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Donghyuk Kim - Publications

Affiliations: 
2014 Bioengineering University of California, San Diego, La Jolla, CA 
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36 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Lee SM, Le HT, Taizhanova A, Nong LK, Park JY, Lee EJ, Palsson BO, Kim D. Experimental promoter identification of a foodborne pathogen subsp. serovar Typhimurium with near single base-pair resolution. Frontiers in Microbiology. 14: 1271121. PMID 38239730 DOI: 10.3389/fmicb.2023.1271121  0.491
2023 Sathesh-Prabu C, Woo J, Kim Y, Kim SM, Lee SB, Jeon CO, Kim D, Lee SK. Comparative Genomic Analysis and BTEX Degradation Pathways of a Thermotolerant PHS1. Journal of Microbiology and Biotechnology. 33: 1-11. PMID 37100759 DOI: 10.41014/jmb.2301.01011  0.315
2023 Gao Y, Bang I, Seif Y, Kim D, Palsson BO. The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets. Nucleic Acids Research. PMID 37026477 DOI: 10.1093/nar/gkad253  0.789
2023 Bang I, Lee SM, Park S, Park JY, Nong LK, Gao Y, Palsson BO, Kim D. Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling. Briefings in Bioinformatics. PMID 36702751 DOI: 10.1093/bib/bbad024  0.615
2023 Park JY, Lee SM, Ebrahim A, Scott-Nevros ZK, Kim J, Yang L, Sastry A, Seo SW, Palsson BO, Kim D. Model-driven experimental design workflow expands understanding of regulatory role of Nac in . Nar Genomics and Bioinformatics. 5: lqad006. PMID 36685725 DOI: 10.1093/nargab/lqad006  0.831
2022 Choe D, Kim U, Hwang S, Seo SW, Kim D, Cho S, Palsson B, Cho BK. Revealing Causes for False-Positive and False-Negative Calling of Gene Essentiality in Escherichia coli Using Transposon Insertion Sequencing. Msystems. e0089622. PMID 36507678 DOI: 10.1128/msystems.00896-22  0.74
2021 Decker KT, Gao Y, Rychel K, Al Bulushi T, Chauhan SM, Kim D, Cho BK, Palsson BO. proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. Nucleic Acids Research. PMID 34791440 DOI: 10.1093/nar/gkab1043  0.698
2020 Nguyen AD, Nam G, Kim D, Lee EY. Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z. Microbial Cell Factories. 19: 131. PMID 32546161 DOI: 10.1186/s12934-020-01382-5  0.334
2020 Hwang J, Bang I, Kim D, Shin SC, Chin YW, Kim TW, Kim HJ. Genome sequence of the potential probiotic eukaryote KCCM 51299. 3 Biotech. 10: 185. PMID 32257741 DOI: 10.1007/s13205-020-02174-9  0.324
2020 Kim YJ, Park JY, Balusamy SR, Huo Y, Nong LK, Thi Le H, Yang DC, Kim D. Comprehensive Genome Analysis on the Novel Species DCY99 Reveals Insights into Iron Tolerance of Ginseng. International Journal of Molecular Sciences. 21. PMID 32188055 DOI: 10.3390/ijms21062019  0.303
2020 Song Y, Lee JS, Shin J, Lee GM, Jin S, Kang S, Lee JK, Kim DR, Lee EY, Kim SC, Cho S, Kim D, Cho BK. Functional cooperation of the glycine synthase-reductase and Wood-Ljungdahl pathways for autotrophic growth of . Proceedings of the National Academy of Sciences of the United States of America. PMID 32170009 DOI: 10.1073/pnas.1912289117  0.341
2019 Sastry AV, Gao Y, Szubin R, Hefner Y, Xu S, Kim D, Choudhary KS, Yang L, King ZA, Palsson BO. The Escherichia coli transcriptome mostly consists of independently regulated modules. Nature Communications. 10: 5536. PMID 31797920 DOI: 10.1038/S41467-019-13483-W  0.815
2019 Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, Monk JM, Lloyd CJ, Sandberg TE, Seo SW, Kim D, Sastry AV, Phaneuf P, Gao Y, Broddrick JT, et al. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Proceedings of the National Academy of Sciences of the United States of America. PMID 31270234 DOI: 10.1073/Pnas.1905039116  0.654
2018 Brunk E, Chang RL, Xia J, Hefzi H, Yurkovich JT, Kim D, Buckmiller E, Wang HH, Cho BK, Yang C, Palsson BO, Church GM, Lewis NE. Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow. Proceedings of the National Academy of Sciences of the United States of America. PMID 30301795 DOI: 10.1073/Pnas.1811971115  0.793
2018 Kabimoldayev I, Nguyen AD, Yang L, Park S, Lee EY, Kim D. Basics of genome-scale metabolic modeling and applications on C1-utilization. Fems Microbiology Letters. PMID 30256945 DOI: 10.1093/Femsle/Fny241  0.396
2018 Gao Y, Yurkovich JT, Seo SW, Kabimoldayev I, Dräger A, Chen K, Sastry AV, Fang X, Mih N, Yang L, Eichner J, Cho BK, Kim D, Palsson BO. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. Nucleic Acids Research. PMID 30137486 DOI: 10.1093/Nar/Gky752  0.802
