Interdisciplinary Program of Integrated OMICS for Biomedical Sciences

Research Output

2013

Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer

Zhang, E. Y., Cristofanilli, M., Robertson, F., Reuben, J. M., Mu, Z., Beavis, R. C., Im, H., Snyder, M., Hofree, M., Ideker, T., Omenn, G. S., Fanayan, S., Jeong, S. K., Paik, Y. K., Zhang, A. F., Wu, S. L. & Hancock, W. S., 2013, In : Journal of Proteome Research. 12, 6, p. 2805-2817 13 p.

Research output: Contribution to journalArticle

29 Citations (Scopus)

Human liver carboxylesterase 1 outperforms alpha-fetoprotein as biomarker to discriminate hepatocellular carcinoma from other liver diseases in Korean patients

Na, K., Jeong, S. K., Lee, M. J., Cho, S. Y., Kim, S. A., Lee, M. J., Song, S. Y., Kim, H., Kim, K. S., Lee, H. W. & Paik, Y. K., 2013 Jul 15, In : International Journal of Cancer. 133, 2, p. 408-415 8 p.

Research output: Contribution to journalArticle

21 Citations (Scopus)

Identification of methyl violet 2B as a novel blocker of focal adhesion kinase signaling pathway in cancer cells

Kim, H., Kim, N. D., Lee, J., Han, G. & Sim, T., 2013 Jul 26, In : Biochemical and Biophysical Research Communications. 437, 2, p. 319-324 6 p.

Research output: Contribution to journalArticle

Interleukin-1β induced by Helicobacter pylori infection enhances mouse gastric carcinogenesis

Shigematsu, Y., Niwa, T., Rehnberg, E., Toyoda, T., Yoshida, S., Mori, A., Wakabayashi, M., Iwakura, Y., Ichinose, M., Kim, Y. J. & Ushijima, T., 2013 Oct 28, In : Cancer Letters. 340, 1, p. 141-147 7 p.

Research output: Contribution to journalArticle

44 Citations (Scopus)

Intermediate filaments of the lung

Yi, H. & Ku, N. O., 2013 Jul, In : Histochemistry and cell biology. 140, 1, p. 65-69 5 p.

Research output: Contribution to journalReview article

7 Citations (Scopus)

Large protein complexes retained in the ER are dislocated by non-COPII vesicles and degraded by selective autophagy

Le Fourn, V., Park, S., Jang, I., Gaplovska-Kysela, K., Guhl, B., Lee, Y., Cho, J. W., Zuber, C. & Roth, J., 2013 Jun, In : Cellular and Molecular Life Sciences. 70, 11, p. 1985-2002 18 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Manufacturing and physicochemical properties of wine using hardy kiwi fruit (Actinidia arguta)

Park, K. L., Hong, S. W., Kim, Y. J., Kim, S. J. & Chung, K. S., 2013 Sep, In : Korean Journal of Microbiology and Biotechnology. 41, 3, p. 327-334 8 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Multiple reaction monitoring of multiple low-abundance transcription factors in whole lung cancer cell lysates

Kim, J. S., Lee, Y., Lee, M. Y., Shin, J., Han, J. M., Yang, E. G., Yu, M. H., Kim, S., Hwang, D. & Lee, C., 2013, In : Journal of Proteome Research. 12, 6, p. 2582-2596 15 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Negative Regulation of Type I IFN Expression by OASL1 Permits Chronic Viral Infection and CD8+ T-Cell Exhaustion

Lee, M. S., Park, C. H., Jeong, Y. H., Kim, Y. J. & Ha, S. J., 2013 Jul, In : PLoS Pathogens. 9, 7, e1003478.

