| SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information K Dührkop, M Fleischauer, M Ludwig, AA Aksenov, AV Melnik, M Meusel, ... Nature methods 16 (4), 299-302, 2019 | 1320 | 2019 |
| Feature-based molecular networking in the GNPS analysis environment LF Nothias, D Petras, R Schmid, K Dührkop, J Rainer, A Sarvepalli, ... Nature methods 17 (9), 905-908, 2020 | 1070 | 2020 |
| Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra K Dührkop, LF Nothias, M Fleischauer, R Reher, M Ludwig, MA Hoffmann, ... Nature Biotechnology 39 (4), 462-471, 2021 | 556 | 2021 |
| High-confidence structural annotation of metabolites absent from spectral libraries MA Hoffmann, LF Nothias, M Ludwig, M Fleischauer, EC Gentry, M Witting, ... Nature biotechnology 40 (3), 411-421, 2022 | 181 | 2022 |
| Database-independent molecular formula annotation using Gibbs sampling through ZODIAC M Ludwig, LF Nothias, K Dührkop, I Koester, M Fleischauer, MA Hoffmann, ... Nature Machine Intelligence 2 (10), 629-641, 2020 | 178* | 2020 |
| Chemically informed analyses of metabolomics mass spectrometry data with Qemistree A Tripathi, Y Vázquez-Baeza, JM Gauglitz, M Wang, K Dührkop, ... Nature Chemical Biology 17 (2), 146-151, 2021 | 100 | 2021 |
| Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints M Ludwig, K Dührkop, S Böcker Bioinformatics 34 (13), i333-i340, 2018 | 55 | 2018 |
| Assigning confidence to structural annotations from mass spectra with COSMIC MA Hoffmann, LF Nothias, M Ludwig, M Fleischauer, EC Gentry, M Witting, ... | 51 | 2021 |
| De Novo Molecular Formula Annotation and Structure Elucidation Using SIRIUS 4 M Ludwig, M Fleischauer, K Dührkop, MA Hoffmann, S Böcker Computational Methods and Data Analysis for Metabolomics, 185-207, 2020 | 34 | 2020 |
| Faster mass decomposition K Dührkop, M Ludwig, M Meusel, S Böcker International Workshop on Algorithms in Bioinformatics, 45-58, 2013 | 17 | 2013 |
| Illuminating the dark metabolome of Pseudo‐nitzschia–microbiome associations I Koester, ZA Quinlan, LF Nothias, ME White, A Rabines, D Petras, ... Environmental Microbiology 24 (11), 5408-5424, 2022 | 15 | 2022 |
| MAD HATTER correctly annotates 98% of small molecule tandem mass spectra searching in PubChem MA Hoffmann, F Kretschmer, M Ludwig, S Böcker Metabolites 13 (3), 314, 2023 | 12 | 2023 |
| Finding characteristic substructures for metabolite classes M Ludwig, F Hufsky, S Elshamy, S Böcker German Conference on Bioinformatics, 23-38, 2012 | 11 | 2012 |
| Studying Charge Migration Fragmentation of Sodiated Precursor Ions in Collision-Induced Dissociation at the Library Scale M Ludwig, CD Broeckling, PC Dorrestein, K Dührkop, EL Schymanski, ... Journal of the American Society for Mass Spectrometry 32 (1), 180-186, 2020 | 5 | 2020 |
| POMAGO: Multiple Genome-Wide Alignment Tool for Bacteria N Wieseke, M Lechner, M Ludwig, M Marz International Symposium on Bioinformatics Research and Applications, 249-260, 2013 | 3 | 2013 |
| Bayesian methods for small molecule identification M Ludwig Friedrich-Schiller-Universität Jena, 2020 | 1 | 2020 |
| SIRIUS 4 K Dührkop, M Fleischauer, M Ludwig, AA Aksenov, AV Melnik, M Meusel, ... Nature Publishing Group, 2019 | 1 | 2019 |
| Exact and heuristic algorithms for Cograph Editing WTJ White, M Ludwig, S Böcker arXiv preprint arXiv:1711.05839, 2017 | 1 | 2017 |