| 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 | 976 | 2019 |
| Searching molecular structure databases with tandem mass spectra using CSI:FingerID K Dührkop, H Shen, M Meusel, J Rousu, S Böcker Proceedings of the National Academy of Sciences 112 (41), 12580-12585, 2015 | 855 | 2015 |
| 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 | 797 | 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 | 373 | 2021 |
| SIRIUS: decomposing isotope patterns for metabolite identification S Böcker, MC Letzel, Z Lipták, A Pervukhin Bioinformatics 25 (2), 218-224, 2009 | 358 | 2009 |
| Fragmentation trees reloaded S Böcker, K Dührkop Journal of cheminformatics 8 (1), 5, 2016 | 205 | 2016 |
| Computational mass spectrometry for metabolomics: identification of metabolites and small molecules S Neumann, S Böcker Analytical and bioanalytical chemistry 398, 2779-2788, 2010 | 197 | 2010 |
| Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spectrometry: a tool for rapid bacterial identification F Von Wintzingerode, S Böcker, C Schlötelburg, NHL Chiu, N Storm, ... Proceedings of the National Academy of Sciences 99 (10), 7039-7044, 2002 | 191 | 2002 |
| Critical assessment of small molecule identification 2016: automated methods EL Schymanski, C Ruttkies, M Krauss, C Brouard, T Kind, K Dührkop, ... Journal of cheminformatics 9, 1-21, 2017 | 185 | 2017 |
| Significance estimation for large scale metabolomics annotations by spectral matching K Scheubert, F Hufsky, D Petras, M Wang, LF Nothias, K Dührkop, ... Nature Communications 8 (1), 1494, 2017 | 179 | 2017 |
| High-throughput MALDI-TOF discovery of genomic sequence polymorphisms P Stanssens, M Zabeau, G Meersseman, G Remes, Y Gansemans, ... Genome research 14 (1), 126-133, 2004 | 178 | 2004 |
| Fragmentation-based methods and systems for sequence variation detection and discovery D Van Den Boom, S Boecker US Patent 7,820,378, 2010 | 177 | 2010 |
| Integrative analysis of multimodal mass spectrometry data in MZmine 3 R Schmid, S Heuckeroth, A Korf, A Smirnov, O Myers, TS Dyrlund, ... Nature biotechnology 41 (4), 447-449, 2023 | 172 | 2023 |
| Towards de novo identification of metabolites by analyzing tandem mass spectra S Böcker, F Rasche Bioinformatics 24 (16), i49-i55, 2008 | 167 | 2008 |
| Computing fragmentation trees from tandem mass spectrometry data F Rasche, A Svatoš, RK Maddula, C Böttcher, S Böcker Analytical Chemistry 83 (4), 1243-1251, 2011 | 164 | 2011 |
| Computational mass spectrometry for small molecules K Scheubert, F Hufsky, S Böcker Journal of cheminformatics 5, 1-24, 2013 | 163 | 2013 |
| Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment R Schmid, D Petras, LF Nothias, M Wang, AT Aron, A Jagels, H Tsugawa, ... Nature communications 12 (1), 3832, 2021 | 156 | 2021 |
| Exact algorithms for cluster editing: Evaluation and experiments S Böcker, S Briesemeister, GW Klau Algorithmica 60 (2), 316-334, 2011 | 156 | 2011 |
| 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 | 134 | 2022 |
| Identifying the unknowns by aligning fragmentation trees F Rasche, K Scheubert, F Hufsky, T Zichner, M Kai, A Svatoš, S Böcker Analytical chemistry 84 (7), 3417-3426, 2012 | 131 | 2012 |
| Partitioning biological data with transitivity clustering T Wittkop, D Emig, S Lange, S Rahmann, M Albrecht, JH Morris, S Böcker, ... Nature methods 7 (6), 419-420, 2010 | 130 | 2010 |
| Computational mass spectrometry for small-molecule fragmentation F Hufsky, K Scheubert, S Böcker TrAC Trends in Analytical Chemistry 53, 41-48, 2014 | 128 | 2014 |
