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2014

Sebastian Böcker and Stephan Wagner
Counting glycans revisited.
J Math Biol, 69(4):799-816, 2014.
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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 and Wolf Zimmermann
Explorative Analysis of Heterogeneous, Unstructured, and Uncertain Data: A Computer Science Perspective on Biodiversity Research.
In Proc. of Data Management Technologies and Applications (DATA 2014), pages 251-257. SciTePress, 2014.
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Kai Dührkop, Franziska Hufsky and Sebastian Böcker
Molecular Formula Identification Using Isotope Pattern Analysis and Calculation of Fragmentation Trees.
Mass Spectrom, 3(special issue 2):S0037, 2014.
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Daniel Doerr, Jens Stoye, Sebastian Böcker and Katharina Jahn
Identifying gene clusters by discovering common intervals in indeterminate strings.
BMC Genomics, 15(Suppl 6):S2, 2014. Proc. of RECOMB Satelite Workshop on Comparative Genomics (RECOMB-CG 2014).
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Franziska Hufsky, Kerstin Scheubert and Sebastian Böcker
Computational mass spectrometry for small molecule fragmentation.
Trends Anal Chem, 53:41-48, 2014.
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Franziska Hufsky, Kerstin Scheubert and Sebastian Böcker
New kids on the block: Novel informatics methods for natural product discovery.
Nat Prod Rep, 31(6):807-817, 2014.
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Filip Kaftan, Vladimir Vrkoslav, Philipp Kynast, Purva Kulkarni, Sebastian Böcker, Josef Cvačka, Markus Knaden and Aleš Svatoš
Mass Spectrometry Imaging of Surface Lipids on Intact Drosophila melanogaster Flies.
J Mass Spectrom, 49(3):223-232, 2014.
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Mayuri Napagoda, Jana Gerstmeier, Andreas Koeberle, Sandra Wesely, Sven Popella, Sybille Lorenz, Kerstin Scheubert, Sebastian Böcker, Aleš Svatoš and Oliver Werz
Munronia pinnata (Wall.) Theob.: Unveiling phytochemistry and dual inhibition of 5-lipoxygenase and microsomal prostaglandin E$_2$ synthase (mPGES)-1.
J Ethnopharmacol, 151(2):882-890, 2014.
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Kerstin Scheubert, Franziska Hufsky and Sebastian Böcker
Multiple Mass Spectrometry Fragmentation Trees Revisited: Boosting Performance and Quality.
In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2014), volume 8701 of Lect Notes Comput Sci, pages 217-231. Springer, Berlin, 2014.
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Volker U. Schwartze, Sascha Winter, Ekaterina Shelest, Marina Marcet-Houben, Fabian Horn, Stefanie Wehner, Jörg Linde, Vito Valiante, Michael Sammeth, Konstantin Riege, Minou Nowrousian, Kerstin Kaerger, Ilse D. Jacobsen, Manja Marz, Axel A. Brakhage, Toni Gabaldón, Sebastian Böcker and Kerstin Voigt
Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial Mucorales (Mucoromycotina).
PLOS Genetics, 10(8):e1004496, 2014.
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Huibin Shen, Kai Dührkop, Sebastian Böcker and Juho Rousu
Metabolite Identification through Multiple Kernel Learning on Fragmentation Trees.
Bioinformatics, 30(12):i157-i164, 2014. Proc. of Intelligent Systems for Molecular Biology (ISMB 2014).
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2013

Sebastian Böcker and Jan Baumbach
Cluster Editing.
In Proc. of Computability in Europe (CIE 2013), volume 7921 of Lect Notes Comput Sci, pages 33-44. Springer, Berlin, 2013.
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Sebastian Böcker, Stefan Canzar and Gunnar W. Klau
The generalized Robinson-Foulds metric.
In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2013), volume 8126 of Lect Notes Comput Sci, pages 156-169. Springer, Berlin, 2013.
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Guillaume Blin, Romeo Rizzi, Florian Sikora and Stéphane Vialette
Minimum Mosaic Inference of a Set of Recombinants.
Int J Found Comput S, 24(1):51, 2013.
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Malte Brinkmeyer, Thasso Griebel and Sebastian Böcker
FlipCut Supertrees: Towards Matrix Representation Accuracy in Polynomial Time.
Algorithmica, 67(2):142-160, 2013.
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Kai Dührkop, Marcus Ludwig, Marvin Meusel and Sebastian Böcker
Faster mass decomposition.
In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2013), volume 8126 of Lect Notes Comput Sci, pages 45-58. Springer, Berlin, 2013.
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Kai Dührkop, Kerstin Scheubert and Sebastian Böcker
Molecular Formula Identification with SIRIUS.
Metabolites, 3:506-516, 2013.
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Sylvain Guillemot and Florian Sikora
Finding and counting vertex-colored subtrees.
Algorithmica, 65(4):828-844, 2013.
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Katharina Jahn, Sascha Winter, Jens Stoye and Sebastian Böcker
Statistics for approximate gene clusters.
BMC Bioinformatics, 14(Suppl 15):S14, 2013. Proc. of RECOMB Satelite Workshop on Comparative Genomics (RECOMB-CG 2013).
[ bib | doi | pmid | abstract ]

