Publications
Dr. Joomyeong Kim – a bibliography:
http://www.ncbi.nlm.nih.gov/myncbi/browse/collection/46109543/?sort=date&direction=descending
– 2019
104. J. Kim, W.D. Frey, K. Sharma, S. Ghimire, R. Teruyama, L. Stubbs (2019). Allele-specific
enhancer interaction at the Peg3 imprinted domain. PLoS ONE 14(10): e0224287. https://doi.org/10.1371/journal.pone.0224287
103. J. Kim (2019). Down-regulation of Aromatase in Peg3-mutant female mice. (submitted).
– 2018
102. J. Kim (2018). Evolution patterns of Peg3 and H19-ICRs. Genomics (in press). https://doi.org/10.1016/j.ygeno.2018.11.025
101. J. Kim, B.P.U. Perera, S. Ghimire (2018). Enhancer-driven alternative promoters of imprinted genes. PLoS ONE 13(11): e0208421. https://doi.org/10.1371/journal.pone.0208421
100. B.P.U. Perera, S. Ghimire, and J. Kim (2018). Circular RNA identified from Peg3 and Igf2r. PLoS ONE 13(9): e0203850. https://doi.org/10.1371/journal.pone.0203850
99. C.L. Bretz and J. Kim (2018). Trans-allelic mutational effects at the Peg3 imprinted locus. PLoS ONE 13(10): e0206112. https://doi.org/10.1371/journal.pone.0206112
98. W.D. Frey, K. Sharma, T.L. Cain, K. Nishimori, R. Teruyama, and J. Kim (2018). Oxytocin receptor is regulated by Peg3. PLoS ONE 13(8): e0202476. https://doi.org/10.1371/journal.pone.0202476
– 2017
97. C.L. Bretz, W.D. Frey, R. Teruyama and J. Kim (2018). Allele and dosage specificity of the Peg3 imprinted domain. PLoS ONE 13(5): e0197069. https://doi.org/10.1371/journal.pone.0197069
96. A. Bakshi, M.B. Ekram and J. Kim (2019). High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS). Methods Mol Biol 1908: 219-228. 10.1007/978-1-4939-9004-7_15
95. A. Bakshi, C.L. Bretz, T.L. Cain and J. Kim (2018). Intergenic and intronic DNA hypomethylated regions as putative regulators of imprinted domains. Epigenomics 10(4): 445-461. https://doi.org/10.2217/epi-2017-0125
94. C.L. Bretz and J. Kim (2017). Transcription-driven DNA methylation setting on the mouse Peg3 locus. Epigenetics 12(11): 945-952. https://doi.org/10.1080/15592294.2017.1377869
93. J. Kwon, H.B. Seo, Y.M. Moon, J.G. Ryu, K.A. Jung, S.Y. Lee, J.Y. Jhun, J.S. Park, S.S. Hwang, J. Kim, G.R. Lee, S.H. Park and M.L. Cho (2018). YinYang1 deficiency ameliorates joint inflammation in a murine model of rheumatoid arthritis by modulating Th17 cell activation.. Immunol Lett 197: 63-69. https://doi.org/10.1016/j.imlet.2018.03.003
92. J. Kim, H. He and H. Kim (2017). Inversion of the Imprinting Control Region of the Peg3 domain. PLoS ONE 12(7): e0181591. https://doi.org/10.1371/journal.pone.0181591
– 2016
91. A. Ye, H. Kim and J. Kim (2017). PEG3 control on the mammalian MSL complex. PLoS ONE 12(6): e0178363. https://doi.org/10.1371/journal.pone.0178363
90. C.L. Bretz, I.M. Langohr and J. Kim (2017). Epigenetic response of imprinted domains during carcinogenesis. Clin Epigenetics 9: 90. https://doi.org/10.1186/s13148-017-0393-8
89. B.P.U. Perera and J. Kim (2016). Sex and tissue specificity of Peg3 promoters. PLoS ONE 11(10): e0164158. https://doi.org/10.1371/journal.pone.0164158
