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김동혁
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<p> 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*. <u>Inorg </u>Chem. 2017 June 30. doi: 10.10</p>
<p> 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. doi:10.1364/OME.7.002272.</p>
<p> 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> 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> 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> 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> 21. Multi-omic data integration enables discovery of hidden biological regularities. Ebrahim A<sup>#</sup>, Brunk E<sup>#</sup>, Tan J<sup>#</sup>, O'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> 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 BØ. <u>Cell Reports</u>. 2015 Aug 25. DOI: http://dx.doi.org/10.1016/j.celrep.2015.07.043.</p>
<p> 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’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. <u>Proc Natl Acad Sci U S A</u>. 2015 Aug 10. pii: 201501384.</p>
<p> 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'Brien EJ, Szubin R, Palsson BØ. <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"> </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'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"> 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 BØ. <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"> 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"> 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"> 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"> 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"> 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 BØ. <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"> 32. The PurR regulon in <em>Escherichia coli</em> K-12 MG1655</a>. Cho BK, Federowicz SA, Embree M, Park YS, Kim D, Palsson BØ. <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"> 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> </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> </p>
<p><strong>Teaching</strong></p>
<ul>
<li>ACE30101 Computational Methods for Chemical Engineering, UNIST, Ulsan, Korea</li>
<li>BT714100 Genomics Programming, Kyung Hee University, Yongin, Korea</li>
<li>BIO10302 Biology, Kyung Hee University, Yongin, Korea</li>
<li>GEN41801 Capstone Design, Kyung Hee University, Yongin, Korea</li>
<li>GEN415 Genomics, Kyung Hee University, Yongin, Korea</li>
<li>GEN306 Molecular Biology Laboratory, Kyung Hee University, Yongin, Korea</li>
</ul>
<p> </p>
<p> </p>
