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<p><strong><span style="font-size:18px">Donghyuk&nbsp;&nbsp;Kim</span></strong></p>
<p>&nbsp;<strong/p> <span style="font-size:12px"p><span style="display:none"strong>&nbsp;- ResearchInterests&nbsp;</strong></p> <p>Systems Biology, Computational Biology, Bioconversion bacterial strains, Bacterial Pathogen</p> <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Interests</spanp> <p><strong>- Education</strong></spanp<p>University of California, San Diego, California, USA, 2014</strongp> <p>- Research&nbsp; Interests : Systems&nbsp;BiologyDegree : Ph.D.,Bioengineering</p> <p>&nbsp;Computational&nbsp;Biology,Thesis : Systems Assessment of Regulator Components in Bacterial Transcription Initiation</p> <p>&nbsp;Bioconversion&nbsp;bacterial&nbsp;strainsAdviser : Dr. Bernhard O. Palsson,&nbsp;Bacterial&nbsp;PathogenSystems Biology Research Group</p>
<p>Seoul National University, Seoul, Korea, 2006</p> <p>&nbsp;&nbsp; Degree : B.S., Computer Science and Engineering</p> <p>&nbsp;&nbsp; Thesis : Pattern Classification and Completion by Probabilistic Library Model</p> <p>&nbsp;&nbsp; Adviser : Dr. Byung- EducationTak Zhang, Biointelligence Lab</p> <p>&nbsp;&nbsp; Degree : B.S., Biological Sciences</p> <p>&nbsp;&nbsp; Thesis : Designing Efficient siRNAs for Gene Silencing</p> <p>&nbsp;&nbsp; Adviser : Dr. V. Narry Kim, RNomics Lab</p>
<p>&nbsp;</p>
 
<p><strong>- Professional Experience</strong></p>
 
<ul>
<li><strong>Assistant Professor</strong>, Department of Chemical Engineering, School of Energy and Chemical Engineering, UNIST, Ulsan, Korea, <em>Jul 2018 ~ Present</em></li>
<li><strong>Assistant Professor</strong>, Department of Genetic Engineering, School of Life Sciences, Kyung Hee University, Yongin, Korea, <em>Mar 2016 ~ Jun 2018</em></li>
<li><strong>Post-Doctoral Researcher</strong>, <a href="http://sbrg.ucsd.edu/" target="_blank">Systems Biology Research Group</a> of Dr. Bernhard Palsson, Department of Bioengineering, University of California, San Diego, <em>Jun 2014 ~ Feb 2016</em></li>
<li><strong>Graduate Student Researcher</strong>, <a href="http://sbrg.ucsd.edu/" target="_blank">Systems Biology Research Group</a> of Dr. Bernhard Palsson, Department of Bioengineering, University of California, San Diego, <em>Sep 2009 ~ May 2014</em></li>
<li><strong>Research Assistant</strong>, <a href="http://www.narrykim.org/en/home" target="_blank">RNomics Lab</a> of Dr. V. Narry Kim, School of Biological Sciences, Seoul National University, <em>Jan 2006 ~ Jan 2007</em></li>
<li><strong>Research Assistant</strong>, <a href="http://bi.snu.ac.kr/" target="_blank">Biointelligence Lab</a>, Computer Science and Engineering, Seoul National University, Seoul, Korea, <em>2005</em></li>
</ul>
<p>&nbsp;</p>
 
<p><strong>- Professional Activity</strong></p>
 
<p> Editor, Journal of Microbiology and Biotechnology, March 2017 ~ Present</p>
 
<p>&nbsp;&nbsp; Committee of Research Affairs, Korean Society of Bioinformatics and Systems Biology, March 2017&nbsp;~ Present</p>
 
<p>&nbsp; &nbsp;Member, The Korean Society for Microbiology and Biotechnology, Jan 2018 ~ Present</p>
 
<p>&nbsp;&nbsp; Member, The Korean Society for Biotechnology and Bioengineering, Sep 2017 ~ Present</p>
 
<p>&nbsp;&nbsp; Member, The Microbiological Society of Korea, Feb 2018 ~ Present</p>
 
<p>&nbsp;&nbsp; Member, The Korean Society of Industrial and Engineering Chemistry, Sep 2017 ~ Present</p>
 
