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Sebastian Böcker
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- affiliation: Friedrich-Schiller-Universität, Jena, Germany
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2020 – today
- 2021
- [i18]Sebastian Böcker, Rebekah L. Gundry, Lennart Martens, Magnus Palmblad
:
Computational Proteomics (Dagstuhl Seminar 21271). Dagstuhl Reports 11(6): 1-13 (2021) - 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) - [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)
2010 – 2019
- 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) - [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 - [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
- [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) - [c39]Céline Brouard, Eric Bach, Sebastian Böcker
, Juho Rousu:
Magnitude-Preserving Ranking for Structured Outputs. ACML 2017: 407-422 - [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) - 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) - [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 - [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
- [j34]Huibin Shen, Kai Dührkop
, Sebastian Böcker
, Juho Rousu:
Metabolite identification through multiple kernel learning on fragmentation trees. Bioinform. 30(12): 157-164 (2014) - [c36]Clemens Beckstein, Sebastian Böcker, Martin Bogdan, Helge Bruehlheide, 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 - [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
- [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) - [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 - [i8]Sebastian Böcker
, Stefan Canzar, Gunnar W. Klau:
The generalized Robinson-Foulds metric. CoRR abs/1307.7824 (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) - [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 - [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] - [i7]Sebastian Böcker:
Ten times eighteen. CoRR abs/1209.1977 (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) - [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 - [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) - 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
2000 – 2009
- 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) - [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
- [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) - [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 - [i3]Sebastian Böcker, Florian Rasche:
Towards de novo identification of metabolites by analyzing tandem mass spectra. Computational Proteomics 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) - [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
- [j4]Sebastian Böcker
:
Sequencing from Compomers: The Puzzle. Theory Comput. Syst. 39(3): 455-471 (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 - [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 - 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) - [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 - 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)
Coauthor Index
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