Kim Lab Home
Publications
Research articles
Billi, A.C.*, Freeberg, M.A.*, Day, A.D., Chun, S.Y., Khivansara, V., and Kim, J.K. A conserved upstream motif orchestrates autonomous, germline-enriched expression of Caenorhabditis elegans piRNAs. PLoS Genetics 9(3): e1003392 (2013).
Freeberg, M.A.*, Han, T.*, Moresco, J.J., Kong, A., Yang, Y-C., Lu, Z.J., Yates III, J.R., and Kim, J.K. Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biology 14(2):R13 (2013). PubMed Link
Tabach, Y., Billi, A.C.*, Hayes, G.D.*, Newman, M.A., Zuk, O., Gabel, H., Kamath, R., Yacoby, K., Chapman, B., Garcia, S.M., Borowsky, M., Kim, J.K., and Ruvkun, G. Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence. Nature 493: 694-698 (2013). PubMed Link
Moissiard, G., Cokus, S., Cary, J., Feng, S., Billi, A.C., Stroud, H., Husmann, D., Zhan, Y., Lajoie, B.R., McCrod, R.P., Hale, C.J., Feng, W., Michaels, S.D., Frand, A.R., Pellegrini, M., Dekker, J., Kim, J.K., and Jacobsen, S. MORC family ATPases required for heterochromatin condensation and gene silencing. Science 336: 1448-1451 (2012). PubMed Link
Billi, A.C., Alessi, A.F., Khivansara, V., Han, T., Freeberg, M., Mitani, S., and Kim, J.K. The Caenorhabditis elegans HEN1 ortholog, HENN-1, methylates and stabilizes select subclasses of germline small RNAs. PLoS Genetics 8(4): e1002617 (2012). PubMed Link
modENCODE Consortium (Gerstein, M.B. et al.,). Integrative analysis of the Caenorhabditis elegans genome by the modENCODE Project. Science 330: 1775-1787 (2010). PubMed Link
Mangone, M.*, Manoharan, A.P.*, Thierry-Mieg, D.*, Thierry-Mieg, J.*, Han, T.*, Mackowiak, S., Mis, E., Zegar, C., Gutwein, M.R., Khivansara, V., Salehi-Ashtiani, K., Harkins, T. Bouffard, P., Suzuki, Y., Sugano, S., Kohara, Y., Rajewsky, N., Piano, F., Gunsalus, K.C., and Kim, J.K. The landscape of C. elegans 3’ UTRs. Science 329: 432-435 (2010). PubMed Link
Han, T., Manoharan, A.P., Harkins, T.T., Bouffard, P., Fitzpatrick, C., Chu, D.S., Thierry-Mieg, D., Thierry-Mieg, J., and Kim, J.K. 26G endo-siRNAs regulate spermatogenic and zygotic gene expression in C. elegans. Proc. Natl. Acad. Sci. USA 106: 18674-18679 (2009). PubMed Link
Friedländer, M.R., Adamidi, C., Han, T., Lebedeva, S., Isenbarger, T.A., Hirst, M., Marra, M., Nusbaum, C., Lee, W.L., Sánchez Alvarado, A., Kim, J.K., and Rajewsky, N. High-resolution discovery and profiling of planarian small RNAs. Proc. Natl. Acad. Sci. USA 106: 11546-11551 (2009). PubMed Link
modENCODE Consortium (Celniker, S.E. et al.,). Unlocking the secrets of the genome. Nature 459: 927-930 (2009). PubMed Link
Simon, D.*, Madison, J.*, Connery, A., Thompson-Peer, K., Soskis, M., Ruvkun, G., Kaplan, J., and Kim, J.K. The microRNA miR-1 regulates a MEF-2-dependent retrograde signal at neuromuscular junctions. Cell 133: 903-915 (2008). PubMed Link
Wang, D., Kennedy, S., Conte, D., Kim, J.K., Gabel, H.W., Kamath, R.S., Mello, C.C., and Ruvkun, G. Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants. Nature 436: 593-597 (2005). PubMed Link
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., and Ruvkun, G. Functional genomic analysis of RNA interference in C.elegans. Science 308: 1164-1167 (2005). PubMed Link
Kim, J., Krichevsky, A., Grad, Y., Hayes, G.D., Kosik, K.S., Church, G.M., and Ruvkun, G. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc. Natl. Acad. Sci. USA 101: 360-365 (2004). PubMed Link
Grad, Y., Aach, J., Hayes, G.D., Reinhart, B.J., Church, G.M., Ruvkun, G., and Kim, J. Computational and experimental identification of C. elegans microRNAs. Molecular Cell 11: 1253-1263 (2003). PubMed Link
*equal contribution
Reviews and commentaries
Billi, A.C., Freeberg, M.A., Kim, J.K. piRNAs and siRNAs collaborate in Caenorhabditis elegans genome defense. Genome Biology 13(7): 164 (2012). PubMed Link
Irminger-Finger, I., Thomson, J.M., Kim, J.K. (editors). MicroRNAs, a superimposed regulatory network for development and disease. Int J Biochem Cell Biol 42: 1234-1235 (2010). PubMed Link
Early papers
Kim, J., Huang, W.P., Stromhaug, P.E., Klionsky, D.J. 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 (2002).
