A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools. - Jirí Novák; Timo Sachsenberg; David Hoksza; Tomás Skopal; Oliver Kohlbacher (PACBB, 2013)

On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications. - Jirí Novák; Timo Sachsenberg; David Hoksza; Tomás Skopal; Oliver Kohlbacher (J. Integr. Bioinform., 2013)

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)

Recommendations for the packaging and containerizing of bioinformatics software. - Björn A. Grüning; Olivier Sallou; Pablo A. Moreno; Felipe da Veiga Leprevost; Hervé Ménager; Dan Søndergaard; Hannes L. Röst; Timo Sachsenberg; Brian O'Connor; Fábio Madeira; Victoria Dominguez Del Angel; Michael R. Crusoe; et al. (F1000Research, 2018)

Computational Methods for Mass Spectrometry-based Study of Protein-RNA or Protein-DNA Complexes and Quantitative Metaproteomics - Timo Sachsenberg (2018)

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)

Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides. - Husen M. Umer; Enrique Audain; Yafeng Zhu; Julianus Pfeuffer; Timo Sachsenberg; Janne Lehtiö; Rui Mamede Branca; Yasset Pérez-Riverol (Bioinform., 2022)

UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis. - Eleftheria Kontou; Axel Walter; Oliver Alka; Julianus Pfeuffer; Timo Sachsenberg; Omkar S. Mohite; Matin Nuhamunada; Oliver Kohlbacher; Tilmann Weber (J. Cheminformatics, 2023)

OpenMS WebApps: Building User-Friendly Solutions for MS Analysis. - Tom David Müller; Arslan Siraj; Axel Walter; Jihyung Kim; Samuel Wein; Johannes von Kleist; Ayesha Feroz; Matteo Pilz; Kyowon Jeong; Justin Cyril Sing; Joshua Charkow; Hannes L. Röst; et al. (CoRR, 2024)