Sebastian Böcker

105 papers A* 1A 1B 6C 15Misc 7Journal 60Unranked 14

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data. J. Cheminformatics Pilleriin Peets, Aristeidis Litos, Kai Dührkop, Daniel R. Garza, Justin J. J. van der Hooft, Sebastian Böcker, Bas E. Dutilh
2024	A*	`conf`	MassSpecGym: A benchmark for the discovery and identification of molecules. NeurIPS 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
2024	J	`jnl`	MassSpecGym: A benchmark for the discovery and identification of molecules. CoRR 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
2021	J	`jnl`	Computational Proteomics (Dagstuhl Seminar 21271). Dagstuhl Reports Sebastian Böcker, Rebekah L. Gundry, Lennart Martens, Magnus Palmblad
2020	J	`jnl`	Computational Metabolomics: From Cheminformatics to Machine Learning (Dagstuhl Seminar 20051). Dagstuhl Reports Sebastian Böcker, Corey Broeckling, Emma Schymanski, Nicola Zamboni
2020	J	`jnl`	Database-independent molecular formula annotation using Gibbs sampling through ZODIAC. Nat. Mach. Intell. 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
2020	J	`jnl`	Publisher Correction: Database-independent molecular formula annotation using Gibbs sampling through ZODIAC. Nat. Mach. Intell. 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
2018	J	`jnl`	Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints. Bioinform. Marcus Ludwig, Kai Dührkop, Sebastian Böcker
2018	C	`conf`	Heuristic Algorithms for the Maximum Colorful Subtree Problem. WABI Kai Dührkop, Marie Anne Lataretu, W. Timothy J. White, Sebastian Böcker
2018	J	`jnl`	Heuristic algorithms for the Maximum Colorful Subtree problem. CoRR Kai Dührkop, Marie Anne Lataretu, W. Timothy J. White, Sebastian Böcker
2018	J	`jnl`	Liquid-chromatography retention order prediction for metabolite identification. Bioinform. Eric Bach, Sándor Szedmák, Céline Brouard, Sebastian Böcker, Juho Rousu
2017	J	`jnl`	Cograph Editing in O(3 CoRR W. Timothy J. White, Marcus Ludwig, Sebastian Böcker
2017	J	`jnl`	Computational Metabolomics (NII Shonan Meeting 2017-3). NII Shonan Meet. Rep. Masanori Arita, Sebastian Böcker, Steffen Neumann
2017	J	`jnl`	Computational Metabolomics: Identification, Interpretation, Imaging (Dagstuhl Seminar 17491). Dagstuhl Reports Theodore Alexandrov, Sebastian Böcker, Pieter C. Dorrestein, Emma Schymanski
2017	J	`jnl`	Critical Assessment of Small Molecule Identification 2016: automated methods. J. Cheminformatics 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
2017	J	`jnl`	LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis. J. Integr. Bioinform. Eudes Barbosa, Richard Röttger, Anne-Christin Hauschild, Siomar de Castro Soares, Sebastian Böcker, Vasco Ariston de Carvalho Azevedo, Jan Baumbach
2017	C	`conf`	Magnitude-Preserving Ranking for Structured Outputs. ACML Céline Brouard, Eric Bach, Sebastian Böcker, Juho Rousu
2016	J	`jnl`	Fast metabolite identification with Input Output Kernel Regression. Bioinform. Céline Brouard, Huibin Shen, Kai Dührkop, Florence d'Alché-Buc, Sebastian Böcker, Juho Rousu
2016	J	`jnl`	Fragmentation trees reloaded. J. Cheminformatics Sebastian Böcker, Kai Dührkop
2015	J	`jnl`	Collecting reliable clades using the Greedy Strict Consensus Merger. PeerJ Prepr. Markus Fleischauer, Sebastian Böcker
2015	J	`jnl`	Computational Metabolomics (Dagstuhl Seminar 15492). Dagstuhl Reports Sebastian Böcker, Juho Rousu, Emma Schymanski
2015	B	`conf`	Fragmentation Trees Reloaded. RECOMB Kai Dührkop, Sebastian Böcker
2015	Misc	`conf`	Speedy Colorful Subtrees. COCOON W. Timothy J. White, Stephan Beyer, Kai Dührkop, Markus Chimani, Sebastian Böcker
2015	J	`jnl`	Ten Times Eighteen. J. Inf. Process. Sebastian Böcker