Wang, C.W., Kim, J., Stromhaug, P., Abeliovich, H., Klionsky, D.J. Apg2 is a novel protein required for the cytoplasm to vacuole targeting, autophagy, and pexophagy pathways. Journal of Biological Chemistry 276:30442-30451 (2001).
Scott, S.V., Guan, J., Hutchins, M.U., Kim, J., Klionsky, D.J. Cvt19 is a receptor for the cytoplasm to vacuole targeting pathway. Molecular Cell 7: 1131-1141 (2001).
Kim, J., Kamada, Y., Stromhaug, P., Guan, J., Hefner-Gravink, A., Baba, M., Dunn, W., Ohsumi, Y., Klionsky, D.J. Cvt9p/Gsa9p functions in sequestering selective cytosolic cargo destined for the vacuole. Journal of Cell Biology 153: 381-396 (2001).
Kim, J., Huang, W.P., Klionsky, D.J. Membrane recruitment of Aut7p in the autophagy and Cvt pathways requires Aut1p, Aut2p and the Apg conjugation system. Journal of Cell Biology 152: 51-64 (2001).
Teter, S.A., Eggerton, K.P., Scott, S.V., Kim, J., Fisher, A.M., Klionsky, D.J. Degradation of lipid vesicles in the yeast vacuole requires function of Cvt17, a putative lipase. Journal of Biological Chemistry 276: 2083-2087 (2001).
Abeliovich, H., Dunn, W., Kim, J., Klionsky, D.J. Dissection of autophagosome biogenesis into distinct nucleation and expansion steps. Journal of Cell Biology 151: 1025-1034 (2000).
Huang, W.-P., Scott, S.V., Kim, J., Klionsky, D.J. 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 (2000).
Noda, T.*, Kim, J.*, Huang, W.P., Baba, M., Tokunaga, C., Ohsumi, Y., Klionsky, D.J. Apg9/Cvt7p is an integral membrane protein required for transport vesicle formation in the Cvt and autophagy pathways. Journal of Cell Biology 148: 465-480 (2000). *equal contribution
Kim, J. and Klionsky, D.J. Autophagy, Cvt pathway, and pexophagy in yeast and mammalian cells. Annual Review of Biochemistry 69: 303-342 (2000).
Kim, J., Scott, S.V., and Klionsky, D.J. Alternative protein sorting pathways. Int. Review of Cytology 198: 153-201 (2000).
Kim, J., Dalton, V.M., Eggerton, K.P., Scott, S.V., Klionsky, D.J. Apg7p/Cvt2p is required for the Cytoplasm-to-vacuole targeting, macroautophagy, and peroxisomal degradation pathways. Molecular Biology of the Cell 10: 1337-1351 (1999).
Kim, J., Scott, S.V., Oda, M.N., Klionsky, D.J. Transport of a large oligomeric protein by the cytoplasm to vacuole protein targeting pathway. Journal of Cell Biology 137: 609-618 (1997).
Kim, J., Alizadeh, P., Harding, T., Hefner-Gravink, A., Klionsky, D.J. 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 (1996).
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. Identification and characterization of glima 38, a glycosylated islet cell membrane antigen, which together with GAD65 and IA2 mark the early phases of autoimmune response in type 1 diabetes. Journal of Clinical Investigation 7: 2772-2283 (1996).
Kim, J., Namchuk, M., Bugawan, D., Fu, Q., Jaffe, M., Shi, Y., Aanstoot, H., Turck, C.W., Erlich, H., Lennon, V., Baekkeskov, S. Higher autoantibody levels and recognition of a linear N-terminal epitope in the autoantigen GAD65 distinguish stiff-man syndrome from insulin dependent diabetes mellitus. Journal of Experimental Medicine 180: 595-606 (1994).
Kim, J., Richter, W., Aanstoot, H.J., Shi, Y., Fu, Q., Rajotte, R., Warnock, G., Baekkeskov, S. Differential expression of GAD65 and GAD67 in human, rat, and mouse pancreatic islets. Diabetes 42: 1799-1808 (1993).
Aanstoot, H.J., Michaels, A., Christgau, S., Shi, Y., Kim, J., Baekkeskov, S. Stiff-Man Syndrome and Type 1 Diabetes Mellitus: Similarities and Differences in Autoimmune Reactions. Motor Unit Hyperactivity States, ed. Layzer, R.B.: 53-67, Raven Press (1993).
Baekkeskov, S., Aanstoot, H.J., Fu, Q., Jaffe, M., Kim, J., Quan, J., Richter, W., Shi, Y. The glutamic acid decarboxylase and 38kD autoantigens in type 1 diabetes: Aspects of structure and epitope recognition. Autoimmunity 15: 24 (1993).
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