Publications

2025

  • X. Li, Kabza, A., Ives, A.N., Thiel, J., Waters, K.M., Qian, WJ., Sims, A.C., Zhang, T. "Proteome-wide characterization of PTMs reveals host cell responses to viral infection and identifies putative antiviral drug targets." 2025. Frontiers in Immunology. Volume 16 - 2025. DOI: 10.3389/fimmu.2025.1587106. 
  • Johnson, Z., Anderson, D., Cheung, S.M., 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.” Front. Microbiol. Sec. Systems Microbiology 16. doi: 10.3389/fmicb.2025.1569559 RESEARCH HIGHLIGHT
  • Gilliam, A., Sadler, N.C., Li, X. et al. Cyanobacterial circadian regulation enhances bioproduction under subjective nighttime through rewiring of carbon partitioning dynamics, redox balance orchestration, and cell cycle modulation. Microb Cell Fact 24, 56 (2025). https://doi.org/10.1186/s12934-025-02665-5 RESEARCH HIGHLIGHT
  • 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

  • Yang, Y., Jerger, A., Feng, S., Wang, Z., Brasfield, C., Cheung, M. S., Zucker, J., & Guan, Q. "Improved enzyme functional annotation prediction using contrastive learning with structural inference." 2024. Communications Biology, 7(1), 1690. https://doi.org/10.1038/s42003-024-07359-z
  • Gluth, A. et al. "Integrative Multi-PTM Proteomics Reveals Dynamic Global, Redox, Phosphorylation, and Acetylation Regulation in Cytokine-Treated Pancreatic Beta Cells." Molecular & Cellular Proteomics 23, 100881 (2024). DOI: 10.1016/j.mcpro.2024.100881
  • Sarkar, S., J. Morris, Y. You, H. Sexmith, S.E. Street, S.M. Thibert, I.K. Attah, C.M. Hutchinson Bunch, I.V. Novikova, J.E. Evans, A.S. Shah, S.M. Gordon, J.P. Segrest, K.E. Bornfeldt, T. Vaisar, J.W. Heinecke, W. Sean Davidson, J.T. Melchior. 2024. "APOA2 increases cholesterol efflux capacity to plasma HDL by displacing the C-terminus of resident APOA1." Journal of Lipid Research, Volume 65, Issue 12, 2024, 100686, ISSN 0022-2275. https://doi.org/10.1016/j.jlr.2024.100686 RESEARCH HIGHLIGHT
  • Degnan D.J., C.W. Strauch, M.Y. Obiri, E.D. VonKaenel, S.J. Kim, J. Kershaw, D.L. Novelli, K. Pazdernik, and L.M Bramer. 2024. "Protein-Protein Interaction Networks Derived from Classical and Machine Learning-Based Natural Language Processing Tools." Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.4c00535 REASEARCH HIGHLIGHT
  • Bohutskyi, P., Pomraning, K.R., Jenkins, J.,  et al. 2024. "Mixed and membrane-separated culturing of synthetic cyanobacteria-yeast consortia reveals metabolic cross-talk mimicking natural cyanolichens." Sci Rep 14, 25303. https://doi.org/10.1038/s41598-024-74743-4 RESEARCH HIGHLIGHT
  • Pomraning, K., S. Deng, R. Duong, J. Czajka, P. Bohutskyi. 2024. “Identification of Yarrowia lipolyticaas a platform for designed consortia that incorporate in situnitrogen fixation to enable ammonia-free bioconversion.” Front. Ind. Microbiol. https://doi.org/10.3389/finmi.2024.1473316 RESEARCH HIGHLIGHT
  • 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, 760-765. New York, New York:Association for Computing Machinery. doi:10.1145/3649476.3660377

2023

  • Mejia-Rodriguez D, H Kim, N Sadler, X Li, P Bohutskyi, M Valiev, WJ Qian, 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 Sci. 2023; e4822. doi:10.1002/pro.4822
    RESEARCH HIGHLIGHT
  • Reichart, NJ, AK Steiger, EM Van Fossen, et al. 2023. "Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing." ISME COMMUN. 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, and JD Zucker, et al. 2023. "Optimal adjustment set for causal query estimation in partially observed biomolecular networks." Bioinformatics 39(Suppl 1). doi: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. doi: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. doi:10.3389/fsysb.2023.981866
  • Leonard B, VG Danna, LJ Gorham, MR Davison, WB Chrisler, D Kim, and RV Gerbasi. 2023. "Shaping Nanobodies and Intrabodies Against Proteoforms." Analytical Chemistry 95, no. 23:8747–8751. doi:10.1021/acs.analchem.3c00958
    RESEARCH HIGHLIGHT
  • Flores JE, DM Claborne, ZD Weller, BJM Webb-Robertson, KM Waters, LM Bramer. 2023. "Missing data in multi-omics integration: Recent advances through artificial intelligence." Frontiers in Artificial Intelligence, DOI: 10.3389/frai.2023.1098308