Interdisciplinary Program of Integrated OMICS for Biomedical Sciences

Research Output

Filter
Review article
2019

Advances in Identifying and Characterizing the Human Proteome

Paik, Y. K., Overall, C. M., Corrales, F., Deutsch, E. W., Lane, L. & Omenn, G. S., 2019 Dec 6, In : Journal of Proteome Research. 18, 12, p. 4079-4084 6 p.

Research output: Contribution to journalReview article

Open Access

Ascaroside pheromones: Chemical biology and pleiotropic neuronal functions

Park, J. Y., Joo, H. J., Park, S. & Paik, Y. K., 2019 Aug 2, In : International journal of molecular sciences. 20, 16, 3898.

Research output: Contribution to journalReview article

Open Access
4 Citations (Scopus)

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0

Deutsch, E. W., Lane, L., Overall, C. M., Bandeira, N., Baker, M. S., Pineau, C., Moritz, R. L., Corrales, F., Orchard, S., Van Eyk, J. E., Paik, Y. K., Weintraub, S. T., Vandenbrouck, Y. & Omenn, G. S., 2019 Dec 6, In : Journal of Proteome Research. 18, 12, p. 4108-4116 9 p.

Research output: Contribution to journalReview article

10 Citations (Scopus)

Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project

Omenn, G. S., Lane, L., Overall, C. M., Corrales, F. J., Schwenk, J. M., Paik, Y. K., Van Eyk, J. E., Liu, S., Pennington, S., Snyder, M. P., Baker, M. S. & Deutsch, E. W., 2019 Dec 6, In : Journal of Proteome Research. 18, 12, p. 4098-4107 10 p.

Research output: Contribution to journalReview article

11 Citations (Scopus)
2018

Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function

Paik, Y. K., Lane, L., Kawamura, T., Chen, Y. J., Cho, J. Y., Labaer, J., Yoo, J. S., Domont, G., Corrales, F., Omenn, G. S., Archakov, A., Encarnación-Guevara, S., Lui, S., Salekdeh, G. H., Cho, J. Y., Kim, C. Y. & Overall, C. M., 2018 Dec 7, In : Journal of Proteome Research. 17, 12, p. 4042-4050 9 p.

Research output: Contribution to journalReview article

15 Citations (Scopus)

Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project

Omenn, G. S., Lane, L., Overall, C. M., Corrales, F. J., Schwenk, J. M., Paik, Y. K., Van Eyk, J. E., Liu, S., Snyder, M., Baker, M. S. & Deutsch, E. W., 2018 Dec 7, In : Journal of Proteome Research. 17, 12, p. 4031-4041 11 p.

Research output: Contribution to journalReview article

30 Citations (Scopus)

The role of keratins in the digestive system: lessons from transgenic mouse models

Yi, H., Yoon, H. N., Kim, S. & Ku, N. O., 2018 Oct 1, In : Histochemistry and cell biology. 150, 4, p. 351-359 9 p.

Research output: Contribution to journalReview article

4 Citations (Scopus)

Toward Completion of the Human Proteome Parts List: Progress Uncovering Proteins That Are Missing or Have Unknown Function and Developing Analytical Methods

Paik, Y. K., Overall, C. M., Corrales, F., Deutsch, E. W., Lane, L. & Omenn, G. S., 2018 Dec 7, In : Journal of Proteome Research. 17, 12, p. 4023-4030 8 p.

Research output: Contribution to journalReview article

8 Citations (Scopus)
2017

Advances in the Chromosome-Centric Human Proteome Project: looking to the future

Paik, Y. K., Omenn, G. S., Hancock, W. S., Lane, L. & Overall, C. M., 2017 Dec 2, In : Expert Review of Proteomics. 14, 12, p. 1059-1071 13 p.

Research output: Contribution to journalReview article

15 Citations (Scopus)

Progress and Future Direction of Chromosome-Centric Human Proteome Project

Paik, Y. K., Overall, C. M., Deutsch, E. W., Van Eyk, J. E. & Omenn, G. S., 2017 Dec 1, In : Journal of Proteome Research. 16, 12, p. 4253-4258 6 p.

Research output: Contribution to journalReview article

10 Citations (Scopus)
2016

ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining

Park, S. H., Lee, S. M., Kim, Y. J. & Kim, S., 2016 Dec 13, In : BMC bioinformatics. 17, 452.