| Unbiased Transcriptional Comparisons of Generalist and Specialist Herbivores Feeding on Progressively Defenseless Nicotiana attenuata Plants G Govind, O Mittapalli, T Griebel, S Allmann, S Böcker, IT Baldwin PLoS one 5 (1), e8735, 2010 | 123 | 2010 |
| Simple but fundamental limitations on supertree and consensus tree methods M Steel, AWM Dress, S Böcker Systematic Biology 49 (2), 363-368, 2000 | 123 | 2000 |
| Metabolite identification through multiple kernel learning on fragmentation trees H Shen, K Dührkop, S Böcker, J Rousu Bioinformatics 30 (12), i157-i164, 2014 | 122 | 2014 |
| 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 | 120 | 2020 |
| Going weighted: Parameterized algorithms for cluster editing S Böcker, S Briesemeister, QBA Bui, A Truß Theoretical Computer Science 410 (52), 5467-5480, 2009 | 119 | 2009 |
| Mining molecular structure databases: Identification of small molecules based on fragmentation mass spectrometry data F Hufsky, S Böcker Mass spectrometry reviews 36 (5), 624-633, 2017 | 116 | 2017 |
| Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS M Ehrich, S Böcker, D van den Boom Nucleic acids research 33 (4), e38-e38, 2005 | 108 | 2005 |
| Novel mass spectrometry-based tool for genotypic identification of mycobacteria M Lefmann, C Honisch, S Böcker, N Storm, F von Wintzingerode, ... Journal of clinical microbiology 42 (1), 339-346, 2004 | 107 | 2004 |
| RNase T1 mediated base‐specific cleavage and MALDI‐TOF MS for high‐throughput comparative sequence analysis R Hartmer, N Storm, S Boecker, CP Rodi, F Hillenkamp, C Jurinke, ... Nucleic acids research 31 (9), e47-e47, 2003 | 102 | 2003 |
| Fast metabolite identification with input output kernel regression C Brouard, H Shen, K Dührkop, F d'Alché-Buc, S Böcker, J Rousu Bioinformatics 32 (12), i28-i36, 2016 | 99 | 2016 |
| Exact and heuristic algorithms for weighted cluster editing S Rahmann, T Wittkop, J Baumbach, M Martin, A Truss, S Böcker Computational Systems Bioinformatics: (Volume 6), 391-401, 2007 | 98 | 2007 |
| Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial … VU Schwartze, S Winter, E Shelest, M Marcet-Houben, F Horn, S Wehner, ... PLoS genetics 10 (8), e1004496, 2014 | 92* | 2014 |
| New kids on the block: novel informatics methods for natural product discovery F Hufsky, K Scheubert, S Böcker Natural product reports 31 (6), 807-817, 2014 | 92 | 2014 |
| Methods for long-range sequence analysis of nucleic acids DJ Van Den Boom, S Boecker | 92 | 2006 |
| 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 | 91 | 2021 |
| Current status of retention time prediction in metabolite identification M Witting, S Böcker Journal of Separation Science 43 (9-10), 1746-1754, 2020 | 91 | 2020 |
| Recovering symbolically dated, rooted trees from symbolic ultrametrics S Böcker, AWM Dress Advances in mathematics 138 (1), 105-125, 1998 | 91 | 1998 |
| A Golden Ratio Parameterized Algorithm for Cluster Editing S Böcker Journal of Discrete Algorithms 16, 79-89, 2012 | 90 | 2012 |
| A fast and simple algorithm for the Money Changing Problem S Bocker, Z Lipták Algorithmica 48 (4), 413-432, 2007 | 88 | 2007 |
| Cluster editing S Böcker, J Baumbach Conference on Computability in Europe, 33-44, 2013 | 84 | 2013 |
| MSNovelist: de novo structure generation from mass spectra MA Stravs, K Dührkop, S Böcker, N Zamboni Nature Methods 19 (7), 865-870, 2022 | 73 | 2022 |
| Liquid-chromatography retention order prediction for metabolite identification E Bach, S Szedmak, C Brouard, S Böcker, J Rousu Bioinformatics 34 (17), i875-i883, 2018 | 71 | 2018 |
| De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation A Bertsch, A Leinenbach, A Pervukhin, M Lubeck, R Hartmer, ... Electrophoresis 30 (21), 3736-3747, 2009 | 71 | 2009 |
| Comprehensive cluster analysis with Transitivity Clustering T Wittkop, D Emig, A Truss, M Albrecht, S Böcker, J Baumbach Nature protocols 6 (3), 285-295, 2011 | 69 | 2011 |
| SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry S Böcker Bioinformatics 19 (suppl_1), i44-i53, 2003 | 69 | 2003 |
| Searching molecular structure databases using tandem MS data: are we there yet? S Böcker Current Opinion in Chemical Biology 36, 1-6, 2017 | 68 | 2017 |
| Even faster parameterized cluster deletion and cluster editing S Böcker, P Damaschke Information Processing Letters 111 (14), 717-721, 2011 | 63 | 2011 |
| Current state-of-the-art of separation methods used in LC-MS based metabolomics and lipidomics EM Harrieder, F Kretschmer, S Böcker, M Witting Journal of Chromatography B 1188, 123069, 2022 | 60 | 2022 |
| Sequencing from compomers: Using mass spectrometry for DNA de novo sequencing of 200+ nt S Böcker Journal of Computational Biology 11 (6), 1110-1134, 2004 | 57 | 2004 |
| Expanding the use of spectral libraries in proteomics EW Deutsch, Y Perez-Riverol, RJ Chalkley, M Wilhelm, S Tate, ... Journal of proteome research 17 (12), 4051-4060, 2018 | 55 | 2018 |
| Computation of median gene clusters S Böcker, K Jahn, J Mixtacki, J Stoye Research in Computational Molecular Biology: 12th Annual International …, 2008 | 53 | 2008 |
| Algorithmic aspects of tree amalgamation S Böcker, D Bryant, AWM Dress, MA Steel Journal of Algorithms 37 (2), 522-537, 2000 | 53 | 2000 |
| EPoS: a modular software framework for phylogenetic analysis T Griebel, M Brinkmeyer, S Böcker Bioinformatics 24 (20), 2399-2400, 2008 | 51 | 2008 |
| Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity JP Shaffer, LF Nothias, LR Thompson, JG Sanders, RA Salido, ... Nature microbiology 7 (12), 2128-2150, 2022 | 49 | 2022 |
| Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints M Ludwig, K Dührkop, S Böcker Bioinformatics 34 (13), i333-i340, 2018 | 46 | 2018 |
| Molecular formula identification with SIRIUS K Dührkop, K Scheubert, S Böcker Metabolites 3 (2), 506-516, 2013 | 46 | 2013 |
| Finding maximum colorful subtrees in practice I Rauf, F Rasche, F Nicolas, S Böcker Journal of Computational Biology 20 (4), 311-321, 2013 | 45 | 2013 |
| Decomposing metabolomic isotope patterns S Böcker, MC Letzel, Z Lipták, A Pervukhin Algorithms in Bioinformatics: 6th International Workshop, WABI 2006, Zurich …, 2006 | 44 | 2006 |
| Peak intensity prediction in MALDI-TOF mass spectrometry: a machine learning study to support quantitative proteomics W Timm, A Scherbart, S Böcker, O Kohlbacher, TW Nattkemper BMC bioinformatics 9, 1-18, 2008 | 43 | 2008 |
| The Money Changing Problem Revisited: Computing the Frobenius Number in Time O(ka1) S Böcker, Z Lipták International Computing and Combinatorics Conference, 965-974, 2005 | 43 | 2005 |
| Fragmentation-based methods and systems for de novo sequencing S Boecker, D Boom US Patent App. 10/830,943, 2005 | 42 | 2005 |
| The generalized Robinson-Foulds metric S Böcker, S Canzar, GW Klau International Workshop on Algorithms in Bioinformatics, 156-169, 2013 | 41 | 2013 |
