Publications / Patents
Papers
# First author, * Corresponding author
Papers in progress
** Characterization and therapeutic potential of newly isolated bacteriophages against Staphylococcus species in bovine mastitis. Cho JH#, Lee GM#, Ko S, Kim Y*, Kim D*. Submitted.
** Biosensor-guided evolution boosts itaconic acid production, unveiling unique insights on the stringent response. Moon JH#, Woo J#, Park JY, Noh MH*, Kim D*, Jung GY*. Submitted.
** An Optimized Method for Reconstruction of Transcriptional Regulatory Networks in Bacteria Using ChIP-exo and RNA-seq Datasets. Jang M#, Park JY#, Kim D*. Submitted.
** Elucidating DNA-binding protein dynamics in Salmonella Typhimurium under macrophages in vivo conditions using a breakthrough low-input ChIP-exo approach. Park JY#, Jang M#, Choi E, Lee SM, Bang I, Woo J, Kim S, Lee EJ*, Kim D*. Submitted.
** Unveiling the novel regulatory roles of RpoD-family sigma factors in Salmonella Typhimurium heat shock response through genome-wide transcriptional network analysis. Park JY#, Jang M#, Lee SM, Lee EJ, Kim D*. Submitted.
** Genome-wide regulon of NtrC reveals genetic regulation under nitrogen limitation in Methylomonas sp. DH-1. Han SJ#, Park JY#, Han YH#, Bang I, Lee OK, Hyung JS, Na JG*, Lee EY*, Kim D*, Seo SW*. Submitted.
** Explanable deep learning for enzyme engineering with leveraging attention analysis of transformer-based model for NAD/NADP cofactor specificity. Kim J#, Woo J#, Park JY, Kim KJ, Kim D. Submitted.
** Developing the PIP-eco pipeline: An integrated genomic approach to identify Escherichia coli with hybrid pathotypes. Ko S, Nguyen HMT, Lee W, Kim D. In revision.
** Behavioral biometric optical tactile sensor that instantaneously decouples dynamic touch signals in real time. Son C#, Kim J#, Kang D#, Park S#, Jeong S, Ahn S, Lim S, Lee DW, Kim D*, Kim J*, Ko H*, Lee J*. Resubmitted.
** Next generation feasibility study model on H2 production process: Machine learning-based framework for feasibility prediction and parametric optimization in methanol steam reforming with membrane filters. Byun M#, Park S#, Lee A, Kim J, Scott-Nevros ZK, Park JY, Lim H*, Kim D*. Appl Energy. Resubmitted.
2024
78. Use of acetate as substrate for sustainable production of homoserine and threonine by Escherichia coli W3110: a modular metabolic engineering approach. Vo TM, Park JY, Kim D, Park S. Metab Eng. Accepted.
** 77. Experimental promoter identification of a food-borne pathogen Salmonella Enterica Subsp. Enterica Serovar Typhimurium with near single base-pair resolution. Lee SM#, Le HT#, Taizhanova A, Nong LK, Park JY, Lee EJ, Palsson BO, Kim D. Front Microbiol. 2024 Jan 04. doi:10.3389/fmicb.2023.1271121.
2023
** 76. Blanket antimicrobial resistance gene database with structural information, BOARDS, provides insights on historical landscape of resistance prevalence and effects of mutations in enzyme structure. Ko S#, Kim J#, Lim J, Lee SM, Park JY, Woo J, Scott-Nevros ZK, Kim JR, Yoon H, Kim D*. mSystems. 2023 Dec 12. doi:10.1128/msystems.00943-23.
** 75. A deep learning-based framework for battery reusability verification: one-step state-of-health estimation of pack and constituent modules using a generative algorithm and graphical representation. Park S#, Lim D#, Lee H, Jung D, Choi Y*, Lim H*, Kim D*. J. Mater. Chem. A. 2023 Oct 17. doi:10.1039/D3TA03603K.
on the media: 분해 없이 소모된 배터리 상태 진단할 수 있는 기술 나왔다
featured on the back cover
74. Design of synthetic promoters for cyanobacteria with generative deep-learning model. Seo E, Choi YN, Shin YR, Kim D, Lee JW. Nucleic Acids Res. 2023 May 29. doi: 10.1093/nar/gkad451.