Research output: Contribution to journalReview article

4 Citations (Scopus)

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1

Deutsch, E. W., Overall, C. M., Van Eyk, J. E., Baker, M. S., Paik, Y. K., Weintraub, S. T., Lane, L., Martens, L., Vandenbrouck, Y., Kusebauch, U., Hancock, W. S., Hermjakob, H., Aebersold, R., Moritz, R. L. & Omenn, G. S., 2016 Nov 4, In : Journal of Proteome Research. 15, 11, p. 3961-3970 10 p.

Research output: Contribution to journalReview article

105 Citations (Scopus)

Interplay of genetic and epigenetic alterations in hepatocellular carcinoma

Lee, S. M., Kim-Ha, J., Choi, W. Y., Lee, J., Kim, D., Lee, J., Choi, E. & Kim, Y. J., 2016 Jul, In : Epigenomics. 8, 7, p. 993-1005 13 p.

Research output: Contribution to journalReview article

16 Citations (Scopus)

Keratins: Biomarkers and modulators of apoptotic and necrotic cell death in the liver

Ku, N. O., Strnad, P., Bantel, H. & Omary, M. B., 2016 Jan 1, In : Hepatology. 64, 3, p. 966-976 11 p.

Research output: Contribution to journalReview article

34 Citations (Scopus)

Progress in the Chromosome-Centric Human Proteome Project as Highlighted in the Annual Special Issue IV

Paik, Y. K., Overall, C. M., Deutsch, E. W., Hancock, W. S. & Omenn, G. S., 2016 Nov 4, In : Journal of Proteome Research. 15, 11, p. 3945-3950 6 p.

Research output: Contribution to journalReview article

14 Citations (Scopus)
2015

Oligoadenylate synthase-like (OASL) proteins: dual functions and associations with diseases

Choi, U. Y. U., Kang, J. S., Hwang, Y. S. A. & Kim, Y. J., 2015 Jan 1, In : Experimental & molecular medicine. 47, p. e144

Research output: Contribution to journalReview article

69 Citations (Scopus)

Quest for missing proteins: Update 2015 on chromosome-centric human proteome project

Horvatovich, P., Lundberg, E. K., Chen, Y. J., Sung, T. Y., He, F., Nice, E. C., Goode, R. J., Yu, S., Ranganathan, S., Baker, M. S., Domont, G. B., Velasquez, E., Li, D., Liu, S., Wang, Q., He, Q. Y., Menon, R., Guan, Y., Corrales, F. J., Segura, V. & 34 others, Casal, J. I., Pascual-Montano, A., Albar, J. P., Fuentes, M., Gonzalez-Gonzalez, M., Diez, P., Ibarrola, N., Degano, R. M., Mohammed, Y., Borchers, C. H., Urbani, A., Soggiu, A., Yamamoto, T., Salekdeh, G. H., Archakov, A., Ponomarenko, E., Lisitsa, A., Lichti, C. F., Mostovenko, E., Kroes, R. A., Rezeli, M., Végvári, Á., Fehniger, T. E., Bischoff, R., Vizcaíno, J. A., Deutsch, E. W., Lane, L., Nilsson, C. L., Marko-Varga, G., Omenn, G. S., Jeong, S. K., Lim, J. S., Paik, Y. K. & Hancock, W. S., 2015 Sep 4, In : Journal of Proteome Research. 14, 9, p. 3415-3431 17 p.

Research output: Contribution to journalReview article

50 Citations (Scopus)

Recent advances in the chromosome-centric human proteome project: Missing proteins in the spot light

Paik, Y. K., Omenn, G. S., Overall, C. M., Deutsch, E. W. & Hancock, W. S., 2015 Sep 4, In : Journal of Proteome Research. 14, 9, p. 3409-3414 6 p.

Research output: Contribution to journalReview article

15 Citations (Scopus)
2014

Genome-wide proteomics, chromosome-centric human proteome project (C-HPP), Part II

Paik, Y. K., Omenn, G. S., Thongboonkerd, V., Marko-Varga, G. & Hancock, W. S., 2014 Jan 3, In : Journal of Proteome Research. 13, 1, p. 1-4 4 p.

Research output: Contribution to journalReview article

16 Citations (Scopus)

Protein-protein interactions and multi-component complexes of aminoacyl-tRNA synthetases.

