Sebastian Böcker

Postal Address

Lehrstuhl für Bioinformatik
Institut für Informatik
Ernst-Abbe-Platz 2
07743 Jena
Phone: +49-3641-9-46450
Fax: +49-3641-9-46452

Selected publications

See here for a complete and up-to-date list of publications. See here for my Google Scholar page.

  • R. Schmid, S. Heuckeroth, A. Korf, [… including S. Böcker], D. Petras, X. Du, and T. Pluskal. Integrative analysis of multimodal mass spectrometry data in MZmine 3. Nature Biotechnology, 2023.
  • J. P. Shaffer, L.-F. Nothias, L. R. Thompson, [… including S. Böcker], J. A. Gilbert, R. Knight & the Earth Microbiome Project 500 (EMP500) Consortium. Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity. Nature Microbiology 7(12):2128-2150, 2022.
  • F. Mock, F. Kretschmer, A. Kriese, S. Böcker, and M. Marz. Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks. Proceedings of the National Academy of Sciences USA 119(35):e2122636119, 2022.
  • M. A. Stravs, K. Dührkop, S. Böcker, and N. Zamboni. MSNovelist: de novo structure generation from mass spectra. Nature Methods 19(7):865–870, 2022.
  • M. A. Hoffmann, L.-F. Nothias, M. Ludwig, M. Fleischauer, E. C. Gentry, M. Witting, P. C. Dorrestein, K. Dührkop, and S. Böcker. High-confidence structural annotation of metabolites absent from spectral libraries. Nature Biotechnology 40(3):411–421, 2022.
  • R. Schmid, D. Petras, L.-F. Nothias, […], S. Böcker, K. L. McPhail, H.-U. Humpf, U. Karst, and P. C. Dorrestein. Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment. Nature Communications 12:3832, 2021.
  • K. Dührkop, L. F. Nothias, M. Fleischauer, R. Reher, M. Ludwig, M. A. Hoffmann, D. Petras, W. H. Gerwick, J. Rousu, P. C. Dorrestein, and S. Böcker. Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra. Nature Biotechnology 39(4):462–471, 2021.
  • A. Tripathi, Y. Vázquez-Baeza, J. M. Gauglitz, M. Wang, K. Dührkop, M. Nothias-Esposito, D. D. Acharya, M. Ernst, J. J. van der Hooft, Q. Zhu, D. McDonald, A. Gonzalez, J. Handelsman, M. Fleischauer, M. Ludwig, S. Böcker, L.-F. Nothias, R. Knight, and P. C. Dorrestein. Chemically-informed analyses of metabolomics mass spectrometry data with Qemistree. Nature Chemical Biology 17(2):146–151, 2021.
  • L.-F. Nothias, D. Petras, R. Schmid, […], S. Böcker, T. Alexandrov, N. Bandeira, M. Wang, and P. C. Dorrestein. Feature-based molecular networking in the GNPS analysis environment. Nature Methods 17(9):905–908, 2020.
  • M. Ludwig, L.-F. Nothias, K. Dührkop, I. Koester, M. Fleischauer, M. A. Hoffmann, D. Petras, F. Vargas, M. Morsy, L. Aluwihare, P. C. Dorrestein, and S. Böcker. Database-independent molecular formula annotation using Gibbs sampling through ZODIAC. Nature Machine Intelligence 2(10):629–641, 2020.
  • K. Dührkop, M. Fleischauer, M. Ludwig, A. A. Aksenov, A. V. Melnik, M. Meusel, P. C. Dorrestein, J. Rousu, and S. Böcker. SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information. Nature Methods 16(4):299–302, 2019.
  • M. Ludwig, K. Dührkop, and S. Böcker. Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints. Bioinformatics 34(13):i333–i340, 2018. Proc. of Intelligent Systems for Molecular Biology (ISMB 2018).
  • E. Bach, S. Szedmak, C. Brouard, S. Böcker, and J. Rousu. Liquid-chromatography retention order prediction for metabolite identification. Bioinformatics 34(17):i875–i883, 2018. Proc. of European Conference on Computational Biology (ECCB 2018).
  • K. Scheubert, F. Hufsky, D. Petras, M. Wang, L.-F. Nothias, K. Dührkop, N. Bandeira, P. C. Dorrestein, and S. Böcker. Significance estimation for large scale metabolomics annotations by spectral matching. Nature Communications 8:1494, 2017.
  • S. Böcker and K. Dührkop. Fragmentation trees reloaded. Journal of Cheminformatics, 8:5, 2016.
  • C. Brouard, H. Shen, K. Dührkop, F. d’Alché-Buc, S. Böcker, and J. Rousu. Fast metabolite identification with input output kernel regression. Bioinformatics, 32(12):i28–i36, 2016. Proc. of Intelligent Systems for Molecular Biology (ISMB 2016).
  • K. Dührkop, H. Shen, M. Meusel, J. Rousu, and S. Böcker. Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proceedings of the National Academy of Sciences USA, 112(41):12580–12585, 2015.
  • K. Dührkop and S. Böcker. Fragmentation trees reloaded. In Proc. of Research in Computational Molecular Biology (RECOMB 2015), volume 9029 of Lect Notes Comput Sci, pages 65–79. Springer, Berlin, 2015.
  • H. Shen, K. Dührkop, S. Böcker, and J. Rousu. Metabolite identification through multiple kernel learning on fragmentation trees. Bioinformatics, 30(12):i157–i164, 2014. Proc. of Intelligent Systems for Molecular Biology (ISMB 2014).
  • T. Wittkop, D. Emig, S. Lange, S. Rahmann, M. Albrecht, J. H. Morris, S. Böcker, J. Stoye, and J. Baumbach. Partitioning biological data with transitivity clustering. Nature Methods 7(6):419–420, 2010.
  • S. Böcker, M. C. Letzel, Z. Liptak, A. Pervukhin. SIRIUS: decomposing isotope patterns for metabolite identification. Bioinformatics 25(2):218-224, 2009.