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Energy and Environment Directorate

Ziyu Dai

Ziyu Dai

Pacific Northwest National Laboratory
PO Box 999
Richland, WA 99352
(509) 375-2169


Ziyu Dai concentrates his work in the area of the molecular biology and biotechnology of eukaryotic systems. He is currently applying his expertise to research on filamentous fungi to develop biobased technology and products, and is heading the fungal genetics component of the Lab's Bio-based Products Initiative. Dr. Dai's diverse experience includes the isolation, analysis, and manipulation of genes. He has isolated a series of eukaryotic genes and examined their functions and regulations in the eukaryotic systems. This work has resulted in two issued patents and five pending patents. Dr. Dai has also studied the transgenic expression of various proteins in green plants, including the expression of various microbial cellulase enzymes and human blood proteins in tobacco and potato plants. He has published extensively in the area of molecular biology, biochemistry, and physiology of green plants.

Education and Credentials

  • Ph.D., Botany, Washington State University, 1993
  • M.S., Agronomy, Southern China Agricultural University, 1986
  • B.S., Agronomy, Southern China Agricultural University, 1983

PNNL Patents

PNNL Publications


  • 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. 2023. "Novel genetic tools improve Penicillium expansum patulin synthase production in Aspergillus niger." FEBS Journal 290, no. 21:5094-5097. PNNL-SA-190084. doi:10.1111/febs.16956
  • 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
  • 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


  • 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


  • 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
  • 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


  • Deng S., Z. Dai, M.S. Swita, K.R. Pomraning, B.A. Hofstad, E.A. Panisko, and S.E. Baker, et al. 2020. "Deletion analysis of the itaconic acid biosynthesis gene cluster components in Aspergillus pseudoterreus ATCC32359." Applied Microbiology and Biotechnology 104, no. 9:3981-3992. PNNL-SA-144713. doi:10.1007/s00253-020-10418-0


  • Collett J.R., J.M. Billing, P.A. Meyer, A.J. Schmidt, A.B. Remington, E. Hawley, and B.A. Hofstad, et al. 2019. "Renewable diesel via hydrothermal liquefaction of oleaginous yeast and residual lignin from bioconversion of corn stover." Applied Energy 233. PNNL-SA-133222. doi:10.1016/j.apenergy.2018.09.115
  • Dai Z., K.R. Pomraning, S. Deng, B.A. Hofstad, E.A. Panisko, D. Rodriguez, and M.G. Butcher, et al. 2019. "Deletion of the ku70 homologue facilitates gene targeting in lipomyces starkeyi strain NRRL Y-11558." Current Genetics 65, no. 1:269-282. PNNL-SA-130042. doi:10.1007/s00294-018-0875-z
  • 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


  • Bredeweg E.L., K.R. Pomraning, Z. Dai, J.B. Nielsen, E.J. Kerkhoven, and S.E. Baker. 2017. "A Molecular Genetic Toolbox for Yarrowia lipolytica." Biotechnology for Biofuels 10. PNNL-SA-118953. doi:10.1186/s13068-016-0687-7
  • Dai Z., S. Deng, D.E. Culley, K.S. Bruno, and J.K. Magnuson. 2017. "Agrobacterium tumefaciens-mediated transformation of oleaginous yeast Lipomyces species." Applied Microbiology and Biotechnology 101, no. 15:6099-6110. PNNL-SA-123451. doi:10.1007/s00253-017-8357-7


  • Mo K., Z. Dai, and D.S. Wunschel. 2016. "Production and Characterization of Desmalonichrome Relative Binding Affinity for Uranyl Ions in Relation to other Siderophores." Journal of Natural Products 79, no. 6:1492-1499. PNNL-SA-113689. doi:10.1021/acs.jnatprod.5b00933
  • Niu J., M. Arentshorst, D. Nair, Z. Dai, S.E. Baker, J. Frisvad, and K.F. Nielsen, et al. 2016. "Identification of a classical mutant in the industrial host Aspergillus niger by systems genetics: LaeA is required for citric acid production and regulates the formation of some secondary metabolites." G3 Genes, Genomes, Genetics 6, no. 1:193-204. PNNL-SA-114553. doi:10.1534/g3.115.024067


  • Guo J., A.Y. Nguyen, Z. Dai, D. Su, M.J. Gaffrey, R.J. Moore, and J.M. Jacobs, et al. 2014. "Proteome-wide Light/Dark Modulation of Thiol Oxidation in Cyanobacteria Revealed by Quantitative Site-Specific Redox Proteomics." Molecular & Cellular Proteomics 13, no. 12:3270-3285. PNNL-SA-100244. doi:10.1074/mcp.M114.041160


  • Dai Z., U.K. Aryal, A.K. Shukla, W. Qian, R.D. Smith, J.K. Magnuson, and W.S. Adney, et al. 2013. "Impact of alg3 gene deletion on growth, development, pigment production, protein secretion, and functions of recombinant Trichoderma reesei cellobiohydrolases in Aspergillus niger." Fungal Genetics and Biology : FG & B 61. PNNL-SA-93855. doi:10.1016/j.fgb.2013.09.004
  • Kim J., Z. Dai, U.K. Aryal, R.J. Moore, D.G. Camp, S.E. Baker, and R.D. Smith, et al. 2013. "Resin-assisted Enrichment of N-terminal Peptides for Characterizing Proteolytic Processing." Analytical Chemistry 85, no. 14:6826-6832. PNNL-SA-92785. doi:10.1021/ac401000q


