K, Lau AL, Yeung SY, Humbert S, Saudou F, Klionsky DJ, Finkbeiner S, Zeitlin SO, Marsh JL, Housman DE, Thompson LM, Steffan JS. (2014) Potential function for the Huntingtin protein as a scaffold for selective autophagy. Proc Natl Acad Sci U S A 111(47):16889-16894. PMCID: PMC4250109. PubMed Link

Jin M, Klionsky DJ. (2014) Regulation of autophagy: modulation of the size and number of autophagosomes. FEBS Lett 588(15):2457-2463. PMCID: PMC4118767. PubMed Link

Jin M, He D, Backues SK, Freeberg MA, Liu X, Kim JK, Klionsky DJ. (2014) Transcriptional regulation by Pho23 modulates the frequency of autophagosome formation. Curr Biol 24(12):1314-1322. PMCID: PMC4169046. PubMed Link

Sasaki T, Lian S, Qi J, Bayliss PE, Carr CE, Johnson JL, Guha S, Kobler P, Catz SD, Gill M, Jia K, Klionsky DJ, Kishi S. (2014) Aberrant autolysosomal regulation is linked to the induction of embryonic senescence: differential roles of Beclin 1 and p53 in vertebrate Spns1 deficiency. PLoS Genet. 10(6):e1004409. PMCID: PMC4072523. PubMed Link

Klionsky DJ, Schulman BA. (2014) Dynamic regulation of macroautophagy by distinctive ubiquitin-like proteins. Nat Struct Mol Biol (4):336-345. PMCID: PMC4036234. PubMed Link

Jin N, Mao K, Jin Y, Tevzadze G, Kauffman EJ, Park S, Bridges D, Loewith R, Saltiel AR, Klionsky DJ, Weisman LS. (2014) Roles for PI(3,5)P2 in nutrient sensing through TORC1. Mol Biol Cell  25(7):1171-1185.PubMed Central PMCID: PMC3967979. PubMed Link

Mao K, Liu X, Feng Y, Klionsky DJ.(2014) The progression of peroxisomal degradation through autophagy requires peroxisomal division.Autophagy 10(4):652-661. PMCID: PMC4091152. Pubmed Link

Varga M, Sass M, Papp D, Takács-Vellai K, Kobolak J, Dinnyés A, Klionsky DJ Vellai T. (2014) Autophagy is required for zebrafish caudal fin regeneration.Cell Death Differ  21(4):547-556. PMCID: PMC3950318. PubMed Link

Klionsky DJ, Eskelinen EL. (2014) The vacuole versus the lysosome: when size matters. Autophagy 10(2):185-187. PubMed PMID: 24343261. PubMed Link

Belaid A, Ndiaye PD, Cerezo M, Cailleteau L, Brest P, Klionsky DJ, Carle GF, Hofman P, Mograbi B. (2014) Autophagy and SQSTM1 on the RHOA(d) again: emerging roles of autophagy in the degradation of signaling proteins.Autophagy  (2):201-208. PubMed PMID: 24300375. PubMed Link

Parzych KR, Klionsky DJ. (2014) An overview of autophagy: morphology, mechanism, and regulation. Antioxid Redox Signal 20(3):460-473. PMCID: PMC3894687. PubMed Link

Füllgrabe J, Klionsky DJ, Joseph B. (2014) The return of the nucleus: transcriptional and epigenetic control of autophagy. Nat Rev Mol Cell Biol  15(1):65-74. PubMed PMID: 24326622. PubMed Link

Feng Y, He D, Yao Z, Klionsky DJ. (2014) The machinery of macroautophagy.Cell Res 24(1):24-41. PMCID: PMC3879710.PubMed Link

Backues SK, Chen D, Ruan J, Xie Z, Klionsky DJ. (2014) Estimating the size and number of autophagic bodies by electron microscopy. Autophagy10(1):155-164. PubMed PMID: 24270884. PubMed Link

Mao K, Chew LH, Yip CK, Klionsky DJ. (2013) The role of Atg29 phosphorylation in PAS assembly. Autophagy (12):2178-2179. PMCID: PMC4028347. PubMed Link

Mao K, Klionsky DJ. (2013) Mitochondrial fission facilitates mitophagy in Saccharomyces cerevisiae. Autophagy (11):1900-2001. PMCID: PMC4028339. PubMed Link

Wang K, Jin M, Liu X, Klionsky DJ. (2013) Proteolytic processing of Atg32 by the mitochondrial i-AAA protease Yme1 regulates mitophagy. Autophagy 9(11):1828-1836. PMCID: PMC4028336. Pubmed Link

Mao K, Klionsky DJ. (2013) Participation of mitochondrial fission during mitophagy. Cell Cycle (19):3131-3132. PMCID: PMC3865006. PubMed Link

Füllgrabe J, Klionsky DJ, Joseph B. (2013) Histone post-translational modifications regulate autophagy flux and outcome. Autophagy (10):1621-1623. PubMed PMID: 23934085. PubMed Link

Belaid A, Ndiaye PD, Klionsky DJ, Hofman P, Mograbi B. (2013) Signalphagy: scheduled signal termination by macroautophagy. Autophagy (10):1629-1630. PubMed PMID: 24004837. PubMed LinkChew LH, Setiaputra D, Klionsky DJ, Yip CK. (2013) Structural characterization of the Saccharomyces cerevisiae autophagy regulatory complex Atg17-Atg31-Atg29. Autophagy (10):1467-1474.PMID: 23939028. Pubmed Link

Loos B, Engelbrecht AM, Lockshin RA, Klionsky DJ, Zakeri Z. (2013) The variability of autophagy and cell death susceptibility: Unanswered questions. Autophagy (9):1270-1285. PMCID: PMC4026026. PubMed Link

Füllgrabe J, Lynch-Day MA, Heldring N, Li W, Struijk RB, Ma Q, Hermanson O, Rosenfeld MG, Klionsky DJ, Joseph B. (2013)  The histone H4 lysine 16 acetyltransferase hMOF regulates the outcome of autophagy. Nature. 500(7463):468-471. PMCID: PMC4006103. PubMed Link

Mao K, Chew LH, Inoue-Aono Y, Cheong H, Nair U, Popelka H, Yip CK, Klionsky DJ. (2013) Atg29 phosphorylation regulates coordination of the Atg17-Atg31-Atg29 complex with the Atg11 scaffold during autophagy initiation. Proc Natl Acad Sci U S A. 110(31):E2875-2884. PMCID: PMC3732952. Pubmed Link

Mao K, Wang K, Liu X, Klionsky DJ. (2013) The scaffold protein Atg11 recruits fission machinery to drive selective mitochondria degradation by autophagy. Dev Cell 26(1):9-18. PMCID: PMC3720741. Pubmed Link

Belaid A, Cerezo M, Chargui A, Corcelle-Termeau E, Pedeutour F, Giuliano S, Ilie M, Rubera I, Tauc M, Barale S, Bertolotto C, Brest P, Vouret-Craviari V, Klionsky DJ, Carle GF, Hofman P, Mograbi B. (2013) Autophagy plays a critical role in the degradation of active RHOA, the control of cell cytokinesis, and genomic stability. Cancer Res. 73(14):4311-4322. PMCID: PMC3740229. PubMed Link

Thompson DA, Klionsky DJ. Autophagy and gene therapy combine in the treatment of liver disease. Autophagy. 2013 Jul;9(7):945-946. PMCID: PMC3722329. Pubmed Link

Reggiori F, Klionsky DJ. (2013) Autophagic processes in yeast: mechanism, machinery and regulation. Genetics 194(2):341-361. PMCID: PMC3664846. PubMed Link

Bernard A, Popelka H, Klionsky DJ. (2013) A unique hairpin-type tail-anchored SNARE starts to solve a long-time puzzle. Autophagy 9(6):813-814. PMCID: PMC3672291. Pubmed Link

Kaiser S.E., Qiu Y., Coats J.E., Mao K., Klionsky D.J., Schulman B.A. (2013). Structures of Atg7-Atg3 and Atg7-Atg10 reveal noncanonical mechanisms of E2 recruitment by the autophagy E1. Autophagy 9(5):778-780. PubMed Link

Jin M., Liu X., Klionsky D.J. (2013). SnapShot: Selective autophagy. Cell 152. PubMed Link

