Publications

  • Gene duplication of SNAPC1 generates transcription factors for snRNAs and sex-specific piRNAs. Benner LK*, Starostik MR*, Tay RJ*, Inoki A, Clark M, Feng S, Schatz MC, Jacobsen SE, Kim JK. https://www.biorxiv.org/content/10.64898/2026.08.31.747621v1 (2026).

  • FOXO/DAF-16 modulates the transcription factor ROR/NHR-23 and inhibits the let-7 microRNA to maintain multipotency during dauer. Galagali H, Wirick MJ, Alessi AF, Starostik MR, Balamurugan P, Giudicelli Sims I, Pene L, Patel R, Feng S, Frand AR, Jacobsen SE, Karp X, and Kim JK. https://www.biorxiv.org/content/10.64898/2026.07.18.739353v1 (2026).

  • Regulation of MORC-1 is key to the CSR-1-mediated germline gene licensing mechanism in C. elegans. Kirshner JA*, Picard CL*, Weiser NE, Mehta N, Feng S, Murphy VN, Vakhnovetsky A, Alessi AF, Xiao C, Inoki K, El Mouridi S, Frøkjær-Jensen C, Jacobsen SE°, and Kim JK°. Science Advances https://www.science.org/doi/10.1126/sciadv.ado4170 (2025). PDF

  • A maternally programmed mechanism enable male offspring to make piRNAs from Y-linked precursor RNAs in Drosophila. Venkei ZG, Gainetdinov I, Bagci A, Starostik MR, Choi CP, Chen P, Balsara C, Whitfield TW, Bell GW, Feng S, Jacobsen SE, Aravin AA, Kim JK, Zamore PD, and Yamashita YM. Nature CellBiology https://doi.org/10.1038/s41556-023-01227-4 (2023). PDF

  • Feedback between a retinoid-related nuclear receptor and the let-7 microRNAs controls the pace and number of molting cycles in C. elegans.‍ ‍Patel R*, Galagali H*, Kim JK°, and Frand AR°. eLife 15(11):e80010 (2022). PDF

  • daf-16/FOXO blocks adult cell fate in Caenorhabditis elegans dater larvae via lin-41/TRIM71.‍ ‍Wirick MJ, Cale AR, Smith IT, Alessi AF, Starostik MR, Cuko L, Lalk K, Schmidt MN, Olson BS, Salomon PM, Santos A, Schmitter-Sánchez, A, Galagali H, Ranke KJ, Wolbert PA, Knoblock ML, Kim JK, and Karp X. PLOS Genetics 17(11):e1009881 (2021). PDF

  • Compartmentalization and metabolic regulation of glycolysis.‍ ‍Fuller GG and Kim JK. Journal of Cell Science 134(20):jcs258469 (2021). PDF

  • SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans. Choi CP*, Tay RJ*, Starostik MR, Feng S, Moresco JJ, Montgomery BE, Xu E, Hammonds MA, Schatz MC, Montgomery TA, Yates JR III, Jacobsen SE, and Kim JK. eLife 10:e60681 (2021). PDF

  • The multifaceted roles of microRNAs in differentiation. Galagali H and Kim JK. Current Opinions in Cell Biology 67:118-140 (2020). PDF

  • RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia. Fuller GG, Han T, Freeberg MA, Moresco JJ, Niaki AG, Roach NP, Yates JR III, Myong S, and Kim JK. eLife 9:e48480 (2020). PDF

  • A kinesin Klp10A mediates cell cycle-dependent shuttling of Piwi between nucleus and nuage.‍ ‍Venkei ZG, Choi CP, Feng S, Chen C, Jacobsen SE, Kim JK, and Yamashita YM. PLoS Genetics 16(3):e1008648 (2020). PDF

  • The full-length transcriptome of C. elegans using direct RNA sequencing. Roach NP, Sadowski N, Alessi AF, Timp W°, Taylor J°, and Kim JK°.  Genome Research 30(2):299-312 (2020). PDF

  • Multigenerational regulation of the C. elegans chromatin landscape by germline small RNAs.‍ ‍Weiser NE and Kim JK. Annual Review of Genetics 53:289-311 (2019). PDF