<p>&nbsp;</p>
 
<p><strong>- Publications</strong></p>
 
<p>&nbsp;1. Deciphering bacterial xylose metabolism and metabolic engineering of industrial microorganisms for use as efficient microbial cell factories. Kim D, Woo HM. <u>Appl Microbiol </u>Biotechnol. In press.</p>
 
<p>&nbsp;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. <u>Plant Pathol </u>J, In Press.</p>
 
<p>&nbsp;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*. <u>Nucleic Acids </u>Res, 2018 Aug 23. doi.org/10.1093/nar/gky752.</p>
 
<p>&nbsp;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. <u>Korean J </u>Microbiol, 2018 Jul 2. doi.org/10.7845/kjm.2018.54.2.152.</p>
 
<p>&nbsp;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. <u>Korean J </u>Microbiol, 2018 Jul 2. doi:10.7845/kjm.2018.54.2.149.</p>
 
<p>&nbsp;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*. <u>Inorganica Chimica </u>Acta. 2018 May 28. doi:10.1016/j.ica.2018.05.035.</p>
 
<p>&nbsp;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*. <u>Metab </u>Eng, 2018 Apr 16. doi: 10.1016/j.ymben.2018.04.010.</p>
 
<p>&nbsp;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. <u>Korean J </u>Microbiol, 2018 Apr 1. doi:10.7845/kjm.2018.7099.</p>
 
<p>&nbsp;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. <u>Korean J </u>Microbiol, 2018 Apr 1. doi:10.7845/kjm.2018.7098.</p>
 
<p>&nbsp;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*. <u>Korean J </u>Microbiol, 2018 Apr 1. doi:10.7845/kjm.2018.7087.</p>
 
<p>&nbsp;11. Isolation and identification of novel equol-producing bacterial strains. Kwon JE, Lim J, Kim I, Kim D*, Kang SC*. <u>PLoS </u>One, 2018 Feb 15;13(2):e0192490. doi:10.1371/journal.pone.0192490</p>
 
<p>&nbsp;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 B&Oslash; *. <u>Nucleic Acids </u>Res. 2018 Jan 31. doi:10.1093/nar/gky069.</p>
 
<p>&nbsp;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. <u>New </u>Phytol. 2017 Nov 14. doi:10.1111/nph.14896.</p>
 
<p>&nbsp;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*. <u>Proc Natl Acad Sci U S </u>A. 2017 Sep 19;114(38):10286-10291. doi:10.1073/pnas.1702581114. Epub 2017 Sep 5.</p>
 
<p>&nbsp;15. Coordination-Driven Self-Assembly Using Ditopic Pyridyl&ndash;Pyrazolyl Donor and p-Cymene Ru(II)&nbsp;Acceptors: [2]Catenane Synthesis and Anticancer Activities. Jo JH#, Singh N#, Kim D#, Cho SM, Mishra A, Kim H, Kang SC*, Chi KW*. <u>Inorg </u>Chem. 2017 June 30. doi: 10.10</p>
 
<p>&nbsp;16. Highly efficient silver nanowire/PEDPT:PSS composite microelectrodes via poly(ethylene glycol) photolithography. Kim D, Ko Y, Kim W, Kim D, You J. <u>Opt Mater Express</u>. 2017 June 8;7(7):2272-2279.&nbsp; doi:10.1364/OME.7.002272.</p>
 
<p>&nbsp;17. Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in <em>Escherichia coli</em> K-12 MG1655. Seo SW<sup>#,*</sup>, Geo Y<sup>#</sup>, Kim D<sup>#</sup>, Szubin R, Cho BK, Palsson BO<sup>*</sup>. <u>Sci Rep</u>. 2017 May 19. doi:10.1038/s41598-017-02110-7.</p>
 
<p>&nbsp;18. Selective bio-oxidation of propane to acetone using methane-oxidizing <em>Methylomonas</em> sp. DH-1. Hur DH, Nguyen TT, Kim D, Lee EY. <u>J Ind Microbiol Biotechnol</u>. 2017 Mar 20. doi: 10.1007/s10295-017-1936-x.</p>
 
<p>&nbsp;19. Elucidation of bacterial translation regulatory networks. Jeong Y, Shin H, Seo SW, Kim D, Cho S, Cho BK. <u>Curr Opin Sys Biol</u>. 2017 Mar 8. doi:10.1016/j.coisb.2017.01.009.</p>
 
