Publications

Updated 2025 March

For the most recently updated publication list see google scholar page.

* denote co-authorship

# denote co-senior authorship

1. *Cardona, C., *Wei, L., *Kim, J., *Angeles, E., Singh, G., Chen, S., Patel, R., Ifediora, N., Cannol, P., Teich, A., Hargus, G., #Chavez, A., #Sproul, A.A. High throughput identification of genetic regulators of microglial inflammatory processes in Alzheimer's disease. Journal of Neuroinflammation. Accepted. (2025).

Before 2025 March

1. Kim J., Kratz A. F., Chen S., Sheng J., Kim H. K., Zhang L., Singh B. K., Chavez A., High-throughput tagging of endogenous loci for rapid characterization of protein function. Science Advances. 10, eadg8771 (2024). Video summary of manuscript.

2. Lee J., Kim J., Kim H., Park H., Kim J. Y., Kim E.-J., Yang Y.-H., Choi K.-Y., Kim B.-G., Constructing multi-enzymatic cascade reactions for selective production of 6-bromoindirubin from tryptophan in Escherichia coli. Biotechnology and Bioengineering. 119, 2938–2949 (2022).

3. Song H., Lee P.-G., Kim J., Kim J., Lee S.-H., Kim H., Lee U.-J., Kim J. Y., Kim E.-J., Kim B.-G., Regioselective one-pot synthesis of hydroxy-(S)-equols using isoflavonoid reductases and monooxygenases and evaluation of the hydroxyequol derivatives as selective estrogen receptor modulators and antioxidants. Frontiers in Bioengineering and Biotechnology 10, 830712 (2022).

4. Song H., Lee P.-G., Kim H., Lee U.-J., Lee S.-H., Kim J., Kim B.-G., Polyphenol-hydroxylating tyrosinase activity under acidic pH enables efficient synthesis of plant catechols and gallols. Microorganisms 9, 1866 (2021).

5. Bae S.-J., Kim S., Park H. J., Kim J., Jin H., Kim B.-G., Hahn J.-S., High-yield production of (R)-acetoin in Saccharomyces cerevisiae by deleting genes for NAD(P)H-dependent ketone reductases producing meso-2,3-butanediol and 2,3-dimethylglycerate. Metabolic Engineering. 66, 68–78 (2021).

6. Park B. G., Kim J., Kim E.-J., Kim Y., Kim J., Kim J. Y., Kim B.-G., Application of Random Mutagenesis and Synthetic FadR Promoter for de novo Production of ω-Hydroxy Fatty Acid in Yarrowia lipolytica. Frontiers in Bioengineering and Biotechnology 9, 624838 (2021).

7. *Lee J., *Kim J., Song J. E., Song W.-S., Kim E.-J., Kim Y.-G., Jeong H.-J., Kim H. R., Choi K.-Y., Kim B.-G.,  Production of Tyrian purple indigoid dye from tryptophan in Escherichia coli. Nature Chemical Biology 17, 104–112 (2021).

8. Lee J., Kim J., Kim H., Kim E.-J., Jeong H.-J., Choi K.-Y., Kim B.-G., Characterization of a tryptophan 6-halogenase from Streptomyces albus and its regioselectivity determinants. ChemBioChem 21, 1446–1452 (2020).

9. Heo K., Park Y.-H., Lee K.-A., Kim J., Ham H.-I., Kim B.-G., Lee W.-J., Seok Y.-J., Sugar-mediated regulation of a c-di-GMP phosphodiesterase in Vibrio cholerae. Nature Communication. 10, 5358 (2019).

10. Yoo H.-W., Kim J., Patil M. D., Park B. G., Joo S.-Y., Yun H., Kim B.-G., Production of 12-hydroxy dodecanoic acid methyl ester using a signal peptide sequence-optimized transporter AlkL and a novel monooxygenase. Bioresource Technology. 291, 121812 (2019).

11. Kim J., Lee J., Lee P.-G., Kim E.-J., Kroutil W., Kim B.-G., Elucidating cysteine-assisted synthesis of indirubin by a flavin-containing monooxygenase. ACS Catalysis 9, 9539–9544 (2019).

12. Kim M., Park B. G., Kim E.-J., Kim J., Kim B.-G., In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by genome-scale metabolic modeling. Biotechnology for Biofuels 12, 187 (2019).

13. Namgung S., Park H. A., Kim J., Lee P.-G., Kim B.-G., Yang Y.-H., Choi K.-Y., Ecofriendly one-pot biosynthesis of indigo derivative dyes using CYP102G4 and PrnA halogenase. Dyes and Pigment 162, 80–88 (2019).

14. Hosseini-Abari A., Emtiazi G., Jazini M., Kim J., Kim B. G., LC/MS detection of oligogalacturonic acids obtained from tragacanth degradation by pectinase producing bacteria. Journal of Basic Microbiology 59, 249–255 (2019).

15. Lee J., Yoo J., Kim J., Jang Y., Shin K., Ha E., Ryu S., Kim B.-G., Wooh S., Char K., Development of multimodal antibacterial surfaces using porous Amine-reactive films incorporating lubricant and silver nanoparticles. ACS Applied Materials and Interfaces 11, 6550–6560 (2019).

16. Paik S.-M., Kim J., Jin E., Jeon N. L., Overproduction of recombinant E. coli malate synthase enhances Chlamydomonas reinhardtii biomass by upregulating heterotrophic metabolism. Bioresource Technology 272, 594–598 (2019).

17. Kim M., Park B. G., Kim J., Kim J. Y., Kim B.-G.,  Exploiting transcriptomic data for metabolic engineering: toward a systematic strain design. Biotechnology Journal 54, 26–32 (2018).

18. Lee P.-G., Lee S.-H., Kim J., Kim E.-J., Choi K.-Y., Kim B.-G., Polymeric solvent engineering for gram/liter scale production of a water-insoluble isoflavone derivative, (S)-equol. Applied Microbiology and Biotechnology 102, 6915–6921 (2018).

19. Song W.-S., Park H.-M., Ha J. M., Shin S. G., Park H.-G., Kim J., Zhang T., Ahn D.-H., Kim S.-M., Yang Y.-H., Jeong J. H., Theberge A. B., Kim B.-G., Lee J. K., Kim Y.-G., Discovery of glycocholic acid and taurochenodeoxycholic acid as phenotypic biomarkers in cholangiocarcinoma. Scientific Reports 8, 11088 (2018).

20. Yoo J., Birke A., Kim J., Jang Y., Song S. Y., Ryu S., Kim B.-S., Kim B.-G., Barz M., Char K., Cooperative catechol-functionalized polypept(o)ide brushes and Ag nanoparticles for combination of protein resistance and antimicrobial activity on metal oxide surfaces. Biomacromolecules 19, 1602–1613 (2018).

21. Kim J., Yoo H.-W., Kim M., Kim E.-J., Sung C., Lee P.-G., Park B. G., Kim B.-G., Rewiring FadR regulon for the selective production of ω-hydroxy palmitic acid from glucose in Escherichia coli. Metabolic Engineering 47, 414–422 (2018).

22. Jung E., Park B. G., Yoo H.-W., Kim J., Choi K.-Y., Kim B.-G., Semi-rational engineering of CYP153A35 to enhance ω-hydroxylation activity toward palmitic acid. Applied Microbiology and Biotechnology 102, 269–277 (2018).

23. Kim J., Lee P.-G., Jung E.-O., Kim B.-G., In vitro characterization of CYP102G4 from Streptomyces cattleya: A self-sufficient P450 naturally producing indigo. Biochimica et Biophysica Acta - Proteins and Proteomics 1866, 60–67 (2018).

24. Lee P.-G., Kim J., Kim E.-J., Lee S.-H., Choi K.-Y., Kazlauskas R. J., Kim B.-G., Biosynthesis of (-)-5-hydroxy-equol and 5-hydroxy-dehydroequol from soy isoflavone, genistein using microbial whole cell bioconversion. ACS Chemical Biology 12, 2883–2890 (2017).

25. Kim H.-J., Jang S., Kim J., Yang Y.-H., Kim Y.-G., Kim B.-G., Choi K.-Y., Biosynthesis of indigo in Escherichia coli expressing self-sufficient CYP102A from Streptomyces cattleya. Dyes and Pigments 140, 29–35 (2017).

26. Park B. G., Kim M., Kim J., Yoo H., Kim B.-G., Systems biology for understanding and engineering of heterotrophic oleaginous microorganisms. Biotechnology Journal 12, 1600104 (2017).

27. Jung E., Park B. G., Ahsan M. M. M., Kim J., Yun H., Choi K.-Y., Kim B.-G., Production of ω-hydroxy palmitic acid using CYP153A35 and comparison of cytochrome P450 electron transfer system in vivo. Applied Microbiology and Biotechnology 100, 10375–10384 (2016).

28. Lee P.-G., Kim J., Kim E.-J., Jung E., Pandey B. P., Kim B.-G., P212A mutant of dihydrodaidzein reductase enhances (S)-equol production and enantioselectivity in a recombinant Escherichia coli whole-cell reaction system. Applied and Environmental Microbiology 82, 1992–2002 (2016).

29. Sung C., Jung E., Choi K.-Y., Bae J.-H., Kim M., Kim J., Kim E.-J., Kim P. I., Kim B.-G., The production of ω-hydroxy palmitic acid using fatty acid metabolism and cofactor optimization in Escherichia coli. Applied Microbiology and Biotechnology 99, 6667–6676 (2015).

30. Kim M., Yi J. S., Kim J., Kim J.-N., Kim M. W., Kim B.-G., Reconstruction of a high-quality metabolic model enables the identification of gene overexpression targets for enhanced antibiotic production in Streptomyces coelicolor A3(2). Biotechnology Journal 9, 1185–1194 (2014).