Staff information

PNNL Publications

2024

• Couvillion S.P., E.S. Nakayasu, B.M. Webb-Robertson, I.H. Yang, J.G. Eder, C.D. Nicora, and L.M. Bramer, et al. 2024. "Associations between SARS-CoV-2 Infection or COVID-19 Vaccination and Human Milk Composition: A Multi-Omics Approach." The Journal of Nutrition 154, no. 12:3566-3574. PNNL-SA-197322. doi:10.1016/j.tjnut.2024.09.032
• Harrison A.L., J.G. Eder, P.M. Lalli, N. Munoz Munoz, Y. Gao, C.S. Clendinen, and D.J. Orton, et al. 2024. "PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data." Journal of the American Society for Mass Spectrometry 35, no. 11:2680-2689. PNNL-SA-197329. doi:10.1021/jasms.4c00146
• 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
• Liu J., S. Cao, K.J. Imbach, M.A. Gritsenko, T.M. Lih, J.E. Kyle, and T.M. Yaron, et al. 2024. "Multi-scale signaling and tumor evolution in high-grade gliomas." Cancer Cell 42, no. 7:P1217-1238.E19. PNNL-SA-189873. doi:10.1016/j.ccell.2024.06.004

2023

• Couvillion S.P., K.E. Mostoller, J.L. Williams, R.M. Pace, I.L. Stohel, H.K. Peterson, and C.D. Nicora, et al. 2023. "Interrogating the role of the milk microbiome in mastitis in the multi-omics era." Frontiers in Microbiology 14. PNNL-SA-180041. doi:10.3389/fmicb.2023.1105675
• Couvillion S.P., R.E. Danczak, D.T. Naylor, M.L. Smith, K.G. Stratton, V.L. Paurus, and K.J. Bloodsworth, et al. 2023. "Rapid remodeling of the soil lipidome in response to a drying-rewetting event." Microbiome 11, no. 2023:34. PNNL-SA-172149. doi:10.1186/s40168-022-01427-4
• 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
• Naasko K.I., D.T. Naylor, E.B. Graham, S.P. Couvillion, R.E. Danczak, N. Tolic, and C.D. Nicora, et al. 2023. "Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry." mBio 14, no. 5:Art. No. e01758-23. PNNL-SA-187582. doi:10.1128/mbio.01758-23
• Tabb D., K. Jeong, K. Druart, M. Gant, K.A. Brown, C.D. Nicora, and M. Zhou, et al. 2023. "Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection." Journal of Proteome Research 22, no. 7:2199-2217. PNNL-SA-178802. doi:10.1021/acs.jproteome.2c00673

2022

• McClure R.S., Y. Farris, R.E. Danczak, W.C. Nelson, H. Song, A. Kessler, and J. Lee, et al. 2022. "Interaction Networks are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes." mSystems 7, no. 5:Art. No. e00372-22. PNNL-SA-169189. doi:10.1128/msystems.00372-22
• Shaffer J.P., L. Nothias, L.R. Thompson, J.G. Sanders, R.A. Salido, S.P. Couvillion, and A. Brejnrod, et al. 2022. "Standardized Multi-omics of Earth’s Microbiomes reveals microbial and metabolite diversity." Nature Microbiology 7, no. 12:2128-2150. PNNL-SA-174662. doi:10.1038/s41564-022-01266-x
• Zhang S., W. Song, L. Nothias, S.P. Couvillion, N. Webster, and T. Thomas. 2022. "Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts." Microbiome 10, no. 1:Art. No. 22. PNNL-SA-163874. doi:10.1186/s40168-021-01220-9

2021

• Brandvold K.R., S.P. Couvillion, T.M. Gibbins, and K.J. Tyrrell. 2021. Illuminating gut microbiome signaling pathways that regulate host circadian rhythms. PNNL-32131. Richland, WA: Pacific Northwest National Laboratory. Illuminating gut microbiome signaling pathways that regulate host circadian rhythms
• Cao X., X. Pan, S.P. Couvillion, T. Zhang, C. Tamez, L.M. Bramer, and J. White, et al. 2021. "Fate, cytotoxicity and cellular metabolomic impact of ingested nanoscale carbon dots using simulated digestion and a triculture small intestinal epithelial model." NanoImpact 23. PNNL-SA-166081. doi:10.1016/j.impact.2021.100349
• Wang L., A. Karpova, M.A. Gritsenko, J.E. Kyle, S. Cao, Y. Li, and D. Rykunov, et al. 2021. "Proteogenomic and Metabolomic Characterization of Human Glioblastoma." Cancer Cell 39, no. 4:509-528.e20. PNNL-SA-151124. doi:10.1016/j.ccell.2021.01.006
• Xu C., S.P. Couvillion, R.L. Sontag, N.G. Isern, Y. Maezato, S.R. Lindemann, and T.R. Chowdhury, et al. 2021. "MetFish: A Metabolomics Pipeline for Studying Microbial Communities in Chemically Extreme Environments." mSystems 6, no. 3:e01058-20. PNNL-SA-132977. doi:10.1128/mSystems.01058-20
• 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., H.M. Heyman, S.P. Couvillion, R.J. Cordero, M.L. Rodrigues, L. Nimrichter, and A. Casadevall, et al. 2021. "Comparative molecular and immunoregulatory analysis of extracellular vesicles from Candida albicans and Candida auris." mSystems 6, no. 4:e00822-21. PNNL-SA-156740. doi:10.1128/mSystems.00822-21
• 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

• Cleare L.G., D. Zamith-Miranda, H.M. Heyman, S.P. Couvillion, L. Nimrichter, M.L. Rodrigues, and E.S. Nakayasu, et al. 2020. "Media Matters! Alterations in the loading and release of Histoplasma capsulatum extracellular vesicles in response to different nutritional milieus." Cellular Microbiology 22, no. 9:Article No. e13217. PNNL-SA-151908. doi:10.1111/cmi.13217
• Couvillion S.P., N. Agrawal, S.M. Colby, K.R. Brandvold, and T.O. Metz. 2020. "Who is metabolizing what? Discovering novel biomolecules in the microbiome and the organisms who make them." Frontiers in Cellular and Infection Microbiology 10. PNNL-SA-153398. doi:10.3389/fcimb.2020.00388
• Khare S., G.M. Deloid, R.M. Molina, K. Gokulan, S.P. Couvillion, K.J. Bloodsworth, and E.K. Eder, et al. 2020. "Effects of ingested nanocellulose on intestinal microbiota and homeostasis in Wistar Han rats." NanoImpact 18. PNNL-SA-149247. doi:10.1016/j.impact.2020.100216

2019

• Couvillion S.P., Y. Zhu, G. Nagy, J.N. Adkins, C.K. Ansong, R.S. Renslow, and P.D. Piehowski, et al. 2019. "New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells." Analyst 144, no. 3:794-807. PNNL-SA-137430. doi:10.1039/C8AN01574K
• Zamith-Miranda D., H.M. Heyman, L.G. Cleare, S.P. Couvillion, G. Clair, E.L. Bredeweg, and A. Gacser, et al. 2019. "Multi-omics signature of Candida Auris, an emerging and multidrug-resistant pathogen." mSystems 4, no. 4:e00257-19. PNNL-SA-140174. doi:10.1128/mSystems.00257-19