  • Beckham G.T., Z. Dai, J.F. Mattews, M. Momany, C.M. Payne, W.S. Adney, and S.E. Baker, et al. 2012. "Harnessing glycosylation to improve cellulase activity." Current Opinion in Biotechnology 23, no. 3:338-345. PNNL-SA-83208. doi:10.1016/j.copbio.2011.11.030
  • Wang L., U.K. Aryal, Z. Dai, A.C. Mason, M.E. Monroe, Z. Tian, and J. Zhou, et al. 2012. "Mapping N-linked Glycosylation Sites in the Secretome and Whole Cells of Aspergillus niger Using Hydrazide Chemistry and Mass Spectrometry." Journal of Proteome Research 11, no. 1:143-56. PNNL-SA-82556. doi:10.1021/pr200916k


  • Andersen M.R., M. Salazar, P. Schaap, P. van de Vondervoort, D.E. Culley, J. Thykaer, and J.C. Frisvad, et al. 2011. "Comparative genomics of citric-acid producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88." Genome Research 21, no. 6:885-897. PNNL-SA-78790. doi:10.1101/gr.112169.110
  • Chou H.L., Z. Dai, C.W. Hsieh, and M.S. Ku. 2011. "High level expression of Acidothermus cellulolyticus ß-1, 4-endoglucanase in transgenic rice enhances the hydrolysis of its straw by cultured cow gastric fluid." Biotechnology for Biofuels 4. PNNL-SA-84795. doi:10.1186/1754-6834-4-58
  • Yang B., Z. Dai, S. Ding, and C.E. Wyman. 2011. "Enzymatic Hydrolysis of Cellulosic Biomass." Biofuels 2, no. 4:421-450. PNNL-SA-81187. doi:10.4155/BFS.11.116
  • Yang B., Z. Dai, S. Ding, and C.E. Wyman. 2011. "Review: Enzymatic Hydrolysis of Cellulosic Biomass." Biofuels 2, no. 4:421-450. PNNL-SA-80964. doi:10.4155/bfs.11.116


  • Lee A., Z. Dai, B. Chen, H. Wu, J. Wang, A. Zhang, and A. Zhang, et al. 2008. "Electrochemical Branched-DNA Assay for Polymerase Chain Reaction-Free Detection and Quantification of Oncogenes in Messenger RNA." Analytical Chemistry 80, no. 24:9402-9410. PNNL-SA-61141. doi:10.1021/ac801263r
  • Taylor L.E., Z. Dai, S.R. Decker, R. Brunecky, W.S. Adney, S. Ding, and M.E. Himmel. 2008. "Heterologous Expression of Glycosyl Hydrolases in planta: A New Departure for Biofuels." Trends in Biotechnology 26, no. 8:413-424. PNNL-SA-60488.


  • Baker S.E., C.F. Wend, A.D. Martinez, J.K. Magnuson, E.A. Panisko, Z. Dai, and K.S. Bruno, et al. 2007. "Genome and Proteome Analysis of Industrial Fungi." In Exploitation of Fungi, edited by GD Robson, P van West and G Gadd. 3-9. New York, New York:Cambridge University Press. PNNL-SA-51617. doi:10.1017/CBO9780511902451.002


  • Dai Z., B.S. Hooker, R.D. Quesenberry, and S.R. Thomas. 2005. "Optimization of Acidothermus Celluloyticus Endoglucanase (E1) Production in Transgenic Tobacco Plants by Transcriptional, Post-transcription and Post-Translational Modification." Transgenic Research 14, no. 5:627-643. PNNL-SA-42943. doi:10.1007/s11248-005-5695-5


  • Dai Z., X. Mao, J.K. Magnuson, and L.L. Lasure. 2004. "Identification of Genes Associated with Morphology in Aspergillus Niger by Using Suppression Subtractive Hybridization." Applied and Environmental Microbiology 70, no. 4:2474-2485. PNNL-SA-40898.


  • Hooker B.S., Z. Dai, D.B. Anderson, R.D. Quesenberry, M.F. Ruth, and S.R. Thomas. 2001. "Production of Microbial Cellulases in Transgenic Crop Plants." In Glycosyl Hydrolases in Biomass Conversion. ACS Symposium Series, edited by ME Himmel, JO Baker, JN Saddler. 55-90. Washington Dc:American Chemical Society. PNNL-SA-32128.
  • Mauzey-Amato J.M., and Z. Dai. 2001. "Functional Analysis of Plant Promoter rpL34 Using the GUS Marker Gene in New Tr,tnsgene Expression Vector pZD428." Journal of Undergraduate Research 1. PNWD-SA-4664.


  • Dai Z., B.S. Hooker, D.B. Anderson, and S.R. Thomas. 2000. "Improved Plant-based Production of E1 endoglucanase Using Potato: Expression Optimization and Tissue Targeting." Molecular Breeding 6, no. 3:277-285. PNNL-SA-32097.


  • Dai Z., B.S. Hooker, R.D. Quesenberry, and J. Gao. 1999. "Expression of Trichoderma reesei exo-cellobiohydrolase I transgenic tobacco leaves and calli." Applied Biochemistry and Biotechnology 77, no. 9:689-699. PNNL-SA-31600.

Energy and Environment

Core Research Areas