<p>&nbsp; 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<sup>#</sup>, Jeong HY<sup>#</sup>, Jeon SH, Kim D, Lee C. <u>J Plant Physiol</u>. 2016 Nov 18. doi: 10.1016/j.jplph.2016.11.006.</p>
 
<p>&nbsp; 21. Multi-omic data integration enables discovery of hidden biological regularities. Ebrahim A<sup>#</sup>, Brunk E<sup>#</sup>, Tan J<sup>#</sup>, O&#39;Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist AM, Palsson BO. <u>Nat Commun</u>. 2016 Oct 26;7:13091. doi: 10.1038/ncomms13091.</p>
 
<p>&nbsp; 22. Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in <em>Escherichia coli</em> K-12 MG1655. Seo SW<sup>#</sup>, Kim D<sup>#</sup>, Szubin R, Palsson B&Oslash;. <u>Cell Reports</u>. 2015 Aug 25. DOI: http://dx.doi.org/10.1016/j.celrep.2015.07.043.</p>
 
<p>&nbsp; 23. A systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Yang L<sup>#</sup>, Tan J<sup>#</sup>, O&rsquo;Brien EJ, Monk JM, Kim D, Li H, Charusanti P, Ebrahim A, Lloyd C, Yurkovich JT, Du B, Dr&auml;ger A, Thomas A, Sun Y, Ma D, Saunders MA, Palsson B&Oslash;. <u>Proc Natl Acad Sci U S A</u>. 2015 Aug 10. pii: 201501384.</p>
 
<p>&nbsp; 24. Decoding the genome-wide GadEWX transcriptional regulatory landscape for acid resistance in <em>Escherichia coli</em>. Seo SW<sup>#</sup>, Kim D<sup>#</sup>, O&#39;Brien EJ, Szubin R, Palsson B&Oslash;. <u>Nat Commun</u>. 2015 Aug 10;6:7970. doi: 10.1038/ncomms8970.</p>
 
<p><a href="http://www.ncbi.nlm.nih.gov/pubmed/25222563" target="_blank">&nbsp; </a><u><a href="http://www.ncbi.nlm.nih.gov/pubmed/25222563" target="_blank">25. Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in <em>Escherichia coli</em></a>. </u>Seo SW<sup>#</sup>, Kim D<sup>#</sup>, Latif H<sup>#</sup>, O&#39;Brien EJ, Szubin R, Palsson BO. <u>Nat Commun</u>. 2014 Sep 15;5:4910. <a href="http://www.nature.com/ncomms/2014/140915/ncomms5910/full/ncomms5910.html" target="_blank">doi: 10.1038/ncomms5910</a>.</p>
 
<p><a href="http://www.ncbi.nlm.nih.gov/pubmed/24699140" target="_blank">&nbsp; 26. Determining the control circuitry of redox metabolism at the genome-scale</a>. Federowicz S, Kim D, Ebrahim A, Lerman JA, Nagarajan H, Cho BK, Zengler K, Palsson B&Oslash;. <u>PLoS Genet</u>. 2014 Apr 3;10(4):e1004264. <a href="http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004264" target="_blank">doi: 10.1371/journal.pgen.1004264</a>. eCollection 2014.</p>
 
<p><a href="http://www.ncbi.nlm.nih.gov/pubmed/24461193" target="_blank">&nbsp; 27. Genome-scale reconstruction of the sigma factor network in <em>Escherichia coli</em>: topology and functional states</a>. Cho BK<sup>#</sup>, Kim D<sup>#</sup>, Knight EM, Zengler K, Palsson BO. <u>BMC Biol</u>. 2014 Jan 24;12(1):4. <a href="http://www.biomedcentral.com/1741-7007/12/4" target="_blank">doi: 10.1186/1741-7007-12-4</a>.</p>
 
<p><a href="http://www.ncbi.nlm.nih.gov/pubmed/23744946" target="_blank">&nbsp; 28. Structural Systems Biology Evaluation of Metabolic Thermotolerance in <em>Escherichia coli</em></a>. Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BO. <u>Science</u>. 2013 Jun 7;340(6137):1220-3. <a href="http://www.sciencemag.org/content/340/6137/1220.long" target="_blank">doi: 10.1126/science.1234012</a>.</p>
 