| A fixed-parameter approach for weighted cluster editing S Böcker, S Briesemeister, QBA Bui, A Trub Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 211-220, 2008 | 41 | 2008 |
| Computing fragmentation trees from metabolite multiple mass spectrometry data K Scheubert, F Hufsky, F Rasche, S Böcker Journal of computational biology 18 (11), 1383-1397, 2011 | 39 | 2011 |
| De novo analysis of electron impact mass spectra using fragmentation trees F Hufsky, M Rempt, F Rasche, G Pohnert, S Böcker Analytica chimica acta 739, 67-76, 2012 | 38 | 2012 |
| Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks F Mock, F Kretschmer, A Kriese, S Böcker, M Marz Proceedings of the National Academy of Sciences 119 (35), e2122636119, 2022 | 36 | 2022 |
| Mass spectrometry imaging of surface lipids on intact Drosophila melanogaster flies F Kaftan, V Vrkoslav, P Kynast, P Kulkarni, S Böcker, J Cvačka, M Knaden, ... Journal of Mass Spectrometry 49 (3), 223-232, 2014 | 36 | 2014 |
| A closer look at the closest string and closest substring problem M Chimani, M Woste, S Böcker 2011 Proceedings of the Thirteenth Workshop on Algorithm Engineering and …, 2011 | 36 | 2011 |
| Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry S Böcker Bioinformatics 23 (2), e5-e11, 2007 | 34 | 2007 |
| Assigning confidence to structural annotations from mass spectra with COSMIC MA Hoffmann, LF Nothias, M Ludwig, M Fleischauer, EC Gentry, M Witting, ... BioRxiv, 2021.03. 18.435634, 2021 | 33 | 2021 |
| Molecular formula identification using isotope pattern analysis and calculation of fragmentation trees K Dührkop, F Hufsky, S Böcker Mass Spectrometry 3 (Special_Issue_2), S0037-S0037, 2014 | 33 | 2014 |
| A faster fixed-parameter approach to drawing binary tanglegrams S Böcker, F Hüffner, A Truss, M Wahlström Parameterized and Exact Computation: 4th International Workshop, IWPEC 2009 …, 2009 | 33 | 2009 |
| Predicting the presence of uncommon elements in unknown biomolecules from isotope patterns M Meusel, F Hufsky, F Panter, D Krug, R Müller, S Böcker Analytical chemistry 88 (15), 7556-7566, 2016 | 32 | 2016 |
| Decomp—from interpreting Mass Spectrometry peaks to solving the Money Changing Problem S Böcker, Z Lipták, M Martin, A Pervukhin, H Sudek Bioinformatics 24 (4), 591-593, 2008 | 32 | 2008 |
| Patching up X-trees S Böcker, AWM Dress, MA Steel Annals of Combinatorics 3 (1), 1-12, 1999 | 31 | 1999 |
| Mapping metabolites from rough terrain: laser ablation electrospray ionization on non-flat samples B Bartels, P Kulkarni, N Danz, S Böcker, HP Saluz, A Svatoš RSC advances 7 (15), 9045-9050, 2017 | 30 | 2017 |
| Efficient mass decomposition S Böcker, Z Lipták Proceedings of the 2005 ACM symposium on Applied computing, 151-157, 2005 | 29 | 2005 |
| Finding approximate gene clusters with Gecko 3 S Winter, K Jahn, S Wehner, L Kuchenbecker, M Marz, J Stoye, S Böcker Nucleic acids research 44 (20), 9600-9610, 2016 | 26 | 2016 |
| Exact ILP solutions for phylogenetic minimum flip problems M Chimani, S Rahmann, S Böcker Proceedings of the First ACM International Conference on Bioinformatics and …, 2010 | 26 | 2010 |
| Automated bond order assignment as an optimization problem AK Dehof, A Rurainski, QBA Bui, S Böcker, HP Lenhof, A Hildebrandt Bioinformatics 27 (5), 619-625, 2011 | 25 | 2011 |
| Determination of glycan structure from tandem mass spectra S Bocker, B Kehr, F Rasche IEEE/ACM Transactions on Computational Biology and Bioinformatics 8 (4), 976-986, 2010 | 25 | 2010 |
