* co-author   † co-corresponding

Venkei Z*, Gainetdinov I*, Bagci A, Starostik MR, Choi CP, Fingerhut JM, Chen P, Balsara C, Whitfield TW, Bell GW, Feng S, Jacobsen SE, Aravin AA, Kim JK, Zamore PD, and Yamashita YM. A maternally programmed intergenerational mechanism enables male offspring to make piRNAs from Y-linked precursor RNAs in Drosophila. Nature Cell Biology (2023).

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

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. daf-16/FOXO blocks adult cell fate in Caenorhabditis elegans dauer larvae via lin-41/TRIM71. PLOS Genetics 17(11):e1009881 (2021).

Fuller GG and Kim JK. Compartmentalization and metabolic regulation of glycolysis. J Cell Sci 134(20):jcs258469 (2021).

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.  SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. eleganseLife 10:e60681 (2021).

Galagali H and Kim JK.  The multifaceted roles of microRNAs in differentiation.  Curr Opin Cell Biol  67:118-140 (2020).

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

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

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).

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).

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.  The gene-silencing protein MORC-1 topologically entraps DNA and forms multimeric assemblies to cause DNA compaction.  Molecular Cell  75:700-710 (2019).

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

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.  FUS regulates activity of microRNA-mediated gene silencing.  Molecular Cell  69:787-801 (2018).

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.  Glycolytic enzymes coalesce in G bodies under hypoxic stress.   Cell Reports  20(4):895-908 (2017).

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).

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

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

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

Chen F, Zhou Y, Qi YB, Khivansara V, Li H, Chun SY, Kim JK, Fu XD, and 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).

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

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

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

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

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

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

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.  Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence.  Nature  493: 694-698 (2013).

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.  MORC family ATPases required for heterochromatin condensation and gene silencing.  Science  336:1448-1451 (2012).

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

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

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

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.  The landscape of C. elegans 3’ UTRs.  Science  329:432-435 (2010).

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

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.  High-resolution discovery and profiling of planarian small RNAs.        Proc. Natl. Acad. Sci. USA  106:11546-11551 (2009).

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

Simon D*, Madison J*, Connery A, Thompson-Peer K, Soskis M, Ruvkun G, Kaplan J, and Kim JK.  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 JK, Gabel HW, Kamath RS, Mello CC, and Ruvkun G.  Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants.   Nature  436:593-597 (2005).

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.  Functional genomic analysis of RNA interference in C. elegans.  Science  308:1164-1167 (2005).

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

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

Past Publications

Kim J, Huang WP, Stromhaug PE, and Klionsky DJ.  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 CW, Kim J, Stromhaug P, Abeliovich H, and Klionsky DJ.  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 SV, Guan J, Hutchins MU, Kim J, and Klionsky DJ.  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, and Klionsky DJ.  Cvt9p/Gsa9p functions in sequestering selective cytosolic cargo destined for the vacuole.  Journal of Cell Biology  153:381-396 (2001).

Kim J, Huang WP, and Klionsky DJ.  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 SA, Eggerton KP, Scott SV, Kim J, Fisher AM, and Klionsky DJ.  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, and Klionsky DJ.  Dissection of autophagosome biogenesis into distinct nucleation and expansion steps.  Journal of Cell Biology  151:1025-1034 (2000).

Huang WP, Scott SV, Kim J, and Klionsky DJ.  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 WP, Baba M, Tokunaga C, Ohsumi Y, and Klionsky DJ.  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).

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

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

Kim J, Dalton VM, Eggerton KP, Scott SV, and Klionsky DJ.  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 SV, Oda MN, and Klionsky DJ.  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, and Klionsky DJ.  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 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.  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 CW, Erlich H, Lennon V, and 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 HJ, Shi Y, Fu Q, Rajotte R, Warnock G, and Baekkeskov, S.  Differential expression of GAD65 and GAD67 in human, rat, and mouse pancreatic islets.  Diabetes  42:1799-1808 (1993).

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