  • The gene-silencing protein MORC-1 topologically entraps DNA and forms multimeric assemblies to cause DNA compaction. Kim H, Yen L, Mullane P, Wongpalee SP, Kirshner JA, Lu H, Mehta N, Xue Y, Johnston JB, Burlingame AL, Kim JK, Loparo JJ, and Jacobsen SE. Molecular Cell 75:700-710 (2019). PDF

  • miRISC composition determines target fates in time and space. Galagali H and Kim JK.  Developmental Cell 47:142-143 (2018). PDF

  • FUS regulates activity of microRNA-mediated gene silencing. 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, and Wang J. Molecular Cell 69:787-801 (2018). PDF

  •  Glycolytic enzymes coalesce in G bodies under hypoxic stress.‍ ‍Jin M*, Fuller G*, Han T*, Yao Y, Alessi AF, Freeberg MA, Roach N, Moresco JJ, Karnovsky A, Baba M, Yates JR III, Gitler AD, Inoki K, Klionsky DJ, and Kim JK. Cell Reports 20(4):895-908 (2017). PDF

  • LARP1 functions as a molecular switch for mTORC1-mediated translation of an essential class of mRNAs.‍ ‍Hong S, Freeberg MA, Kamath A, Han T, Yao Y, Fukuda T, Suzuki T, Kim JK, and Inoki K. eLife 6:e25237 (2017). PDF

  • MORC-1 integrates nuclear RNAi and transgenerational chromatin architecture to promote germline immortality. 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 JK.  Developmental Cell 41:408-423 (2017). PDF

  • Mapping the transcriptome-wide landscape of RBP binding sites using gPAR-CLIP-seq: bioinformatic analysis. Freeberg MA and Kim JK. Methods in Molecular Biology 1361:91-104 (2016). PDF

  • Mapping the transcriptome-wide landscape of RBP binding sites using gPAR-CLIP-seq: experimental procedures. Han T and Kim JK.  Methods in Molecular Biology 1361:77-90 (2016). PDF

  • Context-dependent modulation of Pol II CTD phosphatase SSUP-72 regulates alternative polyadenylation in neuronal development. Chen F, Zhou Y, Qi YB, Khivansara V, Li H, Chun SY, Kim JK, Fu XD, and Jin Y. Genes and Development 29:2377-2390 (2015). PDF

  • Casein kinase II promotes target silencing by miRISC through direct phosphorylation of the DEAD-box helicase CGH-1. Alessi, AF*, Khivansara V*, Han T*, Freeberg MA, Moresco JJ, Tu PG, Montoye E, Yates JR III, Karp X, and Kim JK.  Proc. Nat. Acad Sci. USA 112:E7213-7222 (2015). PDF

  • Transcriptional regulation by Pho23 modulates the frequency of autophagosome formation. Jin M, He D, Backues SK, Freeberg MA, Liu X, Kim JK, and Klionsky DJ. Current Biology 24:1314-22 (2014). PDF

  • Driving glioblastoma growth by alternative polyadenylation. Han T and Kim JK.  Cell Research, doi: 10.1038/cr.2014.88 (2014). PDF

  • Endogenous RNAi pathways in C. elegans. Billi AC, Fischer SE, and Kim JK.  WormBook, doi: 10.1895/wormbook.1.22.2 (2014). PDF

  • A conserved upstream motif orchestrates autonomous, germline-enriched expression of Caenorhabditis elegans piRNAs. Billi AC*, Freeberg MA*, Day AM, Chun SY, Khivansara V, and Kim JK.  PLoS Genetics 9(3):e1003392 (2013). PDF

  • Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Freeberg MA*, Han T*, Moresco JJ, Kong A, Yang Y-C, Lu ZJ, Yates JR III, and Kim JK. Genome Biology 14(2):R13 (2013). PDF

  • Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence. Tabach Y, Billi AC*, Hayes GD*, Newman MA, Zuk O, Gabel H, Kamath R, Yacoby K, Chapman B, Garcia SM, Borowsky M, Kim JK, and Ruvkun G. Nature 493: 694-698 (2013). PDF

