Sebastian Böcker

Orcid: 0000-0002-9304-8091

Affiliations:
  • Friedrich-Schiller-Universität, Jena, Germany


According to our database1, Sebastian Böcker authored at least 84 papers between 2000 and 2024.

Collaborative distances:

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Bibliography

2024
MassSpecGym: A benchmark for the discovery and identification of molecules.
CoRR, 2024

2021
Computational Proteomics (Dagstuhl Seminar 21271).
Dagstuhl Reports, 2021

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

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

Computational Metabolomics: From Cheminformatics to Machine Learning (Dagstuhl Seminar 20051).
Dagstuhl Reports, 2020

2018
Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints.
Bioinform., 2018

Liquid-chromatography retention order prediction for metabolite identification.
Bioinform., 2018

Heuristic Algorithms for the Maximum Colorful Subtree Problem.
Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

2017
Computational Metabolomics (NII Shonan Meeting 2017-3).
NII Shonan Meet. Rep., 2017

LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis.
J. Integr. Bioinform., 2017

Critical Assessment of Small Molecule Identification 2016: automated methods.
J. Cheminformatics, 2017

Computational Metabolomics: Identification, Interpretation, Imaging (Dagstuhl Seminar 17491).
Dagstuhl Reports, 2017

Cograph Editing in O(3<sup>n</sup>n) time and O(2<sup>n</sup>) space.
CoRR, 2017

Magnitude-Preserving Ranking for Structured Outputs.
Proceedings of The 9th Asian Conference on Machine Learning, 2017

2016
Fragmentation trees reloaded.
J. Cheminformatics, 2016

Fast metabolite identification with Input Output Kernel Regression.
Bioinform., 2016

2015
Collecting reliable clades using the Greedy Strict Consensus Merger.
PeerJ Prepr., 2015

Ten Times Eighteen.
J. Inf. Process., 2015

Computational Metabolomics (Dagstuhl Seminar 15492).
Dagstuhl Reports, 2015

Speedy Colorful Subtrees.
Proceedings of the Computing and Combinatorics - 21st International Conference, 2015

2014
Towards the ground truth: Exact algorithms for bioinformatics research (NII Shonan Meeting 2014-2).
NII Shonan Meet. Rep., 2014

Metabolite identification through multiple kernel learning on fragmentation trees.
Bioinform., 2014

Multiple Mass Spectrometry Fragmentation Trees Revisited: Boosting Performance and Quality.
Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

Explorative Analysis of Heterogeneous, Unstructured, and Uncertain Data - A Computer Science Perspective on Biodiversity Research.
Proceedings of the DATA 2014, 2014

2013
Computational mass spectrometry for small molecules.
J. Cheminformatics, 2013

Finding Maximum Colorful Subtrees in Practice.
J. Comput. Biol., 2013

Statistics for approximate gene clusters.
BMC Bioinform., 2013

FlipCut Supertrees: Towards Matrix Representation Accuracy in Polynomial Time.
Algorithmica, 2013

Faster Mass Decomposition.
Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

The Generalized Robinson-Foulds Metric.
Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

Cluster Editing.
Proceedings of the Nature of Computation. Logic, Algorithms, Applications, 2013

2012
Improved Fixed-Parameter Algorithms for Minimum-Flip Consensus Trees.
ACM Trans. Algorithms, 2012

A golden ratio parameterized algorithm for Cluster Editing.
J. Discrete Algorithms, 2012

A note on the parameterized complexity of unordered maximum tree orientation.
Discret. Appl. Math., 2012

Fast alignment of fragmentation trees.
Bioinform., 2012

Finding Characteristic Substructures for Metabolite Classes.
Proceedings of the German Conference on Bioinformatics 2012, 2012

Comparing Fragmentation Trees from Electron Impact Mass Spectra with Annotated Fragmentation Pathways.
Proceedings of the German Conference on Bioinformatics 2012, 2012

2011
Computing bond orders in molecule graphs.
Theor. Comput. Sci., 2011

Determination of Glycan Structure from Tandem Mass Spectra.
IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data.
J. Comput. Biol., 2011

Even faster parameterized cluster deletion and cluster editing.
Inf. Process. Lett., 2011

