Gasch, A. P. et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241–4257 (2000).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Costanzo, M. et al. Environmental robustness of the global yeast genetic interaction network. Science 372, eabf8424 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Causton, H. C. et al. Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell 12, 323–337 (2001).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hohmann, S. & Mager, W. H. Yeast Stress Responses (Springer Science & Business Media, 2007).

Gutin, J., Sadeh, A., Rahat, A., Aharoni, A. & Friedman, N. Condition-specific genetic interaction maps reveal crosstalk between the cAMP/PKA and the HOG MAPK pathways in the activation of the general stress response. Mol. Syst. Biol. 11, 829 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Bahn, Y.-S. et al. Sensing the environment: lessons from fungi. Nat. Rev. Microbiol. 5, 57–69 (2007).

Article  CAS  PubMed  Google Scholar 

Schulz, J. C., Zampieri, M., Wanka, S., von Mering, C. & Sauer, U. Large-scale functional analysis of the roles of phosphorylation in yeast metabolic pathways. Sci. Signal. 7, rs6 (2014).

Article  PubMed  Google Scholar 

Oliveira, A. P. et al. Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis. Sci. Signal. 8, rs4 (2015).

Article  PubMed  Google Scholar 

Paulo, J. A., O’Connell, J. D., Gaun, A. & Gygi, S. P. Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae. Mol. Biol. Cell 26, 4063–4074 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gutin, J., Joseph-Strauss, D., Sadeh, A., Shalom, E. & Friedman, N. Genetic screen of the yeast environmental stress response dynamics uncovers distinct regulatory phases. Mol. Syst. Biol. 15, e8939 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Hillenmeyer, M. E. et al. The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science 320, 362–365 (2008).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brauer, M. J. et al. Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol. Biol. Cell 19, 352–367 (2008).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Viéitez, C. et al. High-throughput functional characterization of protein phosphorylation sites in yeast. Nat. Biotechnol. 40, 382–390 (2022).

Article  PubMed  Google Scholar 

Gruhler, A. et al. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell. Proteom. 4, 310–327 (2005).

Article  CAS  Google Scholar 

Smolka, M. B., Albuquerque, C. P., Chen, S.-H. & Zhou, H. Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. Proc. Natl Acad. Sci. USA 104, 10364–10369 (2007).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Saleem, R. A. et al. Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. Mol. Cell. Proteom. 9, 2076–2088 (2010).

Article  Google Scholar 

Oliveira, A. P. et al. Regulation of yeast central metabolism by enzyme phosphorylation. Mol. Syst. Biol. 8, 623 (2012).

Article  PubMed  PubMed Central  Google Scholar 

Vaga, S. et al. Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast. Mol. Syst. Biol. 10, 767 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Kanshin, E., Bergeron-Sandoval, L.-P., Isik, S. S., Thibault, P. & Michnick, S. W. A cell-signaling network temporally resolves specific versus promiscuous phosphorylation. Cell Rep. 10, 1202–1214 (2015).

Article  CAS  PubMed  Google Scholar 

Kanshin, E., Kubiniok, P., Thattikota, Y., D'Amours, D. & Thibault, P. Phosphoproteome dynamics of Saccharomyces cerevisiae under heat shock and cold stress. Mol. Syst. Biol. 11, 813 (2015).

Article  PubMed  PubMed Central  Google Scholar 

MacGilvray, M. E. et al. Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. PLoS Comput. Biol. 13, e1006088 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Leutert, M., Rodríguez‐Mias, R. A., Fukuda, N. K. & Villén, J. R2‐P2 rapid‐robotic phosphoproteomics enables multidimensional cell signaling studies. Mol. Syst. Biol. 15, e9021 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lanz, M. C. et al. In-depth and 3-dimensional exploration of the budding yeast phosphoproteome. EMBO Rep. 22, e51121 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Holt, L. J. et al. Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science 325, 1682–1686 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Soste, M. et al. A sentinel protein assay for simultaneously quantifying cellular processes. Nat. Methods 11, 1045–1048 (2014).

Article  CAS  PubMed  Google Scholar 

Plank, M. et al. Chemical genetics of AGC-kinases reveals shared targets of Ypk1, protein kinase A and Sch9. Mol. Cell. Proteom. 19, 655–671 (2020).

Article  CAS  Google Scholar 

Dokládal, L. et al. Phosphoproteomic responses of TORC1 target kinases reveal discrete and convergent mechanisms that orchestrate the quiescence program in yeast. Cell Rep. 37, 110149 (2021).

Article  PubMed  Google Scholar 

Bodenmiller, B. et al. Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci. Signal. 3, rs4 (2010).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li, J., Paulo, J. A., Nusinow, D. P., Huttlin, E. L. & Gygi, S. P. Investigation of proteomic and phosphoproteomic responses to signaling network perturbations reveals functional pathway organizations in yeast. Cell Rep. 29, 2092–2104.e4 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

van Wageningen, S. et al. Functional overlap and regulatory links shape genetic interactions between signaling pathways. Cell 143, 991–1004 (2010).

Article  PubMed  PubMed Central  Google Scholar 

da Silveira Dos Santos, A. X. et al. Systematic lipidomic analysis of yeast protein kinase and phosphatase mutants reveals novel insights into regulation of lipid homeostasis. Mol. Biol. Cell 25, 3234–3246 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Lawrence, R. T., Searle, B. C., Llovet, A. & Villén, J. Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry. Nat. Methods 13, 431–434 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Searle, B. C., Lawrence, R. T., MacCoss, M. J. & Villén, J. Thesaurus: quantifying phosphopeptide positional isomers. Nat. Methods 16, 703–706 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Searle, B. C. et al. Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry. Nat. Commun. 9, 5128 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Beausoleil, S. A., Villén, J., Gerber, S. A., Rush, J. & Gygi, S. P. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 24, 1285–1292 (2006).

Article  CAS  PubMed  Google Scholar 

Ochoa, D. et al. The functional landscape of the human phosphoproteome. Nat. Biotechnol. 38, 365–373 (2020).

Article  CAS  PubMed  Google Scholar 

Pentony, M. M., Ward, J. & Jones, D. T. in Proteome Bioinformatics (eds Hubbard, S. J. & Jones, A. R.) 369–393 (Humana Press, 2010).

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar