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ORCIDSebastian Böcker
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- affiliation: Friedrich-Schiller-Universität, Jena, Germany
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Journal Articles
- 2025
[j44]Pilleriin Peets, Aristeidis Litos, Kai Dührkop, Daniel R. Garza, Justin J. J. van der Hooft, Sebastian Böcker, Bas E. Dutilh:
Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data. J. Cheminformatics 17(1): 82 (2025)- 2020
- [j43]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:
Database-independent molecular formula annotation using Gibbs sampling through ZODIAC. Nat. Mach. Intell. 2(10): 629-641 (2020) - [j42]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:
Publisher Correction: Database-independent molecular formula annotation using Gibbs sampling through ZODIAC. Nat. Mach. Intell. 2(11): 727 (2020) - 2018
- [j41]Marcus Ludwig, Kai Dührkop, Sebastian Böcker:
Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints. Bioinform. 34(13): i333-i340 (2018) - [j40]Eric Bach, Sándor Szedmák, Céline Brouard, Sebastian Böcker, Juho Rousu:
Liquid-chromatography retention order prediction for metabolite identification. Bioinform. 34(17): i875-i883 (2018) - 2017
- [j39]Emma Schymanski, Christoph Ruttkies, Martin Krauss, Céline Brouard, Tobias Kind, Kai Dührkop, Felicity Allen, Arpana Vaniya, Dries Verdegem, Sebastian Böcker, Juho Rousu, Huibin Shen, Hiroshi Tsugawa, Tanvir Sajed, Oliver Fiehn, Bart Ghesquière, Steffen Neumann:
Critical Assessment of Small Molecule Identification 2016: automated methods. J. Cheminformatics 9(1): 22:1-22:21 (2017) - [j38]Eudes Barbosa, Richard Röttger, Anne-Christin Hauschild, Siomar de Castro Soares, Sebastian Böcker, Vasco Ariston de Carvalho Azevedo, Jan Baumbach:
LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis. J. Integr. Bioinform. 14(2) (2017) - 2016
- [j37]Céline Brouard, Huibin Shen, Kai Dührkop, Florence d'Alché-Buc, Sebastian Böcker, Juho Rousu:
Fast metabolite identification with Input Output Kernel Regression. Bioinform. 32(12): 28-36 (2016) - [j36]Sebastian Böcker, Kai Dührkop:
Fragmentation trees reloaded. J. Cheminformatics 8(1): 5:1-5:26 (2016) - 2015
- [j35]Sebastian Böcker:
Ten Times Eighteen. J. Inf. Process. 23(3): 258-264 (2015) - 2014
- [j34]Huibin Shen, Kai Dührkop, Sebastian Böcker, Juho Rousu:
Metabolite identification through multiple kernel learning on fragmentation trees. Bioinform. 30(12): 157-164 (2014) - 2013
- [j33]Malte Brinkmeyer, Thasso Griebel, Sebastian Böcker:
FlipCut Supertrees: Towards Matrix Representation Accuracy in Polynomial Time. Algorithmica 67(2): 142-160 (2013) - [j32]Katharina Jahn, Sascha Winter, Jens Stoye, Sebastian Böcker:
Statistics for approximate gene clusters. BMC Bioinform. 14(S-15): S14 (2013) - [j31]Imran Rauf, Florian Rasche, François Nicolas, Sebastian Böcker:
Finding Maximum Colorful Subtrees in Practice. J. Comput. Biol. 20(4): 311-321 (2013) - [j30]Kerstin Scheubert, Franziska Hufsky, Sebastian Böcker:
Computational mass spectrometry for small molecules. J. Cheminformatics 5: 12 (2013) - 2012
- [j29]Franziska Hufsky, Kai Dührkop, Florian Rasche, Markus Chimani, Sebastian Böcker:
Fast alignment of fragmentation trees. Bioinform. 28(12): 265-273 (2012) - [j28]Sebastian Böcker, Peter Damaschke:
A note on the parameterized complexity of unordered maximum tree orientation. Discret. Appl. Math. 160(10-11): 1634-1638 (2012) - [j27]Sebastian Böcker:
A golden ratio parameterized algorithm for Cluster Editing. J. Discrete Algorithms 16: 79-89 (2012) - [j26]Sebastian Böcker, Quang Bao Anh Bui, Anke Truß:
