2025

• Sarkar S, S Feng, HD Mitchell, MR Berger, T Zhang, IK Attah, CM Hutchinson-Bunch, VN Prozapas, K Engbrecht, S King, AC Sims and JT Melchior. 2025. "Human coronavirus-229E hijacks key host-cell RNA processing complexes for replication." Journal of Proteome Research, 24(10), 5026-5045. https://doi.org/10.1021/acs.jproteome.5c00400
• Gluth, A, JB Trejo, JJ Czajka, S Deng, WJ Qian, B Yang, and T Zhang. 2025. "Proteomic insights into the physiology and metabolism of oleaginous yeasts and filamentous fungi."  Frontiers in Microbiology, 16, 1637123. https://doi.org/10.3389/fmicb.2025.1637123 RESEARCH HIGHLIGHT
• Johnson, CGM, Z Johnson, LS Mackey, X Li, NC Sadler, T Zhang, WJ Qian, P Bohutskyi and MS Cheung. 2025. "Multi-omics reveals temporal scales of carbon metabolism in Synechococcus elongatus PCC 7942 under light disturbance." PRX Life 3, 033017. https://doi.org/10.1103/l2dp-kw2t RESEARCH HIGHLIGHT
• Cannon WR, E King, KA Huening, and JA North. 2025. "Redox Poise in R. rubrum phototrophic growth drives large-scale changes in macromolecular pathways." PLoS Computational Biology, 21(6), e1013015. PNNL-SA-194523.  https://doi.org/10.1371/journal.pcbi.1013015
• Li, X, MJ Gaffrey, MA Gritsenko, A Gluth, JB Trejo, NJ Day, PF Wilson, WJ Qian, and T Zhang. 2025. "A mass spectrometry-based proteomics workflow for concurrent profiling of protein thiol oxidation and phosphorylation." Methods in Molecular Biology, 2933, 127-139. https://doi.org:/10.1007/978-1-0716-4574-1_17   
• Gluth, A, JJ Czajka, X Li, KJ Bloodsworth, JG Eder, JE Kyle, RK Chu, B Yang, WJ Qian, P Bohutskyi, and T Zhang. 2025. "Nitrogen limitation causes a seismic shift in redox state and phosphorylation of proteins implicated in carbon flux and lipidome remodeling in Rhodotorula toruloides." Biotechnology for Biofuels and Bioproducts 18, 80. https://doi.org/10.1186/s13068-025-02657-y RESEARCH HIGHLIGHT
• Breysse, EM, O Rodriguez, MR Berger, RS Wooldridge, L Gorham, A Shouaib, AC Sims, JT Melchior, and SM Powell. 2025. "Harnessing nanobodies for precision targeting of proteoforms: Opportunities and challenges in therapeutics and diagnostics." ACS Chemical Biology, 20 (8), 1817-1827. https://doi.org:/10.1021/acschembio.5c00329
• Li, X, A Kabza, AN Ives, J Thiel, KM Waters, WJ Qian, AC Sims, and T Zhang. 2025. "Proteome-wide characterization of PTMs reveals host cell responses to viral infection and identifies putative antiviral drug targets." Frontiers in Immunology, 16, 1587106. https://doi.org/10.3389/fimmu.2025.1587106 RESEARCH HIGHLIGHT
• Johnson, Z, D Anderson, MS Cheung, and P Bohutskyi. 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. https://doi.org/10.3389/fmicb.2025.1569559 RESEARCH HIGHLIGHT
• Gilliam, A, NC Sadler, X Li, M Garcia, Z Johnson, M Velickovic, TM Kim, S Feng, WJ Qian, MS Cheung and P Bohutskyi. 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. https://doi.org/10.1186/s12934-025-02665-5 RESEARCH HIGHLIGHT
• Kim DN, T Yin, T Zhang, AK Im, JR Cort, JC Rozum, DD Pollock, WJ Qian and S Feng. 2025. "Artificial intelligence transforming post-translational modification research." Bioengineering, 12(1), 26. https://doi.org/10.3390/bioengineering12010026