Deffieu M., Bhatia-Kissova I., Salin B., Klionsky D.J., Pinson B., Manon S., Camougrand N. (2013). Increased levels of reduced cytochrome b and mitophagy components are required to trigger nonspecific autophagy following induced mitochondrial dysfunction. Journal of Cell Science 126(2):415-426. PubMed link

Kaiser S.E., Mao K., Taherbhoy A.M., Yu S., Olszewski J.L., Duda D.M., Kurinov I., Deng A., Fenn T.D., Klionsky D.J., Schulman B.A. (2012). Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7-Atg3 and Atg7-Atg10 structures. Nature Structural and Molecular Biology 19(12):1242-1249. PubMed link

Wang K., Yang Z., Liu X., Mao K., Nair U., Klionsky D.J. (2012). Phosphatidylinositol 4-kinases are required for autophagic membrane trafficking. Journal of Biological Chemistry 287(45):37964-37972. PubMed link

Cebollero E., Van Der Vaart A., Zhao M., Rieter E., Klionsky D.J., Helms J.B., Reggiori F. (2012). Phosphatidylinositol-3-phosphate clearance plays a key role in autophagosome completion. Current Biology 22(17):1545-1553. PubMed link

Yen W.-L., Klionsky D.J. (2012). Proteinase protection of prApe1 as a tool to monitor Cvt vesicle/ autophagosome biogenesis. Autophagy 8(8):1245-1249. PubMed link

Bartholomew C.R., Suzuki T., Du Z., Backues S.K., Jin M., Lynch-Day M.A., Umekawa M., Kamath A., Zhao M., Xie Z., Inoki K., Klionsky D.J. (2012). Ume6 transcription factor is part of a signaling cascade that regulates autophagy. Proc Natl Acad Sci U S A 109(28):11206-11210. PubMed link

Yu Z.-Q., Ni T., Hong B., Wang H.-Y., Jiang F.-J., Zou S., Chen Y., Zheng X.-L., Klionsky D.J., Liang Y., Xie Z. (2012). Dual roles of Atg8 - PE deconjugation by Atg4 in autophagy. Autophagy 8(6):883-892. PubMed link

Umekawa M., Klionsky D.J. (2012). Ksp1 kinase regulates autophagy via the target of rapamycin complex 1 (TORC1) pathway. Journal of Biological Chemistry 287(20):16300-16310. PubMed link

Klionsky D.J., Hurley J.H. (2012). Self-eating with your fingers. Cell Research 22(5):783-785. PubMed link

Nair U., Yen W.-L., Mari M., Cao Y., Xie Z., Baba M., Reggiori F., Klionsky D.J. (2012). A role for Atg8-PE deconjugation in autophagosome biogenesis. Autophagy 8(5):780-793. PubMed link

Takahashi R., Miller J.H., Klionsky D.J. (2012). SNARE Dance: A musical interpretation of Atg9 transport to the tubulovesicular cluster. Autophagy 8(3):294-296. PubMed link

Devenish R.J., Klionsky D.J. (2012). Autophagy: Mechanism and physiological relevance 'brewed' from yeast studies. Frontiers in Bioscience S4(4):1354-1363. PubMed link

Bass A., Sauer D., Klionsky D.J. (2011). A PCR analysis of the ubiquitin-like conjugation systems in macroautophagy. Autophagy 7(12):1410-1414. PubMed link

Nair U., Thumm M., Klionsky D.J., Krick R. (2011). GFP-Atg8 protease protection as a tool to monitor autophagosome biogenesis. Autophagy 7(12):1546-1550. PubMed link

Nair U., Jotwani A., Geng J., Gammoh N., Richerson D., Yen W.-L., Griffith J., Nag S., Wang K., Moss T., Baba M., McNew J.A., Jiang X., Reggiori F., Melia T.J., Klionsky D.J. (2011). SNARE proteins are required for macroautophagy. Cell 146(2):290-302. PubMed link

Taylor R.W., Qi J.Y., Talaga A.K., Ma T.P., Pan L., Bartholomew C.R., Klionsky D.J., Moens C.B., Gamse J.T. (2011). Asymmetric inhibition of Ulk2 causes left-right differences in habenular neuropil formation. Journal of Neuroscience 31(27):9869-9878. PubMed link

Nyfeler B., Bergman P., Triantafellow E., Wilson C.J., Zhu Y., Radetich B., Finan P.M., Klionsky D.J., Murphy L.O. (2011). Relieving autophagy and 4EBP1 from rapamycin resistance. Molecular and Cellular Biology 31(14):2867-2876. PubMed link

Mao K., Wang K., Zhao M., Xu T., Klionsky D.J. (2011). Two MAPK-signaling pathways are required for mitophagy in Saccharomyces cerevisiae. Journal of Cell Biology 193(4):755-767. PubMed link

Yuga M., Gomi K., Klionsky D.J., Shintani T. (2011). Aspartyl aminopeptidase is imported from the cytoplasm to the vacuole by selective autophagy in Saccharomyces cerevisiae. Journal of Biological Chemistry 286(15):13704-13713. PubMed link

Backues S.K., Klionsky D.J. (2011). Autophagy gets in on the regulatory act. Journal of Molecular Cell Biology 3(2):76-77. PubMed link

Zhao M., Klionsky D.J. (2011). AMPK-dependent phosphorylation of ULK1 induces autophagy. Cell Metabolism 13(2):119-120. PubMed link

Huang J., Birmingham C.L., Shahnazari S., Shiu J., Zheng Y.T., Smith A.C., Campellone K.G., Heo W.D., Gruenheid S., Meyer T., Welch M.D., Ktistakis N.T., Kim P.K., Klionsky D.J., Brumell J.H. (2011). Antibacterial autophagy occurs at PtdIns(3)P-enriched domains of the endoplasmic reticulum and requires Rab1 GTPase. Autophagy 7(1):17-26. PubMed link

Yen W.-L., Shintani T., Nair U., Cao Y., Richardson B.C., Li Z., Hughson F.M., Baba M., Klionsky D.J. (2010). The conserved oligomeric Golgi complex is involved in double-membrane vesicle formation during autophagy. Journal of Cell Biology 188(1):101-114. PubMed link

Mari M., Griffith J., Rieter E., Krishnappa L., Klionsky D.J., Reggiori F. (2010). An Atg9-containing compartment that functions in the early steps of autophagosome biogenesis. Journal of Cell Biology 190(6):1005-1022. PubMed link

Shahnazari S., Yen W.-L., Birmingham C.L., Shiu J., Namolovan A., Zheng Y.T., Nakayama K., Klionsky D.J., Brumell J.H. (2010). A diacylglycerol-dependent signaling pathway contributes to regulation of antibacterial autophagy. Cell Host and Microbe 8(2):137-146. PubMed link

Brest P., Corcelle E.A., Cesaro A., Chargui A., Belaid A., Klionsky D.J., Vouret-Craviari V., Hebuterne X., Hofman P., Mograbi B. (2010). Autophagy and crohn's disease: At the crossroads of infection, inflammation, immunity, and cancer. Current Molecular Medicine 10(5):486-502. PubMed link

Geng J., Nair U., Yasumura-Yorimitsu K., Klionsky D.J. (2010). Post-golgi sec proteins are required for autophagy in Saccharomyces cerevisiae. Molecular Biology of the Cell 21(13):2257-2269. PubMed link

He C., Klionsky D.J. (2010). Analyzing autophagy in zebrafish. Autophagy 6(5):642-644. PubMed link

Lynch-Day M.A., Bhandari D., Menon S., Huang J., Caid H., Bartholomew C.R., Brumell J.H., Ferro-Novick S., Klionsky D.J. (2010). Trs85 directs a Ypt1 GEF, TRAPPIII, to the phagophore to promote autophagy. Proc Natl Acad Sci U S A 107(17):7811-7816. PubMed link

Yang Z., Geng J., Yen W.-L., Wang K., Klionsky D.J. (2010). Positive or Negative Roles of Different Cyclin-Dependent Kinase Pho85-Cyclin Complexes Orchestrate Induction of Autophagy in Saccharomyces cerevisiae. Molecular Cell 38(2):250-264. PubMed link

