김동혁

Donghyuk  Kim

 

- Research Interests 

Systems Biology, Computational Biology, Bioconversion bacterial strains, Bacterial Pathogen

 

- Education

University of California, San Diego, California, USA, 2014

   Degree : Ph.D., Bioengineering

   Thesis : Systems Assessment of Regulator Components in Bacterial Transcription Initiation

   Adviser : Dr. Bernhard O. Palsson, Systems Biology Research Group

Seoul National University, Seoul, Korea, 2006

   Degree : B.S., Computer Science and Engineering

   Thesis : Pattern Classification and Completion by Probabilistic Library Model

   Adviser : Dr. Byung-Tak Zhang, Biointelligence Lab

   Degree : B.S., Biological Sciences

   Thesis : Designing Efficient siRNAs for Gene Silencing

   Adviser : Dr. V. Narry Kim, RNomics Lab

 

- Professional Activity

 Editor, Journal of Microbiology and Biotechnology, March 2017 ~ Present

   Committee of Research Affairs, Korean Society of Bioinformatics and Systems Biology, March 2017 ~ Present

   Member, The Korean Society for Microbiology and Biotechnology, Jan 2018 ~ Present

   Member, The Korean Society for Biotechnology and Bioengineering, Sep 2017 ~ Present

   Member, The Microbiological Society of Korea, Feb 2018 ~ Present

   Member, The Korean Society of Industrial and Engineering Chemistry, Sep 2017 ~ Present

 

- Publications

 1. Deciphering bacterial xylose metabolism and metabolic engineering of industrial microorganisms for use as efficient microbial cell factories. Kim D, Woo HM. Appl Microbiol Biotechnol. In press.

 2. Genomic characterization of the lytic bacteriophage phiEaP-8 effective against both Erwinia amylovora and Erwinia pyrifoliae causing severe diseases in apple and pear. Park J, Lee GM, Kim D, Park DH, Oh CS. Plant Pathol J, In Press.

 3. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. Gao Y, Yurkovich JT, Seo SW, Kabimoldayev I, Drager A, Chen K, Sastry A, Mih N, Yang L, Eichner J, Cho BK, Kim D*, Palsson BO*. Nucleic Acids Res, 2018 Aug 23. doi.org/10.1093/nar/gky752.

 4. Draft genome sequence of lytic bacteriophage KP1 infecting Klebsiella pneumoniae. Kim Y#, Bang I#, Yeon YE, Park JY, Han BK, Kim H, Ahn JK, Kim D. Korean J Microbiol, 2018 Jul 2. doi.org/10.7845/kjm.2018.54.2.152.

 5. Draft genome sequence of lytic bcteriophage CP3 infecting anaerobic bacterial pathogen Clostridium perfrigens. Kim Y#, Ko S#, Yeon YE, Le HT, Han BK, Kim H, Oh CS, Kim D. Korean J Microbiol, 2018 Jul 2. doi:10.7845/kjm.2018.54.2.149.

 6. Coordination-driven self-assembly and anticancer studies of thiophene-derived donor and arene ruthenium acceptors. Kim T#, Song HS#, Singh J, Kim D, Kim H, Kang SC*, Chi KW*. Inorganica Chimica Acta. 2018 May 28. doi:10.1016/j.ica.2018.05.035.

 7. Systematic metabolic engineering of Methylomicrobium alcaliphilum 20Z for 2,3-butanediol production from methane. Nguyen AD, Hwang IY, Lee OK, Kim D, Kalyuzhnaya MG, Mariyana R, Hadiyati S, Kim MS*, Lee YE*. Metab Eng, 2018 Apr 16. doi: 10.1016/j.ymben.2018.04.010.

 8. Draft Genome Sequence of Lytic Bacteriophage CF1 Infecting Citrobacter freundii Isolates. Kim YJ, Ko S, Yeon YE, Lim J, Han BK, Kim H, Ahn JK, Kim D. Korean J Microbiol, 2018 Apr 1. doi:10.7845/kjm.2018.7099.

 9. Draft Genome Sequence of Lytic Bacteriophage SA7 Infecting Staphylococcus aureus Isolates. Kim YJ, Lee GM, Taizhanova A, Han BK, Kim H, Ahn JK, Kim D. Korean J Microbiol, 2018 Apr 1. doi:10.7845/kjm.2018.7098.

 10. Draft genome sequence of a bacterial plant pathogen Erwinia pyrifoliae strain EpK1/15 isolated from an apple twig showing black shoot blight. Lee GM, Oh EJ, Park J, Ko S, Park DH, Kim D*, Oh CS*. Korean J Microbiol, 2018 Apr 1. doi:10.7845/kjm.2018.7087.

 11. Isolation and identification of novel equol-producing bacterial strains. Kwon JE, Lim J, Kim I, Kim D*, Kang SC*. PLoS One, 2018 Feb 15;13(2):e0192490. doi:10.1371/journal.pone.0192490

 12. Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP. Kim D#,*, Seo SW#, Gao Y#, Nam H, Guzman GI, Cho BK, Palsson BØ *. Nucleic Acids Res. 2018 Jan 31. doi:10.1093/nar/gky069.

 13. Multiple plasmid-borne virulence genes of Clavibacter michiganensis subsp. capsici critical for disease development in pepper. Hwang IS, Oh EJ, Kim D, Oh CS. New Phytol. 2017 Nov 14. doi:10.1111/nph.14896.

 14. Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities. Fang X#, Sastry A#, Mih N, Kim D, Yurkovich JT, Lloyd CJ, Tan J, Gao Y, Yang L*, Palsson BO*. Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):10286-10291. doi:10.1073/pnas.1702581114. Epub 2017 Sep 5.

 15. Coordination-Driven Self-Assembly Using Ditopic Pyridyl–Pyrazolyl Donor and p-Cymene Ru(II) Acceptors: [2]Catenane Synthesis and Anticancer Activities. Jo JH#, Singh N#, Kim D#, Cho SM, Mishra A, Kim H, Kang SC*, Chi KW*. Inorg Chem. 2017 June 30. doi: 10.10