Publications

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Billi A.C.*, Freeberg M.A.*, Day A.M., Chun S.Y., Khivansara V., and Kim, J.K. A conserved upstream motif orchestrates autonomous, germline-enriched expression of Caenorhabditis elegans piRNAs. PLoS Genet 9(3) (2013).File:2013 PLoS Genet Billi.pdf


Freeberg M.A.*, Han, T.*, Moresco, J.J., Kong, A., Yang, Y., Lu, Z.J., Yaters III, J.R., and Kim, J.K. Pervasive and dynamics protein binding sites of the mRNA transcriptome in Saccharomycese cerevisiae. Genome Biology 14(2):R13 (2013).


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., Ruvkun G. Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence. Nature 493(7434): 694 (2013). File:2013 Nature Tabach.pdf


Billi, A.C., Freeberg, M.A., and Kim, J.K. piRNAs and siRNAs collaborate in Caenorhabditis elegans genome defense. Genome Biology 13(7): 164 (2012). File:2012 Genome Biol Billi.pdf


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). File:2012 Science Moissiard.pdf


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) (2012). File:2012 PLoS Genet Billi.pdf


modENCODE Consortium (Gerstein, M.B. et al.,). Integrative analysis of the Caenorhabditis elegans genome by the modENCODE Project. Science 330: 1775-87 (2010). File:2010 Science Gerstein.pdf


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: 432-5 (2010). File:Science2010Mangone.pdf


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: 18674-9 (2009). File:2009 Proc Natl Acad Sci U S A Han.pdf


modENCODE Consortium (Celniker, S.E. et al.,). Unlocking the secrets of the genome. Nature 459: 927-30 (2009). File:Nature2009Celniker.pdf


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: 11546-51 (2009). File:2009 Proc Natl Acad Sci U S A Friedländer.pdf


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). File:Cell2008Simon.pdf


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). File:Nature2005Wang.pdf


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). File:Science2005Kim.pdf


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). File:2004 Proc Natl Acad Sci U S A Kim.pdf


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). File:Molecular Cell2003Grad.pdf