  • MORC family ATPases required for heterochromatin condensation and gene silencing. Moissiard G, Cokus S, Cary J, Feng S, Billi AC, Stroud H, Husmann, D, Zhan Y, Lajoie BR, McCrod RP, Hale CJ, Feng W, Michaels SD, Frand AR, Pellegrini M, Dekker J, Kim JK, and Jacobsen S. Science 336:1448-1451 (2012). PDF

  • piRNAs and siRNAs collaborate in Caenorhabditis elegans genome defense. Billi AC, Freeberg MA, and Kim JK.  Genome Biology 13(7): 164 (2012). PDF

  • The Caenorhabditis elegans HEN1 ortholog, HENN-1, methylates and stabilizes select subclasses of germline small RNAs. Billi AC, Alessi AF, Khivansara V, Han T, Freeberg M, Mitani S, and Kim JK.  PLoS Genetics 8(4):e1002617 (2012). PDF

  • Integrative analysis of the Caenorhabditis elegans genome by the modENCODE Project. modENCODE Consortium (Gerstein MB et al.). Science 330:1775-1787 (2010). PDF

  • The landscape of C. elegans 3’ UTRs. Mangone M*, Manoharan AP*, Thierry-Mieg D*, Thierry-Mieg J*, Han T*, Mackowiak S, Mis E, Zegar C, Gutwein MR, Khivansara V, Salehi-Ashtiani K, Harkins T, Bouffard P, Suzuki Y, Sugano S, Kohara Y, Rajewsky N, Piano F, Gunsalus KC, and Kim JK.  Science 329:432-435 (2010). PDF

  • 26G endo-siRNAs regulate spermatogenic and zygotic gene expression in C. elegans. Han T, Manoharan AP, Harkins TT, Bouffard P, Fitzpatrick C, Chu, DS, Thierry-Mieg D, Thierry-Mieg J, and Kim JK. Proc. Natl. Acad. Sci. USA 106:18674-18679 (2009). PDF

  • High-resolution discovery and profiling of planarian small RNAs. Friedländer MR, Adamidi C, Han T, Lebedeva S, Isenbarger TA, Hirst M, Marra M, Nusbaum C, Lee WL, Sánchez Alvarado A, Kim JK, and Rajewsky N.  Proc. Natl. Acad. Sci. USA 106:11546-11551 (2009). PDF

  • Unlocking the secrets of the genome. modENCODE Consortium (Celniker SE et al.). Nature 459:927-930 (2009). PDF

  • The microRNA miR-1 regulates a MEF-2-dependent retrograde signal at neuromuscular junctions. Simon D*, Madison J*, Connery A, Thompson-Peer K, Soskis M, Ruvkun G, Kaplan J, and Kim JK. Cell 133:903-915 (2008). PDF

  • Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants. Wang D, Kennedy S, Conte D, Kim JK, Gabel HW, Kamath RS, Mello CC, and Ruvkun G.  Nature 436:593-597 (2005). PDF

  • Functional genomic analysis of RNA interference in C. elegans. Kim JK*, Gabel HW*, Kamath RS*, Tewari M, Pasquinelli A, Rual JF, Kennedy S, Dybbs M, Bertin N, Kaplan JM, Vidal M, and Ruvkun G.  Science 308:1164-1167 (2005). PDF

  • Identification of many microRNAs that copurify with polyribosomes in mammalian neurons.  Kim JK, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, and Ruvkun G. Proc. Natl. Acad. Sci. USA 101:360-365 (2004). PDF

  • Computational and experimental identification of C. elegans microRNAs. Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, and Kim JK. Molecular Cell 11:1253-1263 (2003). PDF

  • Past Publications

  • Convergence of multiple autophagy and cytoplasm to vacuole targeting components to a perivacuolar membrane compartment prior to de novo vesicle formation.Kim J, Huang WP, Stromhaug PE, and Klionsky DJ.  Journal of Biological Chemistry 277:763-773 (2002).

  • Apg2 is a novel protein required for the cytoplasm to vacuole targeting, autophagy, and pexophagy pathways. Wang CW, Kim J, Stromhaug P, Abeliovich H, and Klionsky DJ.  Journal of Biological Chemistry 276:30442-30451 (2001).

  • Cvt19 is a receptor for the cytoplasm to vacuole targeting pathway. Scott SV, Guan J, Hutchins MU, Kim J, and Klionsky DJ.  Molecular Cell 7:1131-1141 (2001).