Improved Fixed-Parameter Algorithms for Minimum-Flip Consensus Trees. ACM Trans. Algorithms 8(1): 7:1-7:17 (2012) - 2011
- [j25]Malte Brinkmeyer, Thasso Griebel, Sebastian Böcker:
Polynomial Supertree Methods Revisited. Adv. Bioinformatics 2011: 524182:1-524182:21 (2011) - [j24]Sebastian Böcker, Sebastian Briesemeister, Gunnar W. Klau:
Exact Algorithms for Cluster Editing: Evaluation and Experiments. Algorithmica 60(2): 316-334 (2011) - [j23]Anna Katharina Dehof, Alexander Rurainski, Quang Bao Anh Bui, Sebastian Böcker, Hans-Peter Lenhof, Andreas Hildebrandt:
Automated bond order assignment as an optimization problem. Bioinform. 27(5): 619-625 (2011) - [j22]Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker:
Swiftly Computing Center Strings. BMC Bioinform. 12: 106 (2011) - [j21]Tobias Wittkop, Sven Rahmann, Richard Röttger, Sebastian Böcker, Jan Baumbach:
Extension and Robustness of Transitivity Clustering for Protein-Protein Interaction Network Analysis. Internet Math. 7(4): 255-273 (2011) - [j20]Sebastian Böcker, Peter Damaschke:
Even faster parameterized cluster deletion and cluster editing. Inf. Process. Lett. 111(14): 717-721 (2011) - [j19]Kerstin Scheubert, Franziska Hufsky, Florian Rasche, Sebastian Böcker:
Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data. J. Comput. Biol. 18(11): 1383-1397 (2011) - [j18]Sebastian Böcker, Birte Kehr, Florian Rasche:
Determination of Glycan Structure from Tandem Mass Spectra. IEEE ACM Trans. Comput. Biol. Bioinform. 8(4): 976-986 (2011) - [j17]Sebastian Böcker, Quang Bao Anh Bui, Anke Truß:
Computing bond orders in molecule graphs. Theor. Comput. Sci. 412(12-14): 1184-1195 (2011) - 2009
- [j16]Sebastian Böcker, Matthias C. Letzel, Zsuzsanna Lipták, Anton Pervukhin:
SIRIUS: decomposing isotope patterns for metabolite identification. Bioinform. 25(2): 218-224 (2009) - [j15]Sebastian Böcker, Sebastian Briesemeister, Gunnar W. Klau:
On optimal comparability editing with applications to molecular diagnostics. BMC Bioinform. 10(S-1) (2009) - [j14]Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye:
Computation of Median Gene Clusters. J. Comput. Biol. 16(8): 1085-1099 (2009) - [j13]Sebastian Böcker, Sebastian Briesemeister, Quang Bao Anh Bui, Anke Truß:
Going weighted: Parameterized algorithms for cluster editing. Theor. Comput. Sci. 410(52): 5467-5480 (2009) - 2008
- [j12]Sebastian Böcker, Zsuzsanna Lipták, Marcel Martin, Anton Pervukhin, Henner Sudek:
DECOMP - from interpreting Mass Spectrometry peaks to solving the Money Changing Problem. Bioinform. 24(4): 591-593 (2008) - [j11]Thasso Griebel, Malte Brinkmeyer, Sebastian Böcker:
EPoS: a modular software framework for phylogenetic analysis. Bioinform. 24(20): 2399-2400 (2008) - [j10]Wiebke Timm, Alexandra Scherbart, Sebastian Böcker, Oliver Kohlbacher, Tim W. Nattkemper:
Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics. BMC Bioinform. 9 (2008) - [j9]Sebastian Böcker, Veli Mäkinen:
Combinatorial Approaches for Mass Spectra Recalibration. IEEE ACM Trans. Comput. Biol. Bioinform. 5(1): 91-100 (2008) - 2007
- [j8]Sebastian Böcker, Zsuzsanna Lipták:
A Fast and Simple Algorithm for the Money Changing Problem. Algorithmica 48(4): 413-432 (2007) - [j7]Sebastian Böcker:
Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry. Bioinform. 23(2): 5-12 (2007) - [j6]Hans-Michael Kaltenbach, Andreas Wilke, Sebastian Böcker:
SAMPI: Protein Identification with Mass Spectra Alignments. BMC Bioinform. 8 (2007) - [j5]Sebastian Böcker, Hans-Michael Kaltenbach:
