Staff information

PNNL Publications

2025

• Adamczyk P.A., H. Hwang, T. Chang, Y. Gao, E. Baidoo, J. Kim, and B.M. Webb-Robertson, et al. 2025. "The oleaginous yeast Rhodosporidium toruloides engineered for biomass hydrolysate-derived (E)-a-bisabolene production." Metabolic Engineering 90. PNNL-SA-210177. doi:10.1016/j.ymben.2025.02.014

2024

• Kuri Cruz A., M. Alves, T. Andresson, A.L. Bayless, K.J. Bloodsworth, J.A. Bowden, and K. Bullock, et al. 2024. "Multiplatform metabolomic interlaboratory study of a whole human stool candidate reference material from omnivore and vegan donors." Metabolomics 20. PNNL-SA-198688. doi:10.1007/s11306-024-02185-0
• Walukiewicz H.E., Y. Farris, M.C. Burnet, S.C. Feid, Y. You, H. Kim, and T. Bank, et al. 2024. "Regulation of bacterial stringent response by an evolutionary conserved ribosomal protein L11 methylation." mBio 15, no. 10:Art. No. e01773-24. PNNL-SA-186921. doi:10.1128/mbio.01773-24
• Zheng X., D.H. Ross, E.L. Bredeweg, J.G. Eder, D.J. Orton, M.C. Burnet, and J.E. Kyle, et al. 2024. "A deep learning-guided automated workflow in LipidOz for detailed characterization of fungal fatty acid unsaturation by ozonolysis." Journal of Mass Spectrometry 59, no. 9:e5078. PNNL-SA-197836. doi:10.1002/jms.5078

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
• Coradetti S.T., P.A. Adamczyk, D. Liu, Y. Gao, P.B. Otoupal, G.M. Geiselman, and B.M. Webb-Robertson, et al. 2023. "Engineering Transcriptional Regulation of Pentose Metabolism in Rhodosporidium toruloides for Improved Conversion of Xylose to Bioproducts." Microbial Cell Factories 22. PNNL-SA-177272. doi:10.1186/s12934-023-02148-5
• Couvillion S.P., R.E. Danczak, X. Cao, Q. Yang, T.P. Keerthisinghe, R.S. McClure, and D. Bitounis, et al. 2023. "Graphene oxide exposure alters gut microbial community composition and metabolism in an in vitro human model." NanoImpact 30. PNNL-SA-177384. doi:10.1016/j.impact.2023.100463
• Ross D.H., J. Lee, A. Bilbao, D.J. Orton, J.G. Eder, M.C. Burnet, and B. Kaiser, et al. 2023. "LipidOz Enables Automated Elucidation of Lipid Carbon-Carbon Double Bond Positions from Ozone-Induced Dissociation Mass Spectrometry Data." Communications Chemistry 6. PNNL-SA-180930. doi:10.1038/s42004-023-00867-9

2022

• Lee J., H.D. Mitchell, M.C. Burnet, R. Wu, S.C. Jenson, E.D. Merkley, and E.S. Nakayasu, et al. 2022. "Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics." Journal of Proteome Research 21, no. 8:2023-2035. PNNL-SA-138497. doi:10.1021/acs.jproteome.2c00334
• 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

• Del Cerro C., E. Erickson, T. Dong, A.R. Wong, E. Eder, S.O. Purvine, and H.D. Mitchell, et al. 2021. "Intracellular pathways for lignin catabolism in white-rot fungi." Proceedings of the National Academy of Sciences (PNAS) 118, no. 9:e2017381118. PNNL-SA-155713. doi:10.1073/pnas.2017381118
• Zamith-Miranda D., H.M. Heyman, M.C. Burnet, S.P. Couvillion, X. Zheng, N. Munoz Munoz, and W.C. Nelson, et al. 2021. "A Histoplasma capsulatum lipid metabolic map identifies antifungal targets." mBio 12, no. 6:e02972-21. PNNL-SA-152496. doi:10.1128/mBio.02972-21
• Zamith-Miranda D., R.P. da Silva, S.P. Couvillion, E.L. Bredeweg, M.C. Burnet, C. Coelho, and E. Camacho, et al. 2021. "Omics approaches for understanding biogenesis, composition and functions of fungal extracellular vesicles." Frontiers in Genetics 12. PNNL-SA-161136. doi:10.3389/fgene.2021.648524

