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Energy and Environment Directorate

Kyle Pomraning

Kyle Pomraning

(509) 371-6627


Dr. Pomraning came to PNNL in 2013 as a William Wiley Post-doctoral Fellow and joined the Chemical and Biological Process Development Group in 2016. He has over 10 years of experience working with fungi and expertise in systems biology, genomics, metabolic engineering, and fungal biology.

His current research activities include biological conversion of renewable feedstocks to biofuels and bioproducts. He has worked extensively on multi-omic analyses of biological processes and has experience in metabolic modeling and bioengineering as well as process scale-up to bioreactors.

Research Interests

  • Bioconversion to fuels and chemicals
  • Renewable energy
  • Metabolic engineering
  • Genome regulation
  • Fungal metabolism and physiology

Education and Credentials

  • Ph.D., Molecular and Cellular Biology, Oregon State University
  • B.S., Biological Engineering, Oregon State University

Affiliations and Professional Service

  • Genetics Society of America
  • Society for Industrial Microbiology and Biotechnology

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., 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


  • Pomraning K.R., J.K. Magnuson, A.S. Beliaev, E.A. Hill, A.L. Robles, M.R. Garcia, and T.L. Lemmon. 2022. Enhancing organic matter removal, product recovery, and hydrogen generation from fermentation wastewater. PNNL-33008. Richland, WA: Pacific Northwest National Laboratory. Enhancing organic matter removal, product recovery, and hydrogen generation from fermentation wastewater
  • 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


  • Cordova L.T., B.C. Lad, S.A. Ali, A.J. Schmidt, J.M. Billing, K.R. Pomraning, and B.A. Hofstad, et al. 2020. "Valorizing a Hydrothermal Liquefaction Aqueous Phase through co-production of chemicals and lipids using the oleaginous yeast Yarrowia lipolytica." Bioresource Technology 313. PNNL-SA-153615. doi:10.1016/j.biortech.2020.123639
  • 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


  • 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


  • Deng S., K.R. Pomraning, P. Bohutskyi, and J.K. Magnuson. 2018. "Draft Genome Sequence of Aspergillus oryzae ATCC 12892." Genome Announcements 8, no. 18:Article No. e00251-18. PNNL-SA-132840. doi:10.1128/genomeA.00251-18
  • Pomraning K.R., E.L. Bredeweg, E.J. Kerkhoven, K.W. Barry, S. Haridas, H. Hundley, and K.M. LaButti, et al. 2018. "Regulation of yeast-to-hyphae transition in Yarrowia lipolytica." mSphere 3, no. 6:Article No. e00541-18. PNNL-SA-131456. doi:10.1128/mSphere.00541-18


  • 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
  • Geng T., C.R. Smallwood, E.L. Bredeweg, K.R. Pomraning, A.E. Plymale, S.E. Baker, and J.E. Evans, et al. 2017. "Multimodal Microfluidic Platform for Controlled Culture and Analysis of Unicellular Organisms." Biomicrofluidics 11, no. 5:054104. PNNL-SA-129125. doi:10.1063/1.4986533
  • Pomraning K.R., E.L. Bredeweg, and S.E. Baker. 2017. "Regulation of nitrogen metabolism by GATA zinc-finger transcription factors in Yarrowia lipolytica." mSphere 2, no. 1:Article No. 00038-17. PNNL-SA-122638. doi:10.1128/mSphere.00038-17
  • Tisch D., K.R. Pomraning, J.R. Collett, M. Freitag, S.E. Baker, C. Chen, and P.W. Hsu, et al. 2017. "Omics Analyses of Trichoderma reesei CBS999.97 and QM6a Indicate the Relevance of Female Fertility to Carbohydrate-Active Enzyme and Transporter Levels." Applied and Environmental Microbiology 83, no. 22:e01578-17. PNNL-SA-129552. doi:10.1128/AEM.01578-17


  • Kerkhoven E., K.R. Pomraning, S.E. Baker, and J.B. Nielsen. 2016. "Regulation of amino acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica." npj Systems Biology and Applications 2. PNNL-SA-111282. doi:10.1038/npjsba.2016.5
  • Pomraning K.R., Y. Kim, C.D. Nicora, R.K. Chu, E.L. Bredeweg, S.O. Purvine, and D. Hu, et al. 2016. "Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica." BMC Genomics 17, no. 138:1-18. PNNL-SA-112784. doi:10.1186/s12864-016-2471-2
  • Schmoll M., C. Dattenbock, N. Carreras-Villasenor, A. Mendoza-Mendoza, D. Tisch, M.I. Aleman, and S.E. Baker, et al. 2016. "The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species." Microbiology and Molecular Biology Reviews 80, no. 1:205-327. PNNL-SA-118679. doi:10.1128/MMBR.00040-15


  • Pomraning K.R., and S.E. Baker. 2015. "Draft genome sequence of the dimorphic yeast Yarrowia lipolytica, strain W29." Genome Announcements 3, no. 6:Article No. e01211-15. PNNL-SA-112964. doi:10.1128/genomeA.01211-15
  • Pomraning K.R., S. Wei, S.A. Karagiosis, Y. Kim, A. Dohnalkova, B.W. Arey, and E.L. Bredeweg, et al. 2015. "Comprehensive metabolomic, lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis." PLoS One 10, no. 4:e0123188. PNNL-SA-105704. doi:10.1371/journal.pone.0123188

Energy and Environment

Core Research Areas