Mass spectra alignments and their significance. J. Discrete Algorithms 5(4): 714-728 (2007) - 2006
- [j4]Sebastian Böcker:
Sequencing from Compomers: The Puzzle. Theory Comput. Syst. 39(3): 455-471 (2006) - 2004
- [j3]Sebastian Böcker:
Sequencing from Compomers: Using Mass Spectrometry for DNA de novo Sequencing of 200+ nt. J. Comput. Biol. 11(6): 1110-1134 (2004) - 2002
- [j2]Sebastian Böcker:
Exponentially many supertrees. Appl. Math. Lett. 15(7): 861-865 (2002) - 2000
- [j1]Sebastian Böcker, David Bryant, Andreas W. M. Dress, Mike A. Steel:
Algorithmic Aspects of Tree Amalgamation. J. Algorithms 37(2): 522-537 (2000)
Conference and Workshop Papers
- 2024
- [c41]Roman Bushuiev, Anton Bushuiev, Niek F. de Jonge, Adamo Young, Fleming Kretschmer, Raman Samusevich, Janne Heirman, Fei Wang, Luke Zhang, Kai Dührkop, Marcus Ludwig, Nils A. Haupt, Apurva Kalia, Corinna Brungs, Robin Schmid, Russell Greiner, Bo Wang, David S. Wishart, Liping Liu, Juho Rousu, Wout Bittremieux, Hannes Rost, Tytus D. Mak, Soha Hassoun, Florian Huber, Justin J. J. van der Hooft, Michael A. Stravs, Sebastian Böcker, Josef Sivic, Tomás Pluskal:
MassSpecGym: A benchmark for the discovery and identification of molecules. NeurIPS 2024 - 2018
- [c40]Kai Dührkop, Marie Anne Lataretu, W. Timothy J. White, Sebastian Böcker:
Heuristic Algorithms for the Maximum Colorful Subtree Problem. WABI 2018: 23:1-23:14 - 2017
- [c39]Céline Brouard, Eric Bach, Sebastian Böcker, Juho Rousu:
Magnitude-Preserving Ranking for Structured Outputs. ACML 2017: 407-422 - 2015
- [c38]W. Timothy J. White, Stephan Beyer, Kai Dührkop, Markus Chimani, Sebastian Böcker:
Speedy Colorful Subtrees. COCOON 2015: 310-322 - [c37]Kai Dührkop, Sebastian Böcker:
Fragmentation Trees Reloaded. RECOMB 2015: 65-79 - 2014
- [c36]Clemens Beckstein, Sebastian Böcker, Martin Bogdan, Helge Bruelheide, H. Martin Bücker, Joachim Denzler, Peter Dittrich, Ivo Grosse, Alexander Hinneburg, Birgitta König-Ries, Felicitas Löffler, Manja Marz, Matthias Müller-Hannemann, Martin Winter, Wolf Zimmermann:
Explorative Analysis of Heterogeneous, Unstructured, and Uncertain Data - A Computer Science Perspective on Biodiversity Research. DATA 2014: 251-257 - [c35]Kerstin Scheubert, Franziska Hufsky, Sebastian Böcker:
Multiple Mass Spectrometry Fragmentation Trees Revisited: Boosting Performance and Quality. WABI 2014: 217-231 - 2013
- [c34]Sebastian Böcker, Jan Baumbach:
Cluster Editing. CiE 2013: 33-44 - [c33]Kai Dührkop, Marcus Ludwig, Marvin Meusel, Sebastian Böcker:
Faster Mass Decomposition. WABI 2013: 45-58 - [c32]Sebastian Böcker, Stefan Canzar, Gunnar W. Klau:
The Generalized Robinson-Foulds Metric. WABI 2013: 156-169 - 2012
- [c31]Franziska Hufsky, Sebastian Böcker:
Comparing Fragmentation Trees from Electron Impact Mass Spectra with Annotated Fragmentation Pathways. GCB 2012: 12-22 - [c30]Marcus Ludwig, Franziska Hufsky, Samy Elshamy, Sebastian Böcker:
Finding Characteristic Substructures for Metabolite Classes. GCB 2012: 23-38 - [c29]Imran Rauf, Florian Rasche, François Nicolas, Sebastian Böcker:
Finding Maximum Colorful Subtrees in Practice. RECOMB 2012: 213-223 - 2011
- [c28]Markus Chimani, Matthias Woste, Sebastian Böcker:
A Closer Look at the Closest String and Closest Substring Problem. ALENEX 2011: 13-24 - [c27]Malte Brinkmeyer, Thasso Griebel, Sebastian Böcker:
FlipCut Supertrees: Towards Matrix Representation Accuracy in Polynomial Time. COCOON 2011: 37-48 - [c26]Sebastian Böcker:
A Golden Ratio Parameterized Algorithm for Cluster Editing. IWOCA 2011: 85-95 - [c25]Kerstin Scheubert, Franziska Hufsky, Florian Rasche, Sebastian Böcker:
Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data. RECOMB 2011: 377-391 - 2010
- [c24]Markus Chimani, Sven Rahmann, Sebastian Böcker:
Exact ILP solutions for phylogenetic minimum flip problems. BCB 2010: 147-153 - [c23]Malte Brinkmeyer, Thasso Griebel, Sebastian Böcker:
Polynomial Supertree Methods Revisited. PRIB 2010: 183-194 - [c22]Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker:
Swiftly Computing Center Strings. WABI 2010: 325-336 - 2009
- [c21]Sebastian Böcker, Birte Kehr, Florian Rasche:
Determination of Glycan Structure from Tandem Mass Spectra. COCOON 2009: 258-267 - [c20]Sebastian Böcker, Anton Pervukhin:
Inferring Peptide Composition from Molecular Formulas. COCOON 2009: 277-286 - [c19]Sebastian Böcker, Quang Bao Anh Bui, Patrick Seeber, Anke Truß:
Computing Bond Types in Molecule Graphs. COCOON 2009: 297-306 - [c18]Sebastian Böcker, Falk Hüffner, Anke Truß, Magnus Wahlström:
A Faster Fixed-Parameter Approach to Drawing Binary Tanglegrams. IWPEC 2009: 38-49 - [c17]Sebastian Böcker, Florian Rasche, Tamara Steijger:
Annotating Fragmentation Patterns. WABI 2009: 13-24 - 2008
- [c16]Sebastian Böcker, Sebastian Briesemeister, Quang Bao Anh Bui, Anke Truß:
A Fixed-Parameter Approach for Weighted Cluster Editing. APBC 2008: 211-220 - [c15]Sebastian Böcker, Sebastian Briesemeister, Quang Bao Anh Bui, Anke Truß:
Going Weighted: Parameterized Algorithms for Cluster Editing. COCOA 2008: 1-12 - [c14]Sebastian Böcker, Florian Rasche:
Towards de novo identification of metabolites by analyzing tandem mass spectra. ECCB 2008: 49-55 - [c13]Alexandra Scherbart, Wiebke Timm, Sebastian Böcker, Tim W. Nattkemper:
Improved Mass Spectrometry Peak Intensity Prediction by Adaptive Feature Weighting. ICONIP (1) 2008: 513-520 - [c12]Sebastian Böcker, Quang Bao Anh Bui, Anke Truß:
An Improved Fixed-Parameter Algorithm for Minimum-Flip Consensus Trees. IWPEC 2008: 43-54 - [c11]Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye:
Computation of Median Gene Clusters. RECOMB 2008: 331-345 - [c10]Sebastian Böcker, Sebastian Briesemeister, Gunnar W. Klau:
Exact Algorithms for Cluster Editing: Evaluation and Experiments. WEA 2008: 289-302 - 2007
- [c9]Alexandra Scherbart, Wiebke Timm, Sebastian Böcker, Tim W. Nattkemper:
Neural Network Approach for Mass Spectrometry Prediction by Peptide Prototyping. ICANN (2) 2007: 90-99 - 2006
- [c8]Hans-Michael Kaltenbach, Sebastian Böcker, Sven Rahmann:
Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting. Systems Biology and Computational Proteomics 2006: 29-41 - [c7]Sebastian Böcker, Matthias C. Letzel, Zsuzsanna Lipták, Anton Pervukhin:
Decomposing Metabolomic Isotope Patterns. WABI 2006: 12-23 - 2005
- [c6]Sebastian Böcker, Zsuzsanna Lipták:
The Money Changing Problem Revisited: Computing the Frobenius Number in Time O(k a1). COCOON 2005: 965-974 - [c5]Sebastian Böcker, Hans-Michael Kaltenbach:
Mass Spectra Alignments and Their Significance. CPM 2005: 429-441 - [c4]Sebastian Böcker, Zsuzsanna Lipták:
Efficient mass decomposition. SAC 2005: 151-157 - 2004
- [c3]Sebastian Böcker:
Weighted Sequencing from Compomers: DNA de-novo sequencing from mass spectrometry data in the presence of false negative constraints. German Conference on Bioinformatics 2004: 13-23 - 2003
- [c2]Sebastian Böcker:
SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry. ISMB (Supplement of Bioinformatics) 2003: 44-53 - [c1]Sebastian Böcker:
Sequencing from Compomers: Using Mass Spectrometry for DNA De-Novo Sequencing of 200+ nt. WABI 2003: 476-497
Editorship
- 2012
- [e1]Sebastian Böcker, Franziska Hufsky, Kerstin Scheubert, Jana Schleicher, Stefan Schuster:
