aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. - George Rosenberger; Christina Ludwig; Hannes L. Röst; Ruedi Aebersold; Lars Malmström (Bioinform., 2014)

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. - Hannes L. Röst; George Rosenberger; Ruedi Aebersold; Lars Malmström (Bioinform., 2015)

DIANA - algorithmic improvements for analysis of data-independent acquisition MS data. - Johan Teleman; Hannes L. Röst; George Rosenberger; Uwe Schmitt; Lars Malmström; Johan Malmström; Fredrik Levander (Bioinform., 2015)

Statistical elimination of spectral features with large between-run variation enhances quantitative protein-level conclusions in experiments with data-independent spectral acquisition. - Lin-Yang Cheng; Yansheng Liu; Ching-Yun Chang; Hannes L. Röst; Ruedi Aebersold; Olga Vitek (BMC Bioinform., 2015)

Chapter 10. Data Analysis for Data Independent Acquisition. - Pedro Navarro; Marco Trevisan-Herraz; Hannes L. Röst (Proteome Informatics, 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)

Peak Detection On Data Independent Acquisition Mass Spectrometry Data With Semisupervised Convolutional Transformers. - Leon L. Xu; Hannes L. Röst (CoRR, 2020)

mspack: efficient lossless and lossy mass spectrometry data compression. - Felix Hanau; Hannes L. Röst; Idoia Ochoa (Bioinform., 2021)

MassFormer: Tandem Mass Spectrum Prediction with Graph Transformers. - Adamo Young; Bo Wang 044; Hannes L. Röst (CoRR, 2021)

MassSpecGym: A benchmark for the discovery and identification of molecules. - Roman Bushuiev; Anton Bushuiev; Niek F. de Jonge; Adamo Young; Fleming Kretschmer; Raman Samusevich; Janne Heirman; Fei Wang 062; Luke Zhang; Kai Dührkop; Marcus Ludwig; Nils A. Haupt; et al. (NeurIPS, 2024)

FraGNNet: A Deep Probabilistic Model for Mass Spectrum Prediction. - Adamo Young; Fei Wang 062; David S. Wishart; Bo Wang 044; Hannes L. Röst; Russ Greiner (CoRR, 2024)

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)

Tandem mass spectrum prediction for small molecules using graph transformers. - Adamo Young; Hannes L. Röst; Bo Wang 044 (Nat. Mac. Intell., 2024)

FraGNNet: A Deep Probabilistic Model for Tandem Mass Spectrum Prediction. - Adamo Young; Fei Wang 062; David S. Wishart; Bo Wang 044; Russell Greiner; Hannes Rost (Trans. Mach. Learn. Res., 2025)