Interdisciplinary Program of Integrated OMICS for Biomedical Sciences

Research Output

2010

FISH: Finding of Identical Spectra set for Homogenous peptide using two-stage clustering algorithm

Lee, S., Kwon, M. S., Lee, H. J., Paik, Y. K., Lee, J. K. & Park, T., 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010. p. 73-76 4 p. 5703776. (2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Identification of cdc25 gene in pinewood nematode, Bursaphelenchus xylophilus, and its function in reproduction

Choi, Y. N., Oh, B. K., Kawasaki, I., Oh, W. S., Lee, Y., Paik, Y. K. & Shim, Y. H., 2010 Feb, In : Molecules and cells. 29, 2, p. 195-201 7 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Identification of gp96 as a novel target for treatment of autoimmune disease in mice

Han, J. M., Kwon, N. H., Lee, J. Y., Jeong, S. J., Jung, H. J., Kim, H. R., Li, Z. & Kim, S., 2010, In : PloS one. 5, 3, e9792.

Research output: Contribution to journalArticle

34 Citations (Scopus)

KBH-A42, a histone deacetylase inhibitor, inhibits the growth of doxorubicin-resistant leukemia cells expressing P-glycoprotein

Kang, M. R., Lee, K., Kang, J. S., Lee, C. W., Lee, K. H., Kim, J. H., Yang, J. W., Kim, B. G., Han, G., Kang, J. S., Park, S. K. & Kim, H. M., 2010 Mar, In : Oncology reports. 23, 3, p. 801-809 9 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

MicroRNA expression profile of gastrointestinal stromal tumors is distinguished by 14q loss and anatomic site

Choi, H. J., Lee, H., Kim, H., Kwon, J. E., Kang, H. J., You, K. T., Rhee, H., Noh, S. H., Paik, Y. K., Hyung, W. J. & Kim, H., 2010 Apr 1, In : International Journal of Cancer. 126, 7, p. 1640-1650 11 p.

Research output: Contribution to journalArticle

29 Citations (Scopus)

Natural therapeutic magnesium lithospermate B potently protects the endothelium from hyperglycaemia-induced dysfunction

Kim, S. H., Kim, S. H., Choi, M., Lee, Y., Kim, Y. O., Ahn, D. S., Kim, Y. H., Kang, E. S., Lee, E. J., Jung, M., Cho, J. W., Williams, D. R. & Lee, H. C., 2010 Sep 1, In : Cardiovascular Research. 87, 4, p. 713-722 10 p.

Research output: Contribution to journalArticle

39 Citations (Scopus)

O-GlcNAcylation regulates hyperglycemia-induced GPX1 activation

Yang, W. H., Park, S. Y., Ji, S., Kang, J. G., Kim, J. E., Song, H., Mook-Jung, I., Choe, K. M. & Cho, J. W., 2010 Jan 1, In : Biochemical and Biophysical Research Communications. 391, 1, p. 756-761 6 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Prediction of relative stability between TACE/gelastatin and TACE/gelastatin hydroxamate

Nam, K. Y., Han, G., Kim, H. M. & No, K. T., 2010 Nov 20, In : Bulletin of the Korean Chemical Society. 31, 11, p. 3291-3296 6 p.

Research output: Contribution to journalArticle

Property based optimization of δ-lactam HDAC inhibitors for metabolic stability

Yoon, H. C., Choi, E., Park, J. E., Cho, M., Seo, J. J., Oh, S. J., Kang, J. S., Kim, H. M., Park, S. K., Lee, K. & Han, G., 2010 Nov 15, In : Bioorganic and Medicinal Chemistry Letters. 20, 22, p. 6808-6811 4 p.

Research output: Contribution to journalArticle

13 Citations (Scopus)

Protective effects of magnesium lithospermate B against diabetic atherosclerosis via Nrf2-ARE-NQO1 transcriptional pathway

Hur, K. Y., Kim, S. H., Choi, M. A., Williams, D. R., Lee, Y. H., Kang, S. W., Yadav, U. C. S., Srivastava, S. K., Jung, M., Cho, J. W., Kim, S. G., Kang, E. S., Lee, E. J. & Lee, H. C., 2010 Jul, In : Atherosclerosis. 211, 1, p. 69-76 8 p.