Nair U., Cao Y., Xie Z., Klionsky D.J. (2010). Roles of the lipid-binding motifs of Atg18 and Atg21 in the cytoplasm to vacuole targeting pathway and autophagy. Journal of Biological Chemistry 285(15):11476-11488. PubMed link

Thevissen K., Yen W.-L., Carmona-Gutierrez D., Idkowiak-Baldys J., Aerts A.M., Francois I.E.J.A., Madeo F., Klionsky D.J., Hannun Y.A., Cammue B.P.A. (2010). Skn1 and Ipt1 negatively regulate autophagy in Saccharomyces cerevisiae. FEMS Microbiology Letters 303(2):164-168. PubMed link

Geng J., Klionsky D.J. (2010). Determining Atg protein stoichiometry at the phagophore assembly site by fluorescence microscopy. Autophagy 6(1):144-147. PubMed link

Articles (2004-2009)

Autophagy

Kanki T., Wang K., Baba M., Bartholomew C.R., Lynch-Day M.A., Du Z., Geng J., Mao K., Yang Z., Yen W.-L., Klionsky D.J. (2009). A genomic screen for yeast mutants defective in selective mitochondria autophagy. Molecular Biology of the Cell 20(22):4730-4738. PubMed link

Kanki T., Kang D., Klionsky D.J. (2009). Monitoring mitophagy in yeast: The Om45-GFP processing assay. Autophagy 5(8):1186-1189. PubMed link

Kanki T., Klionsky D.J. (2009). Atg32 is a tag for mitochondria degradation in yeast. Autophagy 5(8):1201-1202. PubMed link

Vellai T., Takacs-Vellai K., Sass M., Klionsky D.J. (2009). The regulation of aging: does autophagy underlie longevity?. Trends in Cell Biology 19(10):487-494. PubMed link

Kanki T., Klionsky D.J. (2009). Mitochondrial abnormalities drive cell death in Wolfram syndrome 2.. Cell Research 19(8):922-923. PubMed link

Kanki T., Wang K., Cao Y., Baba M., Klionsky D.J. (2009). Atg32 Is a Mitochondrial Protein that Confers Selectivity during Mitophagy. Developmental Cell 17(1):98-109. PubMed link

Cao Y., Nair U., Yasumura-Yorimitsu K., Klionsky D.J. (2009). A multiple ATG gene knockout strain for yeast two-hybrid analysis. Autophagy 5(5):699-705. PubMed link

Yorimitsu T., He C., Wang K., Klionsky D.J. (2009). Tap42-associated protein phosphatase type 2A negatively regulates induction of autophagy. Autophagy 5(5):616-624. PubMed link

He C., Bartholomew C.R., Zhou W., Klionsky D.J. (2009). Assaying autophagic activity in transgenic GFP-Lc3 and GFP-Gabarap zebrafish embryos. Autophagy 5(4):520-526. PubMed link

Klionsky D.J. (2009). Crohn's disease, autophagy, and the paneth cell. New England Journal of Medicine 360(17):1785-1786. PubMed link

He C., Baba M., Klionsky D.J. (2009). Double duty of Atg9 self-association in autophagosome biogenesis. Autophagy 5(3):385-387. PubMed link

Xie Z., Nair U., Geng J., Szefler M.B., Rothman E.D., Klionsky D.J. (2009). Indirect estimation of the area density of Atg8 on the phagophore. Autophagy 5(2):217-220. PubMed link

Cheong H., Klionsky D.J. (2008). Biochemical methods to monitor autophagy-related processes in yeast.. Methods in enzymology 451:1-26. PubMed link

Legakis J.E., Klionsky D.J. (2008). Analysis of autophagosome membrane cycling by fluorescence microscopy. Methods in Molecular Biology 445:135-145. PubMed link

Noda T., Klionsky D.J. (2008). The quantitative Pho8Delta60 assay of nonspecific autophagy.. Methods in enzymology 451:33-42. PubMed link

He C., Baba M., Cao Y., Klionsky D.J. (2008). Self-interaction is critical for Atg9 transport and function at the phagophore assembly site during autophagy. Molecular Biology of the Cell 19(12):5506-5516. PubMed link

Kanki T., Klionsky D.J. (2008). Mitophagy in yeast occurs through a selective mechanism. Journal of Biological Chemistry 283(47):32386-32393. PubMed link

Cao Y., Klionsky D.J. (2008). New insights into autophagy using a multiple knockout strain. Autophagy 4(8):1073-1075. PubMed link

Geng J., Klionsky D.J. (2008). Quantitative regulation of vesicle formation in yeast nonspecific autophagy. Autophagy 4(7):955-957. PubMed link

Monastyrska I., Reggiori F., Klionsky D.J. (2008). Harpooning the Cvt complex to the phagophore assembly site. Autophagy 4(7):914-916. PubMed link

Xie Z., Nair U., Klionsky D.J. (2008). Dissecting autophagosome formation: The missing pieces. Autophagy 4(7):920-922. PubMed link

Cao Y., Cheong H., Song H., Klionsky D.J. (2008). In vivo reconstitution of autophagy in Saccharomyces cerevisiae. Journal of Cell Biology 182(4):703-713. PubMed link

Xie Z., Nair U., Klionsky D.J. (2008). Atg8 controls phagophore expansion during autophagosome formation. Molecular Biology of the Cell 19(8):3290-3298. PubMed link

Geng J., Baba M., Nair U., Klionsky D.J. (2008). Quantitative analysis of autophagy-related protein stoichiometry by fluorescence microscopy. Journal of Cell Biology 182(1):129-140. PubMed link

Cheong H., Klionsky D.J. (2008). Dual role of Atg1 in regulation of autophagy-specific PAS assembly in Saccharomyces cerevisiae. Autophagy 4(5):724-726. PubMed link

Monastyrska I., He C., Geng J., Hoppe A.D., Li Z., Klionsky D.J. (2008). Arp2 links autophagic machinery with the actin cytoskeleton. Molecular Biology of the Cell 19(5):1962-1975. PubMed link

Deretic V., Klionsky D.J. (2008). How cells clean house. Scientific American 298(5):74-81. PubMed link

Cheong H., Nair U., Geng J., Klionsky D.J. (2008). The Atg1 kinase complex is involved in the regulation of protein recruitment to initiate sequestering vesicle formation for nonspecific autophagy in Saccharomyces cerevisiae. Molecular Biology of the Cell 19(2):668-681. PubMed link

Yorimitsu T., Zaman S., Broach J.R., Klionsky D.J. (2007). Protein kinase A and Sch9 cooperatively regulate induction of autophagy in Saccharomyces cerevisiae. Molecular Biology of the Cell 18(10):4180-4189. PubMed link

Cao Y., Klionsky D.J. (2007). Physiological functions of Atg6/Beclin 1: A unique autophagy-related protein. Cell Research 17(10):839-849. PubMed link

Legakis J.E., Yen W.-L., Klionsky D.J. (2007). A cycling protein complex required for selective autophagy. Autophagy 3(5):422-432. PubMed link

Huang J., Reggiori F., Klionsky D.J. (2007). The transmembrane domain of acid trehalase mediates ubiquitin-independent multivesicular body pathway sorting. Molecular Biology of the Cell 18(7):2511-2524. PubMed link

Klionsky D.J. (2007). Monitoring autophagy in yeast: The Pho8?60 assay. Methods in Molecular Biology 390:363-371. PubMed link

He C., Klionsky D.J. (2007). Atg9 trafficking in autophagy-related pathways. Autophagy 3(3):271-274. PubMed link

Yen W.-L., Klionsky D.J. (2007). Atg27 is a second transmembrane cycling protein. Autophagy 3(3):254-256. PubMed link

Yang Z., Klionsky D.J. (2007). Permeases recycle amino acids resulting from autophagy. Autophagy 3(2):149-150. PubMed link

Yorimitsu T., Klionsky D.J. (2007). Endoplasmic reticulum stress: A new pathway to induce aytophagy. Autophagy 3(2):160-162. PubMed link

Tal R., Winter G., Ecker N., Klionsky D.J., Abeliovich H. (2007). Aup1p, a yeast mitochondrial protein phosphatase homolog, is required for efficient stationary phase mitophagy and cell survival. Journal of Biological Chemistry 282(8):5617-5624. PubMed link

Yen W.-L., Legalds J.E., Nair U., Klionsky D.J. (2007). Atg27 is required for autophagy-dependent cycling of Atg9. Molecular Biology of the Cell 18(2):581-593. PubMed link

