Interdisciplinary Program of Integrated OMICS for Biomedical Sciences

Research Output

2009

Proteomic analysis of Caenorhabditis elegans.

Jeong, P. Y., Na, K., Jeong, M. J., Chitwood, D., Shim, Y. H. & Paik, Y. K., 2009, In : Methods in molecular biology (Clifton, N.J.). 519, p. 145-169 25 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Proteomic analysis of the sterol-mediated signaling pathway in Caenorhabditis elegans.

Choi, B. K., Shin, Y. K., Lee, E. Y., Jeong, P. Y., Shim, Y. H., Chitwood, D. J. & Paik, Y. K., 2009, In : Methods in molecular biology (Clifton, N.J.). 462, p. 181-195 15 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Proteomic profiling of yeast - and hyphal-specific responses of Candida albicans to the antifungal agent, HWY-289

Kim, K. Y., Shin, Y. K., Kang, K. C., Yoo, J. S., Kim, J. H. & Paik, Y. K., 2009, In : Proteomics - Clinical Applications. 3, 4, p. 452-461 10 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Quantitative analysis of phosphopeptides in search of the disease biomarker from the hepatocellular carcinoma specimen

Lee, H. J., Na, K., Kwon, M. S., Kim, H., Kyoung, S. K. & Paik, Y. K., 2009 Jun, In : Proteomics. 9, 12, p. 3395-3408 14 p.

Research output: Contribution to journalArticle

52 Citations (Scopus)

Requirement of split ends for epigenetic regulation of notch signal-dependent genes during infection-induced hemocyte differentiation

Li, H. J., Jung, K. C., Kim, B., Hwan, S. C., Kim, J., Kim-Ha, J. & Kim, Y. J., 2009 Mar, In : Molecular and cellular biology. 29, 6, p. 1515-1525 11 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Reversine increases the plasticity of lineage-committed cells toward neuroectodermal lineage

Eun, K. L., Bae, G. U., Jueng, S. Y., Jae, C. L., Yae, J. J., Jong, W. P., Jae, H. P., Seong, H. A., Yong, K. K., Wahn, S. C., Kang, J. S., Han, G. & Han, J. W., 2009 Jan 30, In : Journal of Biological Chemistry. 284, 5, p. 2891-2901 11 p.

Research output: Contribution to journalArticle

29 Citations (Scopus)

RhoB induces apoptosis via direct interaction with TNFAIP1 in HeLa cells

Kim, D. M., Chung, K. S., Choi, S. J., Jung, Y. J., Park, S. K., Han, G. H., Ha, J. S., Song, K. B., Choi, N. S., Kim, H. M., Won, M. & Seo, Y. S., 2009 Dec 1, In : International Journal of Cancer. 125, 11, p. 2520-2527 8 p.

Research output: Contribution to journalArticle

49 Citations (Scopus)

Solution structure of the DNA binding domain of rice telomere binding protein RTBP

Ko, S., Yu, E. Y., Shin, J., Yoo, H. H., Tanaka, T., Kim, W. T., Cho, H. S., Lee, W. & Chung, I. K., 2009 Feb 10, In : Biochemistry. 48, 5, p. 827-838 12 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)

The Moscow HUPO human proteome project workshop

Archakov, A., Bergeron, J. J. M., Khlunov, A., Lisitsa, A. & Paik, Y. K., 2009, In : Molecular and Cellular Proteomics. 8, 9, p. 2199-2200 2 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Toward unraveling the complexity of simple epithelial keratins in human disease

Omary, M. B., Ku, N. O., Strnad, P. & Hanada, S., 2009 Jul 1, In : Journal of Clinical Investigation. 119, 7, p. 1794-1805 12 p.

Research output: Contribution to journalReview article

176 Citations (Scopus)

Ubiquitin ligase RLIM modulates telomere length homeostasis through a proteolysis of TRF1

Her, Y. R. & Chung, I. K., 2009 Mar 27, In : Journal of Biological Chemistry. 284, 13, p. 8557-8566 10 p.

Research output: Contribution to journalArticle

42 Citations (Scopus)
2008

AIMP1/p43 downregulates TGF-β signaling via stabilization of smurf2

Lee, Y. S., Han, J. M., Son, S. H., Choi, J. W., Jeon, E. J., Bae, S. C., Park, Y. I. & Kim, S., 2008 Jul 4, In : Biochemical and Biophysical Research Communications. 371, 3, p. 395-400 6 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)

AIMP2/p38, the scaffold for the multi-tRNA synthetase complex, responds to genotoxic stresses via p53

Jung, M. H., Park, B. J., Sang, G. P., Young, S. O., So, J. C., Sang, W. L., Hwang, S. K., Chang, S. H., Cho, M. H. & Kim, S., 2008 Aug 12, In : Proceedings of the National Academy of Sciences of the United States of America. 105, 32, p. 11206-11211 6 p.