<p><a href="http://www.ncbi.nlm.nih.gov/pubmed/23194155" target="_blank">&nbsp; 29. Multiple-omic data analysis of <em>Klebsiella pneumoniae</em> MGH 78578 reveals its transcriptional architecture and regulatory features</a>. Seo JH<sup>#</sup>, Hong JS<sup>#</sup>, Kim D, Cho BK, Huang TW, Tsai SF, Palsson BO, Charusanti P. <u>BMC Genomics</u>. 2012 Nov 29;13:679. <a href="http://www.biomedcentral.com/1471-2164/13/679" target="_blank">doi: 10.1186/1471-2164-13-679</a>.</p>
 
<p><a href="http://www.ncbi.nlm.nih.gov/pubmed/22936779" target="_blank">&nbsp; 30. Network context and selection in the evolution to enzyme specificity</a>. Nam H*, Lewis NE*, Lerman JA, Lee DH, Chang RL, Kim D, Palsson BO. <u>Science</u>. 2012 Aug 31;337(6098):1101-4. <a href="http://www.sciencemag.org/content/337/6098/1101.long" target="_blank">doi: 10.1126/science.1216861</a>.</p>
 
<p><a href="http://www.ncbi.nlm.nih.gov/pubmed/22912590" target="_blank">&nbsp; 31. Comparative analysis of regulatory elements between <em>Escherichia coli</em> and <em>Klebsiella pneumoniae </em>by genome-wide transcription start site profiling</a>. Kim D<sup>#</sup>, Hong JS<sup>#</sup>, Qiu Y, Nagarajan H, Seo JH, Cho BK, Tsai SF, Palsson B&Oslash;. <u>PLoS Genet</u>. 2012;8(8):e1002867. <a href="http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002867" target="_blank">doi: 10.1371/journal.pgen.1002867</a>. Epub 2012 Aug 9.</p>
 
<p><a href="http://www.ncbi.nlm.nih.gov/pubmed/21572102" target="_blank">&nbsp; 32. The PurR regulon in <em>Escherichia coli</em> K-12 MG1655</a>. Cho BK, Federowicz SA, Embree M, Park YS, Kim D, Palsson B&Oslash;. <u>Nucleic Acids Res</u>. 2011 Aug;39(15):6456-64. <a href="http://nar.oxfordjournals.org/content/39/15/6456.long" target="_blank">doi: 10.1093/nar/gkr307</a>. Epub 2011 May 13.</p>
 
<p><a href="http://www.ncbi.nlm.nih.gov/pubmed/19153141" target="_blank">&nbsp; 33. Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer</a>. Kim YK, Yu J, Han TS, Park SY, Namkoong B, Kim DH, Hur K, Yoo MW, Lee HJ, Yang HK, Kim VN. <u>Nucleic Acids Res</u>. 2009 Apr;37(5):1672-81. <a href="http://nar.oxfordjournals.org/content/37/5/1672.long" target="_blank">doi: 10.1093/nar/gkp002</a>. Epub 2009 Jan 19.</p>
 
<p>&nbsp;</p>
 
<p><strong>- Papers in Progress</strong></p>
 
<ol>
<li>Genome-scale metabolic modeling of bacteria for C1 utilization. Kabimoldayev I<sup>#</sup>, Nguyen AD<sup>#</sup>, Park S, Lee EY*, Yang L*, Kim D*. <u>FEMS Microbiol Lett</u>, Resubmitted.</li>
<li>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*. <u>BMC Genomics</u>, Resubmitted.</li>
<li>Characterizing post-translational modifications using a multi-scale workflow. Brunk E<sup>#</sup>, Chang RL, Xia J, Hefzi H, Yurkovich J, Kim D, Buckmiller E, Wang H, Cho BK, Yang C, Palsson BO, Church GM, Lewis NE<sup>#</sup>. <u>Proc Natl Acad Sci U S A</u>, In revision.</li>
</ol>
 
<p>&nbsp;</p>
 
<p><strong>- Teaching</strong></p>
 
<ul>
<li>ACE30101&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Computational Methods for Chemical Engineering, UNIST, Ulsan, Korea</li>
<li>BT714100&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Genomics Programming, Kyung Hee University, Yongin, Korea</li>
<li>BIO10302&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Biology, Kyung Hee University, Yongin, Korea</li>
<li>GEN41801&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Capstone Design, Kyung Hee University, Yongin, Korea</li>
<li>GEN415&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Genomics, Kyung Hee University, Yongin, Korea</li>
<li>GEN306&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Molecular Biology Laboratory, Kyung Hee University, Yongin, Korea</li>
</ul>
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