88. H. Kim, I.M. Langohr, M Faisal, M. McNulty, C. Thorn, and J. Kim (2018). Ablation of Ezh2 in neural crest cells leads to aberrant enteric nervous system development in mice. PLoS ONE 13(8): e0203391. https://doi.org/10.1371/journal.pone.0203391
87. H. He, A. Ye, H. Kim and J. Kim (2016). PEG3 interacts with KAP1 through KRAB-A. PLoS ONE 11(11): e167541. https://doi.org/10.1371/journal.pone.0167541
86. H. He, B.P.U. Perera, A. Ye and J. Kim (2016). Parental and sexual conflicts over the Peg3 imprinted domain. Sci. Rep. 6: 38136. https://doi.org/10.1038/srep38136
85. H. He, A. Ye, B.P.U. Perera and J. Kim (2017). YY1’s role in the Peg3 imprinted domain. Sci. Rep. 7(1): 6427. https://doi.org/10.1038/s41598-017-06817-5
84. J. Kim and A. Ye (2016). Phylogenetic and epigenetic footprinting of the putative enhancers of the Peg3 domain. PLoS ONE 11(4): e0154216. https://doi.org/10.1371/journal.pone.0154216
– 2015
83. B.P.U. Perera and J. Kim (2016). NGS-based 5’RACE for alternative promoters. Anal. Biochem. 494: 82-84. https://doi.org/10.1016/j.ab.2015.11.006
82. B.P.U. Perera and J. Kim (2016). Alternative promoters of Peg3 with maternal specificity. Sci. Rep. 6: 24438. https://doi.org/10.1038/srep24438
81. A. Ye, H. He, and J. Kim (2016). PEG3 binds to H19-ICR as a transcriptional repressor. Epigenetics 11(12):889-900. https://doi.org/10.1080/15592294.2016.1255385
80. A. Bakshi, S.W. Herke, M.A. Batzer, J. Kim (2016). DNA methylation variation of human-specific Alu repeats. Epigenetics 11(2): 163-173. https://doi.org/10.1080/15592294.2015.1130518
79. S. Lee, A. Ye, and J. Kim (2015). DNA-binding motif of the imprinted transcription factor PEG3. PLoS ONE 10(12): e0145531. https://doi.org/10.1371/journal.pone.0145531
78. H. He, A. Ye, and J. Kim (2016). Transcriptional truncation of the long coding imprinted gene Usp29. PLoS ONE 11(6): e0158004. https://doi.org/10.1371/journal.pone.0158004
77. W.D. Frey and J. Kim (2015). Tissue-Specific Contributions of Paternally Expressed Gene 3 in Lactation and Maternal Care of Mus musculus. PLoS ONE 10(12):e0144459. https://doi.org/10.1371/journal.pone.0144459
76. C.L. Bretz, I. Langohr, S. Lee, and J. Kim (2015). Epigenetic instability at imprinting control regions in a KrasG12D T-cell neoplasm. Epigenetics 10(12): 1111-1120. https://doi.org/10.1080/15592294.2015.1110672
75. S. Lee and J. Kim (2016). NGS-based deep bisulfite sequencing. MethodsX 3: 1-7. https://doi.org/10.1016/j.mex.2015.11.008
74. J. Kim, C.L. Bretz, S. Lee (2015). Epigenetic instability of imprinted genes in human cancers. Nucleic Acids Res 43(22): 10689-10699. https://doi.org/10.1093/nar/gkv867
– 2014
73. A. Bakshi, M.B. Ekram, and J. Kim (2015). Locus-specific DNA methylation analysis of retrotransposons in ES, somatic and cancer cells using High-Throughput Targeted Repeat Element Bisulfite Sequencing. Genomics Data 3: 87-89. https://doi.org/10.1016/j.gdata.2014.11.013
72. H. Kim*, and A. Bakshi*, and J. Kim (2015). Retrotransposon-derived promoter of mammalian Aebp2. PLoS ONE 10(4): e016966. (* joint first author). https://doi.org/10.1371/journal.pone.0126966
71. H. He and J. Kim (2014). Regulation and function of the Peg3 imprinted domain. Genomics & Informatics 12(3): 105-113. https://doi.org/10.5808/GI.2014.12.3.105
70. A. Ye, H. He, and J. Kim (2014). Paternally expressed Peg3 controls maternally expressed Zim1 as a trans factor. PLoS ONE 9(9): e108596. https://doi.org/10.1371/journal.pone.0108596
69. A. Bakshi and J. Kim (2014). Retrotransposon-based profiling of mammalian epigenomes: DNA methylation of IAP LTRs in embryonic stem, somatic and cancer cells. Genomics 104: 538-544. https://doi.org/10.1016/j.ygeno.2014.09.009
68. H. Kim, M.B. Ekram, A. Bakshi and J. Kim (2015). AEBP2 as a transcriptional activator and its role in cell migration. Genomics 105: 108-115. https://dx.doi.org/10.1016%2Fj.ygeno.2014.11.007
67. B.P.U. Perera, R. Teruyama and J. Kim (2015). Yy1 gene dosage effect and bi-allelic expression of Peg3. PLoS ONE 10(4): e0119493. https://doi.org/10.1371/journal.pone.0119493
– 2013
66. W.D. Frey and J. Kim (2013). APeg3: Regulation of Peg3 through an evolutionarily conserved ncRNA. Gene 540: 251-257. https://dx.doi.org/10.1016%2Fj.gene.2014.02.056
65. M.B. Ekram and J. Kim (2013). High Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS): Genome-wide DNA methylation analysis of IAPLTR retrotransposon. PLoS ONE 9(7): e101683. https://doi.org/10.1371/journal.pone.0101683
64. J. Kim, W.D. Frey, H. He, H. Kim, M.B. Ekram, A. Bakshi, M. Faisal, B.P.U. Perera, A. Ye, R. Teruyama (2013). Peg3 mutational effects on reproduction and placenta-specific gene families. PLoS ONE 8(12): e85477. https://dx.doi.org/10.1371%2Fjournal.pone.0083359
63. H. Kim, T.J. Kang, and J. Kim (2013). Environmental effects on the epigenetics of neural crest cell development. OA Mol Cell 1(1): 4. http://www.oapublishinglondon.com/article/780
62. M. Faisal, H. Kim, and J. Kim (2014). Sexual differences of imprinted genes’ expression levels. Gene 533: 434-438. https://doi.org/10.1016/j.gene.2013.10.006
61. M.M. Thiaville, H. Kim, W.D. Frey and J. Kim (2013). Identification of an evolutionarily conserved cis-regulatory element controlling the Peg3 imprinted domain. PLoS ONE 8(9): e75417. https://doi.org/10.1371/journal.pone.0075417
– 2012
60. S.S. Hwang, Y.U. Kim, S.W. Jang, B.H. Koh, J. Kim, A. Souabni, M. Busslinger, and G.R. Lee (2012). Transcription factor YY1 is essential for regulation of the Th2 cytokine locus and for Th2 cell differentiation. Proc. Natl. Acad. Sci. U.S.A. 110: 276-281.
59. J. Kim and H. Kim (2012). Recruitment and biological consequences of histone modification H3K27me3 and H3K9me3. ILAR 53(3-4): 232-239.
58. M.M. Thiaville, J.M. Huang, H. Kim, M.B. Ekram, T.Y. Roh, and J. Kim (2012). DNA binding motif and target genes of the imprinted transcription factor PEG3. Gene 512: 314-320. https://doi.org/10.1016/j.gene.2012.10.005
57. M. B. Ekram, K. Kang, H. Kim, and J. Kim (2012). Retrotransposons as a major source of epigenetic variations in the mammalian genome. Epigenetics 7(4): 370-382.
56. J. Kim, M.B. Ekram, H. Kim, M. Faisal, W.D. Frey, J.M. Huang, K. Tran, M.M. Kim, S. Yu (2012). Imprinting Control Region of the Peg3 domain. Hum. Mol. Genet. 21: 2677-2687.
– 2011
55. M.M. Thiaville and J. Kim (2011). Oncogenic potential of YY1 through imprinted genes. Critical Reviews in Oncogenesis 16(3-4): 199-209.
