Müller-Dott, S., Jaehnig, E. J., Munchic, K. P., Jiang, W., Yaron-Barir, T. M., Savage, S. R., Garrido-Rodriguez, M., Johnson, J. L., Lussana, A., Petsalaki, E., Lei, J. T., Dugourd, A., Krug, K., Cantley, L. C., Mani, D. R., Zhang, B., & Saez-Rodriguez, J. (2025). Comprehensive evaluation of phosphoproteomic-based kinase activity inference. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-59779-y

Jiang, W., Jaehnig, E. J., Liao, Y., Shi, Z., Yaron-Barir, T. M., Johnson, J. L., Cantley, L. C., & Zhang, B. (2025). Deciphering the dark cancer phosphoproteome using machine-learned co-regulation of phosphosites. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-57993-2

Klomp, J. E., Diehl, J. N., Klomp, J. A., Edwards, A. C., Yang, R., Morales, A. J., Taylor, K. E., Drizyte-Miller, K., Bryant, K. L., Schaefer, A., Johnson, J. L., Huntsman, E. M., Yaron, T. M., Pierobon, M., Baldelli, E., Prevatte, A. W., Barker, N. K., Herring, L. E., Petricoin, E. F., … Stalnecker, C. A. (2024). Determining the ERK-regulated phosphoproteome driving KRAS-mutant cancer. Science, 384(6700). https://doi.org/10.1126/science.adk0850

Prakash, P., Khodke, P., Balasubramaniam, M., Davids, B.-O., Hollis, T., Davis, J., Kumbhar, B., & Dash, C. (2024). Three prime repair exonuclease 1 preferentially degrades the integration-incompetent HIV-1 DNA through favorable kinetics, thermodynamic, structural, and conformational properties. Journal of Biological Chemistry, 300(7), 107438. https://doi.org/10.1016/j.jbc.2024.107438

Rosenberger, G., Li, W., Turunen, M., He, J., Subramaniam, P. S., Pampou, S., Griffin, A. T., Karan, C., Kerwin, P., Murray, D., Honig, B., Liu, Y., & Califano, A. (2024). Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-47957-3

Johnson, J. L., Yaron, T. M., Huntsman, E. M., Kerelsky, A., Song, J., Regev, A., Lin, T.-Y., Liberatore, K., Cizin, D. M., Cohen, B. M., Vasan, N., Ma, Y., Krismer, K., Robles, J. T., van de Kooij, B., van Vlimmeren, A. E., Andrée-Busch, N., Käufer, N. F., Dorovkov, M. V., … Cantley, L. C. (2023). An atlas of substrate specificities for the human serine/threonine kinome. Nature, 613(7945), 759–766. https://doi.org/10.1038/s41586-022-05575-3

Lieu, Y. K., Liu, Z., Ali, A. M., Wei, X., Penson, A., Zhang, J., An, X., Rabadan, R., Raza, A., Manley, J. L., & Mukherjee, S. (2021). SF3B1 mutant-induced missplicing of MAP3K7 causes anemia in myelodysplastic syndromes. Proceedings of the National Academy of Sciences, 119(1). https://doi.org/10.1073/pnas.2111703119