| Swiftly computing center strings F Hufsky, L Kuchenbecker, K Jahn, J Stoye, S Böcker BMC bioinformatics 12, 1-12, 2011 | 24 | 2011 |
| Classes for the masses: systematic classification of unknowns using fragmentation spectra K Dührkop, LF Nothias, M Fleischauer, M Ludwig, MA Hoffmann, J Rousu, ... BioRxiv, 2020.04. 17.046672, 2020 | 23 | 2020 |
| 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 | 22 | 2020 |
| Magnitude-preserving ranking for structured outputs C Brouard, E Bach, S Böcker, J Rousu Asian Conference on Machine Learning, 407-422, 2017 | 22 | 2017 |
| Determination of 15N-Incorporation into Plant Proteins and their Absolute Quantitation: A New Tool to Study Nitrogen Flux Dynamics and Protein Pool Sizes Elicited … L Ullmann-Zeunert, A Muck, N Wielsch, F Hufsky, MA Stanton, S Bartram, ... Journal of proteome research 11 (10), 4947-4960, 2012 | 22 | 2012 |
| ZODIAC: Database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules M Ludwig, LF Nothias, K Dührkop, I Koester, M Fleischauer, MA Hoffmann, ... biorxiv, 842740, 2019 | 21 | 2019 |
| COCONUT--An efficient tool for estimating copolymer compositions from mass spectra MS Engler, S Crotty, MJ Barthel, C Pietsch, K Knop, US Schubert, ... Analytical chemistry 87 (10), 5223-5231, 2015 | 20 | 2015 |
| Annotating fragmentation patterns S Böcker, F Rasche, T Steijger Algorithms in Bioinformatics: 9th International Workshop, WABI 2009 …, 2009 | 20 | 2009 |
| Faster mass decomposition K Dührkop, M Ludwig, M Meusel, S Böcker Algorithms in Bioinformatics: 13th International Workshop, WABI 2013, Sophia …, 2013 | 19 | 2013 |
| Correcting mass shifts: a lock mass-free recalibration procedure for mass spectrometry imaging data P Kulkarni, F Kaftan, P Kynast, A Svatoš, S Böcker Analytical and bioanalytical chemistry 407, 7603-7613, 2015 | 18 | 2015 |
| Fast alignment of fragmentation trees F Hufsky, K Dührkop, F Rasche, M Chimani, S Böcker Bioinformatics 28 (12), i265-i273, 2012 | 18 | 2012 |
| Secondary ion mass spectrometry imaging and multivariate data analysis reveal co‐aggregation patterns of Populus trichocarpa leaf surface compounds on a … P Kulkarni, M Dost, ÖD Bulut, A Welle, S Böcker, W Boland, A Svatoš The Plant Journal 93 (1), 193-206, 2018 | 17 | 2018 |
| Analysis of different synthetic homopolymers by the use of a new calculation software for tandem mass spectra A Baumgaertel, K Scheubert, B Pietsch, K Kempe, AC Crecelius, S Böcker, ... Rapid Communications in Mass Spectrometry 25 (12), 1765-1778, 2011 | 17 | 2011 |
| Combinatorial approaches for mass spectra recalibration S Bocker, V Makinen IEEE/ACM Transactions on computational Biology and Bioinformatics 5 (1), 91-100, 2008 | 17 | 2008 |
| Munronia pinnata (Wall.) Theob.: Unveiling phytochemistry and dual inhibition of 5-lipoxygenase and microsomal prostaglandin E2 synthase (mPGES)-1 M Napagoda, J Gerstmeier, A Koeberle, S Wesely, S Popella, S Lorenz, ... Journal of ethnopharmacology 151 (2), 882-890, 2014 | 16 | 2014 |
| Bad Clade Deletion supertrees: a fast and accurate supertree algorithm M Fleischauer, S Böcker Molecular biology and evolution 34 (9), 2408-2421, 2017 | 15 | 2017 |
| Extension and robustness of transitivity clustering for protein–protein interaction network analysis T Wittkop, S Rahmann, R Röttger, S Böcker, J Baumbach Internet Mathematics 7 (4), 255-273, 2011 | 15 | 2011 |
Kai DührkopPhD, Lehrstuhl Bioinformatik, Friedrich-Schiller Universität JenaVerified email at uni-jena.de