Research output: Contribution to journalArticle

33 Citations (Scopus)

New synthetic aliphatic sulfonamido-quaternary ammonium salts as anticancer chemotherapeutic agents

Song, D., Yang, J. S., Oh, C., Cui, S., Kim, B. K., Won, M., Lee, J. I., Kim, H. M. & Han, G., 2013, In : European Journal of Medicinal Chemistry. 69, p. 670-677 8 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

NSBP-1 mediates the effects of cholesterol on insulin/IGF-1 signaling in Caenorhabditis elegans

Cheong, M. C., Lee, H. J., Na, K., Joo, H. J., Avery, L., You, Y. J. & Paik, Y. K., 2013 May, In : Cellular and Molecular Life Sciences. 70, 9, p. 1623-1636 14 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

OASL1 inhibits translation of the type i interferon-regulating transcription factor IRF7

Lee, M. S., Kim, B., Oh, G. T. & Kim, Y. J., 2013 Apr, In : Nature Immunology. 14, 4, p. 346-355 10 p.

Research output: Contribution to journalArticle

82 Citations (Scopus)

O-linked β-N-acetylglucosaminidase inhibitor attenuates β-amyloid plaque and rescues memory impairment

Kim, C., Nam, D. W., Park, S. Y., Song, H., Hong, H. S., Boo, J. H., Jung, E. S., Kim, Y., Baek, J. Y., Kim, K. S., Cho, J. W. & Mook-Jung, I., 2013 Jan, In : Neurobiology of Aging. 34, 1, p. 275-285 11 p.

Research output: Contribution to journalArticle

61 Citations (Scopus)

P300-mediated acetylation of TRF2 is required for maintaining functional telomeres

Her, Y. R. & Chung, I. K., 2013 Feb, In : Nucleic acids research. 41, 4, p. 2267-2283 17 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Predisposition to apoptosis in keratin 8-null liver is related to inactivation of NF-κB and SAPKs but not decreased c-Flip

Lee, J., Jang, K. H., Kim, H., Lim, Y., Kim, S., Yoon, H. N., Chung, I. K., Roth, J. & Ku, N. O., 2013 Jul 15, In : Biology Open. 2, 7, p. 695-702 8 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Synthesis and biological evaluation of novel aliphatic amido-quaternary ammonium salts for anticancer chemotherapy: Part II

Yang, J. S., Song, D., Ko, W. J., Kim, B., Kim, B. K., Park, S. K., Won, M., Lee, K., Lee, K., Kim, H. M. & Han, G., 2013, In : European Journal of Medicinal Chemistry. 63, p. 621-628 8 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

The Third ACGG-DB Meeting Report: Towards an international collaborative infrastructure for glycobioinformatics

Aoki-Kinoshita, K. F., Sawaki, H., An, H. J., Cho, J. W., Hsu, D., Kato, M., Kawano, S., Kawasaki, T., Khoo, K. H., Kim, J., Kim, J. D., Li, X., Lütteke, T., Okuda, S., Packer, N. H., Paulson, J. C., Raman, R., Ranzinger, R., Shen, H., Shikanai, T. & 7 others, Yamada, I., Yang, P., Yamaguchi, Y., Ying, W., Yoo, J. S., Zhang, Y. & Narimatsu, H., 2013 Feb, In : Glycobiology. 23, 2, p. 144-146 3 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Transcriptional and epigenetic networks in the development and maturation of dendritic cells

Kim, H. P., Lee, Y. S., Park, J. H. & Kim, Y. J., 2013 Apr, In : Epigenomics. 5, 2, p. 195-204 10 p.

Research output: Contribution to journalReview article

10 Citations (Scopus)
2012

A role for O-GlcNAcylation in setting circadian clock speed

Kim, E. Y., Jeong, E. H., Park, S., Jeong, H. J., Edery, I. & Cho, J. W., 2012 Mar 1, In : Genes and Development. 26, 5, p. 490-502 13 p.

Research output: Contribution to journalArticle

73 Citations (Scopus)

A versatile assay for monitoring in vivo-like transendothelial migration of neutrophils.

Han, S., Yan, J. J., Shin, Y., Jeon, J. J., Won, J., Jeong, H. E., Kamm, R. D., Kim, Y. J. & Chung, S., 2012 Oct 21, In : Lab on a chip. 12, 20, p. 3861-3865 5 p.