2020

• Bhattacharjee A., A.M. Thompson, K.C. Schwarz, M.C. Burnet, Y. Kim, J. Nunez, and S.J. Fansler, et al. 2020. "Soil microbial EPS resiliency is influenced by carbon source accessibility." Soil Biology and Biochemistry 151. PNNL-SA-153321. doi:10.1016/j.soilbio.2020.108037
• Burnet M.C., D. Zamith-Miranda, H.M. Heyman, K.K. Weitz, E.L. Bredeweg, J.D. Nosanchuk, and E.S. Nakayasu. 2020. "Remodeling of the Histoplasma capsulatum membrane induced by monoclonal antibodies." Vaccines 8, no. 2:269. PNNL-SA-152362. doi:10.3390/vaccines8020269
• Chaves J.E., R. Wilton, Y. Gao, N. Munoz Munoz, M.C. Burnet, Z. Schmitz, and J. Rowan, et al. 2020. "Evaluation of chromosomal insertion loci in the Pseudomonas putida KT2440 genome for predictable biosystems design." Metabolic Engineering Communications 11. PNNL-SA-155823. doi:10.1016/j.mec.2020.e00139

2019

• Coelho C., L. Brown, M. Maryam, R. Vij, D.F. Smith, M.C. Burnet, and J.E. Kyle, et al. 2019. "Listeria monocytogenes Virulence Factors, including listeriolysin O, are Secreted in Biologically Active Extracellular Vesicles." Journal of Biological Chemistry 294, no. 4:1202-1217. PNNL-SA-128462. doi:10.1074/jbc.RA118.006472

2018

• Baltazar L.M., D. Zamith-Miranda, M.C. Burnet, H. Choi, L. Nimrichter, E.S. Nakayasu, and J.D. Nosanchuk. 2018. "Concentration-dependent protein loading of extracellular vesicles released by Histoplasma capsulatum after antibody treatment and its modulatory action upon macrophages." Scientific Reports 8, no. 1:Article No. 8065. PNNL-SA-124828. doi:10.1038/s41598-018-25665-5
• Callister S.J., T.L. Fillmore, C.D. Nicora, J.B. Shaw, S.O. Purvine, D.J. Orton, and R.A. White, et al. 2018. "Addressing the challenge of soil metaproteome complexity by improving metaproteome depth of coverage Through two-dimensional liquid chromatography." Soil Biology and Biochemistry 125. PNNL-SA-131999. doi:10.1016/j.soilbio.2018.07.018

2017

• Nakayasu E.S., M.C. Burnet, H.E. Walukiewicz, C.S. Wilkins, A.K. Shukla, S.M. Brooks, and M.J. Plutz, et al. 2017. "Ancient regulatory role of lysine acetylation in central metabolism." mBio 8, no. 6:Article No. e01894-17. PNNL-SA-124565. doi:10.1128/mBio.01894-17

2015

• Burnet M.C., A. Dohnalkova, A.P. Neumann, M.S. Lipton, R.D. Smith, G. Suen, and S.J. Callister. 2015. "Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85." PLoS One 10, no. 12:e0143809. PNNL-SA-111279. doi:10.1371/journal.pone.0143809

2014

• Eletsky A., K. Michalska, S. Houliston, Q. Zhang, M.D. Daily, X. Xu, and H. Cui, et al. 2014. "Structural and Functional Characterization of DUF1471 Domains of Salmonella Proteins SrfN, YdgH/SssB, and YahO." PLoS One 9, no. 7:Article No. e101787. PNNL-SA-101092. doi:10.1371/journal.pone.0101787

2013

• Merkley E.D., E.S. Baker, K.L. Crowell, D.J. Orton, T. Taverner, C. Ansong, and Y.M. Ibrahim, et al. 2013. "Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein-Protein Interactions by Chemical Cross-Linking." Journal of the American Society for Mass Spectrometry 24, no. 3:444-449. PNNL-SA-88464. doi:10.1007/s13361-012-0565-x

2011

• Ansong C., N. Tolic, S.O. Purvine, S. Porwollik, M.B. Jones, H. Yoon, and S.H. Payne, et al. 2011. "Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium." BMC Genomics 12. PNNL-SA-77195. doi:10.1186/1471-2164-12-433