Algorithmic Aspects of Tree Amalgamation. - Sebastian Böcker; David Bryant; Andreas W. M. Dress; Mike A. Steel (J. Algorithms, 2000)

Exponentially many supertrees. - Sebastian Böcker (Appl. Math. Lett., 2002)

SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry. - Sebastian Böcker (ISMB (Supplement of Bioinformatics), 2003)

Weighted Sequencing from Compomers: DNA de-novo sequencing from mass spectrometry data in the presence of false negative constraints. - Sebastian Böcker (German Conference on Bioinformatics, 2004)

Sequencing from Compomers: Using Mass Spectrometry for DNA de novo Sequencing of 200+ nt. - Sebastian Böcker (J. Comput. Biol., 2004)

The Money Changing Problem Revisited: Computing the Frobenius Number in Time O(k a1). - Sebastian Böcker; Zsuzsanna Lipták (COCOON, 2005)

Maximum line-pair stabbing problem and its variations. - Sebastian Böcker; Veli Mäkinen (EuroCG, 2005)

Efficient mass decomposition. - Sebastian Böcker; Zsuzsanna Lipták (SAC, 2005)

Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting. - Hans-Michael Kaltenbach; Sebastian Böcker; Sven Rahmann (Systems Biology and Computational Proteomics, 2006)

Decomposing Metabolomic Isotope Patterns. - Sebastian Böcker; Matthias C. Letzel; Zsuzsanna Lipták; Anton Pervukhin (WABI, 2006)

Sequencing from Compomers: The Puzzle. - Sebastian Böcker (Theory Comput. Syst., 2006)

Neural Network Approach for Mass Spectrometry Prediction by Peptide Prototyping. - Alexandra Scherbart; Wiebke Timm; Sebastian Böcker; Tim W. Nattkemper (ICANN (2), 2007)

A Fast and Simple Algorithm for the Money Changing Problem. - Sebastian Böcker; Zsuzsanna Lipták (Algorithmica, 2007)

Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry. - Sebastian Böcker (Bioinform., 2007)

SAMPI: Protein Identification with Mass Spectra Alignments. - Hans-Michael Kaltenbach; Andreas Wilke; Sebastian Böcker (BMC Bioinform., 2007)

Mass spectra alignments and their significance. - Sebastian Böcker; Hans-Michael Kaltenbach (J. Discrete Algorithms, 2007)

A Fixed-Parameter Approach for Weighted Cluster Editing. - Sebastian Böcker; Sebastian Briesemeister; Quang Bao Anh Bui; Anke Truß (APBC, 2008)

Towards de novo identification of metabolites by analyzing tandem mass spectra. - Sebastian Böcker; Florian Rasche (Computational Proteomics, 2008)

Towards de novo identification of metabolites by analyzing tandem mass spectra. - Sebastian Böcker; Florian Rasche (ECCB, 2008)

Improved Mass Spectrometry Peak Intensity Prediction by Adaptive Feature Weighting. - Alexandra Scherbart; Wiebke Timm; Sebastian Böcker; Tim W. Nattkemper (ICONIP (1), 2008)

An Improved Fixed-Parameter Algorithm for Minimum-Flip Consensus Trees. - Sebastian Böcker; Quang Bao Anh Bui; Anke Truß (IWPEC, 2008)

DECOMP - from interpreting Mass Spectrometry peaks to solving the Money Changing Problem. - Sebastian Böcker; Zsuzsanna Lipták; Marcel Martin; Anton Pervukhin; Henner Sudek (Bioinform., 2008)

EPoS: a modular software framework for phylogenetic analysis. - Thasso Griebel; Malte Brinkmeyer; Sebastian Böcker (Bioinform., 2008)

Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics. - Wiebke Timm; Alexandra Scherbart; Sebastian Böcker; Oliver Kohlbacher; Tim W. Nattkemper (BMC Bioinform., 2008)

Combinatorial Approaches for Mass Spectra Recalibration. - Sebastian Böcker; Veli Mäkinen (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Computing Bond Types in Molecule Graphs. - Sebastian Böcker; Quang Bao Anh Bui; Patrick Seeber; Anke Truß (COCOON, 2009)

Inferring Peptide Composition from Molecular Formulas. - Sebastian Böcker; Anton Pervukhin (COCOON, 2009)

A Faster Fixed-Parameter Approach to Drawing Binary Tanglegrams. - Sebastian Böcker; Falk Hüffner; Anke Truß; Magnus Wahlström (IWPEC, 2009)

Annotating Fragmentation Patterns. - Sebastian Böcker; Florian Rasche; Tamara Steijger (WABI, 2009)

SIRIUS: decomposing isotope patterns for metabolite identification. - Sebastian Böcker; Matthias C. Letzel; Zsuzsanna Lipták; Anton Pervukhin (Bioinform., 2009)

On optimal comparability editing with applications to molecular diagnostics. - Sebastian Böcker; Sebastian Briesemeister; Gunnar W. Klau (BMC Bioinform., 2009)

