PNNL

Dr. Deng has over 14 years of experience in molecular biology. Dr. Deng got her Ph.D degree from Department of Biochemistry & Molecular Genetics in University of Alabama at Birmingham in 2004. Her thesis work studied bacterial chromosome structure, dynamics, gene regulation and functional genomics in Escherichia coli and Salmonella typhimurium. Dr. Deng joined PNNL in 2006 after working for two years as research associate at University of Alabama at Birmingham.

• Utilizing filamentous fungi for converting renewable biomass to fuels, chemicals and enzymes.
• Discovery of genes important for biosynthetic pathways.
• Strain improvement with higher productivity and the use of alternative substrates, which may reduce costs and conserve environment.

• Ph.D., Biochemistry and Molecular Genetics, University of Alabama at Birmingham
• M.S., Clinical Pharmacology, Sun Yat-sen University
• B.S., Clinical Medicine, Zhengzhou University

• U.S. Patent No. 12,338,480, June 24, 2025, "ACONITIC ACID EXPORTER (AEXA) INCREASES ORGANIC ACID PRODUCTION IN ASPERGILLUS (iEdison No. 0685901-20-0043)".
• U.S. Patent No. 11,873,523, January 16, 2024, "ACONITIC ACID EXPORTER (AEXA) INCREASES ORGANIC ACID PRODUCTION IN ASPERGILLUS (iEdison No. 0685901-20-00430)".
• U.S. Patent No. 10,947,548, March 16, 2021, "PRODUCTION OF ORGANIC ACIDS FROM ASPERGILLUS CIS-ACONITIC ACID DECARBOXYLASE (CADA) DELETION STRAINS".
• U.S. Patent No. 9,914,932, March 13, 2018, "Agrobacterium-mediated transformation of lipomyces".

2025

• Czajka J.J., Z. Dai, T. Radivojevic, J. Kim, S. Deng, T.L. Lemmon, and M.S. Swita, et al. 2025. "Enabling malic acid production from corn-stover hydrolysate in Lipomyces starkeyi via metabolic engineering and bioprocess optimization." Microbial Cell Factories 24:Art. No. 117. PNNL-SA-204465. doi:10.1186/s12934-025-02705-0
• Yuan G., A.L. Salalila, S. Hwang, Z. Deng, and S. Deng. 2025. "An Innovative High Throughput Genome Releaser for Rapid and Efficient PCR Screening." Frontiers in Bioengineering and Biotechnology 13. PNNL-SA-206684. doi:10.3389/fbioe.2025.1547909

2024

• Pomraning K.R., S. Deng, R.D. Duong, J.J. Czajka, and P. Bohutskyi. 2024. "Identification of Yarrowia lipolytica as a platform for designed consortia that incorporate in situ nitrogen fixation to enable ammonia-free bioconversion." Frontiers in Industrial Microbiology 2. PNNL-SA-201556. doi:10.3389/finmi.2024.1473316
• Yuan G., A.L. Salalila, S. Hwang, Z. Deng, and S. Deng. 2024. High Throughput Genome Releaser. PNNL-36983. Richland, WA: Pacific Northwest National Laboratory. High Throughput Genome Releaser
• Yuan G., S. Deng, J.J. Czajka, Z. Dai, B.A. Hofstad, J. Kim, and K.R. Pomraning. 2024. "CRISPR-Cas9/Cas12a Systems for efficient genome editing and large genomic fragment deletions in Aspergillus niger." Frontiers in Bioengineering and Biotechnology 12. PNNL-SA-199630. doi:10.3389/fbioe.2024.1452496
• Yuan G., S. Gao, J.J. Czajka, Z. Dai, K.R. Pomraning, R.D. Duong, and B.A. Hofstad, et al. 2024. "Simple and effective Squash-PCR for rapid genotyping of industrial microalgae." Life 14, no. 1:Art. No. 115. PNNL-SA-192108. doi:10.3390/life14010115

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
• 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
• 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

2020

• 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

2019

• 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

2018

• 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

2017

• 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

2014

• Qu Y., J. Feng, S. Deng, L. Cao, Q. Zhang, R. Zhao, and Z. Zhang, et al. 2014. "Structural Analysis of N- and O-glycans Using ZIC-HILIC/Dialysis Coupled to NMR Detection." Fungal Genetics and Biology : FG & B 72. PNNL-SA-101957. doi:10.1016/j.fgb.2014.08.001

2013

• Tamano K., K.S. Bruno, S.A. Karagiosis, D.E. Culley, S. Deng, J.R. Collett, and M. Umemura, et al. 2013. "Increased Production of Fatty Acids and Triglycerides in Aspergillus oryzae by Enhancing Expressions of Fatty Acid Synthesis-Related Genes." Applied Microbiology and Biotechnology 97, no. 1:269-281. PNNL-SA-86701. doi:10.1007/s00253-012-4193-y

2008

• Shi L., S. Deng, M.J. Marshall, Z. Wang, D.W. Kennedy, A. Dohnalkova, and H.M. Mottaz, et al. 2008. "Direct Involvement of Type II Secretion System in Extracellular Translocation of Shewanella Oneidensis Outer Membrane Cytochromes MtrC and OmcA." Journal of Bacteriology 190, no. 15:5512-5516. PNNL-SA-55117. doi:10.1128/JB.00514-08