2018 Nguyen AD, Hwang IY, Lee OK, Kim D, Kalyuzhnaya MG, Mariyana R, Hadiyati S, Kim MS, Lee EY. Systematic metabolic engineering of Methylomicrobium alcaliphilum 20Z for 2,3-butanediol production from methane. Metabolic Engineering. PMID 29673960 DOI: 10.1016/J.Ymben.2018.04.010  0.377
2018 Kim D, Seo SW, Gao Y, Nam H, Guzman GI, Cho BK, Palsson BO. Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP. Nucleic Acids Research. PMID 29394395 DOI: 10.1093/Nar/Gky069  0.813
2017 Hwang IS, Oh EJ, Kim D, Oh CS. Multiple plasmid-borne virulence genes of Clavibacter michiganensis ssp. capsici critical for disease development in pepper. The New Phytologist. PMID 29134663 DOI: 10.1111/Nph.14896  0.388
2017 Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich JT, Lloyd CJ, Gao Y, Yang L, Palsson BO. Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities. Proceedings of the National Academy of Sciences of the United States of America. PMID 28874552 DOI: 10.1073/Pnas.1702581114  0.778
2017 Seo SW, Gao Y, Kim D, Szubin R, Yang J, Cho BK, Palsson BO. Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655. Scientific Reports. 7: 2181. PMID 28526842 DOI: 10.1038/S41598-017-02110-7  0.822
2017 Hur DH, Nguyen TT, Kim D, Lee EY. Selective bio-oxidation of propane to acetone using methane-oxidizing Methylomonas sp. DH-1. Journal of Industrial Microbiology & Biotechnology. PMID 28321646 DOI: 10.1007/S10295-017-1936-X  0.315
2017 Jeong Y, Shin H, Seo SW, Kim D, Cho S, Cho B. Elucidation of bacterial translation regulatory networks Current Opinion in Systems Biology. 2: 84-90. DOI: 10.1016/J.Coisb.2017.01.009  0.709
2016 Nguyen HP, Jeong HY, Jeon SH, Kim D, Lee C. Rice pectin methylesterase inhibitor28 (OsPMEI28) encodes a functional PMEI and its overexpression results in a dwarf phenotype through increased pectin methylesterification levels. Journal of Plant Physiology. 208: 17-25. PMID 27889517 DOI: 10.1016/J.Jplph.2016.11.006  0.336
2016 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. Multi-omic data integration enables discovery of hidden biological regularities. Nature Communications. 7: 13091. PMID 27782110 DOI: 10.1038/Ncomms13091  0.746
2015 Seo SW, Kim D, Szubin R, Palsson BO. Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655. Cell Reports. PMID 26279566 DOI: 10.1016/J.Celrep.2015.07.043  0.789
2015 Yang L, Tan J, O'Brien EJ, Monk JM, Kim D, Li HJ, Charusanti P, Ebrahim A, Lloyd CJ, Yurkovich JT, Du B, Dräger A, Thomas A, Sun Y, Saunders MA, et al. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proceedings of the National Academy of Sciences of the United States of America. PMID 26261351 DOI: 10.1073/Pnas.1501384112  0.784
2015 Seo SW, Kim D, O'Brien EJ, Szubin R, Palsson BO. Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli. Nature Communications. 6: 7970. PMID 26258987 DOI: 10.1038/Ncomms8970  0.836
2014 Seo SW, Kim D, Latif H, O'Brien EJ, Szubin R, Palsson BO. Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. Nature Communications. 5: 4910. PMID 25222563 DOI: 10.1038/Ncomms5910  0.814
2014 Federowicz S, Kim D, Ebrahim A, Lerman J, Nagarajan H, Cho BK, Zengler K, Palsson B. Determining the control circuitry of redox metabolism at the genome-scale. Plos Genetics. 10: e1004264. PMID 24699140 DOI: 10.1371/Journal.Pgen.1004264  0.797
2014 Cho BK, Kim D, Knight EM, Zengler K, Palsson BO. Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states. Bmc Biology. 12: 4. PMID 24461193 DOI: 10.1186/1741-7007-12-4  0.603
2013 Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BO. Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. Science (New York, N.Y.). 340: 1220-3. PMID 23744946 DOI: 10.1126/Science.1234012  0.701
2012 Seo JH, Hong JS, Kim D, Cho BK, Huang TW, Tsai SF, Palsson BO, Charusanti P. Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features. Bmc Genomics. 13: 679. PMID 23194155 DOI: 10.1186/1471-2164-13-679  0.567
2012 Nam H, Lewis NE, Lerman JA, Lee DH, Chang RL, Kim D, Palsson BO. Network context and selection in the evolution to enzyme specificity. Science (New York, N.Y.). 337: 1101-4. PMID 22936779 DOI: 10.1126/Science.1216861  0.777
2012 Kim D, Hong JS, Qiu Y, Nagarajan H, Seo JH, Cho BK, Tsai SF, Palsson BØ. Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. Plos Genetics. 8: e1002867. PMID 22912590 DOI: 10.1371/Journal.Pgen.1002867  0.769
2011 Cho BK, Federowicz SA, Embree M, Park YS, Kim D, Palsson BØ. The PurR regulon in Escherichia coli K-12 MG1655. Nucleic Acids Research. 39: 6456-64. PMID 21572102 DOI: 10.1093/Nar/Gkr307  0.827
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