Research output: Contribution to journalArticle

43 Citations (Scopus)

Protein N-glycosylation, protein folding, and protein quality control

Roth, J., Zuber, C., Park, S., Jang, I., Lee, Y., Kysela, K. G., Le Fourn, V., Santimaria, R., Guhl, B. & Cho, J. W., 2010 Dec, In : Molecules and cells. 30, 6, p. 497-506 10 p.

Research output: Contribution to journalReview article

101 Citations (Scopus)

Rab35 mediates transport of Cdc42 and Rac1 to the plasma membrane during phagocytosis

Shim, J., Lee, S. M., Lee, M. S., Yoon, J., Kweon, H. S. & Kim, Y. J., 2010 Mar, In : Molecular and cellular biology. 30, 6, p. 1421-1433 13 p.

Research output: Contribution to journalArticle

50 Citations (Scopus)

Regulation of dauer formation by O-GlcNAcylation in Caenorhabditis elegans

Lee, J., Kim, K. Y., Lee, J. & Paik, Y. K., 2010 Jan 29, In : Journal of Biological Chemistry. 285, 5, p. 2930-2939 10 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)

Regulation of in vitro Aβ1-40 aggregation mediated by small molecules

Kim, H. Y., Kim, Y., Han, G. & Kim, D. J., 2010, In : Journal of Alzheimer's Disease. 22, 1, p. 73-85 13 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)

Role of lung apolipoprotein A-I in idiopathic pulmonary fibrosis: Antiinflammatory and antifibrotic effect on experimental lung injury and fibrosis

Kim, T. H., Lee, Y. H., Kim, K. H., Lee, S. H., Cha, J. Y., Shin, E. K., Jung, S., Jang, A. S., Park, S. W., Uh, S. T., Kim, Y. H., Park, J. S., Sin, H. G., Youm, W., Koh, E. S., Cho, S. Y., Paik, Y. K., Rhim, T. Y. & Park, C. S., 2010 Sep 1, In : American Journal of Respiratory and Critical Care Medicine. 182, 5, p. 633-642 10 p.

Research output: Contribution to journalArticle

64 Citations (Scopus)

Simple method for quantitative analysis of N-linked glycoproteins in hepatocellular carcinoma specimens

Lee, H. J., Na, K., Choi, E. Y., Kim, K. S., Kim, H. & Paik, Y. K., 2010 Jan 4, In : Journal of Proteome Research. 9, 1, p. 308-318 11 p.

Research output: Contribution to journalArticle

37 Citations (Scopus)

Snail1 is stabilized by O-GlcNAc modification in hyperglycaemic condition

Park, S. Y., Kim, H. S., Kim, N. H., Ji, S., Cha, S. Y., Kang, J. G., Ota, I., Shimada, K., Konishi, N., Nam, H. W., Hong, S. W., Yang, W. H., Roth, J., Yook, J. I. & Cho, J. W., 2010 Nov 17, In : EMBO Journal. 29, 22, p. 3787-3796 10 p.

Research output: Contribution to journalArticle

105 Citations (Scopus)

Structure based optimization of chromen-based TNF-α converting enzyme (TACE) inhibitors on S1′ pocket and their quantitative structure-activity relationship (QSAR) study

Yang, J. S., Chun, K., Park, J. E., Cho, M., Seo, J., Song, D., Yoon, H., Park, C. H., Joe, B. Y., Choi, J. H., Kim, M. H. & Han, G., 2010 Dec 15, In : Bioorganic and Medicinal Chemistry. 18, 24, p. 8618-8629 12 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)

Synthesis and evaluation of benzoxazole derivatives as 5-lipoxygenase inhibitors

Song, H., Oh, S. R., Lee, H. K., Han, G., Kim, J. H., Chang, H. W., Doh, K. E., Rhee, H. K. & Choo, H. Y. P., 2010 Nov 1, In : Bioorganic and Medicinal Chemistry. 18, 21, p. 7580-7585 6 p.

