Graduate School

Heenam Stanley Kim Professor

Heenam Stanley Kim 교수

김희남 / Heenam Stanley Kim

  • Dept
  • RankProfessor
  • Majorgenomics
  • Lab
  • Phone안1422
  • Fax
  • Emailhstanleykim@korea.ac.kr
Papers
Han Song, Junghyun Hwang, Hyojeong Yi, Ricky L. Ulrich, Yan Yu, William C. Nierman, and H. Stanley Kim.. 2010. The early stage of bacterial genome-reductive evolution in the host. PLoS Pathogens. 6(5): e1000922.

Eun Jin Park, Jun-Yong Lee, Jun Hyup Kim, Cheol Jin Lee, H.StanleyKim, and Nam Ki Min. 2010. Investigation of plasma-functionalized multiwalled carbon nanotube film and its application of DNA sensor for Legionella pneumophila detection. TALANTA 82:904-911.

Liliana Losada, Catherine M. Ronning, David DeShazer, Donald Woods, Natalie Fedorova, H. Stanley Kim, Svetlana A. Shabalina, Talima R. Pearson, Lauren Brinkac, Patrick Tan, Tannistha Nandi, Jonathan Crabtree, Jonathan Badger, Steve Beckstrom-Sternberg, Muhammad Saqib, Steven E. Schutzer, Paul Keim, and William C. Nierman. 2010. Genome Biology and Evolution.Vol. 2010, 102-116; doi:10.1093/gbe/evq003 published on February 22, 2010

Jeong, HW, Cheong, HJ, Kim, WJ, Kim, MJ, Song, KJ, Song, JW, Kim,HS, and Roh, KH. 2009. Loss of 29-kilodalton outer membrane protein in the presence of Oxa-51-like enzymes in Acinetobacter baumanniiis associated with decreased imipenem susceptibility. Microbial Drug Resistance. 15 (3): 151-158.

Han Song, Junghyun Hwang, Jaehee Myung, Hyoseok Seo, Hyojeong Yi, Hee-Sun Sim, Bong-Su Kim, William C. Nierman, and H. Stanley Kim. 2009 (Feb). Simple Sequence Repeat (SSR)-based gene diversity inBurkholderia pseudomalleiand Burkholderia mallei. Mol. Cells. 27(2): 237-241.

McDonagh, A., Fedorova, N.D., Crabtree, J., Yu, Y., Kim,H.S., Chen, D., Loss, O., Cairns, T., Goldman, G., Armstrong-James, D., Haynes, K., Haas, H., Schrettl, M., May, G., Nierman, W.C., Bignell, E. Sub-telomere directed gene expression during initiation of invasive aspergillosis. 2008. PLoS Pathogens. 4(9): e1000154.

Sugui, JA, Kim,H.Stanley, Zarember, KA, Chang, YC, Gallin, JI, Nierman, WC, and Kwon-Chung, KJ. 2008. Genes differentially expressed in conidia and hyphae of Aspergillus fumigatusto human neutrophils. PLoS ONE.3(7):e2655.

Markus Schrettl*,H.StanleyKim*,Martin Eisendle, Claudia Kragl, William Nierman, Thorsten Heinekamp, Ernst R. Werner, Ilse Jacobsen, Paul Illmer, Hyojeong Yi, Axel A. Brakhage, and Hubertus Haas. 2008. SreA-mediated iron regulation in Aspergillus fumigatus. Molecular Microbiology. 70(1): 27-43.
*Co-first author.