German Conference on Bioinformatics 2012, GCB 2012, Jena, Germany, September 20-22, 2012. OASIcs 26, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2012, ISBN 978-3-939897-44-6 [contents]
Informal and Other Publications
- 2024
- [i19]Roman Bushuiev, Anton Bushuiev, Niek F. de Jonge, Adamo Young, Fleming Kretschmer, Raman Samusevich, Janne Heirman, Fei Wang, Luke Zhang, Kai Dührkop, Marcus Ludwig, Nils A. Haupt, Apurva Kalia, Corinna Brungs, Robin Schmid, Russell Greiner, Bo Wang, David S. Wishart, Li-Ping Liu, Juho Rousu, Wout Bittremieux, Hannes Rost, Tytus D. Mak, Soha Hassoun, Florian Huber, Justin J. J. van der Hooft, Michael A. Stravs, Sebastian Böcker, Josef Sivic, Tomás Pluskal:
MassSpecGym: A benchmark for the discovery and identification of molecules. CoRR abs/2410.23326 (2024) - 2021
- [i18]Sebastian Böcker, Rebekah L. Gundry, Lennart Martens, Magnus Palmblad:
Computational Proteomics (Dagstuhl Seminar 21271). Dagstuhl Reports 11(6): 1-13 (2021) - 2020
- [i17]Sebastian Böcker, Corey Broeckling, Emma Schymanski, Nicola Zamboni:
Computational Metabolomics: From Cheminformatics to Machine Learning (Dagstuhl Seminar 20051). Dagstuhl Reports 10(1): 144-159 (2020) - 2018
- [i16]Kai Dührkop, Marie Anne Lataretu, W. Timothy J. White, Sebastian Böcker:
Heuristic algorithms for the Maximum Colorful Subtree problem. CoRR abs/1801.07456 (2018) - 2017
- [i15]W. Timothy J. White, Marcus Ludwig, Sebastian Böcker:
Cograph Editing in O(3nn) time and O(2n) space. CoRR abs/1711.05839 (2017) - [i14]Theodore Alexandrov, Sebastian Böcker, Pieter C. Dorrestein, Emma Schymanski:
Computational Metabolomics: Identification, Interpretation, Imaging (Dagstuhl Seminar 17491). Dagstuhl Reports 7(12): 1-17 (2017) - [i13]Masanori Arita, Sebastian Böcker, Steffen Neumann:
Computational Metabolomics (NII Shonan Meeting 2017-3). NII Shonan Meet. Rep. 2017 (2017) - 2015
- [i12]Sebastian Böcker, Juho Rousu, Emma Schymanski:
Computational Metabolomics (Dagstuhl Seminar 15492). Dagstuhl Reports 5(11): 180-192 (2015) - [i11]Markus Fleischauer, Sebastian Böcker:
Collecting reliable clades using the Greedy Strict Consensus Merger. PeerJ Prepr. 3: e1297 (2015) - 2014
- [i10]Kai Dührkop, Sebastian Böcker:
Fragmentation trees reloaded. CoRR abs/1412.1929 (2014) - [i9]Sebastian Böcker, Gunnar W. Klau, Veli Mäkinen, Hon Wai Leong:
Towards the ground truth: Exact algorithms for bioinformatics research (NII Shonan Meeting 2014-2). NII Shonan Meet. Rep. 2014 (2014) - 2013
- [i8]Sebastian Böcker, Stefan Canzar, Gunnar W. Klau:
The generalized Robinson-Foulds metric. CoRR abs/1307.7824 (2013) - 2012
- [i7]Sebastian Böcker:
Ten times eighteen. CoRR abs/1209.1977 (2012) - 2011
- [i6]Sebastian Böcker:
Towards a Data Reduction for the Minimum Flip Supertree Problem. CoRR abs/1104.4471 (2011) - [i5]François Nicolas, Sebastian Böcker:
Various complexity results for computational mass spectrometry problems. CoRR abs/1109.3367 (2011) - [i4]Sebastian Böcker, Quang Bao Anh Bui, François Nicolas, Anke Truß:
Intractability of the Minimum-Flip Supertree problem and its variants. CoRR abs/1112.4536 (2011) - 2008
- [i3]Sebastian Böcker, Florian Rasche:
Towards de novo identification of metabolites by analyzing tandem mass spectra. Computational Proteomics 2008 - 2005
- [i2]Sebastian Böcker, Veli Mäkinen:
Combinatorial Approaches for Mass Spectra Recalibration. Computational Proteomics 2005 - [i1]Sebastian Böcker, Veli Mäkinen:
Maximum line-pair stabbing problem and its variations. EuroCG 2005: 183-186
Coauthor Index
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