Staff information

PNNL Publications

2025

• Gilliam A.K., N.C. Sadler, X. Li, M.R. Garcia, Z.D. Johnson, M. Velickovic, and Y. Kim, et al. 2025. "Cyanobacterial circadian regulation enhances bioproduction under subjective nighttime through rewiring of carbon partitioning dynamics, redox balance orchestration, and cell cycle modulation." Microbial Cell Factories 24:Art. No. 56. PNNL-SA-206759. doi:10.1186/s12934-025-02665-5
• 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

• Feng S., A. Calinawan, P. Pugliese, P. Wang, M. Ceccarelli, F. Petralia, and S. Gosline. 2024. "Decomprolute is a benchmarking platform designed for multiomics-based tumor deconvolution." Cell Reports Methods 4, no. 2:Art. No. 100708. PNNL-SA-180136. doi:10.1016/j.crmeth.2024.100708
• 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
• Yang Y., A.R. Jerger, S. Feng, Z. Wang, C.D. Brasfield, M.S. Cheung, and J.D. Zucker, et al. 2024. "Improved Enzyme Functional Annotation Prediction Using Contrastive Learning with Structural Inference." Communications Biology 7, no. _:Art. No. 1690. PNNL-SA-198399. doi:10.1038/s42003-024-07359-z
• Yang Y., Z. Wang, P. Ahadian, A.R. Jerger, J.D. Zucker, S. Feng, and M.S. Cheung, et al. 2024. "A Deep Multimodal Representation Learning Framework for Accurate Molecular Properties Prediction." In Proceedings of the Great Lakes Symposium on VLSI (GLSVLSI 2024), June 12-14, 2024, Clearwater, FL, edited by I. Partin-Vaisband, et al, 760-765. New York, New York:Association for Computing Machinery. PNNL-SA-200837. doi:10.1145/3649476.3660377

2023

• Dakup P.P., S. Feng, T. Shi, J.M. Jacobs, H. Wiley, and W. Qian. 2023. "Targeted quantification of protein phosphorylation and its contributions towards mathematical modeling of signaling pathways." Molecules 28, no. 3:Art. No. 1143. PNNL-SA-179947. doi:10.3390/molecules28031143
• Li X., A. Gluth, S. Feng, W. Qian, and B. Yang. 2023. "Harnessing redox proteomics to study metabolic regulation and stress response in lignin-fed Rhodococci." Biotechnology for Biofuels and Bioproducts 16, no. 2024:Art. No. 180. PNNL-SA-189367. doi:10.1186/s13068-023-02424-x

2022

• Li X., T. Zhang, N.J. Day, S. Feng, M.J. Gaffrey, and W. Qian. 2022. "Defining the S-glutathionylation Proteome by Biochemical and Mass Spectrometric Approaches." Antioxidants 11, no. 11:Art. No. 2272. PNNL-SA-179617. doi:10.3390/antiox11112272
• Woo J., G. Clair, S.M. Williams, S. Feng, C. Tsai, R.J. Moore, and W.B. Chrisler, et al. 2022. "Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering." Cell Systems 13, no. 5:426-434.e4. PNNL-SA-156470. doi:10.1016/j.cels.2022.02.003

2021

• Feng S., E. Heath, B.A. Jefferson, C.A. Joslyn, H.J. Kvinge, H.D. Mitchell, and B.L. Praggastis, et al. 2021. "Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response." BMC Bioinformatics 22, no. 1:287. PNNL-SA-155930. doi:10.1186/s12859-021-04197-2
• Li X., N.J. Day, S. Feng, M.J. Gaffrey, T. Lin, V.L. Paurus, and M.E. Monroe, et al. 2021. "Mass spectrometry-based direct detection of multiple types of protein thiol modifications in pancreatic beta cells under endoplasmic reticulum stress." Redox Biology 46. PNNL-SA-163313. doi:10.1016/j.redox.2021.102111
• McDermott J.E., S. Feng, C.H. Chang, D.J. Schmidt, and V.G. Danna. 2021. Structural- and Functional-Informed Machine Learning for Protein Function Prediction. PNNL-32088. Richland, WA: Pacific Northwest National Laboratory. Structural- and Functional-Informed Machine Learning for Protein Function Prediction
• Woo J., S.M. Williams, L. Markillie, S. Feng, C. Tsai, V. Aguilera-Vazquez, and R.L. Sontag, et al. 2021. "High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip." Nature Communications 12, no. 1:Art. No. 6246. PNNL-SA-159977. doi:10.1038/s41467-021-26514-2