PNNL

Song Feng studies complex systems—especially biological ones—by integrating both mechanism-based and data-driven approaches to understand their dynamics, evolution, control, and design. His ultimate goal is to understand the design principles of complex systems, whether physical, biological, or social. Such design principles will guide the field of research in de novo design or systematic control of these complex systems. 

• Complex systems
• Computational biology
• Machine learning
• Scientific computing
• Synthetic biology

• PhD in Biological Sciences, The University of Warwick
• MS in Bioscience, King Abdullah University of Science and Technology
• BS in Biotechnology, Zhejiang University

• American Mathematical Society
• London Mathematical Society

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
• Ushakumary M., S. Feng, G. Bandyopadhyay, H.M. Olson, K.K. Weitz, H.L. Huyck, and C. Poole, et al. 2025. "Cell population-resolved multiomics atlas of the developing lung." American Journal of Respiratory Cell and Molecular Biology 72, no. 5:484-495. PNNL-SA-196107. doi:10.1165/rcmb.2024-0105OC

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

• 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

2019

• Lin YT, Feng S, Hlavacek WS. Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networks. J Chem Phys. 2019 Jun 28;150(24):244101. PubMed PMID: 31255063; PubMed Central PMCID: PMC7043856.
• Suderman R, Mitra ED, Lin YT, Erickson KE, Feng S, Hlavacek WS. Generalizing Gillespie's Direct Method to Enable Network-Free Simulations. Bull Math Biol. 2019 Aug;81(8):2822-2848. PubMed PMID: 29594824; PubMed Central PMCID: PMC6162171.
• Shirin A, Klickstein IS, Feng S, Lin YT, Hlavacek WS, Sorrentino F. Prediction of Optimal Drug Schedules for Controlling Autophagy. Sci Rep. 2019 Feb 5;9(1):1428. PubMed PMID: 30723233; PubMed Central PMCID: PMC6363771.

2018

• Jiang X, Zerfaß C, Feng S, Eichmann R, Asally M, Schäfer P, Soyer OS. Impact of spatial organization on a novel auxotrophic interaction among soil microbes. ISME J. 2018 Jun;12(6):1443-1456. PubMed PMID: 29572468; PubMed Central PMCID: PMC5955953.

2017

• Cavaliere M, Feng S, Soyer OS, Jiménez JI. Cooperation in microbial communities and their biotechnological applications. Environ Microbiol. 2017 Aug;19(8):2949-2963. PubMed PMID: 28447371; PubMed Central PMCID: PMC5575505.

2016

• Feng S, Sáez M, Wiuf C, Feliu E, Soyer OS. Core signalling motif displaying multistability through multi-state enzymes. J R Soc Interface. 2016 Oct;13(123)PubMed PMID: 27733693; PubMed Central PMCID: PMC5095215.
• Feng S, Ollivier JF, Soyer OS. Enzyme sequestration as a tuning point in controlling response dynamics of signalling networks. PLoS Comput Biol. 2016 May;12(5):e1004918. PubMed PMID: 27163612; PubMed Central PMCID: PMC4862689.

2015

• Feng S, Ollivier JF, Swain PS, Soyer OS. BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling. Nucleic Acids Res. 2015 Oct 30;43(19):e123. PubMed PMID: 26101250; PubMed Central PMCID: PMC4627059.
• Feng S, Ollivier JF, Swain PS, Soyer OS. BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling. Nucleic Acids Res. 2015 Oct 30;43(19):e123. PubMed PMID: 26101250; PubMed Central PMCID: PMC4627059.