54. K. Kang, J. Kim, J.H. Chung and D. Lee (2011). An integrative analysis tool to identify genome-wide cis-regulatory modules: Combinatorial CRM Decoder (CCD). Nucleic Acids Research 39: e116.
53. H. Kim, K. Kang, M.B. Ekram, T.Y. Roh and J. Kim (2011). Aebp2 as an epigenetic regulator for neural crest cells. PLoS ONE 6(9): e25174.
52. J.D. Kim, H. Kim, M.B. Ekram, S. Yu, C. Faulk, and J. Kim (2011). Rex1/Zfp42 as an epigenetic regulator for genomic imprinting. Hum. Mol. Genet. 20: 1353-1362.
– 2010
51. J. Kim (2010). Genomic imprinting and transcription factor YY1. Forum on Immunopathological Diseases and Therapeutics 1:1-16.
– 2009
50. C.D. Faulk and J. Kim (2009). YY1’s DNA-Binding Motifs in Mammalian Olfactory Receptor Genes. BMC Genomics 10: 576.
49. J.D. Kim, S. Yu, and J. Kim (2009). YY1 is autoregulated through its own DNA-binding sites. BMC Mol Biol. 10: 85.
48. J.D. Kim, K. Kang, and J. Kim (2009). YY1’s role in DNA methylation of Peg3 and Xist. Nucleic Acids Research 37: 5656-5664.
47. J.M. Huang, S. Yu, and J. Kim (2009). Identification of an antisense transcript to ZIM2 in the primate lineage. Gene 445: 1-6.
46. C.D. Faulk and J. Kim (2009). Position-based clustering of expression data. CSH Protocols 4(9): 1-6 (doi: 10.1101/pdb.prot5280).
45. J.M. Huang and J. Kim (2009). DNA methylation analysis of the mammalian PEG3 imprinted domain. Gene 442: 18-25.
44. H. Kim, K. Kang, and J. Kim (2009). AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2. Nucleic Acids Research 37: 2940-2950.
43. K. Kang, J.H. Chung, and J. Kim (2009). Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1 and CTCF binding sites. Nucleic Acids Research 37: 2003-2013.
42. J.D. Kim and J. Kim (2009). YY1’s longer DNA-binding motif. Genomics 93: 152-158.
– 2008
41. J.D. Kim, S. Yu, J.H. Choo, and J. Kim (2008). Two evolutionarily conserved sequence elements for Peg3/Usp29 transcription. BMC Mol Biol. 9: 108.
40. J. Kim (2008). Multiple YY1 and CTCF binding sites in Imprinting Control Regions. Epigenetics 3: 115-118.
39. J. Kim and J.D. Kim (2008). In vivo YY1-knockdown effects on genomic imprinting. Hum. Mol. Genet. 17: 391-401.
38. J.H. Choo J.D. Kim and J. Kim (2008). Imprinting of an evolutionarily conserved antisense transcript gene APeg3. Gene 409: 28-33.
– 2007
37. J.H. Choo, J.D. Kim, and J. Kim (2007). MacroH2A1 knockdown effects on the Peg3 imprinted domain. BMC Genomics 8: 479-485.
36. J.D. Kim, C. Faulk, and J. Kim (2007). Retroposition and DNA-binding motifs of YY1, YY2 and REX1. Nucleic Acids Research 35: 3442-3452.
35. J. Kim, A. Bergmann, J.H. Choo, and L. Stubbs (2007). Genomic organization and imprinting of the Peg3 domain in bovine. Genomics 90: 85-92.
34. J.D. Kim, A.K. Hinz, J.H. Choo, L. Stubbs, and J. Kim (2007). YY1 as a controlling factor for the Peg3 and Gnas imprinted domains. Genomics 89: 262-269.
– 2006
33. J.D. Kim, A.K. Hinz, A. Bergmann, J.M. Thompson, I. Ovcharenko, L. Stubbs, and J. Kim (2006). Identification of clustered YY1 binding sites in imprinting control regions. Genome Research 16: 901-911.
32. J.M. Huang, J.D. Kim, H. Kim, and J. Kim (2006). An improved cloning strategy for ChIP-derived DNA fragments. Anal. Biochem. 356: 145-147.
