Publications

  1. Roach NP, Sadowski N, Alessi AF, Timp W, Taylor J, and Kim, JK. The full-length transcriptome of C. elegans using direct RNA sequencing. Genome Research 30(2):299-312 (2020).
  2. Weiser NE and Kim, JK. Multigenerational regulation of the C. elegans chromatin landscape by germline small RNAs. Annual Review of Genetics 53:289-311 (2019).
  3. Kim H, Yen L, Mullane P, Wongpalee SP, Kirshner JA, Lu H, Mehta N, Xue Y, Johnston JB, Burlingame AL, Kim JK, Loparo JJ, Jacobsen SE. The gene-silencing protein MORC-1 topologically entraps DNA and forms multimeric assemblies to cause DNA compaction. Molecular Cell 75:700-710 (2019).
  4. Galagali H and Kim JK. miRISC composition determines target fates in time and space. Developmental Cell 47:142-143 (2018).
  5. Zhang T*, Wu Y*, Mullane P, Ji YJ, Liu H, Lu H, Arora A, Hwang H, Alessi AF, Niaki AG, Periz G, Guo L, Wang H, Elkayam E, Joshua-Tor L, Myong S, Kim JK, Shorter J, Ong S, Leung AKL, Wang J. FUS regulates activity of microRNA-mediated gene silencing. Molecular Cell 69:787-801 (2018).
  6. Jin M*, Fuller G*, Han T*, Yao Y, Alessi AF, Freeberg MA, Roach N, Moresco JJ, Karnovsky A, Baba M, Yates III JR, Gitler AD, Inoki K, Klionsky DJ, and Kim JK. Glycolytic enzymes coalesce in G bodies under hypoxic stress. Cell Reports 20(4): 895-908 (2017).
  7. Hong S, Freeberg MA, Kamath A, Han T, Yao Y, Fukuda T, Suzuki T, Kim JK, and Inoki K. LARP1 functions as a molecular switch for mTORC1-mediated translation of an essential class of mRNAs. eLife 6:e25237 (2017).
  8. Weiser NE, Yang DX, Feng S, Kalinava N, Brown KC, Khankiar J, Freeberg MA, Snyder MJ, Csankovszki G, Chan RC, Gu SG, Montgomery TA, Jacobsen SE, and Kim, J.K. MORC-1 integrates nuclear RNAi and transgenerational chromatin architecture to promote germline immortality. Developmental Cell 41: 408-423 (2017).
  9. Freeberg M.A. and Kim, J.K. Mapping the Transcriptome-Wide Landscape of RBP Binding Sites Using gPAR-CLIP-seq: Bioinformatic Analysis. Methods in Molecular Biology 1361:91-104 (2016).
  10. Han T. and Kim, J.K. Mapping the Transcriptome-Wide Landscape of RBP Binding Sites Using gPAR-CLIP-seq: Experimental Procedures. Methods in Molecular Biology 1361:77-90 (2016).
  11. Chen F., Zhou Y., Qi Y.B., Khivansara V., Li H., Chun S.Y., Kim, J.K., Fu X.D., Jin Y. Context-dependent modulation of Pol II CTD phosphatase SSUP-72 regulates alternative polyadenylation in neuronal development. Genes and Development 29:2377-2390 (2015).
  12. Alessi, A.F.*, Khivansara, V.*, Han, T.*, Freeberg, M.A., Moresco, J.J., Tu, P.G., Montoye, E., Yates III, J.R., Karp, X., and Kim, J.K. Casein kinase II promotes target silencing by miRISC through direct phosphorylation of the DEAD-box helicase CGH-1. Proc. Nat. Acad Sci. (2015).
  13. Jin, M., He, D., Backues, S.K., Freeberg, M.A., Liu, X., Kim, J.K., and Klionsky, D.J. Transcriptional Regulation by Pho23 Modulates the Frequency of Autophagosome Formation. Current Biology 24:1314-22 (2014).
  14. Han, T. and Kim, J.K. Driving glioblastoma growth by alternative polyadenylation. Cell Research, doi: 10.1038/cr.2014.88 (2014).
  15. Billi, A.C., Fischer, S.E., Kim, J.KEndogenous RNAi pathways in C. elegans. WormBook, doi/10.1895/wormbook.1.22.2 (2014).
  16. Billi, A.C.*, Freeberg, M.A.*, Day, A.M., Chun, S.Y., Khivansara, V., and Kim, J.KA conserved upstream motif orchestrates autonomous, germline-enriched expression of Caenorhabditis elegans. PLoS Genetics  9(3): e1003392 (2013).
  17. 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).
  18. 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).
  19. 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).
  20. Billi, A.C., Freeberg, M.A., Kim, J.K. piRNAs and siRNAs collaborate in Caenorhabditis elegans genome defense. Genome Biology  13(7): 164 (2012).
  21. 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).
  22. modENCODE Consortium (Gerstein, M.B. et al.,). Integrative analysis of the Caenorhabditis elegans genome by the modENCODE Project.  Science  330: 1775-1787 (2010).
  23. 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).
  24. 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 elegans. Proc. Natl. Acad. Sci. USA  106: 18674-18679 (2009).
  25. 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. 106: 11546-11551 (2009).
  26. modENCODE Consortium (Celniker, S.E. et al.,). Unlocking the secrets of the genome. Nature 459: 927-930 (2009).
  27. 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).
  28. 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).
  29. 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 elegans. Science 308:1164-1167 (2005).
  30. Kim, J.K., 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).
  31. Grad, Y., Aach, J., Hayes, G.D., Reinhart, B.J., Church, G.M., Ruvkun, G., and Kim, J.K. Computational and experimental identification of elegans microRNAs. Molecular Cell 11: 1253-1263 (2003).

*equal contribution

 

Past Publications


  1. 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).
  2. 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).
  3. 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).
  4. 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).
  5. 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).
  6. 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).
  7. 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).
  8. 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).
  9. 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).
  10. Kim, J.and Klionsky, D.J.  Autophagy, Cvt pathway, and pexophagy in yeast and mammalian cells. Annual Review of Biochemistry  69: 303-342 (2000).
  11. Kim, J., Scott, S.V., and Klionsky, D.J.  Alternative protein sorting pathways.  Review of Cytology 198: 153-201 (2000).
  12. 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).
  13. 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).
  14. 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).
  15. 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).
  16. 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).
  17. 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).
  18. 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).
  19. 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).