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Resources

News & Publications

JUNE 30, 2026
Research Highlight

Redox Post-Translational Modifications Rewire Metabolic Control in Cyanobacteria

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Abstract illustration of cyanobacteria.
APRIL 15, 2026
Article

Predicting Viral Hijacking Through Genome-Scale Modeling

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Photograph of vessels filled with bacteria
SEPTEMBER 24, 2025
Research Highlight

Redox-Driven Protein Complexes Signal Metabolic Modulation in Cyanobacteria

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Culture of a freshwater bacterium called Synechococcus elongatus PCC 7942 (displayed as a green liquid in glass bottles) are subjected to light changes over periods of time.
JULY 23, 2024
News Release

PNNL Scientists Tap Nation’s Fastest Computers to Explore Critical Science Questions

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Photograph of Daniel Mejia Rodriguez standing near a powerful computer.
SEPTEMBER 11, 2023
Article

PNNL BRaVEly Supports National Preparedness Efforts Against Pathogenic Threats

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image of a blue virus against a black background

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

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ASCR Discovery: Pandemic Preparedness

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