** 73. Comparative genomic analysis and BTEX degradation pathways of a thermotolerant Cupriavidus cauae PHS1. Sathesh-Prabu C#, Woo J#, Kim Y#, Kim SM, Lee SB, Jeon CO*, Kim D*, Lee SK*. J Microbiol Biotechnol. 2023 Apr 10. doi:10.4014/jmb.2301.01011.
** 72. The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets. Gao Y#, Bang I#, Seif Y, Kim D*, Palsson BO*. Nucleic Acids Res. 2023 Apr 07. doi:10.1093/nar/gkad253.
on the media: 한국을 빛내는 사람들, 김동혁
** 71. Deep-learning based spatio-temporal generative model on assessing state-of-health for Li-ion batteries with partially-cycled profiles. Park S#, Lee H#, Scott-Nevros ZK, Lim D, Seo DH, Choi Y*, Lim H*, Kim D*. Mater Horiz. 2023 Feb 20. doi:10.1039/D3MH00013C.
on the media: 딥러닝 기반 배터리 진단 모델 개발
featured on the back cover
** 70. Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling. Bang I#, Lee SM#, Park S#, Park JY, Nong LK, Gao Y, Palsson BO, Kim D. Brief Bioinform. 2023 Jan 25. doi:10.1093/bib/bbad024.
on the media: 한국을 빛내는 사람들, 김동혁
** 69. Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli. Park JY, Lee SM, Ebrahim A, Scott-Nevros ZK, Kim J, Yang L, Sastry A, Seo SW*, Palsson BO*, Kim D*. NAR Genom Bioinform. 2023 Jan 20. doi:10.1093/nargab/lqad006.
** 68. Characterization of Klebsiella pneumoniae bacteriophages, KP1 and KP12, with deep learning-based structure prediction. Kim YJ#, Lee SM#, Nong LK#, Kim J, Kim SB, Kim D. Front Microbiol. 2023 Jan 24. doi:10.3389/fmicb.2022.990910.
** 67. A Machine Learning Approach Reveals a Microbiota Signature for Infection with Mycobacterium avium subsp paratuberculosis in cattle. Lee SM#, Park HT#, Park S, Lee J, Kim D, Yoo HS*, Kim D*. Microbiol Spectr. 2023 Jan 19. doi:10.1128/spectrum.03134-22.
76. Ko and Kim et al. mSystems. 2023.
75. Park and Lim et al. J. Mater. Chem. A. 2023.
72. Gao and Bang et al. Nucleic Acids Res. 2023.
71. Park and Lee et al. Mater Horiz. 2023.
70. Bang, Lee, and Park et al. Brief Bioinform. 2023.
2022
66. Revealing Causes for False-Positive and False-Negative Calling of Gene Essentiality in Escherichia coli Using Transposon Insertion Sequencing. Choe D, Kim U, Hwang S, Seo SW, Kim D, Cho S, Palsson B, Cho BK. mSystems. 2022 Dec 12. doi:10.1128/msystems.00896-22.
** 65. ChEAP: ChIP-exo Analysis Pipeline and the investigation of Escherichia coli RpoN protein-DNA interactions. Bang I#, Nong LK#, Park JY, Le HT, Lee SM, Kim D. Comput Struct Biotechnol J. 2022 Dec 02. doi:10.1016/j.csbj.2022.11.053.
** 64. Characterization of an Entner-Doudoroff pathway-activated Escherichia coli. Kim YE#, Cho KH#, Bang I#, Kim CH, Ryu YS, Kim Y, Choi EM, Nong LK, Kim D*, Lee SK*. Biotechnol Biofuels Bioprod. 2022 Nov 09. doi.org/10.1186/s13068-022-02219-6
** 63. Pan-genome analysis reveals comparative genomic features of central metabolic pathways in Methylorubrum extorquens. Lee GM, Scott-Nevros ZK, Lee SM, Kim D. Biotechnol Bioprocess Eng. 2022 Sep 29. doi:10.1007/s12257-022-0154-1.
** 62. Delineating transcriptional crosstalk between Mycobacterium avium subsp. paratuberculosis and human THP-1 cell at early stage of infection via dual RNA-seq analysis. Park HT#, Lee SM#, Ko S, Kim S, Park HE, Shin MK, Kim D*, Yoo HS*. Vet Res. 2022 Sep 13. doi:10.1186/s13567-022-01089-y.
61. Comparative genomic analysis of plasmids encoding metallo-β-Lactamase NDM-5 in Enterobacteriaceae Korean isolates from Companion dogs. Kyung SM, Choi SW, Lim J, Shim S, Kim S, Im YB, Lee NE, Hwang CY, Kim D, Yoo HS. Sci Rep. 2022 Jan 28. doi:10.1038/s41598-022-05585-1.
60. proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. Decker K#, Gao Y#, Rychel K#, Al Bulushi T, Chauhan S, Kim D, Cho BK, Palsson B. Nucleic Acids Res. 2022 Jan 7. doi:10.1093/nar/gkab1043.
65. Bang and Nong et al. Comput Struct Biotechnol J. 2022.
64. Kim, Cho, and Bang et al. Biotechnol Biofuels Bioprod. 2022.
2021
59. Real-time PCR for Salmonella serotyping Rapid real-time PCR for Salmonella serotyping based on novel unique gene markers by pangenome analysis. Yang SM, Kim E, Kim D, Kim HB, Baek J, Ko S, Kim D, Yoon H, Kim HY. Front Microbiol. 2021 Sep 21. doi:10.3389/fmicb.2021.750379.
58. Enhanced production of nonanedioic acid from nonanoic acid by engineered Escherichia coli. Lee Y, Sathesh-Prabu C, Kwak GH, Bang I, Jung HW, Kim D, Lee SK. Biotechnol J. 2021 May 08. doi:10.1002/biot.202000416.
** 57. Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes. Lim J#, Park HT#, Ko S, Park HE, Lee GM, Kim S, Shin MK, Yoo HS*, Kim D*. Vet Res. 2021 Mar 18. doi:10.1186/s13567-021-00905-1.
on the media: BRIC 농림성과
56. Alpha-2-macroglobulin as a new promising biomarker improving the diagnostic sensitivity of bovine paratuberculosis. Park HE, Park JS, Park HT, Choi JG, Shin JI, Jung M, Kang HL, Baik SC, Lee WK, Kim D, Yoo HS*, Shin MK*. Front Vet Sci. 2021 Mar 05. doi:10.3389/fvets.2021.637716.
Conference
* 1. Feasibility prediction model for hydrogen production system of methanol steam reforming with membrane filters by machine learning regression algorithm. Byun M, Park S, Kim D*, Lim H*. International Conference on Applied Energy. 2021 Nov 29. (conference paper)
2020
** 55. Genome-wide Identification of DNA-protein Interaction to Reconstruct Bacterial Transcription Regulatory Network. Park JY#, Rimal H#, Bang I, Nong LK, Kim D. Biotechnol Bioprocess Eng. 2020 Dec 29. doi:10.1007/s12257-020-0030-9.
54. Development of a genoserotyping method for Salmonella Infantis detection on the basis of pan-genome analysis. Yang SM, Baek J, Kim E, Kim HB, Ko S, Kim D, Yoon H*, Kim HY*. Microorganisms. 2020 Dec 29. doi:10.3390/microorganisms9010067.