Research output: Contribution to journalArticle

48 Citations (Scopus)

Differential gel-based proteomic approach for cancer biomarker discovery using human plasma

Na, K., Lee, M. J., Jeong, H. J., Kim, H. & Paik, Y. K., 2012, Difference Gel Electrophoresis (DIGE): Methods and Protocols. p. 223-237 15 p. (Methods in Molecular Biology; vol. 854).

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)

Early-stage formation of an epigenetic field defect in a mouse colitis model, and non-essential roles of T-and B-cells in DNA methylation induction

Katsurano, M., Niwa, T., Yasui, Y., Shigematsu, Y., Yamashita, S., Takeshima, H., Lee, M. S., Kim, Y. J., Tanaka, T. & Ushijima, T., 2012 Jan 19, In : Oncogene. 31, 3, p. 342-351 10 p.

Research output: Contribution to journalArticle

52 Citations (Scopus)

Enhanced delivery of T cells to tumor after chemotherapy using membrane-anchored, apoptosis-targeted peptide

He, X., Bonaparte, N., Kim, S., Acharya, B., Lee, J. Y., Chi, L., Lee, H. J., Paik, Y. K., Moon, P. G., Baek, M. C., Lee, E. K., Kim, J. H., Kim, I. S. & Lee, B. H., 2012 Sep 28, In : Journal of Controlled Release. 162, 3, p. 521-528 8 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Gene expression profiling of KBH-A42, a novel histone deacetylase inhibitor, in human leukemia and bladder cancer cell lines

Kang, M. R., Kang, J. S., Yang, J. W., Kim, B. G., Kim, J. A., Jo, Y. N., Lee, K., Lee, C. W., Lee, K. H., Yun, J., Kim, H. M., Han, G., Kang, J. S. & Park, S. K., 2012 Jan, In : Oncology Letters. 3, 1, p. 113-118 6 p.

Research output: Contribution to journalArticle

13 Citations (Scopus)

Genome-wide analysis of DNA methylation and the gene expression change in lung cancer

Kwon, Y. J., Lee, S. J., Koh, J. S., Kim, S. H., Lee, H. W., Kang, M. C., Bae, J. B., Kim, Y. J. & Park, J. H., 2012 Jan, In : Journal of Thoracic Oncology. 7, 1, p. 20-33 14 p.

Research output: Contribution to journalArticle

63 Citations (Scopus)

Hsp90 rescues PTK6 from proteasomal degradation in breast cancer cells

Kang, S. A., Cho, H. S., Yoon, J. B., Chung, I. K. & Lee, S. T., 2012 Oct 15, In : Biochemical Journal. 447, 2, p. 313-320 8 p.

Research output: Contribution to journalArticle

21 Citations (Scopus)

Identification of CD23 as a functional receptor for the proinflammatory cytokine AIMP1/p43

Kwon, H. S., Park, M. C., Kim, D. G., Cho, K., Park, Y. W., Han, J. M. & Kim, S., 2012, In : Journal of cell science. 125, 19, p. 4620-4629 10 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Induction of aberrant trimethylation of histone H3 lysine 27 by inflammation in mouse colonic epithelial cells

Takeshima, H., Ikegami, D., Wakabayashi, M., Niwa, T., Kim, Y. J. & Ushijima, T., 2012 Dec, In : Carcinogenesis. 33, 12, p. 2384-2390 7 p., bgs294.

Research output: Contribution to journalArticle

20 Citations (Scopus)

Keratins: Markers and modulators of liver disease

Strnad, P., Paschke, S., Jang, K. H. & Ku, N. O., 2012 May, In : Current Opinion in Gastroenterology. 28, 3, p. 209-216 8 p.

Research output: Contribution to journalReview article

30 Citations (Scopus)

Leucyl-tRNA synthetase is an intracellular leucine sensor for the mTORC1-signaling pathway

Han, J. M., Jeong, S. J., Park, M. C., Kim, G., Kwon, N. H., Kim, H. K., Ha, S. H., Ryu, S. H. & Kim, S., 2012 Apr 13, In : Cell. 149, 2, p. 410-424 15 p.