2014	C	`conf`	Explorative Analysis of Heterogeneous, Unstructured, and Uncertain Data - A Computer Science Perspective on Biodiversity Research. DATA 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
2014	J	`jnl`	Fragmentation trees reloaded. CoRR Kai Dührkop, Sebastian Böcker
2014	J	`jnl`	Metabolite identification through multiple kernel learning on fragmentation trees. Bioinform. Huibin Shen, Kai Dührkop, Sebastian Böcker, Juho Rousu
2014	C	`conf`	Multiple Mass Spectrometry Fragmentation Trees Revisited: Boosting Performance and Quality. WABI Kerstin Scheubert, Franziska Hufsky, Sebastian Böcker
2014	J	`jnl`	Towards the ground truth: Exact algorithms for bioinformatics research (NII Shonan Meeting 2014-2). NII Shonan Meet. Rep. Sebastian Böcker, Gunnar W. Klau, Veli Mäkinen, Hon Wai Leong
2013	C	`conf`	Cluster Editing. CiE Sebastian Böcker, Jan Baumbach
2013	J	`jnl`	Computational mass spectrometry for small molecules. J. Cheminformatics Kerstin Scheubert, Franziska Hufsky, Sebastian Böcker
2013	C	`conf`	Faster Mass Decomposition. WABI Kai Dührkop, Marcus Ludwig, Marvin Meusel, Sebastian Böcker
2013	J	`jnl`	Finding Maximum Colorful Subtrees in Practice. J. Comput. Biol. Imran Rauf, Florian Rasche, François Nicolas, Sebastian Böcker
2013	J	`jnl`	FlipCut Supertrees: Towards Matrix Representation Accuracy in Polynomial Time. Algorithmica Malte Brinkmeyer, Thasso Griebel, Sebastian Böcker
2013	J	`jnl`	Statistics for approximate gene clusters. BMC Bioinform. Katharina Jahn, Sascha Winter, Jens Stoye, Sebastian Böcker
2013	C	`conf`	The Generalized Robinson-Foulds Metric. WABI Sebastian Böcker, Stefan Canzar, Gunnar W. Klau
2013	J	`jnl`	The generalized Robinson-Foulds metric. CoRR Sebastian Böcker, Stefan Canzar, Gunnar W. Klau
2012	J	`jnl`	A golden ratio parameterized algorithm for Cluster Editing. J. Discrete Algorithms Sebastian Böcker
2012	J	`jnl`	A note on the parameterized complexity of unordered maximum tree orientation. Discret. Appl. Math. Sebastian Böcker, Peter Damaschke
2012	—	`conf`	Comparing Fragmentation Trees from Electron Impact Mass Spectra with Annotated Fragmentation Pathways. GCB Franziska Hufsky, Sebastian Böcker
2012	J	`jnl`	Fast alignment of fragmentation trees. Bioinform. Franziska Hufsky, Kai Dührkop, Florian Rasche, Markus Chimani, Sebastian Böcker
2012	—	`conf`	Finding Characteristic Substructures for Metabolite Classes. GCB Marcus Ludwig, Franziska Hufsky, Samy Elshamy, Sebastian Böcker
2012	B	`conf`	Finding Maximum Colorful Subtrees in Practice. RECOMB Imran Rauf, Florian Rasche, François Nicolas, Sebastian Böcker
2012	—	`ed.`	German Conference on Bioinformatics 2012, GCB 2012, Jena, Germany, September 20-22, 2012. GCB Sebastian Böcker, Franziska Hufsky, Kerstin Scheubert, Jana Schleicher, Stefan Schuster
2012	J	`jnl`	Improved Fixed-Parameter Algorithms for Minimum-Flip Consensus Trees. ACM Trans. Algorithms Sebastian Böcker, Quang Bao Anh Bui, Anke Truß
2012	J	`jnl`	Ten times eighteen CoRR Sebastian Böcker
2011	A	`conf`	A Closer Look at the Closest String and Closest Substring Problem. ALENEX Markus Chimani, Matthias Woste, Sebastian Böcker
2011	C	`conf`	A Golden Ratio Parameterized Algorithm for Cluster Editing. IWOCA Sebastian Böcker
2011	J	`jnl`	Automated bond order assignment as an optimization problem. Bioinform. Anna Katharina Dehof, Alexander Rurainski, Quang Bao Anh Bui, Sebastian Böcker, Hans-Peter Lenhof, Andreas Hildebrandt
2011	B	`conf`	Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data. RECOMB Kerstin Scheubert, Franziska Hufsky, Florian Rasche, Sebastian Böcker
2011	J	`jnl`	Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data. J. Comput. Biol. Kerstin Scheubert, Franziska Hufsky, Florian Rasche, Sebastian Böcker