** 53. Systems evaluation reveals novel transporter YohJK renders 3-hydroxypropionate tolerance in Escherichia coli. Nguyen-Vo TP#, Ko S#, Ryu H, Kim JR, Kim D*, Park S*. Sci Rep. 2020 Nov 04. doi:10.1038/s41598-020-76120-3.
** 52. Comparative genome analysis reveals an evolutionary trace in the genomes of Erwinia pyrifoliae, a black shoot blight pathogen in apple and pear. Lee GM, Ko S, Oh EJ, Song YR, Kim D*, Oh CS*. Plant Pathol J. 2020 Oct 1. doi:10.5423/PPJ.OA.06.2020.0097.
51. Adaptive laboratory evolution of Escherichia coli lacking cellular byproduct formation for enhanced acetate utilization through compensatory ATP consumption. Seong W, Han GH, Lim HS, Baek JI, Kim SJ, Kim D, Kim SK, Lee H, Kim H, Lee SG*, Lee DH*. Metab Eng. 2020 Sep 12. doi:10.1016/j.ymben.2020.09.005.
** 50. Genomic and phenotypic characterization of a lytic bacteriophage CF1 infecting multi-drug resistant Citrobacter freundii. Kim Y#, Ko S#, Yeon YE, Kim H, Oh CS, Ahn JK*, Kim D*. Biotechnol Bioprocess Eng. 2020 Jun 29. doi:10.1007/s12257-019-0505-8.
** 49. Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z. Nguyen AD#, Nam G#, Kim D*, Lee EY*. Microb Cell Fact. 2020 Jun 16. doi:10.1186/s12934-020-01382-5.
48. Unlocking the biosynthesis of sesquiterpenoids from methane via the methylerythritol phosphate pathway in methanotrophic bacteria, using α-humulene as a model compound. Nguyen AD, Kim D, Lee EY. Metab Eng. 2020 May 5. doi:10.1016/j.ymben.2020.04.011.
47. Metabolic engineering of Escherichia coli for 2,3-butanediol production from cellulosic biomass by using glucose-inducible gene expression system. Sathesh-Prabu C#, Kim D#, Lee SK. Bioresour Technol. 2020 Apr 10. doi:10.1016/j.biortech.2020.123361.
46. Near-complete genome sequence of a potential eukaryotic probiotic Saccharomyces cerevisiae KCCM 51299: Application of genomic data in the food industry. Hwang J#, Bang I#, Kim D, Shin SC, Chin YW, Kim TW, Kim HJ. 3 Biotech. 2020 Mar 30. doi:.
** 45. Comprehensive genomic analysis on the novel species Sphingomonas panacis DCY99T reveals insights into iron tolerance of ginseng. Kim YJ#,*, Park JY#, Balusamy SR, Huo Y, Nong LK, Le HT, Yang DC, Kim D*. Int J Mol Sci. 2020 Mar 16. doi:10.3390/ijms21062019.
* 44. Functional cooperation of the glycine synthase-reductase and Wood-Ljungdahl pathways for autotrophic growth of Clostridium drakei. Song Y, Lee JS, Shin J, Lee GM, Jin S, Kang SG, Lee JK, Kim DR, Lee EY, Kim SC, Cho S, Kim D*, Cho BK*. Proc Natl Acad Sci U S A. 2020 Mar 13. doi:10.1073/pnas.1912289117.
on the media: 한국을 빛내는 사람들, 김동혁
43. Prevalence of extended-spectrum β-lactamases in the local farm environment and livestock: challenges to mitigate antimicrobial resistance. Lee S, Mir RA, Park SH, Kim D, Kim HY, Boughton RK, Morris JG, Jeong KC. Crit Rev Microbiol. 2020 Jan 24. doi: 10.1080/1040841X.2020.1715339.
53. Nguyen-Vo and Ko et al. Sci Rep. 2020.
44. Song et al. Proc Natl Acad Sci U S A. 2020.
2019
42. The Escherichia coli Transcriptome Mostly Consists of Independently Regulated Modules. Anand VS, Gao Y, Szubin R, Hefner Y, Xu S, Kim D, Choudhary KS, Yang L, King ZA, Palsson BO. Nat Commun. 2019 Dec 04. doi:10.1038/s41467-019-13483-w.