Moon, JH., Park, A.K., Jang, E.H, Kim,H.S., Chi, Y.M. 2008. Crystal structure of a PduO-type ATP:cobalamin adenosyltransferase from Burkholderia thailandensis. Proteins. 72(3): 1066-1070.
Kim, HS*., Lee, HJ, Myung, JH, Piper, K.R., and Farrand, S. K. 2008. Opine-based Agrobacteriumcompetitiveness: dual expression control of the agrocinopine catabolism (acc) operon by agrocinopines and phosphate levels. J. Bacteriol. 190(10): 3700-3711.
First and corresponding author

Ruchi Bhabhra,Richie, D.L., H.StanleyKim, William Nierman, Fortwendel, J., Aris, J.P., Judith C. Rhodes, David S. Askew. 2008. Impaired ribosome biogenesis disrupts the integration between mophogenesis and nuclear duplication during the germination of Aspergillus fumigatus. Eukaryotic Cell.7(4): 575-583.

Chopra, P., Kang, J., Yang, J., Cho, H.J., Kim,H.S., Lee, M.-G. 2008. Microarray data mining using landmark gene-guided clustering.BMC bioinformatics. 9: 92

Wilkinson, J.R., Yu, J., Abbas, H.K., Scheffler, B.E., Kim,H.S., Nierman, W.C., Bhatnagar, D., and Cleveland,T.E.2007.AflatoxinformationandgeneexpressioninresponsetocarbonsourcemediashiftinAspergillus parasiticus. Food Additives and Contaminants, October, 24(10): 1-10.

Mark A. Schell, Ricky L. Ulrich, Wilson J. Ribot, Ernst E. Brueggemann, Harry B. Hines, Dan Chen, Lyla Lipscomb, H.StanleyKim, Jan Mrazek, William C. Nierman, and David DeShazer. 2007. Type VI secretion is a major virulence determinant in Burkholderia mallei. Molecular Microbiology, 64(6): 1466-1485.

Perrin, R. M., Fedorova, N. D., Bok, J.W., Cramer Jr, R. A., J., Wortman, J. R., Kim,H.S.,Nierman, W. C., and Keller, N. P. 2007. Transcriptional regulation of chemical diversity in Aspergillus fumigatusby LaeA. PLoS Pathogens 3 (4): 508-517.

Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen J, Ronning CM, Barbazuk WB, Blanchard M, Field C, Halling C, Hinkle G, Iartchuk O, KimHS, Mackenzie C, Madupu R, Miller N, Shvartsbeyn A, Sullivan SA, Vaudin M, Wiegand R, Kaplan HB. 2006. Evolution of sensory complexity recorded in a myxobacterial genome. Proc. Natl. Acad. Sci. USA, 103(41):15200-15205.

Romero, C. M., D. DeShazer, T. Feldblyum, J. Ravel, D. Woods, H.S.Kim, Y. Yu, Ronning, C.M., and W. C. Nierman. 2006. Genome sequence alterations detected upon passage of Burkholderia malleiATCC23344 in culture and in mammalian hosts. BMC Genomics, 7:228.

Yu, Y., Kim,H.S.,Hoon, C.H., Rodrigues, F., Hoon, S.S., Derr, A., Engels, R., DeShazer, D., Birren, B., Nierman, W.C., and Tan, P. 2006. Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis. BMC Microbiology, 6:46.

Marcia Eliana da Silva Ferreira, Marcela Savoldi, Axel A. Brakhage, Maria Helena S. Goldman, H.StanleyKim, William Nierman, Gustavo H. Goldman. 2006. Transcriptome analysis of Aspergillus fumigatus exposed to voriconazole. Curr. Genet, 50(1):32-44.

Jiujiang Yu, Thomas E. Cleveland, Bruce C. Campbell, Jeffery R. Wilkinson, Jong H. Kim, H.StanleyKim, and William C. Nierman. 2006. Aspergillus flavus Expressed Sequence Tags and Microarray as Tools in Understanding Aflatoxin Biosynthesis. Mycotoxin Research. 22:16-21.