Research output: Contribution to journalArticle

69 Citations (Scopus)

Antiinflammatory activity of methanol extract isolated from stem bark of Magnolia kobus

Kane, J. S., Lee, K. H., Han, M. H., Lee, H., Ahn, J. M., Han, S. B., Han, G., Lee, K., Park, S. K. & Kim, H. M., 2008 Jul, In : Phytotherapy Research. 22, 7, p. 883-888 6 p.

Research output: Contribution to journalArticle

33 Citations (Scopus)

Application of a peptide-based PF2D platform for quantitative proteomics in disease biomarker discovery

Lee, H. J., Kang, M. J., Lee, E. Y., Sang, Y. C., Kim, H. & Paik, Y. K., 2008 Aug, In : Proteomics. 8, 16, p. 3371-3381 11 p.

Research output: Contribution to journalArticle

34 Citations (Scopus)

Cancer and epigenetics

Bae, J. B. & Kim, Y. J., 2008, In : Animal Cells and Systems. 12, 3, p. 117-125 9 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Chromen-based TNF-α converting enzyme (TACE) inhibitors: Design, synthesis, and biological evaluation

Chun, K., Park, S. K., Kim, H. M., Choi, Y., Kim, M. H., Park, C. H., Joe, B. Y., Chun, T. G., Choi, H. M., Lee, H. Y., Hong, S. H., Kim, M. S., Nam, K. Y. & Han, G., 2008 Jan 1, In : Bioorganic and Medicinal Chemistry. 16, 1, p. 530-535 6 p.

Research output: Contribution to journalArticle

29 Citations (Scopus)
19 Citations (Scopus)

Epigenetic regulation and the variability of gene expression

Choi, J. K. & Kim, Y. J., 2008 Feb, In : Nature Genetics. 40, 2, p. 141-147 7 p.

Research output: Contribution to journalArticle

80 Citations (Scopus)

Establishment of a PF2D-MS/MS platform for rapid profiling and semiquantitative analysis of membrane protein biomarkers

Lee, H. J., Kwon, M. S., Lee, E. Y., Sang, Y. C. & Paik, Y. K., 2008 Jun, In : Proteomics. 8, 11, p. 2168-2177 10 p.

Research output: Contribution to journalArticle

22 Citations (Scopus)

Histone deacetylase inhibitor KBH-A42 inhibits cytokine production in RAW 264.7 macrophage cells and in vivo endotoxemia model

Choi, Y., Park, S. K., Hwan, M. K., Jong, S. K., Yeo, D. Y., Sang, B. H., Jeung, W. H., Jee, S. Y. & Han, G., 2008 Oct, In : Experimental and Molecular Medicine. 40, 5, p. 574-581 8 p.

Research output: Contribution to journalArticle

50 Citations (Scopus)

Human Proteinpedia enables sharing of human protein data [4]