Computation of Median Gene Clusters. - Sebastian Böcker; Katharina Jahn 001; Julia Mixtacki; Jens Stoye (J. Comput. Biol., 2009)

Going weighted: Parameterized algorithms for cluster editing. - Sebastian Böcker; Sebastian Briesemeister; Quang Bao Anh Bui; Anke Truß (Theor. Comput. Sci., 2009)

Exact ILP solutions for phylogenetic minimum flip problems. - Markus Chimani; Sven Rahmann; Sebastian Böcker (BCB, 2010)

A Closer Look at the Closest String and Closest Substring Problem. - Markus Chimani; Matthias Woste; Sebastian Böcker (ALENEX, 2011)

Polynomial Supertree Methods Revisited. - Malte Brinkmeyer; Thasso Griebel; Sebastian Böcker (Adv. Bioinformatics, 2011)

Exact Algorithms for Cluster Editing: Evaluation and Experiments. - Sebastian Böcker; Sebastian Briesemeister; Gunnar W. Klau (Algorithmica, 2011)

Automated bond order assignment as an optimization problem. - Anna Katharina Dehof; Alexander Rurainski; Quang Bao Anh Bui; Sebastian Böcker; Hans-Peter Lenhof; Andreas Hildebrandt 001 (Bioinform., 2011)

Swiftly Computing Center Strings. - Franziska Hufsky; Léon Kuchenbecker; Katharina Jahn 001; Jens Stoye; Sebastian Böcker (BMC Bioinform., 2011)

Towards a Data Reduction for the Minimum Flip Supertree Problem - Sebastian Böcker (CoRR, 2011)

Various complexity results for computational mass spectrometry problems - François Nicolas; Sebastian Böcker (CoRR, 2011)

Intractability of the Minimum-Flip Supertree problem and its variants - Sebastian Böcker; Quang Bao Anh Bui; François Nicolas; Anke Truß (CoRR, 2011)

Extension and Robustness of Transitivity Clustering for Protein-Protein Interaction Network Analysis. - Tobias Wittkop; Sven Rahmann; Richard Röttger; Sebastian Böcker; Jan Baumbach (Internet Math., 2011)

Even faster parameterized cluster deletion and cluster editing. - Sebastian Böcker; Peter Damaschke (Inf. Process. Lett., 2011)

Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data. - Kerstin Scheubert; Franziska Hufsky; Florian Rasche; Sebastian Böcker (J. Comput. Biol., 2011)

Determination of Glycan Structure from Tandem Mass Spectra. - Sebastian Böcker; Birte Kehr; Florian Rasche (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Computing bond orders in molecule graphs. - Sebastian Böcker; Quang Bao Anh Bui; Anke Truß (Theor. Comput. Sci., 2011)

Comparing Fragmentation Trees from Electron Impact Mass Spectra with Annotated Fragmentation Pathways. - Franziska Hufsky; Sebastian Böcker (GCB, 2012)

Finding Characteristic Substructures for Metabolite Classes. - Marcus Ludwig; Franziska Hufsky; Samy Elshamy; Sebastian Böcker (GCB, 2012)

Fast alignment of fragmentation trees. - Franziska Hufsky; Kai Dührkop; Florian Rasche; Markus Chimani; Sebastian Böcker (Bioinform., 2012)

A note on the parameterized complexity of unordered maximum tree orientation. - Sebastian Böcker; Peter Damaschke (Discret. Appl. Math., 2012)

A golden ratio parameterized algorithm for Cluster Editing. - Sebastian Böcker (J. Discrete Algorithms, 2012)

Improved Fixed-Parameter Algorithms for Minimum-Flip Consensus Trees. - Sebastian Böcker; Quang Bao Anh Bui; Anke Truß (ACM Trans. Algorithms, 2012)

Cluster Editing. - Sebastian Böcker; Jan Baumbach (CiE, 2013)

The Generalized Robinson-Foulds Metric. - Sebastian Böcker; Stefan Canzar; Gunnar W. Klau (WABI, 2013)

Faster Mass Decomposition. - Kai Dührkop; Marcus Ludwig; Marvin Meusel; Sebastian Böcker (WABI, 2013)

FlipCut Supertrees: Towards Matrix Representation Accuracy in Polynomial Time. - Malte Brinkmeyer; Thasso Griebel; Sebastian Böcker (Algorithmica, 2013)

Statistics for approximate gene clusters. - Katharina Jahn 001; Sascha Winter; Jens Stoye; Sebastian Böcker (BMC Bioinform., 2013)

Finding Maximum Colorful Subtrees in Practice. - Imran Rauf; Florian Rasche; François Nicolas; Sebastian Böcker (J. Comput. Biol., 2013)

Computational mass spectrometry for small molecules. - Kerstin Scheubert; Franziska Hufsky; Sebastian Böcker (J. Cheminformatics, 2013)