Extension and Robustness of Transitivity Clustering for Protein-Protein Interaction Network Analysis.
Internet Math., 2011

Intractability of the Minimum-Flip Supertree problem and its variants
CoRR, 2011

Various complexity results for computational mass spectrometry problems
CoRR, 2011

Towards a Data Reduction for the Minimum Flip Supertree Problem
CoRR, 2011

Swiftly Computing Center Strings.
BMC Bioinform., 2011

Automated bond order assignment as an optimization problem.
Bioinform., 2011

Exact Algorithms for Cluster Editing: Evaluation and Experiments.
Algorithmica, 2011

Polynomial Supertree Methods Revisited.
Adv. Bioinformatics, 2011

A Closer Look at the Closest String and Closest Substring Problem.
Proceedings of the Thirteenth Workshop on Algorithm Engineering and Experiments, 2011

2010
Exact ILP solutions for phylogenetic minimum flip problems.
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

2009
Going weighted: Parameterized algorithms for cluster editing.
Theor. Comput. Sci., 2009

Computation of Median Gene Clusters.
J. Comput. Biol., 2009

On optimal comparability editing with applications to molecular diagnostics.
BMC Bioinform., 2009

SIRIUS: decomposing isotope patterns for metabolite identification.
Bioinform., 2009

Annotating Fragmentation Patterns.
Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

A Faster Fixed-Parameter Approach to Drawing Binary Tanglegrams.
Proceedings of the Parameterized and Exact Computation, 4th International Workshop, 2009

Inferring Peptide Composition from Molecular Formulas.
Proceedings of the Computing and Combinatorics, 15th Annual International Conference, 2009

Computing Bond Types in Molecule Graphs.
Proceedings of the Computing and Combinatorics, 15th Annual International Conference, 2009

2008
Combinatorial Approaches for Mass Spectra Recalibration.
IEEE ACM Trans. Comput. Biol. Bioinform., 2008

Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics.
BMC Bioinform., 2008

EPoS: a modular software framework for phylogenetic analysis.
Bioinform., 2008

DECOMP - from interpreting Mass Spectrometry peaks to solving the Money Changing Problem.
Bioinform., 2008

An Improved Fixed-Parameter Algorithm for Minimum-Flip Consensus Trees.
Proceedings of the Parameterized and Exact Computation, Third International Workshop, 2008

Improved Mass Spectrometry Peak Intensity Prediction by Adaptive Feature Weighting.
Proceedings of the Advances in Neuro-Information Processing, 15th International Conference, 2008

Towards <i>de novo</i> identification of metabolites by analyzing tandem mass spectra.
Proceedings of the ECCB'08 Proceedings, 2008

Towards de novo identification of metabolites by analyzing tandem mass spectra.
Proceedings of the Computational Proteomics, 02.03. - 07.03.2008, 2008

A Fixed-Parameter Approach for Weighted Cluster Editing.
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

2007
Mass spectra alignments and their significance.
J. Discrete Algorithms, 2007

SAMPI: Protein Identification with Mass Spectra Alignments.
BMC Bioinform., 2007

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

A Fast and Simple Algorithm for the Money Changing Problem.
Algorithmica, 2007

Neural Network Approach for Mass Spectrometry Prediction by Peptide Prototyping.
Proceedings of the Artificial Neural Networks, 2007

2006
Sequencing from Compomers: The Puzzle.
Theory Comput. Syst., 2006

Decomposing Metabolomic Isotope Patterns.
Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting.
Proceedings of the Systems Biology and Computational Proteomics, 2006

2005
Efficient mass decomposition.
Proceedings of the 2005 ACM Symposium on Applied Computing (SAC), 2005

Maximum line-pair stabbing problem and its variations.
Proceedings of the (Informal) Proceedings of the 21st European Workshop on Computational Geometry, 2005

The Money Changing Problem Revisited: Computing the Frobenius Number in Time O(k a<sub>1</sub>).
Proceedings of the Computing and Combinatorics, 11th Annual International Conference, 2005

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

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

2003
SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry.
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2002
Exponentially many supertrees.
Appl. Math. Lett., 2002

2000
Algorithmic Aspects of Tree Amalgamation.
J. Algorithms, 2000


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