Search and Decoy: The Automatic Identification of Mass Spectra. - Martin Eisenacher; Michael Kohl; Michael Turewicz; Markus-Hermann Koch; Julian Uszkoreit; Christian Stephan (Quantitative Methods in Proteomics, 2012)

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics. - Yasset Pérez-Riverol; Julian Uszkoreit; Aniel Sánchez; Tobias Ternent; Noemi del-Toro; Henning Hermjakob; Juan Antonio Vizcaíno; Rui Wang (Bioinform., 2015)

Ten Simple Rules for Taking Advantage of Git and GitHub. - Yasset Pérez-Riverol; Laurent Gatto; Rui Wang; Timo Sachsenberg; Julian Uszkoreit; Felipe da Veiga Leprevost; Christian Fufezan; Tobias Ternent; Stephen J. Eglen; Daniel S. Katz; Tom J. Pollard; Alexander Konovalov 001; et al. (PLoS Comput. Biol., 2016)

BioContainers: an open-source and community-driven framework for software standardization. - Felipe da Veiga Leprevost; Björn A. Grüning; Saulo Aflitos; Hannes L. Röst; Julian Uszkoreit; Harald Barsnes; Marc Vaudel; Pablo A. Moreno; Laurent Gatto; Jonas Weber; Mingze Bai; Rafael C. Jiménez; et al. (Bioinform., 2017)

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)

Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases. - Gerhard Mayer; Wolfgang Müller 001; Karin Schork; Julian Uszkoreit; Andreas Weidemann; Ulrike Wittig; Maja Rey; Christian Quast; Janine Felden; Frank Oliver Glöckner; Matthias Lange 001; Daniel Arend; et al. (Briefings Bioinform., 2021)

ProtGraph: a tool for the quick and comprehensive exploration and exploitation of the peptide search space derived from protein sequence databases using graphs. - Dominik Lux; Katrin Marcus-Alic; Martin Eisenacher; Julian Uszkoreit (Briefings Bioinform., 2024)