Cao Y., Klionsky D.J. (2007). Atg26 is not involved in autophagy-related pathways in Saccharomyces cerevisiae. Autophagy 3(1):17-20. PubMed link

Yorimitsu, T., & Klionsky, D.J. (2007). Eating the endoplasmic reticulum: quality control by autophagy. Trends Cell Biol. 17, 279-85. PubMed link

Klionsky, D.J., Cuervo, A.M., & Seglen, P.O. (2007). Methods for monitoring autophagy from yeast to human. Autophagy 3, 181-206. PubMed link

Rubinsztein, D.C., Gestwicki, J.E., Murphy, L.O., and Klionsky, D.J. (2007). Potential therapeutic applications of autophagy. Nat Rev Drug Discov 6, 304-12. PubMed link

He, C., Song, H., Yorimitsu, T., Monastyrska, I., Yen, W.-L., Legakis, J.E., & Klionsky, D.J. (2006). Recruitment of Atg9 to the pre-autophagosomal structure by Atg11 is essential for selective autophagy in budding yeast. Journal of Cell Biology 175, 925-935. [Cover illustration] PubMed link

Yang, Z., Huang, J., Geng, J., Nair, U., & Klionsky, D.J. (2006). Atg22 recycles amino acids to link the degradative and recycling functions of autophagy. Molecular Biology of the Cell 17, 5094-5104. PubMed link

Yorimitsu, T., Nair, U., Yang, Z., & Klionsky, D.J. (2006). Endoplasmic reticulum stress triggers autophagy. Journal of Biological Chemistry 281, 30299-30304. PubMed link

Monastyrska, I., & Klionsky, D.J. (2006). Autophagy in organelle homeostasis: Peroxisome turnover. Molecular Aspects of Medicine 27, 483-494. PubMed link

Reggiori, F., & Klionsky, D.J. (2006). Atg9 sorting from mitochondria is impaired in early secretion and VFT complex mutants in Saccharomyces cerevisiae. Journal of Cell Science 119, 2903-2911. PubMed link

Legakis, J.E., & Klionsky, D.J. (2006). Overview of autophagy. In Autophagy in Immunity and Infection. A Novel Immune Effector (Deretic, V. ed). Wiley-VCH, Weinheim, pp. 3-17.

Klionsky, D.J. (2006). Good riddance to bad rubbish. Nature 441, 819-820. PubMed link

He, C., & Klionsky, D.J. (2006). Autophagy and neurodegeneration. ACS Chemical Biology 1, 211-213. PubMed link

Monastyrska, I., Shintani, T., Klionsky, D. J., & Reggiori, F. (2006). Atg11 directs autophagosome cargoes to the PAS along actin cables. Autophagy, 2, 119-121. PubMed link

Reggiori, F., & Klionsky, D. J. (2006). Atg9 sorting from mitochondria is impaired in early secretion and VFT-complex mutants in Saccharomyces cerevisiae. Journal of Cell Science, 119, 2903-2911. PubMed link

Nazarko, T. Y., Huang, J., Nicaud, J. M., Klionsky, D. J., & Sibirny, A. A. (2005). Trs85 is required for macroautophagy, pexophagy and cytoplasm to vacuole targeting in Yarrowia apolytica and Saccharomyces rereviesioue. Autophagy, 1, 37-45. PubMed link

Reggiori, F., Shintani, T., Nair, U., & Klionsky, D. J. (2005). Atg9 cycles between mitochondria and the pre-autophagosomal structure in yeasts. Autophagy, 1, 101-109. PubMed link

Towns, R., Kabeya, Y., Yoshimori, T., Guo, C. F., Shangguan, Y., Hong, S., Kaplan, M., Klionsky, D. J., & Wiley, J. W. (2005). Sera from patients with type 2 diabetes and neuropathy induce autophagy and colocalization with mitochondria in SY5Y cells. Autophagy, 1, 163-170. PubMed link

Reggiori, F., & Klionsky, D. J. (2005). Autophagosomes: Biogenesis from scratch? Current Opinion in Cell Biology, 17, 415-422. PubMed link

Yorimitsu, T., & Klionsky, D. J. (2005). Atg11 links cargo to the vesicle forming machinery in the cytoplasm to vacuole targeting pathway. Molecular Biology of the Cell, 16, 1593-1605. PubMed link

Cheong, H., Yorimitsu, T., Reggiori, F., Legakis, J. E., Wang, C. W., & Klionsky, D. J. (2005). Atg17 regulates the magnitude of the autophagic response. Molecular Biology of the Cell, 16, 3438-3453. PubMed link

Reggiori, F., Monastyrska, L., Shintani, T., & Klionsky, D. J. (2005). The actin cytoskeleton is required for selective types of autophagy, but not nonspecific autophagy, in the yeast Saccharomyces cerevisiae. Molecular Biology of the Cell, 16, 5843-5856. PubMed link

Teaching/Learning

Klionsky, D.J. (2006). Why don’t we teach the telephone book? The Teaching Professor 20, 7.

Klionsky, D.J., & Kumar, A. (2006). A systems biology approach to learning autophagy. Autophagy 2, 12-23.

Klionsky, D.J. (2007). Malpractice insurance for university professors? The Teaching Professor 21, 6.

Articles (1998-2004)

Reggiori, F., Tucker, K. A., Stromhaug, P. E., & Klionsky, D. J. (2004). The Atg1-Atg13 complex regulates Atg9 and Atg23 retrieval transport from the pre-autophagosomal structure. Developmental Cell, 6, 79-90. PubMed link

Budovskaya, Y. V., Stephan, J. S., Reggiori, F., Klionsky, D. J., & Herman, P. K. (2004). The Ras/cAMP-dependent protein kinase signaling pathway regulates an early step of the autophagy process in Saccharomyces cerevisiae. Journal of Biological Chemistry, 279, 20663-20671. PubMed link

Shintani, T., & Klionsky, D. J. (2004). Cargo proteins facilitate the formation of transport vesicles in the cytoplasm-to-vacuole targeting pathway. Journal of Biological Chemistry, 279, 29889-29894. PubMed link

Stromhaug, P. E., Reggiori, F., Guan, J., Wang, C. W., Klionsky, D. J. (2004). Atg21 is a phosphoinositide binding protein required for efficient lipidation and localization of Atg8 during uptake of aminopeptidase I by selective autophagy. Molecular Biology of the Cell, 15, 3553-3566. PubMed link

Reggiori, F., Wang, C. W., Stromhaug, P. E., Shintani, T., & Klionsky, D. J. (2003). Vps51 is part of the yeast Vps53 tethering complex essential for retrograde traffic from the early endosome and Cvt vesicle completion. Journal of Biological Chemistry, 278, 5009-5020. PubMed link

Tucker, K. A., Reggiori, F., Dunn, W. A., & Klionsky, D. J. (2003). Atg23 is essential for the cytoplasm-to-vacuole targeting pathway and efficient autophagy but not pexophagy. Journal of Biological Chemistry, 278, 48445-48452. PubMed link

Wang, C. W., Stromhaug, P. E., Kauffmann, E. J., Weisman, L. S., & Klionsky, D. J. (2003). Yeast homotypic vacuole fusion requires the Ccz1-Mon1 complex during the tethering/docking stage. Journal of Cell Biology, 163, 973-985. PubMed link

Abeliovich, H., Zhang, C., Dunn, W. A., Shokat, K. M., & Klionsky, D. J. (2003). Chemical genetic analysis of Apg1 reveals a nonkinase role in the induction of autophagy. Molecular Biology of the Cell, 14, 477-490. PubMed link

Wang, C. W., & Klionsky, D. J. (2003). The molecular mechanism of autophagy. Molecular Medicine, 9, 65-76. PubMed link

Shintani, T., Huang, W. P., Stromhaug, P. E., & Klionsky, D. J. (2002). Mechanism of cargo selection in the cytoplasm-to-vacuole targeting pathway. Developmental Cell, 3, 825-837. PubMed link

Kim, J., Huang, W. P., Stromhaug, P. E., & Klionsky, D. J. (2002). Convergence of multiple autophagy and cytoplasm-to-vacuole targeting components to a perivacuolar membrane compartment prior to de novo vesicle formation. Journal of Biological Chemistry, 277, 763-773. PubMed link