31. S. Huntley, D.M. Baggot, A.T. Hamilton, M. Tran-Gyamfi, S. Hammond, S. Yang, J. Kim, L. Gordon, E. Branscomb, and L. Stubbs. (2006). A comprehensive catalog of human KRAB-associated zinc finger genes: insights to the evolutionary history of a large family of transcriptional repressors. Genome Research 16: 669-677.
30. J.H. Choo, J.D. Kim, J.H. Chung, L. Stubbs, and J. Kim (2006). Allele-specific deposition of macroH2A1 in imprinting control regions. Hum. Mol. Genet. 15: 717-724.
29. C. Luo, X. Lu, L. Stubbs, and J. Kim (2006). Rapid evolution of a recently retroposed transcription factor YY2 in mammalian genomes. Genomics 87: 348-355.
– 2005
28. J. Kim and L. Stubbs (2005). Rapidly evolving imprinted loci. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley Publishers, West Sussex, UK.
– 2004
27. J. Kim, A. Bergmann, S. Lucas, R. Stone, and L. Stubbs (2004). Lineage-specific imprinting and evolution of the zinc finger gene ZIM2. Genomics 84: 47-58.
26. A.T. Hamilton, S. Huntley, J. Kim, E. Branscomb, and L. Stubbs (2004). Lineage-specific expansion of KRAB zinc-finger transcription factor genes: implications for the evolution of vertebrate regulatory networks. Cold Spring Harbor Symposium on Quantitative Biology, Volume 68: The genome of Homo Sapiens.
25. S. Huntley, A.T. Hamiton, J. Kim, E. Branscomb, and L. Stubbs (2004). Tandem gene family expansion and genomic diversity. In Comparative genomics: A guide to the analysis of eukaryotic genomes. M. Adams, ed., Humana Press.
– Prior to 2004
24. S-H, Kim, S., Parrinello, J. Kim, and J. Campisi (2003). Mus musculus and Mus spretus Homologues of the Human Telomere-Associated Protein TIN2. Genomics 81: 422-432.
23. J. Kim, A. Kollhoff, A. Bergmann, and L. Stubbs (2003). Methylation-sensitive binding of transcription factor YY1 to an insulator sequence within the paternally expressed imprinted gene, Peg3. Hum. Mol. Genet. 12: 233-245.
22. P. Dehal, P. Predki, A. Olsen, A. Kobayashi, P. Folta, S. Lucas, M. Land, A. Terry, C. Zhou, S. Rash, Q. Zhang, L. Gordon, J. Kim, C. Elkin, M. Pollard, P. Richardson, D. Rokhsar, E. Uberbacher, T. Hawkins, E. Branscomb, and L. Stubbs (2001). Comparison of human chromosome 19 and related regions in mouse: conservative and lineage specific evolution. Science 293: 104-111.
21. J. Kim, A. Bergmann, E. Wehri, X. Lu, and L. Stubbs (2001). Imprinting and evolution of two Kruppel-type zinc-finger genes, Zim3 and ZNF264, located in the PEG3/USP29-imprinted domain. Genomics 77: 91-98.
20. J. Kim, L. Gordon, P. Dehal, H. Badri, M. Christensen, M. Groza, C. Ha, S. Hammond, M. Vargas, E. Wehri, M. Wagner, A. Olsen, and L. Stubbs (2001). Homology-driven assembly of a sequence-ready mouse bac contig map spanning regions related to the 46-mb gene-rich euchromatic segments of human chromosome 19. Genomics 74: 129-141.
19. J. Kim, V. Noskov, X. Lu, A. Bergmann, X. Ren, T. Warth, P. Richardson, N. Kouprina, and L. Stubbs (2000). Discovery of a novel, paternally expressed ubiquitin-specific processing protease gene through comparative analysis of an imprinted region of mouse chromosome 7 and human chromosome 19q13.4. Genome Research 10: 1138-1147.
18. W.R. Liu, J. Kim, C. Nwankwo, L.K. Ashworth, and J.P. Arm (2000). Genomic organization of the human leukocyte immunoglobulin-like receptors within the leukocyte complex on chromosome 19q13.4. J. Immunogenetics 51: 659-669.
