Staff information

PNNL Publications

2025

• Kim D., T. Yin, T. Zhang, A.K. Im, J.R. Cort, J.C. Rozum, and D.D. Pollock, et al. 2025. "Artificial Intelligence Transforming Post-Translational Modification Research." Bioengineering 12, no. 1:Art. No. 26. PNNL-SA-205285. doi:10.3390/bioengineering12010026

2024

• George A.D., W.E. Anthony, A.D. McNaughton, T.T. Lin, V. Torres-Rodriguez, S.M. Mahserejian, and S.L. Altus, et al. 2024. Multi-scale Simulation, Calibration, and Optimization of Calcium Carbonate Precipitation in Microbial Communities. PNNL-36693. Richland, WA: Pacific Northwest National Laboratory. Multi-scale Simulation, Calibration, and Optimization of Calcium Carbonate Precipitation in Microbial Communities
• Gluth A., X. Li, M.A. Gritsenko, M.J. Gaffrey, D. Kim, P.M. Lalli, and R.K. Chu, et al. 2024. "Integrative Multi-PTM Proteomics Reveals Dynamic Global, Redox, Phosphorylation, and Acetylation Regulation in Cytokine-treated Pancreatic Beta Cells." Molecular & Cellular Proteomics 23, no. 12:100881. PNNL-SA-202916. doi:10.1016/j.mcpro.2024.100881
• Kim D., A.D. McNaughton, and N. Kumar. 2024. "Leveraging Artificial Intelligence to Expedite Antibody Design and Enhance Antibody-Antigen Interactions." Bioengineering (Basel) 11, no. 2:Art. No. 185. PNNL-SA-194122. doi:10.3390/bioengineering11020185
• Meng Q., S. Moinuddin, R.M. Celoy, C. Smith, R.P. Young, M.A. Costa, and R.A. Freeman, et al. 2024. "Dirigent isoflavene-forming PsPTS2: 3D Structure, stereochemical and kinetic characterization comparison with pterocarpan-forming PsPTS1 homolog in pea." Journal of Biological Chemistry 300, no. 3:Art. No. 105647. PNNL-SA-188847. doi:10.1016/j.jbc.2024.105647

2023

• George A.D., D. Kim, T.H. Moser, I.T. Gildea, J.E. Evans, and M.S. Cheung-Wyker. 2023. "Graph identification of proteins in tomograms (GRIP-Tomo)." Protein Science 32, no. 1:Art. No. e4538. PNNL-SA-178301. doi:10.1002/pro.4538
• Gosline S., D. Kim, P. Pande, D.G. Thomas, L. Truong, P. Hoffman, and M. Barton, et al. 2023. "The Superfund Research Program Analytics Portal: linking environmental chemical exposure to biological phenotypes." Scientific Data 10. PNNL-SA-177557. doi:10.1038/s41597-023-02021-5
• Leonard B., V.G. Danna, L.J. Gorham, M.R. Davison, W.B. Chrisler, D. Kim, and R.V. Gerbasi. 2023. "Shaping Nanobodies and Intrabodies Against Proteoforms." Analytical Chemistry 95, no. 23:8747-8751. PNNL-SA-182135. doi:10.1021/acs.analchem.3c00958

2022

• Kim D., A.J. August, H.J. Kvinge, and J. Evans. 2022. Structures via Reasoning - Applying AI to Cryo Electron Microscopy to Reveal Structural Variability. PNNL-33162. Richland, WA: Pacific Northwest National Laboratory. Structures via Reasoning - Applying AI to Cryo Electron Microscopy to Reveal Structural Variability
• Rivera B.N., L.B. Wilson, D. Kim, P. Pande, K.A. Anderson, S.C. Tilton, and R.L. Tanguay. 2022. "A Comparative Multi-System Approach to Characterizing Bioactivity of Commonly Occurring Chemicals." International Journal of Environmental Research and Public Health 19, no. 7:Art. No. 3829. PNNL-SA-170471. doi:10.3390/ijerph19073829

2020

• Kim D., D. Gront, and K. Sanbonmatsu. 2020. "Practical considerations for atomistic structure modeling with Cryo-EM maps." Journal of Chemical Information and Modeling 60, no. 5:2436-2442. PNNL-SA-150966. doi:10.1021/acs.jcim.0c00090