Kim, J. H., Han, J. M. & Kim, S., 2014, In : Topics in current chemistry. 344, p. 119-144 26 p.

Research output: Contribution to journalReview article

21 Citations (Scopus)
2013

A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17

Liu, S., Im, H., Bairoch, A., Cristofanilli, M., Chen, R., Deutsch, E. W., Dalton, S., Fenyo, D., Fanayan, S., Gates, C., Gaudet, P., Hincapie, M., Hanash, S., Kim, H., Jeong, S. K., Lundberg, E., Mias, G., Menon, R., Mu, Z., Nice, E. & 11 others, Paik, Y. K., Uhlen, M., Wells, L., Wu, S. L., Yan, F., Zhang, F., Zhang, Y., Snyder, M., Omenn, G. S., Beavis, R. C. & Hancock, W. S., 2013 Jan 4, In : Journal of Proteome Research. 12, 1, p. 45-57 13 p.

Research output: Contribution to journalReview article

31 Citations (Scopus)

A first step toward completion of a genome-wide characterization of the human proteome

Marko-Varga, G., Omenn, G. S., Paik, Y-K. & Hancock, W. S., 2013 Jan 4, In : Journal of Proteome Research. 12, 1, p. 1-5 5 p.

Research output: Contribution to journalReview article

69 Citations (Scopus)

Intermediate filaments of the lung

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

Research output: Contribution to journalReview article

6 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 1, In : Epigenomics. 5, 2, p. 195-204 10 p.

Research output: Contribution to journalReview article

10 Citations (Scopus)
2012

Keratins: Markers and modulators of liver disease

Strnad, P., Paschke, S., Jang, K. H. & Ku, N. O., 2012 May 1, In : Current Opinion in Gastroenterology. 28, 3, p. 209-216 8 p.

Research output: Contribution to journalReview article

30 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)
2010

Caenorhabditis elegans proteomics comes of age

Shim, Y. H. & Paik, Y. K., 2010 Feb 1, In : Proteomics. 10, 4, p. 846-857 12 p.

Research output: Contribution to journalReview article

11 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 1, In : Molecules and cells. 30, 6, p. 497-506 10 p.

Research output: Contribution to journalReview article

101 Citations (Scopus)
2009

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)
2008

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)
2007

Epigenomics: Novel aspect of genomic regulation

Hwan, S. C., Jong, H. P. & Kim, Y. J., 2007 Mar 1, In : Journal of Biochemistry and Molecular Biology. 40, 2, p. 151-155 5 p.

Research output: Contribution to journalReview article

10 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 1, In : Hepatology. 46, 5, p. 1639-1649 11 p.

Research output: Contribution to journalReview article

114 Citations (Scopus)
2006

Biomarker discovery from the plasma proteome using multidimensional fractionation proteomics

Lee, H. J., Lee, E. Y., Kwon, M. S. & Paik, Y. K., 2006 Feb 1, In : Current Opinion in Chemical Biology. 10, 1, p. 42-49 8 p.

Research output: Contribution to journalReview article

89 Citations (Scopus)

C. elegans: An invaluable model organism for the proteomics studies of the cholesterol-mediated signaling pathway

Paik, Y. K., Jeong, S. K., Lee, E. Y., Jeong, P. Y. & Shim, Y. H., 2006 Aug 21, In : Expert Review of Proteomics. 3, 4, p. 439-453 15 p.

Research output: Contribution to journalReview article

10 Citations (Scopus)

Guidelines for the next 10 years of proteomics

Wilkins, M. R., Appel, R. D., Van Eyk, J. E., Chung, M. C. M., Görg, A., Hecker, M., Huber, L. A., Langen, H., Link, A. J., Paik, Y. K., Patterson, S. D., Pennington, S. R., Rabilloud, T., Simpson, R. J., Weiss, W. & Dunn, M. J., 2006 Jan, In : Proteomics. 6, 1, p. 4-8 5 p.

Research output: Contribution to journalReview article

262 Citations (Scopus)

'Heads and tails' of intermediate filament phosphorylation: multiple sites and functional insights

Omary, M. B., Ku, N. O., Tao, G. Z., Toivola, D. M. & Liao, J., 2006 Jul 1, In : Trends in Biochemical Sciences. 31, 7, p. 383-394 12 p.