Michael S. Price, Jiujiang Yu, William C. Nierman, H.StanleyKim, Bethan Pritchard, Deepak Bhatnagar, Thomas E. Cleveland, and Gary A. Payne. 2006. The aflatoxin pathway regulatory gene aflRregulates genes outside of the aflatoxin biosynthetic cluster. FEMS Microbiol. Lett. 255(2): 275-9.
Ricky L. Ulrich, Melanie P. Ulrich, Mark A. Schell, H.Stanley.Kim, and David DeShazer. 2006. Development of a PCR Assay for the Specific Identification of Burkholderia malleiand Differentiation from Burkholderia pseudomalleiand Other Closely Related BurkholderiaSpecies. Diagn. Microbiol. Infect. Dis. 55(1): 37-45.

Ronning, C., Fedorova,N.D.,Bowyer,P.,Coulson,R.,Goldman,G.,Kim,H.S.,et al. 2005. Genomics of Aspergillus fumigatus. Rev. Iberoam. Micol. 22: 224-229.

William Nierman, Arnab Pain, Michael J. Anderson, Jennifer Wortman , H.StanleyKim, et.al. 2005. Genomic sequence of the pathogenic and allergenic Aspergillus fumigatus. Nature. 438:1151-1156.

Kim, HS.,Schell, M.A., Yu, Y., Ulrich, R.L, Sarria, S., Nierman, W.C., and DeShazer, D. 2005. Bacterial genome adaptation to niches: Divergence of the potential virulence genes in three Burkholderia species. BMC Genomics. 6:174.

Donald C. Sheppard, Lisa Y. Chiang, Thomas Doedt, H.StanleyKim, William C. Nierman, Scott G. Filler. 2005. The Aspergillus fumigatusStuA protein governs the upregulation of a discrete transcriptional program during the acquisition of developmental competence. Mol. Biol. Cell.16(12):5866-79.

Tuanyok, A., Kim,H.S., Yu, Y., Nierman, W.C., and Woods, DE. 2005. Genome-wide expression analysis of iron regulation in Burkholderia pseudomallei and Burkholderia mallei using DNA microarrays. FEMS Microbiol. Lett. 252: 327-335.

Nierman, W.C., May, G., Kim,H.S., Anderson,M.J.,Chen,D.,andDenning,D.2005 (May). What the Aspergillus genomes have told us. Medical Mycology. 43, supplement 1: 3-5.
Kim, H.S,Yu, Y., Snesrud, E.C., Moy, L.P., Linford, L.D., Haas, B.J., Nierman, C.W., and J. Quackenbush. 2005. Transcriptional divergence of the duplicated oxidative-stress-responsive genes in the Arabidopsisgenome. Plant J.41: 212-220.

William C. Nierman, David DeShazer, H.StanleyKim, Herve Tettelin, Karen E. Nelson, Tamara Feldblyum, Ricky L. Ulrich, Catherine M. Ronning, Lauren M. Brinkac, Sean C. Daugherty, Tanja D. Davidsen, Robert T. Deboy, Dimitrov, Robert J. Dodson, A. Scott Durkin, Michelle L. Gwinn, Daniel H. Haft, Hoda Khouri, James F. Kolonay, Ramana Madupu, Yasmin Mohammoud, William C. Nelson, Diana Radune, Claudia M. Romero, Saul Sarria, J. Selengut, Christine Shamblin, S. A. Sullivan, Owen White, Yan Yu, N. Zafar, L. Zhou,and Claire M. Fraser. 2004. Structural flexibility in the Burkholderiagenome. Proc. Natl. Acad. Sci. USA 101(39): 14246-14251.

Moore, R.A., Reckseidler-Zenteno, S., Kim,H.,Nierman W., Yu, Y., Tuanyok, A., Warawa, J., DeShazer, D., and D.E. Woods. 2004. Contribution of gene loss to the pathogenic evolution of Burkholderia pseudomalleiand Burkholderia mallei. Infect. Immun.72: 4172-4187.

Kim, H.,Snesrud, E.C., Hass, B., Cheung, F., Town, C.D., and J. Quackenbush. 2003. Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray. Genome Research. 13: 327-340.
Kim, H.,Zhao, B., Snesrud, E.C., Haas, B.J., Town, C.D., and J. Quackenbush. 2002. Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses. BioTechniques. 33: 924-930.