  • Cvt9p/Gsa9p functions in sequestering selective cytosolic cargo destined for the vacuole. Kim J, Kamada Y, Stromhaug P, Guan J, Hefner-Gravink A, Baba M, Dunn W, Ohsumi Y, and Klionsky DJ. Journal of Cell Biology 153:381-396 (2001).

  • Membrane recruitment of Aut7p in the autophagy and Cvt pathways requires Aut1p, Aut2p and the Apg conjugation system. Kim J, Huang WP, and Klionsky DJ. Journal of Cell Biology 152:51-64 (2001).

  • Degradation of lipid vesicles in the yeast vacuole requires function of Cvt17, a putative lipase. Teter SA, Eggerton KP, Scott SV, Kim J, Fisher AM, and Klionsky DJ.  Journal of Biological Chemistry 276:2083-2087 (2001).

  • Dissection of autophagosome biogenesis into distinct nucleation and expansion steps. Abeliovich H, Dunn W, Kim J, and Klionsky DJ. Journal of Cell Biology 151:1025-1034 (2000).

  • The itinerary of a vesicle component, Aut7p/Cvt5p, terminates in the yeast vacuole via the autophagy/Cvt pathways. Huang WP, Scott SV, Kim J, and Klionsky DJ.  Journal of Biological Chemistry 275:5845-5851 (2000).

  • Apg9/Cvt7p is an integral membrane protein required for transport vesicle formation in the Cvt and autophagy pathways. Noda T*, Kim J*, Huang WP, Baba M, Tokunaga C, Ohsumi Y, and Klionsky DJ.  Journal of Cell Biology 148:465-480 (2000).

  • Autophagy, Cvt pathway, and pexophagy in yeast and mammalian cells. Kim J and Klionsky DJ.  Annual Review of Biochemistry 69: 303-342 (2000).

  • Alternative protein sorting pathways. Kim J, Scott SV, and Klionsky DJ.  Review of Cytology 198:153-201 (2000).

  • Apg7p/Cvt2p is required for the cytoplasm-to-vacuole targeting, macroautophagy, and peroxisomal degradation pathways. Kim J, Dalton VM, Eggerton KP, Scott SV, and Klionsky DJ. Molecular Biology of the Cell 10:1337-1351 (1999).

  • Transport of a large oligomeric protein by the cytoplasm to vacuole protein targeting pathway. Kim J, Scott SV, Oda MN, and Klionsky DJ.  Journal of Cell Biology 137:609-618 (1997).

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

  • 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. Aanstoot HJ, Kang SM, Kim J, Lindsay LA, Roll U, Knip M, Atkinson M, Mose-Larsen P, Fey S, Ludvigsson J, Landin M, Bruining J, Maclaren N, Akerblom HK, and Baekkeskov S.  Journal of Clinical Investigation 7:2772-2283 (1996).

  • Higher autoantibody levels and recognition of a linear N-terminal epitope in the autoantigen GAD65 distinguish stiff-man syndrome from insulin dependent diabetes mellitus. Kim J, Namchuk M, Bugawan D, Fu Q, Jaffe M, Shi Y, Aanstoot H, Turck CW, Erlich H, Lennon V, and Baekkeskov S.  Journal of Experimental Medicine 180:595-606 (1994).

  • Differential expression of GAD65 and GAD67 in human, rat, and mouse pancreatic islets. Kim J, Richter W, Aanstoot HJ, Shi Y, Fu Q, Rajotte R, Warnock G, and Baekkeskov, S. Diabetes 42:1799-1808 (1993).

  • Stiff-Man Syndrome and Type 1 Diabetes Mellitus: similarities and differences in autoimmune reactions. Aanstoot HJ, Michaels A, Christgau S, Shi Y,  Kim J, and Baekkeskov, S.  Motor Unit Hyperactivity States ed. Layzer, R.B.: 53-67, Raven Press (1993).

  • The glutamic acid decarboxylase and 38kD autoantigens in type 1 diabetes: aspects of structure and epitope recognition. Baekkeskov S, Aanstoot HJ, Fu Q, Jaffe M, Kim J, Quan J, Richter W, and Shi Y.  Autoimmunity 15:24 (1993).

    * co-author   ° co-corresponding