Fast alignment of fragmentation trees. - Franziska Hufsky; Kai Dührkop; Florian Rasche; Markus Chimani; Sebastian Böcker (Bioinform., 2012)

Faster Mass Decomposition. - Kai Dührkop; Marcus Ludwig; Marvin Meusel; Sebastian Böcker (WABI, 2013)

Metabolite identification through multiple kernel learning on fragmentation trees. - Huibin Shen; Kai Dührkop; Sebastian Böcker; Juho Rousu (Bioinform., 2014)

Speedy Colorful Subtrees. - W. Timothy J. White; Stephan Beyer; Kai Dührkop; Markus Chimani; Sebastian Böcker (COCOON, 2015)

Fast metabolite identification with Input Output Kernel Regression. - Céline Brouard; Huibin Shen; Kai Dührkop; Florence d'Alché-Buc; Sebastian Böcker; Juho Rousu (Bioinform., 2016)

Fragmentation trees reloaded. - Sebastian Böcker; Kai Dührkop (J. Cheminformatics, 2016)

Critical Assessment of Small Molecule Identification 2016: automated methods. - Emma Schymanski; Christoph Ruttkies; Martin Krauss; Céline Brouard; Tobias Kind; Kai Dührkop; Felicity Allen; Arpana Vaniya; Dries Verdegem; Sebastian Böcker; Juho Rousu; Huibin Shen; et al. (J. Cheminformatics, 2017)

Heuristic Algorithms for the Maximum Colorful Subtree Problem. - Kai Dührkop; Marie Anne Lataretu; W. Timothy J. White; Sebastian Böcker (WABI, 2018)

Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints. - Marcus Ludwig; Kai Dührkop; Sebastian Böcker (Bioinform., 2018)

Computational methods for small molecule identification. - Kai Dührkop (2018)

Computational Methods for Small Molecule Identification. - Kai Dührkop (Ausgezeichnete Informatikdissertationen, 2018)

Computational methods for small molecule identification. - Kai Dührkop (it Inf. Technol., 2019)

Database-independent molecular formula annotation using Gibbs sampling through ZODIAC. - Marcus Ludwig; Louis-Félix Nothias; Kai Dührkop; Irina Koester; Markus Fleischauer; Martin A. Hoffmann; Daniel Petras; Fernando Vargas; Mustafa Morsy; Lihini Aluwihare; Pieter C. Dorrestein; Sebastian Böcker (Nat. Mach. Intell., 2020)

Publisher Correction: Database-independent molecular formula annotation using Gibbs sampling through ZODIAC. - Marcus Ludwig; Louis-Félix Nothias; Kai Dührkop; Irina Koester; Markus Fleischauer; Martin A. Hoffmann; Daniel Petras; Fernando Vargas; Mustafa Morsy; Lihini Aluwihare; Pieter C. Dorrestein; Sebastian Böcker (Nat. Mach. Intell., 2020)

Deep kernel learning improves molecular fingerprint prediction from tandem mass spectra. - Kai Dührkop (Bioinform., 2022)

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)

Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data. - Pilleriin Peets; Aristeidis Litos; Kai Dührkop; Daniel R. Garza; Justin J. J. van der Hooft; Sebastian Böcker; Bas E. Dutilh (J. Cheminformatics, 2025)