Research output: Contribution to journalArticle

20 Citations (Scopus)

The Asia Oceania Human Proteome Organisation Membrane Proteomics Initiative. Preparation and characterisation of the carbonate-washed membrane standard

Peng, L., Kapp, E. A., Fenyö, D., Kwon, M. S., Jiang, P., Wu, S., Jiang, Y., Aguilar, M. I., Ahmed, N., Baker, M. S., Cai, Z., Chen, Y. J., Van Chi, P., Chung, M. C. M., He, F., Len, A. C. L., Liao, P. C., Nakamura, K., Ngai, S. M., Paik, Y. K. & 12 others, Pan, T. L., Poon, T. C. W., Hosseini Salekdeh, G., Simpson, R. J., Sirdeshmukh, R., Srisomsap, C., Svasti, J., Tyan, Y. C., Dreyer, F. S., McLauchlan, D., Rawson, P. & Jordan, T. W., 2010 Nov, In : Proteomics. 10, 22, p. 4142-4148 7 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)

The loss of phenol sulfotransferase 1 in hepatocellular carcinogenesis

Yeo, M., Na, Y. M., Kim, D. K., Kim, Y. B., Wang, H. J., Lee, J. A., Cheong, J. Y., Lee, K. J., Paik, Y. K. & Cho, S. W., 2010 Jan, In : Proteomics. 10, 2, p. 266-276 11 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)
11 Citations (Scopus)

Tyrosylprotein sulfotransferase regulates collagen secretion in Caenorhabditis elegans.

Kim, T. H., Kim, D. H., Nam, H. W., Park, S. Y., Shim, J. & Cho, J. W., 2010 Apr, In : Molecules and cells. 29, 4, p. 413-418 6 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)
2009
22 Citations (Scopus)

A HUPO test sample study reveals common problems in mass spectrometry-based proteomics

Bell, A. W., Deutsch, E. W., Au, C. E., Kearney, R. E., Beavis, R., Sechi, S., Nilsson, T., Bergeron, J. J. M., Beardslee, T. A., Chappell, T., Meredith, G., Sheffield, P., Gray, P., Hajivandi, M., Pope, M., Predki, P., Kullolli, M., Hincapie, M., Hancock, W. S., Jia, W. & 82 others, Song, L., Li, L., Wei, J., Yang, B., Wang, J., Ying, W., Zhang, Y., Cai, Y., Qian, X., He, F., Meyer, H. E., Stephan, C., Eisenacher, M., Marcus, K., Langenfeld, E., May, C., Carr, S. A., Ahmad, R., Zhu, W., Smith, J. W., Hanash, S. M., Struthers, J. J., Wang, H., Zhang, Q., An, Y., Goldman, R., Carlsohn, E., van der Post, S., Hung, K. E., Sarracino, D. A., Parker, K., Krastins, B., Kucherlapati, R., Bourassa, S., Poirier, G. G., Kapp, E., Patsiouras, H., Moritz, R., Simpson, R., Houle, B., LaBoissiere, S., Metalnikov, P., Nguyen, V., Pawson, T., Wong, C. C. L., Cociorva, D., Yates, J. R., Ellison, M. J., Lopez-Campistrous, A., Semchuk, P., Wang, Y., Ping, P., Elia, G., Dunn, M. J., Wynne, K., Walker, A. K., Strahler, J. R., Andrews, P. C., Hood, B. L., Bigbee, W. L., Conrads, T. P., Smith, D., Borchers, C. H., Lajoie, G. A., Bendall, S. C., Speicher, K. D., Speicher, D. W., Fujimoto, M., Nakamura, K., Paik, Y. K., Cho, S. Y., Kwon, M. S., Lee, H. J., Jeong, S. K., Chung, A. S., Miller, C. A., Grimm, R., Williams, K., Dorschel, C., Falkner, J. A., Martens, L. & Vizcaíno, J. A., 2009, In : Nature Methods. 6, 6, p. 423-430 8 p.

Research output: Contribution to journalArticle

247 Citations (Scopus)

AIMP2 promotes TNFα-dependent apoptosis via ubiquitin-mediated degradation of TRAF2

Choi, J. W., Kim, D. G., Park, M. C., Um, J. Y., Han, J. M., Park, S. G., Choi, E. C. & Kim, S., 2009 Aug 1, In : Journal of cell science. 122, 15, p. 2710-2715 6 p.

Research output: Contribution to journalArticle

43 Citations (Scopus)

An international showcase of the rapid expansion of epigenetics

Choi, J. K. & Kim, Y. J., 2009 Dec, In : Epigenomics. 1, 2, p. 235-237 3 p.