Nice, D. C., Sato, T. K., Stromhaug, P. E., Emr, S. D., & Klionsky, D. J. (2002). Cooperative binding of the cytoplasm-to-vacuole targeting pathway proteins, Cvt13 and Cvt20, to phosphatidylinositol 3-phosphate at the pre-autophagosomal structure is required for selective autophagy. Journal of Biological Chemistry, 277, 30198-30207. PubMed link

Wang, C. W., Stromhaug, P. E., Shima, J., & Klionsky, D. J. (2002). The Ccz1-Mon1 protein complex is required for the late step of multiple vacuole delivery pathways. Journal of Biological Chemistry, 277, 47917-47927. PubMed link

Teter, S. A., Eggerton, K. P., Scott, S. V., Kim, J., Fischer, A. M., Klionsky, D. J. (2001). Degradation of lipid vesicles in the yeast vacuole requires function of Cvt17, a putative lipase. Journal of Biological Chemistry, 276, 2083-2087. PubMed link

Hutchins, M. U., & Klionsky, D. J. (2001). Vacuolar localization of oligomeric alpha-mannosidase requires the cytoplasm-to-vacuole targeting and autophagy pathway components in Saccharomyces cerevisiae. Journal of Biological Chemistry, 276, 20491-20498. PubMed link

Wang, C. W., Kim, J., Huang, W. P., Abeliovich, H., Stromhaug, P. E., Dunn, W. A., & Klionsky, D. J. (2001). Apg2 is a novel protein required for the cytoplasm-to-vacuole targeting, autophagy, and pexophagy pathways. Journal of Biological Chemistry, 276, 30442-30451. PubMed link

Kim, J., Huang, W. P., & Klionsky, D. J. (2001). Membrane recruitment of Aut7p in the autophagy and cytoplasm-to-vacuole targeting pathways requires Aut1p, Aut2p, and the autophagy conjugation complex. Journal of Cell Biology, 152, 51-64. PubMed link

Kim, J., Kamada, Y., Stromhaug, P. E., Guan, J., Hefner-Gravink, A., Baba, M., Scott, S. V., Ohsumi, Y., Dunn, W. A., & Klionsky, D. J. (2001). Cvt9/Gsa9 functions in sequestering selective cytosolic cargo destined for the vacuole. Journal of Cell Biology, 153, 381-396. PubMed link

Guan, J., Stromhaug, P. E., George, M. D., Habibzadegah-Tari, P., Bevan, A., Dunn, W. A., & Klionsky, D. J. (2001). Cvt18/Gsa12 is required for cytoplasm-to-vacuole transport, pexophagy, and autophagy in Saccharomyces cerevisiae and Pichia pastoris. Molecular Biology of the Cell, 12, 3821-3838. PubMed link

Scott, S. V., Guan, J., Hutchins, M. U., Kim, J., & Klionsky, D. J. (2001). Cvt19 is a receptor for the cytoplasm-to-vacuole targeting pathway. Molecular Cell, 7, 1131-1141. PubMed link

Huang, W. P., Scott, S. V., Kim J., & Klionsky, D. J. (2000). The itinerary of a vesicle component, Aut7p/Cvt5p, terminates in the yeast vacuole via the autophagy/Cvt pathways. Journal of Biological Chemistry, 275, 5845-5851. PubMed link

Scott, S. V., Nice, D. C., Nau, J. J., Weisman, L. S., Kamada, Y., Keizer-Gunnink, I., Funakoshi, T., Veenhuis, M., Ohsumi, Y., & Klionsky, D. J. (2000). Apg13p and Vac8p are part of a complex of phosphoproteins that are required for cytoplasm-to-vacuole targeting. Journal of Biological Chemistry, 275, 25840-25849. PubMed link

Noda, T., Kim, J., Huang, W. P., Baba, M., Tokunaga, C., Ohsumi, Y., & Klionsky, D. J. (2000). Apg9p/Cvt7p is an integral membrane protein required for transport vesicle formation in the Cvt and autophagy pathways. Journal of Cell Biology, 148, 465-479. PubMed link

Abeliovich, H., Dunn, W. A., Kim, J., & Klionsky, D. J. (2000). Dissection of autophagosome biogenesis into distinct nucleation and expansion steps. Journal of Cell Biology, 151, 1025-1033. PubMed link

George, M. D., Baba, M., Scott, S. V., Mizushima, N., Garrison, B. S., Ohsumi, Y., & Klionsky, D. J. (2000). Apg5p functions in the sequestration step in the cytoplasm-to-vacuole targeting and macroautophagy pathways. Molecular Biology of the Cell, 11, 969-982. PubMed link

Klionsky, D. J., & Tomashek, J. J. (1999). An interactive exercise to learn eukaryotic cell structure & organelle function. American Biology Teacher, 61, 539-542.

Hutchins, M. U., Veenhuis, M., & Klionsky, D. J. (1999). Peroxisome degradation in Saccharomyces cerevisiae is dependent on machinery of macroautophagy and the Cvt pathway. Journal of Cell Science, 112, 4079-4087. PubMed link

Kim, J., Dalton, V. M., Eggerton, K. P., Scott, S. V., & Klionsky, D. J. (1999). Apg7p/Cvt2p is required for the cytoplasm-to-vacuole targeting, macroautophagy, and peroxisome degradation pathways. Molecular Biology of the Cell, 10, 1337-1351. [Correction: 10, U5-U6.] PubMed link

Teter, S. A., & Klionsky, D. J. (1999). How to get a folded protein across a membrane. Trends in Cell Biology, 9, 428-431. PubMed link

Scott, S. V., & Klionsky, D. J. (1998). Delivery of proteins and organelles to the vacuole from the cytoplasm. Current Opinion in Cell Biology, 10, 523-529. PubMed link

Fleckenstein, D., Rohde, M., Klionsky, D. J., & Rudiger, M. (1998). Yel013p (Vac8p), an armadillo repeat protein related to plakoglobin and importin alpha, is associated with the yeast vacuole membrane. Journal of Cell Science, 111, 3109-3118. PubMed link

Mizushima, N., Noda, T., Yoshimori, T., Tanaka, Y., Ishii, T., George, M. D., Klionsky, D. J., Ohsumi, M., & Ohsumi, Y. (1998). A protein conjugation system essential for autophagy. Nature, 395, 395-398. PubMed link

Articles (1989-1997)

Tomashek, J. J., Garrison, B. S., & Klionsky, D. J. (1997). Reconstitution in vitro of the V-1 complex from the yeast vacuolar proton-translocating ATPase - Assembly recapitulates mechanism. Journal of Biological Chemistry, 272, 16618-16623. PubMed link

Tomashek, J. J., Graham, L. A., Hutchins, M. U., Stevens, T. H., & Klionsky, D. J. (1997). V-1-situated stalk subunits of the yeast vacuolar proton-translocating ATPase. Journal of Biological Chemistry, 272, 26787-26793. PubMed link

Kim, J., Scott, S. V., Oda, M. N., & Klionsky, D. J. (1997). Transport of a large oligomeric protein by the cytoplasm-to-vacuole protein targeting pathway. Journal of Cell Biology, 137, 609-618. PubMed link

Scott, S. V., Baba, M., Ohsumi, Y., & Klionsky, D. J. (1997). Aminopeptidase I is targeted to the vacuole by a nonclassical vesicular mechanism. Journal of Cell Biology, 138, 37-44. PubMed link

Baba, M., Osumi, M., Scott, S. V., Klionsky, D. J., & Ohsumi, Y. (1997). Two distinct pathways for targeting proteins from the cytoplasm to the vacuole/lysosome. Journal of Cell Biology, 139, 1687-1695. PubMed link

Matoba, S., Morano, K. A., Klionsky, D. J., Kim, K., & Ogrydziak, D. M. (1997). Dipeptidyl aminopeptidase processing and biosynthesis of alkaline extracellular protease from Yarrowia lipolytica. Microbiology (UK), 143, 3263-3272. PubMed link

Scott, S. V., & Klionsky, D. J. (1997). Nonclassical protein sorting. Trends in Cell Biology, 7, 225-229. PubMed link

Kim, J., Alizadeh, P., Harding, T., Hefner-Gravink, A., & Klionsky, D. J. (1996). Disruption of the yeast ATH1 gene confers better survival after dehydration, freezing, and ethanol shock: Potential commercial applications. Applied and Environmental Microbiology, 62, 1563-1569. PubMed link

Nelson, N., & Klionsky, D. J. (1996). Vacuolar H+-ATPase: From mammals to yeast and back. Experientia, 52, 1101-1110. PubMed link

Alizadeh, P., & Klionsky, D. J. (1996). Purification and biochemical characterization of the ATH1 gene product, vacuolar acid trehalase, from Saccharomyces cerevisiae. FEBS Letters, 391, 273-278. PubMed link

Tomashek, J. J., Sonnenburg, J. L., Artimovich, J. M., & Klionsky, D. J. (1996). Resolution of subunit interactions and cytoplasmic subcomplexes of the yeast vacuolar proton-translocating ATPase. Journal of Biological Chemistry, 271, 10397-10404. PubMed link

Harding, T. M., Hefner-Gravink, A., Thumm, M., & Klionsky, D. J. (1996). Genetic and phenotypic overlap between autophagy and the cytoplasm-to-vacuole protein targeting pathway. Journal of Biological Chemistry, 271, 17621-17624. PubMed link

Oda, M. N., Scott, S. V., Hefner-Gravink, A., Caffarelli, A. D., & Klionsky, D. J. (1996). Identification of a cytoplasm-to-vacuole targeting determinant in aminopeptidase I. Journal of Cell Biology, 132, 999-1010. PubMed link

Wang, Y. X., Zhao, H. R., Harding, T. M., deMesquita, D. S. G., Woldringh, C. L., Klionsky, D. J., Munn, A. L., & Weisman, L. S. (1996). Multiple classes of yeast mutants are defective in vacuole partitioning yet target vacuole proteins correctly. Molecular Biology of the Cell, 7, 1375-1389. PubMed link

Scott, S. V., Hefner-Gravink, A., Morano, K. A., Noda, T., Ohsumi, Y., & Klionsky, D. J. (1996). Cytoplasm-to-vacuole targeting and autophagy employ the same machinery to deliver proteins to the yeast vacuole. Proceedings of the National Academy of Sciences of the USA, 93, 12304-12308. PubMed link

Harding, T. M., Morano, K. A., Scott, S. V., & Klionsky, D. J. (1995). Isolation and characterization of yeast mutants in the cytoplasm-to-vacuole protein targeting pathway. Journal of Cell Biology, 131, 591-602. PubMed link

Scott, S. V., & Klionsky, D. J. (1995). In vitro reconstitution of cytoplasm-to-vacuole protein targeting in yeast. Journal of Cell Biology, 131, 1727-1735. PubMed link

Destruelle, M., Holzer, H., & Klionsky, D. J. (1995). Isolation and characterization of a novel yeast gene, Ath1, that is required for vacuolar acid trehalase activity. Yeast, 11, 1015-1025. PubMed link

Morano, K. A., & Klionsky, D. J. (1994). Differential effects of compartment deacidification on the targeting of membrane and soluble proteins to the vacuole in yeast. Journal of Cell Science, 107, 2813-2824. PubMed link

Destruelle, M., Holzer, H., & Klionsky, D. J. (1994). Identification and characterization of a novel yeast gene - The Ygp1 gene product is a highly glycosylated secreted protein that is synthesized in response to nutrient limitation. Molecular and Cellular Biology, 14, 2740-2754. PubMed link

Yaver, D. S., Nelson, H., Nelson, N., & Klionsky, D. J. (1993). Vacuolar ATPase mutants accumulate precursor proteins in a pre-vacuolar compartment. Journal of Biological Chemistry, 268, 10564-10572. PubMed link

Klionsky, D. J., Nelson, H., & Nelson, N. (1992). Compartment acidification is required for efficient sorting of proteins to the vacuole in Saccharomyces cerevisiae. Journal of Biological Chemistry, 267, 3416-3422. PubMed link

Klionsky, D. J., Cueva, R., & Yaver, D. S. (1992). Aminopeptidase I of Saccharomyces cerevisiae is localized to the vacuole independent of the secretory pathway. Journal of Cell Biology, 119, 287-299. PubMed link

Klionsky, D. J., Nelson, H., Nelson, N., & Yaver, D. S. (1992). Mutations in the yeast vacuolar ATPase result in the mislocalization of vacuolar proteins. Journal of Experimental Biology, 172, 83-92. PubMed link

Klionsky, D. J., & Emr, S. D. (1989). Membrane protein sorting - Biosynthesis, transport and processing of yeast vacuolar alkaline phosphatase. EMBO Journal, 8, 2241-2250. PubMed link

Articles (1982-1988)

Banta, L. M., Robinson, J. S., Klionsky, D. J., & Emr, S. D. (1988). Organelle assembly in yeast - Characterization of yeast mutants defective in vacuolar biogenesis and protein sorting. Journal of Cell Biology, 107, 1369-1383. PubMed link

Klionsky, D. J., Banta, L. M., & Emr, S. D. (1988). Intracellular sorting and processing of a yeast vacuolar hydrolase - Proteinase A propeptide contains vacuolar targeting information. Molecular and Cellular Biology, 8, 2105-2116. PubMed link

Robinson, J. S., Klionsky, D. J., Banta, L. M., & Emr, S. D. (1988). Protein sorting in Saccharomyces cerevisiae: Isolation of mutants defective in the delivery and processing of multiple vacuolar hydrolases. Molecular and Cellular Biology, 8, 4936-4948. PubMed link

Bedwell, D. M., Klionsky, D. J., & Emr, S. D. (1987). The yeast F1 ATPase beta-subunit precursor contains functionally redundant mitochondrial protein import information. Molecular and Cellular Biology, 7, 4038-4047. PubMed link

Klionsky, D. J., & Simoni, R. D. (1985). Assembly of a functional F1 of the proton-translocating ATPase of Escherichia coli. Journal of Biological Chemistry, 260, 1200-1206. PubMed link

Aris, J. P., Klionsky, D. J., & Simoni, R. D. (1985). The F0 subunits of the Escherichia coli F1F0-ATP synthase are sufficient to form a functional proton pore. Journal of Biological Chemistry, 260, 1207-1215. PubMed link

Klionsky, D. J., Brusilow, W. S. A., & Simoni, R. D. (1984). In vivo evidence for the role of the epsilon subunit as an inhibitor of the proton-translocating ATPase of Escherichia coli. Journal of Bacteriology, 160, 1055-1060. PubMed link

Humbert, R., Brusilow, W. S. A., Gunsalus, R. P., Klionsky, D. J., & Simoni, R. D. (1983). Escherichia coli mutants defective in the UNCH gene. Journal of Bacteriology, 153, 416-422. PubMed link

Klionsky, D. J., Brusilow, W. S. A., & Simoni, R. D. (1983). Assembly of a functional F0 of the proton-translocating ATPase of Escherichia coli. Journal of Biological Chemistry, 258, 136-143. PubMed link

Brusilow, W. S. A., Klionsky, D. J., & Simoni, R. D. (1982). Differential polypeptide synthesis of the proton-translocating ATPase of Escherichia coli. Journal of Bacteriology, 151, 1363-1371. PubMed link

Review Articles

Klionsky D.J.(2013). Ancient autophagy. Autophagy 9(4):445-446.

Klionsky D.J.(2013). Finding autophagy :It's a question of how you look at it. Autophagy 9(3):267.

Klionsky D.J.(2012). The autophagy community. Autophagy 8(7):1003.

Shimada Y., Klionsky D.J. (2012). Autophagy contributes to lysosomal storage disorders. Autophagy 8(5):715-716. PubMed link

Klionsky D.J. (2012). A human autophagy interaction network. Autophagy 8(4):439-441. PubMed link

Klionsky D.J., et al.(2012). Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy 8(4):445-544.

Umekawa M., Klionsky D.J.(2012). The cytoplasm-to-vacuole targeting pathway: A historical perspective. International Journal of Cell Biology 142634.