Research output: Contribution to journalReview article

209 Citations (Scopus)
2005

Interactions between subunits of Drosophila Mediator and activator proteins

Kim, Y. J. & Lis, J. T., 2005 May 1, In : Trends in Biochemical Sciences. 30, 5, p. 245-249 5 p.

Research output: Contribution to journalReview article

32 Citations (Scopus)

Overview of innate immunity in Drosophila

Kim, T. & Kim, Y. J., 2005, In : Journal of biochemistry and molecular biology. 38, 2, p. 121-127 7 p.

Research output: Contribution to journalReview article

Open Access
71 Citations (Scopus)

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

Omenn, G. S., States, D. J., Adamski, M., Blackwell, T. W., Menon, R., Hermjakob, H., Apweiler, R., Haab, B. B., Simpson, R. J., Eddes, J. S., Kapp, E. A., Moritz, R. L., Chan, D. W., Rai, A. J., Admon, A., Aebersold, R., Eng, J., Hancock, W. S., Hefta, S. A., Meyer, H. & 20 others, Paik, Y. K., Yoo, J. S., Ping, P., Pounds, J., Adkins, J., Qian, X., Wang, R., Wasinger, V., Wu, C. Y., Zhao, X., Zeng, R., Archakov, A., Tsugita, A., Beer, I., Pandey, A., Pisano, M., Andrews, P., Tammen, H., Speicher, D. W. & Hanash, S. M., 2005 Aug 1, In : Proteomics. 5, 13, p. 3226-3245 20 p.

Research output: Contribution to journalReview article

595 Citations (Scopus)
2004

Carbohydrate arrays for functional studies of carbohydrates

Shin, I., Cho, J. W. & Boo, D. W., 2004 Sep, In : Combinatorial Chemistry and High Throughput Screening. 7, 6, p. 565-574 10 p.

Research output: Contribution to journalReview article

36 Citations (Scopus)

Studying simple epithelial keratins in cells and tissues

Ku, N. O., Toivola, D. M., Zhou, Q., Tao, G. Z., Zhong, B. & Omary, M. B., 2004 Jan 1, In : Methods in cell biology. 2004, 78, p. 489-517 29 p.

Research output: Contribution to journalReview article

62 Citations (Scopus)
2003

Molecular network and functional implications of macromolecular tRNA synthetase complex

Han, J. M., Kim, J. Y. & Kim, S., 2003 Apr 18, In : Biochemical and Biophysical Research Communications. 303, 4, p. 985-993 9 p.

Research output: Contribution to journalReview article

41 Citations (Scopus)
1999

The cytoskeleton of digestive epithelia in health and disease

Ku, N. O., Zhou, X., Toivola, D. M. & Omary, M. B., 1999 Dec, In : American Journal of Physiology - Gastrointestinal and Liver Physiology. 277, 6 40-6, p. G1108-G1137

Research output: Contribution to journalReview article

165 Citations (Scopus)
1998

Keratin modifications and solubility properties in epithelial cells and in vitro.

Omary, M. B., Ku, N. O., Liao, J. & Price, D., 1998, In : Sub-cellular biochemistry. 31, p. 105-140 36 p.

Research output: Contribution to journalReview article

172 Citations (Scopus)
1997

Intermediate filament proteins of the liver: Emerging disease association and functions

Omary, M. B. & Ku, N. O. N., 1997 Jan 1, In : Hepatology. 25, 5, p. 1043-1048 6 p.

Research output: Contribution to journalReview article

88 Citations (Scopus)
1996

Implications of intermediate filament protein phosphorylation

Ku, N. O., Liao, J., Chou, C. F. & Omary, M. B., 1996 Dec 1, In : Cancer and Metastasis Reviews. 15, 4, p. 429-444 16 p.

Research output: Contribution to journalReview article

92 Citations (Scopus)

Mediator of transcriptional regulation

Björklund, S. & Kim, Y-J., 1996 Jan 1, In : Trends in Biochemical Sciences. 21, 9, p. 335-337 3 p.

Research output: Contribution to journalReview article

103 Citations (Scopus)

Two-dimensional gel analysis of glandular keratin intermediate filament phosphorylation

Liao, J., Ku, N. O. & Omary, M. B., 1996 Nov, In : Electrophoresis. 17, 11, p. 1671-1676 6 p.

Research output: Contribution to journalReview article

24 Citations (Scopus)