Mathivanan, S., Ahmed, M., Ahn, N. G., Alexandre, H., Amanchy, R., Andrews, P. C., Bader, J. S., Balgley, B. M., Bantscheff, M., Bennett, K. L., Björling, E., Blagoev, B., Bose, R., Brahmachari, S. K., Burlingame, A. S., Bustelo, X. R., Cagney, G., Cantin, G. T., Cardasis, H. L., Celis, J. E. & 140 others, Chaerkady, R., Chu, F., Cole, P. A., Costello, C. E., Cotter, R. J., Crockett, D., DeLany, J. P., De Marzo, A. M., DeSouza, L. V., Deutsch, E. W., Dransfield, E., Drewes, G., Droit, A., Dunn, M. J., Elenitoba-Johnson, K., Ewing, R. M., Eyk, J. V., Faca, V., Falkner, J., Fang, X., Fenselau, C., Figeys, D., Gagné, P., Gelfi, C., Gevaert, K., Gimble, J. M., Gnad, F., Goel, R., Gromov, P., Hanash, S. M., Hancock, W. S., Harsha, H. C., Hart, G., Hays, F., He, F., Hebbar, P., Helsens, K., Hermeking, H., Hide, W., Hjernø, K., Hochstrasser, D. F., Hofmann, O., Horn, D. M., Hruban, R. H., Ibarrola, N., James, P., Jensen, O. N., Jensen, P. H., Jung, P., Kandasamy, K., Kheterpal, I., Kikuno, R. F., Korf, U., Körner, R., Kuster, B., Kwon, M. S., Lee, H. J., Lee, Y. J., Lefevre, M., Lehvaslaiho, M., Lescuyer, P., Levander, F., Lim, M. S., Löbke, C., Loo, J. A., Mann, M., Martens, L., Martinez-Heredia, J., McComb, M., McRedmond, J., Mehrle, A., Menon, R., Miller, C. A., Mischak, H., Mohan, S. S., Mohmood, R., Molina, H., Moran, M. F., Morgan, J. D., Moritz, R., Morzel, M., Muddiman, D. C., Nalli, A., Navarro, J. D., Neubert, T. A., Ohara, O., Oliva, R., Omenn, G. S., Oyama, M., Paik, Y. K., Pennington, K., Pepperkok, R., Periaswamy, B., Petricoin, E. F., Poirier, G. G., Prasad, T. S. K., Purvine, S. O., Rahiman, B. A., Ramachandran, P., Ramachandra, Y. L., Rice, R. H., Rick, J., Ronnholm, R. H., Salonen, J., Sanchez, J. C., Sayd, T., Seshi, B., Shankari, K., Sheng, S. J., Shetty, V., Shivakumar, K., Simpson, R. J., Sirdeshmukh, R., Michael Siu, K. W., Smith, J. C., Smith, R. D., States, D. J., Sugano, S., Sullivan, M., Superti-Furga, G., Takatalo, M., Thongboonkerd, V., Trinidad, J. C., Uhlen, M., Vandekerckhove, J., Vasilescu, J., Veenstra, T. D., Vidal-Taboada, J. M., Vihinen, M., Wait, R., Wang, X., Wiemann, S., Wu, B., Xu, T., Yates, J. R., Zhong, J., Zhou, M., Zhu, Y., Zurbig, P. & Pandey, A., 2008 Feb, In : Nature Biotechnology. 26, 2, p. 164-167 4 p.

Research output: Contribution to journalLetter

126 Citations (Scopus)

Identification and functional analysis of antifungal immune response genes in Drosophila

Li, H. J., Shim, J., Joon, S. Y., Kim, B., Kim, J., Kim-Ha, J. & Kim, Y. J., 2008 Oct, In : PLoS Pathogens. 4, 10, e1000168.

Research output: Contribution to journalArticle

28 Citations (Scopus)

Inhibition of acyl-coenzyme A: Cholesterol acyltransferase stimulates cholesterol efflux from macrophages and stimulates farnesoid X receptor in hepatocytes

An, S., Jang, Y. S., Park, J. S., Kwon, B. M., Paik, Y. K. & Jeong, T. S., 2008 Aug 31, In : Experimental and Molecular Medicine. 40, 4, p. 407-417 11 p.

Research output: Contribution to journalArticle

13 Citations (Scopus)

Inhibition of developmental processes by flavone in Caenorhabditis elegans and its application to the pinewood nematode,Bursaphelenchus xylophilus

Lee, Y. U., Kawasaki, I., Lim, Y., Oh, W. S., Paik, Y. K. & Shim, Y. H., 2008 Aug 31, In : Molecules and cells. 26, 2, p. 171-174 4 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)

Inhibition of skin inflammation and atopic dermatitis by topical application of a novel ceramide derivative, K112PC-5, in mice

Kang, J. S., Lee, C. W., Lee, K., Han, M. H., Lee, H., Youm, J. K., Jeong, S. K., Park, B. D., Han, S. B., Han, G., Park, S. K. & Kim, H. M., 2008 Aug, In : Archives of pharmacal research. 31, 8, p. 1004-1009 6 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

IntelliMS: A platform to efficiently manage and visualize tandem mass spectral data

Kwon, M. S., Lee, H. J., Jeong, S. K., Lee, E. Y., Cho, S. Y. & Paik, Y. K., 2008 Dec, In : Proteomics. 8, 23-24, p. 4910-4913 4 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

In vitro metabolism of KBH-A40, a novel δ-lactam-based histone deacetylase (HDAC) inhibitor, in human liver microsomes and serum

Kim, H. M., Oh, S. J., Park, S. K., Han, G., Kim, K., Lee, K. S., Kang, J. S., Nam, M. & Lee, K., 2008 Mar, In : Xenobiotica. 38, 3, p. 281-293 13 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Microarray analysis of the gene expression profiles of SL2 cells stimulated by LPS/PGN and curdlan