Research output: Contribution to journalArticle

A novel γ-lactam-based histone deacetylase inhibitor potently inhibits the growth of human breast and renal cancer cells

Kwon, H. K., Ahn, S. H., Park, S. H., Park, J. H., Park, J. W., Kim, H. M., Park, S. K., Lee, K., Lee, C. W., Choi, E., Han, G. & Han, J. W., 2009 Oct, In : Biological and Pharmaceutical Bulletin. 32, 10, p. 1723-1727 5 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

A novel δ-lactam-based histone deacetylase inhibitor, KBH-A42, induces cell cycle arrest and apoptosis in colon cancer cells

Kang, M. R., Kang, J. S., Han, S. B., Kim, J. H., Kim, D. M., Lee, K., Lee, C. W., Lee, K. H., Lee, C. H., Han, G., Kang, J. S., Kim, H. M. & Park, S. K., 2009 Sep 1, In : Biochemical Pharmacology. 78, 5, p. 486-494 9 p.

Research output: Contribution to journalArticle

22 Citations (Scopus)

BiomarkerDigger: A versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers

Jeong, S. K., Kwon, M. S., Lee, E. Y., Lee, H. J., Sang, Y. C., Kim, H., Jong, S. Y., Omenn, G. S., Aebersold, R., Hanash, S. & Paik, Y. K., 2009 Jul, In : Proteomics. 9, 14, p. 3729-3740 12 p.

Research output: Contribution to journalArticle

21 Citations (Scopus)

Caenorhabditis elegans utilizes dauer pheromone biosynthesis to dispose of toxic peroxisomal fatty acids for cellular homoeostasis

Joo, H. J., Yim, Y. H., Jeong, P. Y., Jin, Y. X., Lee, J. E., Kim, H., Jeong, S. K., Chitwood, D. J. & Paik, Y. K., 2009 Aug 15, In : Biochemical Journal. 422, 1, p. 61-71 11 p.

Research output: Contribution to journalArticle

58 Citations (Scopus)

Caveolae-mediated entry of Salmonella typhimurium in a human M-cell model

Lim, J. S., Na, H. S., Lee, H. C., Choy, H. E., Park, S. C., Han, J. M. & Cho, K. A., 2009 Dec 25, In : Biochemical and Biophysical Research Communications. 390, 4, p. 1322-1327 6 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)

Chemoenzymatic syntheses of carbasugar analogues of nucleoside diphosphate sugars: UDP-carba-Gal, UDP-carba-GlcNAc, UDP-carba-Glc, and GDP-carba-Man

Seo, K. C., Kwon, Y. G., Kim, D. H., Jang, I. S., Cho, J. W. & Chung, S. K., 2009, In : Chemical Communications. 13, p. 1733-1735 3 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Effects of sterols on the development and aging of Caenorhabditis elegans.

Lee, E. Y., Jeong, P. Y., Kim, S. Y., Shim, Y. H., Chitwood, D. J. & Paik, Y. K., 2009, In : Methods in molecular biology (Clifton, N.J.). 462, p. 167-179 13 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Endogenous cGMP regulates adult longevity via the insulin signaling pathway in Caenorhabditis elegans

Hahm, J. H., Kim, S. & Paik, Y. K., 2009, In : Aging Cell. 8, 4, p. 473-483 11 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)

Excessive O-GlcNAcylation of proteins suppresses spontaneous cardiogenesis in ES cells

Kim, H. S., Park, S. Y., Choi, Y. R., Kang, J. G., Joo, H. J., Moon, W. K. & Cho, J. W., 2009 Aug 6, In : FEBS Letters. 583, 15, p. 2474-2478 5 p.

Research output: Contribution to journalArticle

26 Citations (Scopus)

Expression patterns of aurora kinase B, heat shock protein 47, and periostin in esophageal squamous cell carcinoma

Kwon, Y. J., Lee, S. J., Koh, J. S., Kim, S. H., Kim, Y. J. & Park, J. H., 2009, In : Oncology Research. 18, 4, p. 141-151 11 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Human plasma carboxylesterase 1, a novel serologic biomarker candidate for hepatocellular carcinoma

Na, K., Lee, E. Y., Lee, H. J., Kim, K. Y., Lee, H., Jeong, S. K., Jeong, A. S., Sang, Y. C., Kim, S. A., Si, Y. S., Kyung, S. K., Sung, W. C., Kim, H. & Paik, Y. K., 2009 Aug, In : Proteomics. 9, 16, p. 3989-3999 11 p.