17. J. Kim, A. Bergmann, and L. Stubbs (2000). Exon sharing of a human zinc-finger gene, ZIM2, and paternally expressed gene, PEG3. Genomics 64: 114-118.
16. J. Kim, X. Lu, and L. Stubbs (1999). Zim1, a maternally expressed mouse Kruppel-type zinc-finger gene located in proximal chromosome 7. Hum. Mol. Genet. 8: 847-854.
15. M. Shannon, J. Kim, L. Ashworth, E. Branscomb, and L. Stubbs (1998). Tandem zinc-finger gene families in mammals: insights and unanswered questions. DNA Seq. 8: 303-315.
14. J. Kim, Y.S. Park, J.H. Chung, L. Stubbs (1997). The gene encoding sepiapterin reductase is located in central mouse chromosome 6. Mamm. Genome 8: 942.
13. J. Kim, E. Carver, and L. Stubbs (1997). Amplification and sequencing of end fragments from bacterial artificial chromosome (BAC) clones by single-primer PCR. Anal. Biochem. 253: 272-275.
12. J. Kim, L. Ashworth, E. Branscomb, and L. Stubbs (1997). The human homolog of a mouse imprinted gene, Peg3, maps to a zinc-finger-rich region of human chromosome 19q13.4. Genome Research 7: 532-540.
11. D.H. Kass, J. Kim, A. Rao, and P.L. Deininger (1997). Evolution of B2 Repeats: The Muroid Explosion. Genetica. 99: 1-13.
10. T.H. Shaikh, J. Kim. M.A. Batzer, and P.L. Deininger (1997). Isolation and sequencing of cDNA derived from RNA polymerase III-directed primary Alu transcripts and small cytoplasmic Alu (scAlu) transcripts. J. Mol. Biol. 271: 222-234.
9. J. Kim and P.L. Deininger (1996). Recent amplification of rat ID elements. J. Mol. Biol. 261: 322-327.
8. L.J. Stubbs, E.A. Carver, M.E. Shannon, J. Kim, J. Geisler, E.E. Generoso, B.G. Stanford, W.C. Dunn, H. Mohrenweiser, W. Zimmermann, S.M. Watt, and L.K. Ashworth (1996). Detailed comparative map of human chromosome 19q and related regions of the mouse genome. Genomics 35: 499-508.
7. P.L. Deininger, H. Tiedge, J. Kim, and J. Brosius (1996). The BC1 RNA gene as a master gene for ID amplification: Evolution, Expression and Function. In Cohn WE, Moldave K (eds) Progress in Nucleic Acid Research and Molecular Biology. Academic Press. 52: 67-88.
6. D.H. Kass, J. Kim, and P.L. Deininger (1996). Sporadic amplification of ID elements in rodents. J. Mol. Evol. 42: 7-14.
5. S.S. Arcot, T.H. Shaikh, J. Kim, L. Bennett, M. Alegria-Hartman, D. Nelson, P.L. Deininger, and M.A. Batzer (1995). Sequence diversity and chromosomal distribution of young Alu repeats. Gene 163: 273-278.
4. C. Ahn, S.-I. Park, J. Kim, and J. Yim (1995). Affinity labeling of E. coli GTP cyclohydrolase I by a dialdehyde derivative of guanosine triphosphate. J. Biochem. Mol. Biol. 28: 72-78.
3. J. Kim, D.H. Kass, and P.L. Deininger (1995). Transcription and processing of ID elements in germ line and somatic cells. Nucleic Acids Research 23: 2245-2251.
2. J. Kim, J.A. Martignetti, M.R. Shen, J. Brosius, and P.L. Deininger (1994). Rodent BC1 RNA gene as a master gene for ID element amplification. Proc. Natl. Acad. Sci. U.S.A. 91: 3607-3611.
1. M.A. Batzer, H.A. Bazan, J. Kim, S.L. Morrow, T.H. Shaikh, S. Arcot, and P.L. Deininger (1992). Large scale subcloning of bacteriophage lambda Zap clones. Biotechniques 12: 370-371.