Resources
News & Publications
Redox Post-Translational Modifications Rewire Metabolic Control in Cyanobacteria
Predicting Viral Hijacking Through Genome-Scale Modeling
Redox-Driven Protein Complexes Signal Metabolic Modulation in Cyanobacteria
PNNL Scientists Tap Nation’s Fastest Computers to Explore Critical Science Questions
PNNL BRaVEly Supports National Preparedness Efforts Against Pathogenic Threats
Research Publications
Yang, Y.; Jerger, A.; Feng, S.; Wang, Z.; et al. 2024. “Improved enzyme functional annotation prediction using contrastive learning with structural inference,” Communications Biology, 7, 1690. DOI: 10.1038/s42003-024-07359-z
Chan, A.; Tajkhorshid, E.; Luther-Schulten, Z.; and Sener, M. 2024. “Modeling Diffusive Motion of Ferredoxin and Plastocyanin on the PSI Domain of Procholorococcus marinus MIT9313,” The Journal of Physical Chemistry B, 129 (1): 52–70. DOI: 10.1021/acs.jpcb.4c05001
Johnson, C.G.M.; Johnson, Z.; Mackey, L.S.; Li, X.; et al. 2025. “Multi-Omics Reveals Temporal Scales of Carbon Metabolism in Synechococcus Elongatus PCC 7942 Under Light Disturbance,” PRX Life, 3, 033017. DOI: 10.1103/l2dp-kw2t
Gilliam, A.; Sadler, N.C.; Li, X.; Garcia, M.; 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, 56. DOI: 10.1186/s12934-025-02665-5
Johnson, Z.; Anderson, D.; Cheung, M.S.; and Bohutskyi, P. 2025. “Gene network centrality analysis identifies key regulators coordinating day-night metabolic transitions in Synechococcus elongatus PCC 7942 despite limited accuracy in predicting direct regulator-gene interactions,” Frontiers in Microbiology, 16:1569559. DOI: 10.3389/fmicb.2025.1569559
Samantray, S.; Lockwood, M.; Andersen, A.; Kim, H.; et al. 2025. “PTM-Psi on the Cloud: A Cloud-Compatible Workflow for Scalable, High-Throughput Simulation of Post-Translational Modifications in Protein Complexes,” Journal of Chemical Information and Modeling, 65 (20). DOI: 10.1002/pro.70721
George, A.; Bilbao, A.; Agarwal, K.; Mejia-Rodriguez, D.; et al. 2025. “ADEPT: A Pedagogical Framework for Integrating Agentic AI with Deterministic Scientific Workflows,” Zenodo. DOI: /10.5281/zenodo.17636798
Rozum, J.C.; Sineath, W.; Bohutskyi, P.; Quenneville, J.; et al. 2026. “Synergy and antagonism in a genome-scale model of metabolic hijacking by bacteriophages,” Science Advances, 12, 14. DOI: 10.1126/sciadv.aeb764
Bohutskyi, P.; Parvate, A.D.; Sadler, N.C.; Chrisler, W.B.; et al. 2026. “Systematic scale-up and enhanced purification of marine cyanophage P-SSP7,” Frontiers in Microbiology, 17:1776133. DOI: 10.3389/fmicb.2026.1776133
Boise, N.R.; Leiser, O.P.; Jones, K.; Peter-Frank, M.; et al. 2026. “Sampling microbial dynamics in the Salish Sea estuary: evaluating methods to capture cyanobacteria and cyanophage,” Frontiers in Marine Science, 13:1769457. DOI: 10.3389/fmars.2026.1769457
Li, C.; George, A.; Neff, R.; Kim, D.N.; et al. 2026. “Graph identification of proteins in tomograms (GRIP-Tomo) 2.0: Topologically aware classification for proteins,” Protein Science, 35(9):e70721. DOI: 10.1002/pro.70721
Kim, H.; Feng, S.; Bohutskyi, P.; Li, X.; et al. 2026. “Thiol post-translational modifications modulate allosteric regulation of the OpcA–G6PDH complex through conformational gate control,” Protein Science, 35(5):e70561. DOI: 10.1002/pro.70561
Johnson, Z.; Yang, B.; and Bohutskyi, P. 2026. “From photosynthetic electron flow to gene regulation: redox signal transduction in cyanobacteria,” FEMS Microbiology Reviews, Volume 50, fuag030. DOI: 10.1093/femsre/fuag030