Research Focus
Joonhoon Kim is a scientist at Pacific Northwest National Laboratory and serves as the Director of Fungal Biotechnology at JBEI. He earned his BS in Chemical Engineering from POSTECH in South Korea and his PhD in Chemical Engineering from the University of Wisconsin-Madison. His research interests include computational and systems biology approaches and their application to metabolic engineering of microorganisms. At JBEI, he has been working on development of recombinant fungal protein expression systems to produce lignocellulose deconstruction enzymes, and reconstruction of metabolic pathways in fungi to understand the utilization of carbon sources derived from lignocellulosic biomass.
Projects
- Develop and extend genome-scale metabolic models for fungi
- Identify catabolic pathways and transporters for lignin-derived intermediates using multi-omics approaches and metabolic modeling
- Engineer fungal hosts for conversion of depolymerized lignin and polysaccharides to bioproduct and biofuel precursors
Featured Publications
- “Advances in genome-scale metabolic models of industrially important fungi,” Current Opinion in Biotechnology (2023)
- “Identification of a specific exporter that enables high production of aconitic acid in Aspergillus pseudoterreus,” Metabolic Engineering (2023)
- “Engineering Rhodosporidium toruloides for production of 3-hydroxypropionic acid from lignocellulosic hydrolysate,” Metabolic Engineering (2023)
- “PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements,” Nature Communications (2023)
- “Metabolic engineering to improve production of 3-hydroxypropionic acid from corn-stover hydrolysate in Aspergillus species,” Biotechnology for Biofuels and Bioproducts (2023)
- “Multi-omics driven metabolic network reconstruction and analysis of lignocellulosic carbon utilization in Rhodosporidium toruloides,” Frontiers in Bioengineering and Biotechnology (2021)
- “Machine learning for metabolic engineering: A review,” Metabolic Engineering (2021)
- “A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides,” Microbial Cell Factories (2019)
- “Systems Metabolic Engineering of Escherichia coli Improves Coconversion of Lignocellulose-Derived Sugars,” Biotechnology Journal (2019)
- “Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli,” Metabolic Engineering (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 (2018)