You can see a complete and up-to-date list at Google Scholar
Selected publications:
Ochoa D, et al. The functional landscape of the human phosphoproteome Nature Biotechnology 2019 09 Dec
Strumillo MJ, et al. Conserved phosphorylation hotspots in eukaryotic protein domain families. Nature Comm. 2019 10, 1977
Wagih O et al. A resource of variant effect predictions of single nucleotide variants in model organisms. Mol Sys Bio 2018 14, e8430
Galardini M et al. Phenotype inference in an Escherichia coli strain panel. eLife 2017;6:e31035
Gonçalves E, et al. Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer. Cell Syst. 2017 Oct 25;5(4):386-398.e4.
Studer RA, et al. Evolution of protein phosphorylation across 18 fungal species Science 2016 Vol. 354, Issue 6309, pp. 229-232