Nair U., Klionsky D.J. (2011). Activation of autophagy is required for muscle homeostasis during physical exercise. Autophagy 7(12):1405-1406. PubMed link

Klionsky D.J., Baehrecke E.H., Brumell J.H., Chu C.T., Codogno P., Cuervo A.M., Debnath J., Deretic V., Elazar Z., Eskelinen E.-L., Finkbeiner S., Fueyo-Margareto J., Gewirtz D., Jaattela M., Kroemer G., Levine B., Melia T.J., Mizushima N., Rubinsztein D.C., Simonsen A., Thorburn A., Thumm M., Tooze S.A. (2011). A comprehensive glossary of autophagy-related molecules and processes (2 nd edition). Autophagy 7(11):1273-1294. PubMed link

Klionsky D.J., Meijer A.J. (2011). From the urea cycle to autophagy: Alfred J. Meijer. Autophagy 7(8):805-813. PubMed link

Klionsky D.J., Nemchenko A. (2011). There is more to autophagy than induction: Regulating the roller coaster. Autophagy 7(8):801-802. PubMed link

Kanki T., Klionsky D.J., Okamoto K. (2011). Mitochondria autophagy in yeast. Antioxidants and Redox Signaling 14(10):1989-2001. PubMed link

Wang K., Klionsky D.J. (2011). Mitochondria removal by autophagy. Autophagy 7(3):297-300. PubMed link

Klionsky D.J., Seglen P.O. (2010). The Norse god of autophagy. Autophagy 6(8):1017-1031. PubMed link

Inoue Y., Klionsky D.J. (2010). Regulation of macroautophagy in Saccharomyces cerevisiae. Seminars in Cell and Developmental Biology 21(7):664-670. PubMed link

Yang Z., Klionsky D.J. (2010). Eaten alive: A history of macroautophagy. Nature Cell Biology 12(9):814-822. PubMed link

Munakata N., Klionsky D.J. (2010). "Autophagy suite": Atg9 cycling in the cytoplasm to vacuole targeting pathway. Autophagy 6(6):679-685. PubMed link

Klionsky D.J., Codogno P., Cuervo A.M., Deretic V., Elazar Z., Fueyo-Margareto J., Gewirtz D.A., Kroemer G., Levine B., Mizushima N., Rubinsztein D.C., Thumm M., Tooze S.A.(2010). A comprehensive glossary of autophagy-related molecules and processes. Autophagy 6(4):438-448.

Dice J.F., Klionsky D.J. (2010). Artophagy: The art of autophagy - Macroautophagy. Autophagy 6(3):320-321. PubMed link

Lynch-Day M.A., Klionsky D.J. (2010). The Cvt pathway as a model for selective autophagy. FEBS Letters 584(7):1359-1366. PubMed link

Yang Z., Klionsky D.J. (2010). Mammalian autophagy: Core molecular machinery and signaling regulation. Current Opinion in Cell Biology 22(2):124-131. PubMed link

Goodsell D.S., Klionsky D.J. (2010). Artophagy: The art of autophagy - The Cvt pathway. Autophagy 6(1):3-6. PubMed link

Yang Z., Klionsky D.J.(2009). An overview of the molecular mechanism of autophagy. Current Topics in Microbiology and Immunology 335(1):1-32. PubMed link

He C., Klionsky D.J. (2009). Regulation mechanisms and signaling pathways of autophagy. Annual Review of Genetics 43:67-93. PubMed link

Monastyrska I., Rieter E., Klionsky D.J., Reggiori F. (2009). Multiple roles of the cytoskeleton in autophagy. Biological Reviews 84(3):431-448. PubMed link

Rubinsztein D.C., Cuervo A.M., Ravikumar B., Sarkar S., Korolchuk V., Kaushik S., Klionsky D.J. (2009). In search of an "autophagomometer". Autophagy 5(5):585-589. PubMed link

Klionsky D.J., et al. (2009). Guidelines for the use and interpretation of assays for monitoring cell death in higher eukaryotes. Cell Death and Differentiation 16(8):1093-1107. PubMed link

Klionsky D.J., Elazar Z., Seglen P.O., Rubinsztein D.C. (2008). Does bafilomycin A1 block the fusion of autophagosomes with lysosomes?. Autophagy 4(7):849-850. PubMed link

Yen W.-L., Klionsky D.J. (2008). How to live long and prosper: Autophagy, mitochondria, and aging. Physiology 23(5):248-262. PubMed link

Geng J., Klionsky D.J. (2008). The Atg8 and Atg12 ubiquitin-like conjugation systems in macroautophagy. 'Protein Modifications: Beyond the Usual Suspects' Review Series. EMBO Reports 9(9):859-864. PubMed link

Klionsky D.J. (2008). Autophagy revisited: A conversation with Christian de Duve. Autophagy 4(6):740-743. PubMed link

Mizushima N., Levine B., Cuervo A.M., Klionsky D.J. (2008). Autophagy fights disease through cellular self-digestion. Nature 451(7182):1069-1075. PubMed link

Klionsky D.J., et al. (2008). Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes. Autophagy 4(2):151-175. PubMed link

Mizushima N., Klionsky D.J. (2007). Protein turnover via autophagy: Implications for metabolism. Annual Review of Nutrition 27:19-40. PubMed link

Klionsky D.J. (2007). Autophagy: From phenomenology to molecular understanding in less than a decade. Nature Reviews Molecular Cell Biology 8(11):931-937. PubMed link

Xie Z., Klionsky D.J. (2007). Autophagosome formation: Core machinery and adaptations. Nature Cell Biology 9(10):1102-1109. PubMed link

Mijaljica D., Prescott M., Klionsky D.J., Devenish R.J. (2007). Autophagy and vacuole homeostasis: A case for self-degradation? Autophagy 3(5):417-421. PubMed link

Huang J., Klionsky D.J. (2007). Autophagy and human disease. Cell Cycle 6(15):1837-1849. PubMed link

Yorimitsu T., Klionsky D.J. (2007). Eating the endoplasmic reticulum: quality control by autophagy. Trends in Cell Biology 17(6):279-285. PubMed link

Klionsky D.J., Cuervo A.M., Seglen P.O. (2007). Methods for monitoring autophagy from yeast to human. Autophagy 3(3):181-206. PubMed link

Rubinsztein D.C., Gestwicki J.E., Murphy L.O., Klionsky D.J. (2007). Potential therapeutic applications of autophagy. Nature Reviews Drug Discovery 6(4):304-312. PubMed link

Klionsky, D. J., & Kumar, A. (2006). A systems biology approach to learning autophagy. Autophagy, 2, 12-23.

Yorimitsu, T., & Klionsky, D. J. (2005). Autophagy: Molecular machinery for self-eating. Cell Death and Differentiation, 12 (Suppl. 2), 1542-1552.

Nair, U., & Klionsky, D. J. (2005). Molecular mechanisms and regulation of specific and nonspecific autophagy pathways in yeast. Journal of Biological Chemistry, 280, 41785-41788.

Klionsky, D. J. (2005). The molecular machinery of autophagy: Unanswered questions. Journal of Cell Science, 118, 7-18.

Levine, B., & Klionsky, D. J. (2004). Development by self-digestion: Molecular mechanisms and biological functions of autophagy. Developmental Cell, 6, 463-477.

Reggiori, F., Wang, C. W., Nair, U., Shintani, T., Abeliovich, H., & Klionsky, D. J. (2004). Early stages of the secretory pathway, but not endosomes, are required for Cvt vesicle and autophagosome assembly in Saccharomyces cerevisiae. Molecular Biology of the Cell, 15, 2189-2204.

Shintani, T., & Klionsky, D. J. (2004). Autophagy in health and disease: A double-edged sword. Science, 306, 990-995.

Huang, W. P., & Klionsky, D. J. (2002). Autophagy in yeast: A review of the molecular machinery. Cell Structure and Function, 27, 409-420.

Khalfan, W. A., & Klionsky, D. J. (2002). Molecular machinery required for autophagy and the cytoplasm to vacuole targeting (Cvt) pathway in S. cerevisiae. Current Opinion in Cell Biology, 14, 468-475.

Reggiori, F., & Klionsky, D. J. (2002). Autophagy in the eukaryotic cell. Eukaryotic cell, 1, 11-21.

Abeliovich, A., & Klionsky, D. J. (2001). Autophagy in yeast: Mechanistic insights and physiological function. Microbiology and Molecular Biology Reviews, 65, 463-479.

Stromhaug, P. E., & Klionsky, D. J. (2001). Approaching the molecular mechanism of autophagy. Traffic, 2, 524-531.