Research output: Contribution to journalArticle

450 Citations (Scopus)

Neutrophils promote mycobacterial trehalose dimycolate-induced lung inflammation via the mincle pathway

Lee, W. B., Kang, J. S., Yan, J. J., Lee, M. S., Jeon, B. Y., Cho, S. N. & Kim, Y. J., 2012 Apr, In : PLoS Pathogens. 8, 4, e1002614.

Research output: Contribution to journalArticle

89 Citations (Scopus)

Nictation, a dispersal behavior of the nematode Caenorhabditis elegans, is regulated by IL2 neurons

Lee, H., Choi, M. K., Lee, D., Kim, H. S., Hwang, H., Kim, H., Park, S., Paik, Y. K. & Lee, J., 2012 Jan, In : Nature Neuroscience. 15, 1, p. 107-112 6 p.

Research output: Contribution to journalArticle

74 Citations (Scopus)

Normalization using a tagged-internal standard assay for analysis of antibody arrays and the evaluation of serological biomarkers for liver disease

Kong, D. H., Jung, J. W., Na, K., Jeong, S. K., Paik, Y. K., Jung, S. H., Suh, I. B., Kim, Y. M. & Ha, K. S., 2012 Mar 9, In : Analytica Chimica Acta. 718, p. 92-98 7 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Nuclear import of htert requires a bipartite nuclear localization signal and Akt-mediated phosphorylation

Chung, J., Khadka, P. & Chung, I. K., 2012 Jun 1, In : Journal of cell science. 125, 11, p. 2684-2697 14 p.

Research output: Contribution to journalArticle

57 Citations (Scopus)

O-GlcNAc modification of PPARγ reduces its transcriptional activity

Ji, S., Park, S. Y., Roth, J., Kim, H. S. & Cho, J. W., 2012 Jan 27, In : Biochemical and Biophysical Research Communications. 417, 4, p. 1158-1163 6 p.

Research output: Contribution to journalArticle

41 Citations (Scopus)

Panelcomposer: A web-based panel construction tool for multivariate analysis of disease biomarker candidates

Jeong, S. K., Na, K., Kim, K. Y., Kim, H. & Paik, Y. K., 2012 Dec 7, In : Journal of Proteome Research. 11, 12, p. 6277-6281 5 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

PDHK-2 deficiency is associated with attenuation of lipase-mediated fat consumption for the increased survival of caenorhabditis elegans dauers

Kim, S., Shin, E. J., Hahm, J. H., Park, P. J., Hwang, J. E. & Paik, Y. K., 2012 Jul 27, In : PloS one. 7, 7, e41755.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Property-based optimization of hydroxamate-based γ-lactam HDAC inhibitors to improve their metabolic stability and pharmacokinetic profiles

Choi, E., Lee, C., Cho, M., Seo, J. J., Yang, J. S., Oh, S. J., Lee, K., Park, S. K., Kim, H. M., Kwon, H. J. & Han, G., 2012 Dec 13, In : Journal of Medicinal Chemistry. 55, 23, p. 10766-10770 5 p.

Research output: Contribution to journalArticle

23 Citations (Scopus)

Quantitative proteomic analysis of human embryonic stem cell differentiation by 8-Plex iTRAQ labelling

Jadaliha, M., Lee, H. J., Pakzad, M., Fathi, A., Jeong, S. K., Cho, S. Y., Baharvand, H., Paik, Y. K. & Salekdeh, G. H., 2012 Jun 18, In : PloS one. 7, 6, e38532.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Secreted human glycyl-tRNA synthetase implicated in defense against ERK-activated tumorigenesis

Park, M. C., Kang, T., Jin, D., Han, J. M., Kim, S. B., Park, Y. J., Cho, K., Park, Y. W., Guo, M., He, W., Yang, X. L., Schimmel, P. & Kim, S., 2012 Mar 13, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 11, p. E640-E647