** 41. Genome-scale evaluation of core one-carbon metabolism in gammaproteobacterial methanotrophs grown on methane and methanol. Nguyen AD#, Park JY#, Hwang IY#, Hamilton R, Kalyuzhnaya MG, Kim D*, Lee EY*. Metab Eng. 2019 Oct 15. pii: S1096-7176(19)30307-6. doi: 10.1016/j.ymben.2019.10.004.
40. Photoluminescent and internal reflection scattering of hyaluronic acid-zinc oxide-ginsenoside Rh2 nanoparticles and their potential Cas9 apoptotic mechanism towards cancer cell lines. Kim YJ#,*, Perumalsamy H#, Castro-Aceituno V, Kim D, Markus J, Lee S, Park SY, Kim S, Yang DC. Int J Nanomedicine. 2019 Sep 17;2019(14):8195-8208. doi:10.2147/IJN.S221328.
39. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, Monk JM, Lloyd CJ, Sandberg TE, Seo SW, Kim D, Anand VS, Phaneuf P, Gao Y, Broddrick JT, Chen K, Heckmann D, Szubin R, Hefner Y, Feist AM, Palsson BO. Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):14368-14373. doi: 10.1073/pnas.1905039116. Epub 2019 Jul 3.
** 38. Fermentation product with new equol-producing Lactobacillus paracasei as a probiotic-like product candidate for prevention of skin and intestinal disorder. Kwon JE#, Lim J#, Bang I, Kim I, Kim D*, Kang SC*. J Sci Food Agric. 2019 Feb 14. doi.org/10.1002/jsfa.9648.
* 37. A comparative transcriptome analysis of the novel obligate methanotroph Methylomonas sp. DH-1 reveals key differences in transcriptional responses in C1 and secondary metabolite pathways during growth on methane and methanol. Nguyen AD, Kim D*, Lee EY*. BMC Genomics. 2019 Feb 12. doi.org/10.1186/s12864-019-5487-6.
** 36. Genomic characterization of a newly isolated rhizobacteria Sphingomonas panacis reveals plant growth promoting effect to rice. Kim YJ#,*, Lim J#, Sukweenadhi J, Seok JW, Lee SW, Park JC, Taizhanova A, Kim D*, Yang DC. Biotechnol Bioprocess Eng, 2019 Feb 08. doi.org/10.1007/s12257-018-0386-2.
41. Nguyen, Park and Hwang et al. Metab Eng. 2019.
37. Nguyen et al. BMC Genomics. 2019.
2018
35. Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale 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. 2018 Oct 9. doi.org/10.1073/pnas.1811971115.
34. 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. 2018 Oct 1. doi.org/10.5423/PPJ.NT.06.2018.0100.
** 33. Basics of genome-scale metabolic modeling and applications on C1-utilization. Kabimoldayev I#, Nguyen AD#, Yang L#, Park S, Lee EY, Kim D. FEMS Microbiol Lett. 2018 Sep 25. doi.org/10.1093/femsle/fny241.
contribution to the thematic issue on industrial microbiology
32. Deciphering bacterial xylose metabolism and metabolic engineering of industrial microorganisms for use as efficient microbial cell factories. Kim D, Woo HM. Appl Microbiol Biotechnol. 2018 Sep 20. doi.org/10.1007/s00253-018-9353-2.
* 31. 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 Nov 16;46(20):10682-10696. doi.org/10.1093/nar/gky752.
on the media: 한국을 빛내는 사람들, 김동혁
33. Kabimoldayev et al. FEMS Microbiol Lett. 2018.
31. Gao et al. Nucleic Acids Res. 2018.
Before UNIST
2018
30. 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.
29. 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.
28. 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.