2024

• Yang, Y, A Jerger, S Feng, Z Wang, C Brasfield, MS Cheung, J Zucker, and Q Guan. 2024. "Improved enzyme functional annotation prediction using contrastive learning with structural inference." Communications Biology, 7(1), 1690. https://doi.org/10.1038/s42003-024-07359-z
• Gluth, A, X Li, MA Gritsenko, MJ Gaffrey, DN Kim, PM Lalli, RK Chu, NJ Day, TJ Sagendorf, ME Monroe, S Feng, T Liu, B Yang, WJ Qian, and Tong Zhange. 2024. "Integrative multi-PTM proteomics reveals dynamic global, redox, phosphorylation, and acetylation regulation in cytokine-treated pancreatic beta cells." Molecular & Cellular Proteomics, 23 (12), 100881. https://doi.org/10.1016/j.mcpro.2024.100881 RESEARCH HIGHLIGHT
• Sarkar, S, J Morris, Y You, H Sexmith, SE Street, SM Thibert, IK Attah, CM Hutchinson Bunch, IV Novikova, JE Evans, AS Shah, SM Gordon, JP Segrest, KE Bornfeldt, T Vaisar, JW Heinecke, W Sean Davidson, and JT Melchior. 2024. "APOA2 increases cholesterol efflux capacity to plasma HDL by displacing the C-terminus of resident APOA1." Journal of Lipid Research, 65 (12),100686. https://doi.org/10.1016/j.jlr.2024.100686 RESEARCH HIGHLIGHT
• Degnan DJ, CW Strauch, MY Obiri, ED VonKaenel, SJ Kim, J Kershaw, DL Novelli, K Pazdernik, and LM Bramer. 2024. "Protein-protein interaction networks derived from classical and machine learning-based natural language processing tools." Journal of Proteome Research, 23(12), 5395-5404. https://doi.org/10.1021/acs.jproteome.4c00535 REASEARCH HIGHLIGHT
• Bohutskyi, P, KR Pomraning, JP Jenkins, YM Kim, BP Poirier, MJ Betenbaugh and JK Magnuson. 2024. "Mixed and membrane-separated culturing of synthetic cyanobacteria-yeast consortia reveals metabolic cross-talk mimicking natural cyanolichens." Scientific Reports, 14, 25303. https://doi.org/10.1038/s41598-024-74743-4 RESEARCH HIGHLIGHT
• Pomraning, K., S Deng, R Duong, J Czajka, and P Bohutskyi. 2024. “Identification of Yarrowia lipolytica as a platform for designed consortia that incorporate in situ nitrogen fixation to enable ammonia-free bioconversion.” Frontiers in Industrial Microbiology, 2, 1473316. https://doi.org/10.3389/finmi.2024.1473316 RESEARCH HIGHLIGHT
• Yang Y, Z Wang, P Ahadian, AR Jerger, JD Zucker, S Feng, F Cheung, and Q Guan. 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, 760-765.  https://doi.org/10.1145/3649476.3660377

2023

• Mejia-Rodriguez D, H Kim, N Sadler, X Li, P Bohutskyi, M Valiev, WJ Qian, and MS Cheung. 2023. “PTM-Psi: A python package to facilitate the computational investigation of post-translational modification on protein structures and their impacts on dynamics and functions.” Protein Science, 32(12), e4822. https://doi.org/10.1002/pro.4822 RESEARCH HIGHLIGHT
• Reichart, NJ, AK Steiger, EM Van Fossen, R McClure, HS Overkleeft, and AT Wright. 2023. "Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing." ISME Communications, 3, 106. https://doi.org/10.1038/s43705-023-00305-w RESEARCH HIGHLIGHT
• Taheri SM, V Tewari, R Kapre, E Rahiminasab, K Sachs, CT Hoyt, JD Zucker, and O Vitek. 2023. "Optimal adjustment set for causal query estimation in partially observed biomolecular networks." Bioinformatics, 39 (Suppl 1), i494-i503. https://doi.org/10.1093/bioinformatics/btad270   
• Li X, A Gluth, T Zhang, and W Qian. 2023. "Thiol redox proteomics: Characterization of thiol-based post-translational modifications." Proteomics, 23 (13-14), 2200194. https://doi.org/10.1002/pmic.202200194
• King E, JT Holzer, JA North, and WR Cannon. 2023. "An approach to learn regulation to maximize growth and entropy production rates in metabolism." Frontiers in Systems Biology, 3, 981866. https://doi.org/10.3389/fsysb.2023.981866
• Leonard B, VG Danna, LJ Gorham, MR Davison, WB Chrisler, D Kim, and VR Gerbasi. 2023. "Shaping nanobodies and intrabodies against proteoforms." Analytical Chemistry, 95 (23), 8747–8751. https://doi.org/10.1021/acs.analchem.3c00958
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• Flores JE, DM Claborne, ZD Weller, BJM Webb-Robertson, KM Waters, and LM Bramer. 2023. "Missing data in multi-omics integration: Recent advances through artificial intelligence." Frontiers in Artificial Intelligence, 6, 1098308. https://doi.org/10.3389/frai.2023.1098308