Kim, J., & Klionsky, D. J. (2000). Autophagy, cytoplasm-to-vacuole targeting pathway, and pexophagy in yeast and mammalian cells. Annual Review of Biochemistry, 69, 303-342.

Kim, J., Scott, S. V., & Klionsky, D. J. (2000). Alternative protein sorting pathways. International Review of Cytology - A Survey of Cell Biology, 198, 153-201.

Klionsky, D. J., & Emr, S. D. (2000). Cell biology - Autophagy as a regulated pathway of cellular degradation. Science, 290, 1717-1721.

Teter, S. A., & Klionsky, D. J. (2000). Transport of proteins to the yeast vacuole: Autophagy, cytoplasm-to-vacuole targeting, and role of the vacuole in degradation. Seminars in Cell & Developmental Biology, 11, 173-179.

Klionsky, D. J. (1998). Nonclassical protein sorting to the yeast vacuole. Journal of Biological Chemistry, 273, 10807-10810.

Klionsky, D. J. (1997). Protein transport from the cytoplasm into the vacuole. Journal of Membrane Biology, 157, 105-115.

Klionsky, D. J., Herman, P. K., & Emr, S. D. (1990). The fungal vacuole - Composition, function, and biogenesis. Microbiological Reviews, 54, 266-292.

Editorial Material

Klionsky D.J. (2012). Look people, "Atg" is an abbreviation for "autophagy- related." That's it. Autophagy 8(9):1281-1282. PubMed link

Klionsky D.J., Bruford E.A., Cherry J.M., Hodgkin J., Laulederkind S.J.F., Singer A.G. (2012). In the beginning there was babble.... Autophagy 8(8):1165-1167.

Klionsky D.J. (2012). Protocols, toolboxes and resource papers. Autophagy 8(3):291. PubMed link

Klionsky D.J. (2012). Do you want to read about a biochemic and genetical analysis of the physiologic role of the autophagical process? No.. Autophagy 8(2):153-154. PubMed link

Klionsky D.J. (2012). Do you want to read about a biochemic and genetical analysis of the physiologic role of the autophagical process? No. Autophagy 8(2).

Klionsky D.J. (2011). For the last time, it is GFP-Atg8, not Atg8-GFP (and the same goes for LC3). Autophagy 7(10):1093-1094. PubMed link

Meijer A.J., Klionsky D.J. (2011). Vps34 is a phosphatidylinositol 3-kinase, not a phosphoinositide 3-kinase. Autophagy 7(6):563-564. PubMed link

Klionsky D.J. (2011). The autophagosome is overrated!. Autophagy 7(4):353-354. PubMed link

Thumm M., Klionsky D.J. (2011). New thoughts regarding Atg8 and ubiquitination. Autophagy 7(2):125-126. PubMed link

Klionsky D.J. (2011). Taking the plunge. Autophagy 7(1):1.

Klionsky D.J. (2010). What were you thinking? Do not manipulate those data. Autophagy 6(8):1007-1008.

Klionsky D.J. (2010). The molecular machinery of autophagy and its role in physiology and disease. Seminars in Cell and Developmental Biology 21(7):663. PubMed link

Klionsky D.J. (2010). An autophagy glossary. Autophagy 6(4):437.

Klionsky D.J. (2010). J. Fred "Paulo" dice: In memoriam. Autophagy 6(3):319.

Klionsky D.J., Lane J.D. (2010). Alternative macroautophagy. Autophagy 6(2):201. PubMed link

Klionsky D.J. (2010). Artophagy. Autophagy 6(1):1-2.

Klionsky D.J. (2009). Looking ahead: Online protocols. Autophagy 5(6):757.

Klionsky D.J. (2009). Location, location, location? No. catalog number. Autophagy 5(4):441.

Klionsky D.J. (2009). Autophagy in mammalian systems, Part B. Preface.. Methods in enzymology 452:xxi-xxii. PubMed link

Klionsky D.J. (2009). A work in progress. Autophagy 5(3):289. PubMed link

Klionsky D.J. (2009). Crohn disease and autophagy. Autophagy 5(2):139. PubMed link

Klionsky D.J. (2009). Preface. Methods in Enzymology 451(C):xxi-xxii.

Klionsky D.J. (2008). Achieve fame and (save your lab a) fortune!. Autophagy 4(8):977.

Klionsky D.J. (2008). A reagent forum. Autophagy 4(6):739.

Klionsky D.J. (2008). How we do business (or, why does it take other journals so long to review your paper?). Autophagy 4(5):551-554. PubMed link

Klionsky D.J. (2008). Getting into the flow. Autophagy 4(2):139-140. PubMed link

Klionsky D.J. (2007). Forward to the past. Autophagy 3(6):541.

Klionsky D.J., Cuervo A.M., Dunn Jr. W.A., Levine B., Van Der Klei I., Seglen P.O. (2007). How shall i eat thee?. Autophagy 3(5):413-416. PubMed link

Klionsky D.J. (2007). The importance of diversity. Autophagy 3(2):83-84. PubMed link

Klionsky D.J. (2007). Looking back on two years of Autophagy. Autophagy 3(1):1-3.

Klionsky, D. J. (2006). Learning about autophagy. Autophagy, 2, 1.

Klionsky, D. J. (2006). What can we learn from trypanosomes? Autophagy, 2, 63-64.

Klionsky, D. J. (2006). How selective is autophagy? Autophagy, 2, 151-152.

Klionsky, D. J. (2006). Neurodegeneration - Good riddance to bad rubbish. Nature, 441, 819-820.

Klionsky, D. J., Meijer, A. J., Codogno, P., Neufeld, T. P., & Scott, R. C. (2005). Autophagy and p70S6 kinase. Autophagy, 1, 59-61.

Klionsky, D. J. (2005). The correct way to monitor autophagy in higher eukaryotes. Autophagy, 1, 65.

Klionsky, D. J. (2005). How to keep up in an expanding field: Addenda. Autophagy, 1, 129-130.

Klionsky, D. J. (2005). Autophagy. Current Biology, 15, R282-R283.

Klionsky, D. J. (2004). Cell Biology - Regulated self-cannibalism. Nature, 431, 31-32.

Letters

Klionsky D.J. (2009). Putting the upper-division cart before the introductory horse. CBE Life Sciences Education 8(3):155-156.
Klionsky D.J. (2008). The quiz factor. CBE Life Sciences Education 7(3):265-266.
Klionsky, D. J., Cregg, J. M., Dunn, W. A., Emr, S. D., Sakai, Y., Sandoval, I. V., Sibirny, A., Subramani, S., Thumm, M., Veenhuis, M., Ohsumi, Y. (2003). A unified nomenclature for yeast autophagy-related genes. Developmental Cell, 5, 539-545.

Notes

Mijaljica D., Nazarko T.Y., Brumell J.H., Huang W.-P., Komatsu M., Prescott M., Simonsen A., Yamamoto A., Zhang H., Klionsky D.J., Devenish R.J.(2012). Receptor protein complexes are in control of autophagy. Autophagy 8(11):1701-1705.

Backues S.K., Klionsky D.J.(2012). Atg11: A Rab-dependent, coiled-coil membrane protein that acts as a tether for autophagy. Autophagy 8(8):1275-1278.

Klionsky D.J., Bergamini E.(2012). Searching for the fountain of autophagy-dependent youth: Ettore Bergamini. Autophagy 8(8):1169-1174.

Chen Y., Klionsky D.J. (2011). The regulation of autophagy - Unanswered questions. Journal of Cell Science 124(2):161-170.

Klionsky D.J., Dice J.F. (2009). Chaperone-mediated autophagy: The heretofore untold story of J. Fred "Paulo" Dice. Autophagy 5(8):1079-1084.

Klionsky D.J., Deter R.L. (2008). In the autophagy trenches: The early research career of Russell L. Deter. Autophagy 4(8):978-981.

Klionsky, D. J., & Emr, S. D. (1990). A new class of lysosomal vacuolar protein sorting signals. Journal of Biological Chemistry, 265, 5349-5352.

Klionsky, D. J., Skalnik, D. G., & Simoni, R. D. (1986). Differential translation of the genes encoding the proton-translocating ATPase of Escherichia coli. Journal of Biological Chemistry, 261, 8096-8099.