Predicting post-translational lysine acetylation using support vector machines. - Florian Gnad; Shubin Ren; Chunaram Choudhary; Jürgen Cox; Matthias Mann 002 (Bioinform., 2010)

1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data. - Jürgen Cox; Matthias Mann 002 (BMC Bioinform., 2012)

Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins. - Stefka Tyanova; Jürgen Cox; Jesper V. Olsen; Matthias Mann 002; Dmitrij Frishman (PLoS Comput. Biol., 2013)

IKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data. - Marcel Mischnik; Francesca Sacco; Jürgen Cox; Hans-Christoph Schneider; Matthias Schäfer; Manfred Hendlich; Daniel Crowther; Matthias Mann 002; Thomas Klabunde (Bioinform., 2016)

Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry. - Tikira Temu; Matthias Mann 002; Markus Räschle; Jürgen Cox (Bioinform., 2016)

The PRIDE database and related tools and resources in 2019: improving support for quantification data. - Yasset Pérez-Riverol; Attila Csordas; Jingwen Bai 003; Manuel Bernal Llinares; Suresh Hewapathirana; Deepti Jaiswal Kundu; Avinash Inuganti; Johannes Griss; Gerhard Mayer; Martin Eisenacher; Enrique Pérez; Julian Uszkoreit; et al. (Nucleic Acids Res., 2019)

Benchmarking differential expression, imputation and quantification methods for proteomics data. - Miao-Hsia Lin; Pei-Shan Wu; Tzu-Hsuan Wong; I-Ying Lin; Johnathan Lin; Jürgen Cox; Sung-Huan Yu (Briefings Bioinform., 2022)

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. - Yingying Sun; Jun A; Zhiwei Liu; Rui Sun; Liujia Qian; Samuel H. Payne; Wout Bittremieux; Markus Ralser; Chen Li 021; Yi Chen; Zhen Dong; Yasset Pérez-Riverol; et al. (CoRR, 2025)