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Energy and Environment Directorate

Joonhoon Kim

(509) 372-6176

PNNL Patents

PNNL Publications

2024

  • Czajka J.J., Y. Han, J. Kim, S.J. Mondo, B.A. Hofstad, A.L. Robles, and S. Haridas, et al. 2024. "Genome-Scale Model Development and Genomic Sequencing of the Oleaginous Clade Lipomyces." Frontiers in Bioengineering and Biotechnology 12. PNNL-SA-193362. doi:10.3389/fbioe.2024.1356551
  • Kim J. 2024. Accelerating Engineered Microbe Optimization through Machine Learning and Multi-Omics Datasets - CRADA 422 (Abstract). PNNL-35277. Richland, WA: Pacific Northwest National Laboratory.

2023

  • Bilbao A., N. Munoz Munoz, J. Kim, D.J. Orton, Y. Gao, K. Poorey, and K.R. Pomraning, et al. 2023. "PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements." Nature Communications 14, no. 2023:2461. PNNL-SA-174727. doi:10.1038/s41467-023-37031-9
  • Dai Z., K.R. Pomraning, S. Deng, J. Kim, K.B. Campbell, A.L. Robles, and B.A. Hofstad, et al. 2023. "Metabolic engineering to improve production of 3-hydroxypropionic acid from corn-stover hydrolysate in Aspergillus species." Biotechnology for Biofuels and Bioproducts 16. PNNL-SA-182738. doi:10.1186/s13068-023-02288-1
  • Deng S., J. Kim, K.R. Pomraning, Y. Gao, J.E. Evans, B.A. Hofstad, and Z. Dai, et al. 2023. "Identification of a specific exporter that enables high production of aconitic acid in Aspergillus pseudoterreus." Metabolic Engineering 80. PNNL-SA-181297. doi:10.1016/j.ymben.2023.09.011
  • Han Y., A. Tafur Rangel, K.R. Pomraning, E.J. Kerkhoven, and J. Kim. 2023. "Advances in genome-scale metabolic models of industrially important fungi." Current Opinion in Biotechnology 84. PNNL-SA-188501. doi:10.1016/j.copbio.2023.103005
  • Liu D., H. Hwang, P.B. Otoupal, G.M. Geiselman, J. Kim, K.R. Pomraning, and Y. Kim, et al. 2023. "Engineering Rhodosporidium toruloides for Production of 3-Hydroxypropionic Acid from Lignocellulosic Hydrolysate." Metabolic Engineering 78. PNNL-SA-185285. doi:10.1016/j.ymben.2023.05.001
  • Yuan G., J.J. Czajka, Z. Dai, D. Hu, K.R. Pomraning, B.A. Hofstad, and J. Kim, et al. 2023. "Rapid and robust squashed spore/colony PCR of industrially important fungi." Fungal Biology and Biotechnology 10. PNNL-SA-186830. doi:10.1186/s40694-023-00163-0

2022

  • Pomraning K.R., Z. Dai, N. Munoz Munoz, Y. Kim, Y. Gao, S. Deng, and T.L. Lemmon, et al. 2022. "Itaconic acid production is regulated by laeA in Aspergillus pseudoterreus." Metabolic Engineering Communications 15. PNNL-SA-171876. doi:10.1016/j.mec.2022.e00203

2021

  • Dai Z., K.R. Pomraning, E.A. Panisko, B.A. Hofstad, K.B. Campbell, J. Kim, and A.L. Robles, et al. 2021. "Genetically engineered oleaginous yeast Lipomyces starkeyi for sesquiterpene a-zingiberene production." ACS Synthetic Biology 10, no. 5:1000-1008. PNNL-SA-156626. doi:10.1021/acssynbio.0c00503
  • Kim J., S.T. Coradetti, Y. Kim, Y. Gao, J. Yaegashi, J.D. Zucker, and N. Munoz Munoz, et al. 2021. "Multi-omics driven metabolic network reconstruction and analysis of lignocellulosic carbon utilization in Rhodosporidium toruloides." Frontiers in Bioengineering and Biotechnology 8. PNNL-SA-156767. doi:10.3389/fbioe.2020.612832
  • Kirby J., G.M. Geiselman, J. Yaegashi, J. Kim, X. Zhuang, M. Tran-Gyamfi, and J. Prahl, et al. 2021. "Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass." Biotechnology for Biofuels 14, no. 1:Article No. 101. PNNL-SA-162406. doi:10.1186/s13068-021-01950-w
  • Lawson C., J.M. Marti, T. Radivojevic, S.R. Jonnalagadda, R. Gentz, N.J. Hillson, and S. Peisert, et al. 2021. "Machine learning for metabolic engineering: A review." Metabolic Engineering 63. PNNL-SA-158037. doi:10.1016/j.ymben.2020.10.005
  • Pomraning K.R., Z. Dai, N. Munoz Munoz, Y. Kim, Y. Gao, S. Deng, and J. Kim, et al. 2021. "Integration of proteomics and metabolomics into the Design, Build, Test, Learn cycle to improve 3-hydroxypropionic acid production in Aspergillus pseudoterreus." Frontiers in Bioengineering and Biotechnology 9. PNNL-SA-149911. doi:10.3389/fbioe.2021.603832
  • Roy S., T. Radivojevic, M. Forrer, J.M. Marti, S.R. Jonnalagadda, T. Backman, and W. Morrell, et al. 2021. "Multiomics data collection, visualization, and utilization for guiding metabolic engineering." Frontiers in Bioengineering and Biotechnology 9. PNNL-SA-159094. doi:10.3389/fbioe.2021.612893

2019

  • Kim J., M. Tremaine, J. Grass, H. Purdy, R. Landick, P.J. Kiley, and J.L. Reed. 2019. "Systems Metabolic Engineering of Escherichia coli Improves Coconversion of Lignocellulose-Derived Sugars." Biotechnology Journal 14, no. 9:Article No. 1800441. PNNL-SA-148827. doi:10.1002/biot.201800441
  • Pomraning K.R., J.R. Collett, J. Kim, E.A. Panisko, D.E. Culley, Z. Dai, and S. Deng, et al. 2019. "Transcriptomic analysis of the oleaginous yeast Lipomyces starkeyi during lipid accumulation on enzymatically treated corn stover hydrolysate." Biotechnology for Biofuels 12. PNNL-SA-142743. doi:10.1186/s13068-019-1510-z

2018

  • George K.W., M.G. Thompson, J. Kim, E. Baidoo, G. Wang, V. Benites, and C.J. Petzold, et al. 2018. "Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli." Metabolic Engineering 47. PNNL-SA-138198. doi:10.1016/j.ymben.2018.03.004
  • Reilly M.C., J. Kim, J.J. Lynn, B.A. Simmons, J.M. Gladden, J.K. Magnuson, and S.E. Baker. 2018. "Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger." Applied Microbiology and Biotechnology 102, no. 4:1797-1807. PNNL-SA-132880. doi:10.1007/s00253-017-8717-3

Energy and Environment

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