Research output: Contribution to journalArticle

74 Citations (Scopus)

Identification and characterization of a dual-acting antinematodal agent against the pinewood nematode, Bursaphelenchus xylophilus

Oh, W. S., Jeong, P. Y., Joo, H. J., Lee, J. E., Moon, Y. S., Cheon, H. M., Kim, J. H., Lee, Y. U., Shim, Y. H. & Paik, Y. K., 2009 Nov 11, In : PloS one. 4, 11, e7593.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Implications of the nucleosome code in regulatory variation adaptation and evolution

Choi, J. K. & Kim, Y. J., 2009 Jul 1, In : Epigenetics. 4, 5, p. 18-22 5 p.

Research output: Contribution to journalArticle

Implications of the nucleosome code in regulatory variation adaptation and evolution

Choi, J. K. & Kim, Y. J., 2009 Jul 1, In : Epigenetics. 4, 5, p. 291-295 5 p.

Research output: Contribution to journalArticle

Open Access
7 Citations (Scopus)

Interview with Dr. Young-Ki Paik, President of the Human Proteome Organization (HUPO): Pharmacoproteomics and the approaching wave of "proteomics diagnostics"

Paik, Y. K., Graham, J. E., Jones, M., McDonald, F., Holmes, C. & Ozdemir, V., 2009 Dec, In : Current Pharmacogenomics and Personalized Medicine. 7, 4, p. 243-248 6 p.

Research output: Contribution to journalComment/debate

5 Citations (Scopus)

Intrinsic variability of gene expression encoded in nucleosome positioning sequences

Choi, J. K. & Kim, Y. J., 2009 Apr, In : Nature Genetics. 41, 4, p. 498-503 6 p.

Research output: Contribution to journalArticle

98 Citations (Scopus)

Isolating bronchial epithelial cell preparations from gross lung specimens

Kwon, Y. J., Lee, S. J., Koh, J. S., Kim, Y. J. & Park, J. H., 2009 Sep, In : In Vitro Cellular and Developmental Biology - Animal. 45, 9, p. 496-499 4 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

LysRS Serves as a Key Signaling Molecule in the Immune Response by Regulating Gene Expression

Yannay-Cohen, N., Carmi-Levy, I., Kay, G., Yang, C. M., Han, J. M., Kemeny, D. M., Kim, S., Nechushtan, H. & Razin, E., 2009 Jun 12, In : Molecular Cell. 34, 5, p. 603-611 9 p.

Research output: Contribution to journalArticle

101 Citations (Scopus)

Molecular time-course and the metabolic basis of entry into Dauer in Caenorhabditis elegans

Jeong, P. Y., Kwon, M. S., Joo, H. J. & Paik, Y. K., 2009 Jan 8, In : PloS one. 4, 1, e4162.

Research output: Contribution to journalArticle

35 Citations (Scopus)

Non-histone nuclear factor HMGB1 is phosphorylated and secreted in colon cancers

Kang, H. J., Lee, H., Choi, H. J., Youn, J. H., Shin, J. S., Ahn, Y. H., Yoo, J. S., Paik, Y. K. & Kim, H., 2009 Aug, In : Laboratory Investigation. 89, 8, p. 948-959 12 p.

Research output: Contribution to journalArticle

47 Citations (Scopus)

Nucleosome deposition and DNA methylation at coding region boundaries

Choi, J. K., Bae, J. B., Lyu, J., Kim, T. Y. & Kim, Y. J., 2009 Sep 1, In : Genome biology. 10, 9, R89.

Research output: Contribution to journalArticle

62 Citations (Scopus)

O-GlcNAc protein modification in cancer cells increases in response to glucose deprivation through glycogen degradation

Kang, J. G., Park, S. Y., Ji, S., Jang, I., Park, S., Kim, H. S., Kim, S. M., Yook, J. I., Park, Y. I., Roth, J. & Cho, J. W., 2009 Dec 11, In : Journal of Biological Chemistry. 284, 50, p. 34777-34784 8 p.

Research output: Contribution to journalArticle

53 Citations (Scopus)

Plasma protein profiles in early asthmatic responses to inhalation allergen challenge

Rhim, T., Choi, Y. S., Nam, B. Y., Uh, S. T., Park, J. S., Kim, Y. H., Paik, Y. K. & Park, C. S., 2009 Jan, In : Allergy: European Journal of Allergy and Clinical Immunology. 64, 1, p. 47-54 8 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)