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

 16. Highly efficient silver nanowire/PEDPT:PSS composite microelectrodes via poly(ethylene glycol) photolithography. Kim D, Ko Y, Kim W, Kim D, You J. Opt Mater Express. 2017 June 8;7(7):2272-2279.  doi:10.1364/OME.7.002272.

 17. Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655. Seo SW^#,*, Geo Y^#, Kim D^#, Szubin R, Cho BK, Palsson BO^*. Sci Rep. 2017 May 19. doi:10.1038/s41598-017-02110-7.

 18. Selective bio-oxidation of propane to acetone using methane-oxidizing Methylomonas sp. DH-1. Hur DH, Nguyen TT, Kim D, Lee EY. J Ind Microbiol Biotechnol. 2017 Mar 20. doi: 10.1007/s10295-017-1936-x.

 19. Elucidation of bacterial translation regulatory networks. Jeong Y, Shin H, Seo SW, Kim D, Cho S, Cho BK. Curr Opin Sys Biol. 2017 Mar 8. doi:10.1016/j.coisb.2017.01.009.

  20. Rice pectin methylesterase inhibitor28 (OsPMEI28) encodes a functional PMEI and its overexpression results in a dwarf phenotype through increased pectin methylesterification levels. Nguyen HP^#, Jeong HY^#, Jeon SH, Kim D, Lee C. J Plant Physiol. 2016 Nov 18. doi: 10.1016/j.jplph.2016.11.006.

  21. Multi-omic data integration enables discovery of hidden biological regularities. Ebrahim A^#, Brunk E^#, Tan J^#, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist AM, Palsson BO. Nat Commun. 2016 Oct 26;7:13091. doi: 10.1038/ncomms13091.

  22. Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655. Seo SW^#, Kim D^#, Szubin R, Palsson BØ. Cell Reports. 2015 Aug 25. DOI: http://dx.doi.org/10.1016/j.celrep.2015.07.043.

  23. A systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Yang L^#, Tan J^#, O’Brien EJ, Monk JM, Kim D, Li H, Charusanti P, Ebrahim A, Lloyd C, Yurkovich JT, Du B, Dräger A, Thomas A, Sun Y, Ma D, Saunders MA, Palsson BØ. Proc Natl Acad Sci U S A. 2015 Aug 10. pii: 201501384.

  24. Decoding the genome-wide GadEWX transcriptional regulatory landscape for acid resistance in Escherichia coli. Seo SW^#, Kim D^#, O'Brien EJ, Szubin R, Palsson BØ. Nat Commun. 2015 Aug 10;6:7970. doi: 10.1038/ncomms8970.

  25. Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. Seo SW^#, Kim D^#, Latif H^#, O'Brien EJ, Szubin R, Palsson BO. Nat Commun. 2014 Sep 15;5:4910. doi: 10.1038/ncomms5910.

  26. Determining the control circuitry of redox metabolism at the genome-scale. Federowicz S, Kim D, Ebrahim A, Lerman JA, Nagarajan H, Cho BK, Zengler K, Palsson BØ. PLoS Genet. 2014 Apr 3;10(4):e1004264. doi: 10.1371/journal.pgen.1004264. eCollection 2014.

  27. Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states. Cho BK^#, Kim D^#, Knight EM, Zengler K, Palsson BO. BMC Biol. 2014 Jan 24;12(1):4. doi: 10.1186/1741-7007-12-4.

  28. Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli. Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BO. Science. 2013 Jun 7;340(6137):1220-3. doi: 10.1126/science.1234012.

  29. Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features. Seo JH^#, Hong JS^#, Kim D, Cho BK, Huang TW, Tsai SF, Palsson BO, Charusanti P. BMC Genomics. 2012 Nov 29;13:679. doi: 10.1186/1471-2164-13-679.

  30. Network context and selection in the evolution to enzyme specificity. Nam H*, Lewis NE*, Lerman JA, Lee DH, Chang RL, Kim D, Palsson BO. Science. 2012 Aug 31;337(6098):1101-4. doi: 10.1126/science.1216861.

  31. Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. Kim D^#, Hong JS^#, Qiu Y, Nagarajan H, Seo JH, Cho BK, Tsai SF, Palsson BØ. PLoS Genet. 2012;8(8):e1002867. doi: 10.1371/journal.pgen.1002867. Epub 2012 Aug 9.

  32. The PurR regulon in Escherichia coli K-12 MG1655. Cho BK, Federowicz SA, Embree M, Park YS, Kim D, Palsson BØ. Nucleic Acids Res. 2011 Aug;39(15):6456-64. doi: 10.1093/nar/gkr307. Epub 2011 May 13.

  33. Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer. Kim YK, Yu J, Han TS, Park SY, Namkoong B, Kim DH, Hur K, Yoo MW, Lee HJ, Yang HK, Kim VN. Nucleic Acids Res. 2009 Apr;37(5):1672-81. doi: 10.1093/nar/gkp002. Epub 2009 Jan 19.

 

Papers in Progress

1. Genome-scale metabolic modeling of bacteria for C1 utilization. Kabimoldayev I^#, Nguyen AD^#, Park S, Lee EY*, Yang L*, Kim D*. FEMS Microbiol Lett, Resubmitted.
2. Comparative transcriptome analysis of a novel obligate Methylomonas sp. DH-1 reveals key differences in the transcriptional responses of C1 and secondary metabolite pathways during growth on methane and methanol. Nguyen AD, Kim D*, Lee EY*. BMC Genomics, Resubmitted.
3. Characterizing post-translational modifications using a multi-scale workflow. Brunk E^#, Chang RL, Xia J, Hefzi H, Yurkovich J, Kim D, Buckmiller E, Wang H, Cho BK, Yang C, Palsson BO, Church GM, Lewis NE^#. Proc Natl Acad Sci U S A, In revision.

 

Teaching

• ACE30101      Computational Methods for Chemical Engineering, UNIST, Ulsan, Korea
• BT714100       Genomics Programming, Kyung Hee University, Yongin, Korea
• BIO10302       Biology, Kyung Hee University, Yongin, Korea
• GEN41801      Capstone Design, Kyung Hee University, Yongin, Korea
• GEN415          Genomics, Kyung Hee University, Yongin, Korea
• GEN306          Molecular Biology Laboratory, Kyung Hee University, Yongin, Korea