2011	J	`jnl`	Computing bond orders in molecule graphs. Theor. Comput. Sci. Sebastian Böcker, Quang Bao Anh Bui, Anke Truß
2011	J	`jnl`	Determination of Glycan Structure from Tandem Mass Spectra. IEEE ACM Trans. Comput. Biol. Bioinform. Sebastian Böcker, Birte Kehr, Florian Rasche
2011	J	`jnl`	Even faster parameterized cluster deletion and cluster editing. Inf. Process. Lett. Sebastian Böcker, Peter Damaschke
2011	J	`jnl`	Exact Algorithms for Cluster Editing: Evaluation and Experiments. Algorithmica Sebastian Böcker, Sebastian Briesemeister, Gunnar W. Klau
2011	J	`jnl`	Extension and Robustness of Transitivity Clustering for Protein-Protein Interaction Network Analysis. Internet Math. Tobias Wittkop, Sven Rahmann, Richard Röttger, Sebastian Böcker, Jan Baumbach
2011	Misc	`conf`	FlipCut Supertrees: Towards Matrix Representation Accuracy in Polynomial Time. COCOON Malte Brinkmeyer, Thasso Griebel, Sebastian Böcker
2011	J	`jnl`	Intractability of the Minimum-Flip Supertree problem and its variants CoRR Sebastian Böcker, Quang Bao Anh Bui, François Nicolas, Anke Truß
2011	J	`jnl`	Polynomial Supertree Methods Revisited. Adv. Bioinformatics Malte Brinkmeyer, Thasso Griebel, Sebastian Böcker
2011	J	`jnl`	Swiftly Computing Center Strings. BMC Bioinform. Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker
2011	J	`jnl`	Towards a Data Reduction for the Minimum Flip Supertree Problem CoRR Sebastian Böcker
2011	J	`jnl`	Various complexity results for computational mass spectrometry problems CoRR François Nicolas, Sebastian Böcker
2010	—	`conf`	Exact ILP solutions for phylogenetic minimum flip problems. BCB Markus Chimani, Sven Rahmann, Sebastian Böcker
2010	—	`conf`	Polynomial Supertree Methods Revisited. PRIB Malte Brinkmeyer, Thasso Griebel, Sebastian Böcker
2010	C	`conf`	Swiftly Computing Center Strings. WABI Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker
2009	—	`conf`	A Faster Fixed-Parameter Approach to Drawing Binary Tanglegrams. IWPEC Sebastian Böcker, Falk Hüffner, Anke Truß, Magnus Wahlström
2009	C	`conf`	Annotating Fragmentation Patterns. WABI Sebastian Böcker, Florian Rasche, Tamara Steijger
2009	J	`jnl`	Computation of Median Gene Clusters. J. Comput. Biol. Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye
2009	Misc	`conf`	Computing Bond Types in Molecule Graphs. COCOON Sebastian Böcker, Quang Bao Anh Bui, Patrick Seeber, Anke Truß
2009	Misc	`conf`	Determination of Glycan Structure from Tandem Mass Spectra. COCOON Sebastian Böcker, Birte Kehr, Florian Rasche
2009	J	`jnl`	Going weighted: Parameterized algorithms for cluster editing. Theor. Comput. Sci. Sebastian Böcker, Sebastian Briesemeister, Quang Bao Anh Bui, Anke Truß
2009	Misc	`conf`	Inferring Peptide Composition from Molecular Formulas. COCOON Sebastian Böcker, Anton Pervukhin
2009	J	`jnl`	On optimal comparability editing with applications to molecular diagnostics. BMC Bioinform. Sebastian Böcker, Sebastian Briesemeister, Gunnar W. Klau
2009	J	`jnl`	SIRIUS: decomposing isotope patterns for metabolite identification. Bioinform. Sebastian Böcker, Matthias C. Letzel, Zsuzsanna Lipták, Anton Pervukhin
2008	B	`conf`	A Fixed-Parameter Approach for Weighted Cluster Editing. APBC Sebastian Böcker, Sebastian Briesemeister, Quang Bao Anh Bui, Anke Truß
2008	—	`conf`	An Improved Fixed-Parameter Algorithm for Minimum-Flip Consensus Trees. IWPEC Sebastian Böcker, Quang Bao Anh Bui, Anke Truß
2008	J	`jnl`	Combinatorial Approaches for Mass Spectra Recalibration. IEEE ACM Trans. Comput. Biol. Bioinform. Sebastian Böcker, Veli Mäkinen
2008	B	`conf`	Computation of Median Gene Clusters. RECOMB Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye
2008	J	`jnl`	DECOMP - from interpreting Mass Spectrometry peaks to solving the Money Changing Problem. Bioinform. Sebastian Böcker, Zsuzsanna Lipták, Marcel Martin, Anton Pervukhin, Henner Sudek
2008	J	`jnl`	EPoS: a modular software framework for phylogenetic analysis. Bioinform. Thasso Griebel, Malte Brinkmeyer, Sebastian Böcker
2008	—	`conf`	Exact Algorithms for Cluster Editing: Evaluation and Experiments. WEA Sebastian Böcker, Sebastian Briesemeister, Gunnar W. Klau
2008	C	`conf`	Going Weighted: Parameterized Algorithms for Cluster Editing. COCOA Sebastian Böcker, Sebastian Briesemeister, Quang Bao Anh Bui, Anke Truß
2008	—	`conf`	Improved Mass Spectrometry Peak Intensity Prediction by Adaptive Feature Weighting. ICONIP (1) Alexandra Scherbart, Wiebke Timm, Sebastian Böcker, Tim W. Nattkemper
2008	J	`jnl`	Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics. BMC Bioinform. Wiebke Timm, Alexandra Scherbart, Sebastian Böcker, Oliver Kohlbacher, Tim W. Nattkemper
2008	C	`conf`	Towards ECCB Sebastian Böcker, Florian Rasche
2008	—	`conf`	Towards de novo identification of metabolites by analyzing tandem mass spectra. Computational Proteomics Sebastian Böcker, Florian Rasche
2007	J	`jnl`	A Fast and Simple Algorithm for the Money Changing Problem. Algorithmica Sebastian Böcker, Zsuzsanna Lipták
2007	J	`jnl`	Mass spectra alignments and their significance. J. Discrete Algorithms Sebastian Böcker, Hans-Michael Kaltenbach
2007	—	`conf`	Neural Network Approach for Mass Spectrometry Prediction by Peptide Prototyping. ICANN (2) Alexandra Scherbart, Wiebke Timm, Sebastian Böcker, Tim W. Nattkemper
2007	J	`jnl`	SAMPI: Protein Identification with Mass Spectra Alignments. BMC Bioinform. Hans-Michael Kaltenbach, Andreas Wilke, Sebastian Böcker
2007	J	`jnl`	Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry. Bioinform. Sebastian Böcker
2006	C	`conf`	Decomposing Metabolomic Isotope Patterns. WABI Sebastian Böcker, Matthias C. Letzel, Zsuzsanna Lipták, Anton Pervukhin
2006	—	`conf`	Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting. Systems Biology and Computational Proteomics Hans-Michael Kaltenbach, Sebastian Böcker, Sven Rahmann
2006	J	`jnl`	Sequencing from Compomers: The Puzzle. Theory Comput. Syst. Sebastian Böcker
2005	—	`conf`	Combinatorial Approaches for Mass Spectra Recalibration. Computational Proteomics Sebastian Böcker, Veli Mäkinen
2005	Misc	`conf`	Efficient mass decomposition. SAC Sebastian Böcker, Zsuzsanna Lipták
2005	B	`conf`	Mass Spectra Alignments and Their Significance. CPM Sebastian Böcker, Hans-Michael Kaltenbach
2005	C	`conf`	Maximum line-pair stabbing problem and its variations. EuroCG Sebastian Böcker, Veli Mäkinen
2005	Misc	`conf`	The Money Changing Problem Revisited: Computing the Frobenius Number in Time O(k a COCOON Sebastian Böcker, Zsuzsanna Lipták
2004	J	`jnl`	Sequencing from Compomers: Using Mass Spectrometry for DNA de novo Sequencing of 200+ nt. J. Comput. Biol. Sebastian Böcker
2004	—	`conf`	Weighted Sequencing from Compomers: DNA de-novo sequencing from mass spectrometry data in the presence of false negative constraints. German Conference on Bioinformatics Sebastian Böcker
2003	—	`conf`	SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry. ISMB (Supplement of Bioinformatics) Sebastian Böcker
2003	C	`conf`	Sequencing from Compomers: Using Mass Spectrometry for DNA De-Novo Sequencing of 200+ nt. WABI Sebastian Böcker
2002	J	`jnl`	Exponentially many supertrees. Appl. Math. Lett. Sebastian Böcker
2000	J	`jnl`	Algorithmic Aspects of Tree Amalgamation. J. Algorithms Sebastian Böcker, David Bryant, Andreas W. M. Dress, Mike A. Steel