Jin, L. H., Choi, J. K., Cho, H. S., Shim, J. & Kim, Y. J., 2008 Jun 30, In : Molecules and cells. 25, 4, p. 553-558 6 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Moving AHEAD with an international human epigenome project

Jones, P. A., Archer, T. K., Baylin, S. B., Beck, S., Berger, S., Bernstein, B. E., Carpten, J. D., Clark, S. J., Costello, J. F., Doerge, R. W., Esteller, M., Feinberg, A. P., Gingeras, T. R., Greally, J. M., Henikoff, S., Herman, J. G., Jackson-Grusby, L., Jenuwein, T., Jirtle, R. L., Kim, Y. J. & 14 others, Laird, P. W., Lim, B., Martienssen, R., Polyak, K., Stunnenberg, H., Tlsty, T. D., Tycko, B., Ushijima, T., Zhu, J., Pirrotta, V., Allis, C. D., Elgin, S. C., Rine, J. & Wu, C., 2008 Aug 7, In : Nature. 454, 7205, p. 711-715 5 p.

Research output: Contribution to journalReview article

132 Citations (Scopus)

NFκB activation is associated with its O-GlcNAcylation state under hyperglycemic conditions

Won, H. Y., Sang, Y. P., Hyung, W. N., Do, H. K., Jeong, G. K., Eun, S. K., Yu, S. K., Hyun, C. L., Kwan, S. K. & Cho, J. W., 2008 Nov 11, In : Proceedings of the National Academy of Sciences of the United States of America. 105, 45, p. 17345-17350 6 p.

Research output: Contribution to journalArticle

135 Citations (Scopus)

Regulation of telomeric repeat binding factor 1 binding to telomeres by casein kinase 2-mediated phosphorylation

Mi, K. K., Mi, R. K., Hyung, W. N., Bae, Y. S., Yu, S. K. & In, K. C., 2008 May 16, In : Journal of Biological Chemistry. 283, 20, p. 14144-14152 9 p.

Research output: Contribution to journalArticle

31 Citations (Scopus)

Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes

Choi, J. K., Hwang, S. & Kim, Y. J., 2008 Aug 20, In : PloS one. 3, 8, e3002.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Synthesis of amide and urea derivatives of benzothiazole as Raf-1 inhibitor

Song, E. Y., Kaur, N., Park, M. Y., Jin, Y., Lee, K., Kim, G., Lee, K. Y., Yang, J. S., Shin, J. H., Nam, K. Y., No, K. T. & Han, G., 2008 Jul, In : European Journal of Medicinal Chemistry. 43, 7, p. 1519-1524 6 p.

Research output: Contribution to journalArticle

57 Citations (Scopus)

The efficiency of RNA interference in Bursaphelenchus xylophilus

Park, J. E., Lee, K. Y., Lee, S. J., Oh, W. S., Jeong, P. Y., Woo, T., Kim, C. B., Paik, Y. K. & Koo, H. S., 2008 Jul 31, In : Molecules and cells. 26, 1, p. 81-86 6 p.

Research output: Contribution to journalArticle

31 Citations (Scopus)
2007

Activation of MEK-ERK by heregulin-β1 promotes the development of cardiomyocytes derived from ES cells

Kim, H. S., Cho, J. W., Hidaka, K. & Morisaki, T., 2007 Sep 28, In : Biochemical and Biophysical Research Communications. 361, 3, p. 732-738 7 p.

Research output: Contribution to journalArticle

33 Citations (Scopus)

Aminoacyl-tRNA synthetase-interacting multifunctional protein 1/p43 controls endoplasmic reticulum retention of heat shock protein gp96: Its pathological implications in lupus-like autoimmune diseases

Jung, M. H., Sang, G. P., Liu, B., Park, B. J., Jin, Y. K., Cheng, H. J., Yeong, W. S., Li, Z. & Kim, S., 2007 Jun, In : American Journal of Pathology. 170, 6, p. 2042-2054 13 p.

Research output: Contribution to journalArticle

33 Citations (Scopus)

Antitumor activity of cytokine-induced killer cells against human lung cancer

Kim, H. M., Lim, J., Park, S. K., Kang, J. S., Lee, K., Lee, C. W., Lee, K. H., Yun, M. J., Yang, K. H., Han, G., Kwon, S. W., Kim, Y. & Han, S. B., 2007 Dec 15, In : International Immunopharmacology. 7, 13, p. 1802-1807 6 p.