Research output: Contribution to journalArticle

71 Citations (Scopus)
11 Citations (Scopus)

Standard guidelines for the chromosome-centric human proteome project

Paik, Y. K., Omenn, G. S., Uhlen, M., Hanash, S., Marko-Varga, G., Aebersold, R., Bairoch, A., Yamamoto, T., Legrain, P., Lee, H. J., Na, K., Jeong, S. K., He, F., Binz, P. A., Nishimura, T., Keown, P., Baker, M. S., Yoo, J. S., Garin, J., Archakov, A. & 3 others, Bergeron, J., Salekdeh, G. H. & Hancock, W. S., 2012 Apr 6, In : Journal of Proteome Research. 11, 4, p. 2005-2013 9 p.

Research output: Contribution to journalReview article

118 Citations (Scopus)

Structure-activity relationship of novel lactam based histone deacetylase inhibitors as potential anticancer drugs

Yang, J. S., Chun, T. G., Nam, K. Y., Kim, H. M. & Han, G., 2012 Jun 20, In : Bulletin of the Korean Chemical Society. 33, 6, p. 2063-2066 4 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Structure and property based design, synthesis and biological evaluation of γ-lactam based HDAC inhibitors: Part II

Lee, C., Choi, E., Cho, M., Lee, B., Oh, S. J., Park, S. K., Lee, K., Kim, H. M. & Han, G., 2012 Jun 15, In : Bioorganic and Medicinal Chemistry Letters. 22, 12, p. 4189-4192 4 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)

The AAA-ATPase NVL2 is a telomerase component essential for holoenzyme assembly

Her, J. & Chung, I. K., 2012 Jan 20, In : Biochemical and Biophysical Research Communications. 417, 3, p. 1086-1092 7 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)

The characteristics of genome-wide DNA methylation in naïve CD4+ T cells of patients with psoriasis or atopic dermatitis

Han, J., Park, S. G., Bae, J. B., Choi, J. K., Lyu, J. M., Park, S. H., Kim, H. S., Kim, Y. J., Kim, S. & Kim, T. Y., 2012 May 25, In : Biochemical and Biophysical Research Communications. 422, 1, p. 157-163 7 p.

Research output: Contribution to journalArticle

33 Citations (Scopus)

The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome

Paik, Y. K., Jeong, S. K., Omenn, G. S., Uhlen, M., Hanash, S., Cho, S. Y., Lee, H. J., Na, K., Choi, E. Y., Yan, F., Zhang, F., Zhang, Y., Snyder, M., Cheng, Y., Chen, R., Marko-Varga, G., Deutsch, E. W., Kim, H., Kwon, J. Y., Aebersold, R. & 7 others, Bairoch, A., Taylor, A. D., Kim, K. Y., Lee, E. Y., Hochstrasser, D., Legrain, P. & Hancock, W. S., 2012 Mar, In : Nature Biotechnology. 30, 3, p. 221-223 3 p.

Research output: Contribution to journalLetter

226 Citations (Scopus)

The proto-oncoprotein KR-POK represses transcriptional activation of CDKN1A by MIZ-1 through competitive binding

Lee, K. M., Choi, W. I., Koh, D. I., Kim, Y. J., Jeon, B. N., Yoon, J. H., Lee, C. E., Kim, S. H., Oh, J. & Hur, M. W., 2012 Mar 15, In : Oncogene. 31, 11, p. 1442-1458 17 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Uniting ENCODE with genome-wide proteomics

Paik, Y. K. & Hancock, W. S., 2012 Nov, In : Nature Biotechnology. 30, 11, p. 1065-1067 3 p.

Research output: Contribution to journalArticle

34 Citations (Scopus)
2011

A new versatile peptide-based size exclusion chromatography platform for global profiling and quantitation of candidate biomarkers in hepatocellular carcinoma specimens

Lee, H. J., Na, K., Kwon, M. S., Park, T., Kim, K. S., Kim, H. & Paik, Y. K., 2011 May, In : Proteomics. 11, 10, p. 1976-1984 9 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)