Explorative Analysis of Heterogeneous, Unstructured, and Uncertain Data - A Computer Science Perspective on Biodiversity Research. - 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; et al. (DATA, 2014)

Multiple Mass Spectrometry Fragmentation Trees Revisited: Boosting Performance and Quality. - Kerstin Scheubert; Franziska Hufsky; Sebastian Böcker (WABI, 2014)

Metabolite identification through multiple kernel learning on fragmentation trees. - Huibin Shen; Kai Dührkop; Sebastian Böcker; Juho Rousu (Bioinform., 2014)

Towards the ground truth: Exact algorithms for bioinformatics research (NII Shonan Meeting 2014-2). - Sebastian Böcker; Gunnar W. Klau; Veli Mäkinen; Hon Wai Leong (NII Shonan Meet. Rep., 2014)

Speedy Colorful Subtrees. - W. Timothy J. White; Stephan Beyer; Kai Dührkop; Markus Chimani; Sebastian Böcker (COCOON, 2015)

Computational Metabolomics (Dagstuhl Seminar 15492). - Sebastian Böcker; Juho Rousu; Emma Schymanski (Dagstuhl Reports, 2015)

Ten Times Eighteen. - Sebastian Böcker (J. Inf. Process., 2015)

Collecting reliable clades using the Greedy Strict Consensus Merger. - Markus Fleischauer; Sebastian Böcker (PeerJ Prepr., 2015)

Fast metabolite identification with Input Output Kernel Regression. - Céline Brouard; Huibin Shen; Kai Dührkop; Florence d'Alché-Buc; Sebastian Böcker; Juho Rousu (Bioinform., 2016)

Fragmentation trees reloaded. - Sebastian Böcker; Kai Dührkop (J. Cheminformatics, 2016)

Magnitude-Preserving Ranking for Structured Outputs. - Céline Brouard; Eric Bach 002; Sebastian Böcker; Juho Rousu (ACML, 2017)

Cograph Editing in O(3nn) time and O(2n) space. - W. Timothy J. White; Marcus Ludwig; Sebastian Böcker (CoRR, 2017)

Computational Metabolomics: Identification, Interpretation, Imaging (Dagstuhl Seminar 17491). - Theodore Alexandrov; Sebastian Böcker; Pieter C. Dorrestein; Emma Schymanski (Dagstuhl Reports, 2017)

Critical Assessment of Small Molecule Identification 2016: automated methods. - Emma Schymanski; Christoph Ruttkies; Martin Krauss; Céline Brouard; Tobias Kind; Kai Dührkop; Felicity Allen; Arpana Vaniya; Dries Verdegem; Sebastian Böcker; Juho Rousu; Huibin Shen; et al. (J. Cheminformatics, 2017)

LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis. - Eudes Barbosa; Richard Röttger; Anne-Christin Hauschild; Siomar de Castro Soares; Sebastian Böcker; Vasco Ariston de Carvalho Azevedo; Jan Baumbach (J. Integr. Bioinform., 2017)

Computational Metabolomics (NII Shonan Meeting 2017-3). - Masanori Arita; Sebastian Böcker; Steffen Neumann (NII Shonan Meet. Rep., 2017)

Heuristic Algorithms for the Maximum Colorful Subtree Problem. - Kai Dührkop; Marie Anne Lataretu; W. Timothy J. White; Sebastian Böcker (WABI, 2018)

Liquid-chromatography retention order prediction for metabolite identification. - Eric Bach 002; Sándor Szedmák; Céline Brouard; Sebastian Böcker; Juho Rousu (Bioinform., 2018)

Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints. - Marcus Ludwig; Kai Dührkop; Sebastian Böcker (Bioinform., 2018)

Computational Metabolomics: From Cheminformatics to Machine Learning (Dagstuhl Seminar 20051). - Sebastian Böcker; Corey Broeckling; Emma Schymanski; Nicola Zamboni (Dagstuhl Reports, 2020)

Database-independent molecular formula annotation using Gibbs sampling through ZODIAC. - 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 (Nat. Mach. Intell., 2020)

Publisher Correction: Database-independent molecular formula annotation using Gibbs sampling through ZODIAC. - 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 (Nat. Mach. Intell., 2020)

Computational Proteomics (Dagstuhl Seminar 21271). - Sebastian Böcker; Rebekah L. Gundry; Lennart Martens; Magnus Palmblad (Dagstuhl Reports, 2021)

MassSpecGym: A benchmark for the discovery and identification of molecules. - Roman Bushuiev; Anton Bushuiev; Niek F. de Jonge; Adamo Young; Fleming Kretschmer; Raman Samusevich; Janne Heirman; Fei Wang 062; Luke Zhang; Kai Dührkop; Marcus Ludwig; Nils A. Haupt; et al. (NeurIPS, 2024)

Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data. - Pilleriin Peets; Aristeidis Litos; Kai Dührkop; Daniel R. Garza; Justin J. J. van der Hooft; Sebastian Böcker; Bas E. Dutilh (J. Cheminformatics, 2025)