Research output: Contribution to journalArticle

50 Citations (Scopus)

Anti-tumor activity of ex vivo expanded cytokine-induced killer cells against human hepatocellular carcinoma

Kim, H. M., Lim, J., Yoon, Y. D., Ahn, J. M., Kang, J. S., Lee, K., Park, S. K., Jeong, Y. J., Kim, J. M., Han, G., Yang, K. H., Kim, Y. J., Kim, Y. & Han, S. B., 2007 Dec 15, In : International Immunopharmacology. 7, 13, p. 1793-1801 9 p.

Research output: Contribution to journalArticle

40 Citations (Scopus)

Cloning, characterization and expression of a gene encoding dihydroxyacetone synthase in Mycobacterium sp. strain JC1 DSM 3803

Seo, J. G., Park, S. W., Park, H., Kim, S. Y., Ro, Y. T., Kim, E., Cho, J. W. & Kim, Y. M., 2007 Dec, In : Microbiology. 153, 12, p. 4174-4182 9 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Down-regulation of NF-κB target genes by the AP-1 and STAT complex during the innate immune response in Drosophila

Lark, K. K., Un, Y. C., Hwan, S. C., Jung, S. L., Lee, W. B., Kim, J., Jeong, K., Shim, J., Kim-Ha, J. & Kim, Y. J., 2007 Sep, In : PLoS Biology. 5, 9, p. 2064-2076 13 p.

Research output: Contribution to journalArticle

21 Citations (Scopus)

Epigenomics: Novel aspect of genomic regulation

Hwan, S. C., Jong, H. P. & Kim, Y. J., 2007 Mar, In : Journal of biochemistry and molecular biology. 40, 2, p. 151-155 5 p.

Research output: Contribution to journalReview article

10 Citations (Scopus)

Human ACAT inhibitory effects of shikonin derivatives from Lithospermum erythrorhizon

An, S., Park, Y. D., Paik, Y. K., Jeong, T. S. & Lee, W. S., 2007 Feb 15, In : Bioorganic and Medicinal Chemistry Letters. 17, 4, p. 1112-1116 5 p.

Research output: Contribution to journalArticle

38 Citations (Scopus)

HUPO Plasma Proteome Project 2007 workshop report

Omenn, G. S., Aerbersold, R. & Paik, Y. K., 2007 Dec, In : Molecular and Cellular Proteomics. 6, 12, p. 2252-2253 2 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Inhibition of human ovarian tumor growth by cytokine-induced killer cells

Hwan, M. K., Jong, S. K., Lim, J., Park, S. K., Lee, K., Yeo, D. Y., Chang, W. L., Ki, H. L., Han, G., Yang, K. H., Yeon, J. K., Kim, Y. & Han, S. B., 2007 Nov 30, In : Archives of pharmacal research. 30, 11, p. 1464-1470 7 p.

Research output: Contribution to journalArticle

45 Citations (Scopus)

Keratin 18 overexpression but not phosphorylation or filament organization blocks mouse mallory body formation

Harada, M., Strnad, P., Resurreccion, E. Z., Ku, N. O. & Omary, M. B., 2007 Jan, In : Hepatology. 45, 1, p. 88-96 9 p.

Research output: Contribution to journalArticle

27 Citations (Scopus)

Keratins let liver live: Mutations predispose to liver disease and crosslinking generates Mallory-Denk bodies

Ku, N. O., Strnad, P., Zhong, B. H., Tao, G. Z. & Omary, M. B., 2007 Nov, In : Hepatology. 46, 5, p. 1639-1649 11 p.

Research output: Contribution to journalReview article

114 Citations (Scopus)

Modification of cap group in δ-lactam-based histone deacetylase (HDAC) inhibitors

Kim, H. M., Hong, S. H., Kim, M. S., Lee, C. W., Kang, J. S., Lee, K., Park, S. K., Han, J. W., Lee, H. Y., Choi, Y., Kwon, H. J. & Han, G., 2007 Nov 15, In : Bioorganic and Medicinal Chemistry Letters. 17, 22, p. 6234-6238 5 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)

Overview and introduction to clinical proteomics

Paik, Y. K., Kim, H., Lee, E. Y., Kwon, M. S. & Cho, S. Y., 2007 Aug 31, Clinical Proteomics - Methods and Protocols. p. 1-31 31 p. (Methods in Molecular Biology; vol. 428).

Research output: Chapter in Book/Report/Conference proceedingChapter

20 Citations (Scopus)