27. 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 EY*. Metab Eng. 2018 May;47:323-333. doi: 10.1016/j.ymben.2018.04.010. Epub 2018 Apr 16.
26. Draft genome sequence of lytic bacteriophage CF1 infecting Citrobacter freundii isolates. Kim Y, 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.
25. Draft genome sequence of lytic bacteriophage SA7 infecting Staphylococcus aureus isolates. Kim Y, Lee GM, Taizhanova A, Han BK, Kim H, Ahn JK, Kim D. Korean J Microbiol. 2018 Apr 1. doi:10.7845/kjm.2018.7098.
24. 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.
* 23. Isolation and identification of new bacterial stains producing equol from Pueraria lobata extract fermentation. Kwon JE, Lim J, Kim I, Kim D*, Kang SC*. PLoS One. 2018 Feb 15;13(2):e0192490. doi: 10.1371/journal.pone.0192490.
22. 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.
on the media: 한국을 빛내는 사람들, 김동혁
2017
21. 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.
20. 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.
19. 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: 10.1021/acs.inorgchem.7b01101.
18. 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 genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655. Seo SW#,*, Gao Y#, Kim D#, Szubin R, Yang J, Cho BK, Palsson BO*. Sci Rep. 2017 May 19;7(1):2181. doi: 10.1038/s41598-017-02110-7.
16. 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.
15. 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.
14. 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. 2017 Jan 31. doi: 10.1016/j.jplph.2016.11.006.
2016
13. 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.
2015
12. 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 Rep. 2015 Aug 25;12(8):1289-99. doi: 10.1016/j.celrep.2015.07.043. Epub 2015 Aug 13.
11. 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;112(34):10810-5. doi: 10.1073/pnas.1501384112. Epub 2015 Aug 10.
10. Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress 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.
on the media: 한국을 빛내는 사람들
2014
9. 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.
on the media: 한국을 빛내는 사람들
8. 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.
7. 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.
2013
6. 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.
2012
5. 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.
4. 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.
3. 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.
2011
2. 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.
2009
1. 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 D, 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.
Patents
2024
Lim H, Kim D, Choi Y, Park S, Lee H, Battery state prediction system and battery state prediction method. UTP23334KR-00, filed Feb 05, 2024.
2023
Lim H, Choi Y, Kim D, Kim H, Ni A, Uwitonze H, Mohan NV, and Ahmad S. CFD and Machine Learning-Based Battery SOC/SOH Prediction System. UTP23504KR-00, filed December 06, 2023.
Lim H, Choi Y, Kim D, Kim H, Ni A, Uwitonze H, Mohan NV, and Ahmad S. CFD and Transfer Learning-Based Battery SOC/SOH Prediction System. UTP23505KR-00, filed December 06, 2023.
Kim D, Ko S, Kim H-Y, and Yoon H. Multiplex PCR kit for detecting vancomycin, methicillin, erythromycin and tetracycline resistant strains. KR Patent 10-2023-0068269, filed May 26, 2023.
2022
Kim D, Ko S, Kim H-Y, and Yoon H. Multiplex PCR kit for detecting colistin and quinolone resistant strains. KR Patent 10-2022-0108902, filed Aug 30, 2022.
2021
Kim D, Ko S, Kim H-Y, and Yoon H. Multiplex PCR kit for detecting ESBL resistant strains. KR Patent 10-2021-0192946, filed Dec 30, 2021.
Kim H-Y, Yang S-M, Yoon H, and Kim D. PCR primer set for detecting Salmonella serovars and uses thereof. KR Patent 10-2021-0119597, filed Dec 30, 2021 (10-2635-1430000, granted Feb 05, 2024)
2020
Kim D, Lim J, Yoo H S, and Park H-T. Biomarker for discrimination of Mycobacterium aviumM subsp. paratuberculosis subtype and use thereof. KR Patent 10-2020-0115887, filed Sep 10, 2020 (10-2359-8380000, granted Feb 03, 2022)