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Assistant Professor of Human Genetics Assistant Research Professor, Life Sciences Institute |
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| 6183A LSI 210 Washtenaw Ave. Ann Arbor, MI 48109 -2216 |
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Our lab studies how microRNAs and other emerging classes of small RNAs regulate fundamental biological processes including neuronal and muscle development, germline maintenance, and oncogenic cell proliferation. Using functional genomic, genetic, biochemical, and cell biology strategies, our lab investigates the molecular mechanisms of both the small RNAs and new candidate RNAi factors that we have identified by genome-wide screens.
2006 Biological Sciences Scholar, University of Michigan
2006 MGH Fund for Medical Discovery Fellowship
2003 - 2006 Helen Hay Whitney Postdoctoral Fellowship
2001 - 2006 Postdoctoral Fellowship, Harvard Medical School, MGH
1994 - 2000 Ph.D., Biochemistry and Molecular Biology, U.C., Davis
1990 - 1994 Research associate, U.C., San Francisco
1986 - 1990 B.S., Molecular Biophysics and Biochem., Yale University
Ting Han, Arun Prasad Manoharan, Tim T. Harkins, Pascal Bouffard, Colin Fitzpatrick, Diana S. Chu, Danielle Thierry-Mieg, Jean Thierry-Mieg, and John K. Kim. (2009) 26G endo-siRNAs regulate spermatogenic and zygotic gene expression in C. elegans. PNAS, In Press.
Simon, D.J., Madison, J.M., Connery, A.L., Thompson-Peer, K.L., Soskis, M., Ruvkun, G.B., Kaplan, J.M., Kim, J.K. The microRNA miR-1 regulates a MEF-2-dependent retrograde signal at neuromuscular junctions. Cell 133:903-915 (2008).
Wang, D., Kennedy, S., Conte, D., Kim, J.K., Gabel, H.W., Kamath, R.S., Mello, C.C., & Ruvkun, G. (2005). Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants. Nature, 436, 593-597.
Kim, J.K., Gabel, H.W., Kamath, R.S., Tewari, M., Pasquinelli, A., Rual, J.F., Kennedy, S., Dybbs, M., Bertin, N., Kaplan, J.M., Vidal,M., & Ruvkun, G. (2005). Functional genomic analysis of RNA interference in C.elegans. Science, 308, 1164-1167.
Kim, J., Krichevsky, A., Grad, Y., Hayes, G.D., Kosik, K.S., Church, G.M., & Ruvkun, G. (2004). Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proceedings of the National Academy of Sciences of the USA, 101, 360-365.
Grad, Y., Aach, J., Hayes, G.D., Reinhart, B.J., Church, G.M., Ruvkun, G., & Kim, J. (2003). Computational and experimental identification of C. elegans microRNAs. Molecular Cell, 11, 1253-1263.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Aanstoot, H.J., Kang, S.M., Kim, J., Lindsay, L.A., Roll, U., Knip, M., Atkinson, M., Mose-Larsen, P., Fey, S., Ludvigsson, J., Landin, M., Bruining, J., Maclaren, N., Akerblom, H.K., & Baekkeskov, S.(1996). Identification and characterization of glima 38, a glycosylated islet cell membrane antigen, which together with GAD(65) and IA2 marks the early phases of autoimmune response in type 1 diabetes. Journal of Clinical Investigation, 97, 2772-2783.
Kim, J., Namchuk, M., Bugawan, T., Fu, Q., Jaffe, M., Shi, Y.G., Aanstoot, H.J., Turck, C.W., Erlich, H., Lennon, V., & Baekkeskov, S.(1994). Higher autoantibody levels and recognition of a linear NH2-terminal epitope in the autoantigen GAD(65) distinguish stiff man syndrome from insulin-dependent diabetes mellitus. Journal of Experimental Medicine, 180, 595-606.
Kim, J., Richter, W., Aanstoot, H.J., Shi, Y.G., Fu, Q., Rajotte, R., Warnock, G., & Baekkeskov, S. (1993). Differential expression of GAD(65) and GAD(67) in human, rat, and mouse pancreatic islets. Diabetes, 42, 1799-1808.
Review Articles
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, 198,153-201.
Patents
Kim, J., Gabel, H., Kamath, R., Ruvkun, G. (2005). Compositions and Methods that Modulate RNA Interference. Patent application filed. Serial No. 11/106,238.
Baekkeskov, S., Richter, W., Shi, Y., Namchuk, M., Kim, J. (1997). Reagents and Methods for the Diagnosis and Treatment of Diabetes and Stiff Man Syndrome. United States Patent 5,691,448
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