Sepulveda-Torres, L. C., A. Huang, H.Kim,and C. S. Criddle. 2002. Analysis of regulatory elements and genes required for carbon tetrachloride degradation in Pseudomonas stutzeristrain KC. J. Mol. Micro. Biotechnol.4: 151-161.
Kim, H.and S. K. Farrand.1998. Opine catabolic loci from Agrobacteriumplasmids confer chemotaxis to their cognate substrates. Molec. Plant-Microbe Interact.11:131-143.

Kim, H.and S. K. Farrand.1997. Characterization of the acc operon from the nopaline-type Ti plasmid pTiC58, which encodes utilization of agrocinopines A and B and susceptibility to agrocin 84. J. Bacteriol. 179:7559-7572.

Hayman, G. T., Beck Von Bodman, S., Kim,H., Jiang, P., and S. K. Farrand. 1993. Genetic analysis of the agrocinopine catabolic region of Agrobacterium tumefaciensTi plasmid pTiC58, which encodes genes required for opine and agrocin 84 transport. J. Bacteriol. 175:5575-5584.
Lab Intro
1. Profile
Microbial Genomics for pathogens and human commensal bacteria

Dr. Kim joined Korea University Medical College in the spring semester of 2006, after 18 years of professional life in the United States of America. He is a microbial geneticist by training, a graduate from the Department of Microbiology of the University of lllinois at Urbana-Champaign receiving Master’s and Ph. D. degrees. He augmented and broadened his biological background during the postdoctoral years at the Stanford University studying environmental microbiology and the newly-born microarray technology at the time. In 2001, he moved to TIGR (The Institute for Genomic Research, Rockville, Maryland), which is now called J. Craig Venter Institute (http://www.jcvi.org), and obtained hands-on experiences on cutting edge bioinformatics and genomics while conducting various functional genomic projects, including those with a plant (i.e. Arabidopsis thaliana), a few bacteria (i.e. Burkholderia spp. and Myxococcus), and a couple of fungal species (i.e. Aspergillus fumigatus and Aspergillus flavus), as a staff scientist until the time he left the institute to become a Korea University faculty.

In his new lab in Korea University, Dr. Kim is continuing his work at TIGR (J. Craig Venter Institute) with a few important human pathogens that belong to Burkholderia and Aspergillus. He is interested in identifying virulence genes in these pathogens and understanding their roles in pathogenesis. The knowledge accumulated through his studies will be used to develop accurate diagnostic tools for the pathogen infections and, ultimately, therapeutic means and vaccines.

His research is being expanded and covers more bacterial pathogens, including Legionella pneumophila and Streptococcus pneumoniae. The main tools for research are bioinformatics for genome sequence analyses and comparisons, microarray-based functional genomics, and classical microbial genetics. Dr. Kim’s laboratory is well equipped for such research, with custom microarray construction capability. In this golden era of genomics with rich public genome resources, there is no doubt that the present is an exciting time for microbial genomic studies to fight better in our old war against infectious diseases.

Also being developed in his lab are the new studies with human commensal bacteria, especially those in the guts. Animals including humans exhibit distinct patterns of gut microbiota (microbial community) based on their genetic, physiological, and pathological characteristics. A variety of diseases, including Inflammatory bowel Disease, Coloncancer, autism, atopic diseases, and obesity, have been implicated with specific composition of the gut microbiota. This suggests that gut microbial profiles could be used as health indicators and also as the subjects for treatments. This area of research is new in the world and is considered to be of tremendous impact in the future microbiological research and in medicine.

2. Research Area

◈ Genomics and bioinformatics of human pathogens, mainly bacterial and fungal
◈ Evolution of virulence genes in microorganisms
◈ Genomics and bioinformatics of potential biowarfare agents
◈ Biomarker selection from pathogens for the use of precise detection and future development of therapeutics and vaccines.
◈ Studies on human symbiotic microbiota and microbiome in relation to human health

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