Steffen Neumann, Florian Rasche, Sebastian Wolf and Sebastian Böcker
Metabolite Identification and Computational Mass Spectrometry.
In The Handbook of Plant Metabolomics, Metabolite Profiling and Networking, of Molecular Plant Biology Handbook Series, chapter 16, pages 271-285. Wiley-VCH Verlag, 2013.
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Imran Rauf, Florian Rasche, François Nicolas and Sebastian Böcker
Finding Maximum Colorful Subtrees in practice.
J Comput Biol, 20(4):1-11, 2013.
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Kerstin Scheubert, Franziska Hufsky and Sebastian Böcker
Computational Mass Spectrometry for Small Molecules.
J Cheminform, 5:12, 2013.
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2012

Sebastian Böcker
Comment on ''An Efficient Method to Calculate the Aggregated Isotopic Distribution and Exact Center-Masses'' by Claesen et al..
J Am Soc Mass Spectrom, 23(10):1826-1827, 2012.
[ bib | doi | pmid | pdf | abstract ]

Sebastian Böcker
A golden ratio parameterized algorithm for Cluster Editing.
J Discrete Algorithms, 16:79-89, 2012.
[ bib | doi | pdf | abstract ]

Sebastian Böcker
Ten times eighteen.
Technical report, Cornell University Library, 2012. arXiv:1209.1977v1.
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Sebastian Böcker, Quang Bao Anh Bui and Anke Truss
Improved Fixed-Parameter Algorithms for Minimum-Flip Consensus Trees.
ACM Trans Algorithms, 8(1):17 pages, 2012. Article 7.
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Sebastian Böcker and Peter Damaschke
A Note on the Parameterized Complexity of Unordered Maximum Tree Orientation.
Discrete Appl Math, 160(10-11):1634-1638, 2012.
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Guillaume Blin, Paola Bonizzoni, Riccardo Dondi, Romeo Rizzi and Florian Sikora
Complexity Insights of the Minimum Duplication Problem.
In Proc. of Current Trends in Theory and Practice of Computer Science (SOFSEM 2012), volume 7147 of Lect Notes Comput Sci, pages 153-164. Springer, Berlin, 2012.
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Guillaume Blin, Paola Bonizzoni, Riccardo Dondi and Florian Sikora
On the Parameterized Complexity of the Repetition Free Longest Common Subsequence Problem.
Inform Process Lett, 112(7):272 - 276, 2012.
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Franziska Hufsky and Sebastian Böcker
Comparing Fragmentation Trees from Electron Impact Mass Spectra with Annotated Fragmentation Pathways.
In Proc. of German Conference on Bioinformatics (GCB 2012), volume 26 of OpenAccess Series in Informatics (OASIcs), pages 12-22. Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, 2012.
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Franziska Hufsky, Kai Dührkop, Florian Rasche, Markus Chimani and Sebastian Böcker
Fast alignment of fragmentation trees.
Bioinformatics, 28:i265-i273, 2012. Proc. of Intelligent Systems for Molecular Biology (ISMB 2012).
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Franziska Hufsky, Martin Rempt, Florian Rasche, Georg Pohnert and Sebastian Böcker
De Novo Analysis of Electron Impact Mass Spectra Using Fragmentation Trees.
Anal Chim Acta, 739:67-76, 2012.
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Marcus Ludwig, Franziska Hufsky, Samy Elshamy and Sebastian Böcker
Finding Characteristic Substructures for Metabolite Classes.
In Proc. of German Conference on Bioinformatics (GCB 2012), volume 26 of OpenAccess Series in Informatics (OASIcs), pages 23-38. Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, 2012.
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Florian Rasche, Kerstin Scheubert, Franziska Hufsky, Thomas Zichner, Marco Kai, Aleš Svatoš and Sebastian Böcker
Identifying the unknowns by aligning fragmentation trees.
Anal Chem, 84(7):3417-3426, 2012.
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Imran Rauf, Florian Rasche, François Nicolas and Sebastian Böcker
Finding Maximum Colorful Subtrees in practice.
In Proc. of Research in Computational Molecular Biology (RECOMB 2012), volume 7262 of Lect Notes Comput Sci, pages 213-223. Springer, Berlin, 2012.
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Romeo Rizzi and Florian Sikora
Some results on more flexible versions of Graph Motif.
In Proc. of Computer Science Symposium in Russia (CSR 2012), volume 7353 of Lect Notes Comput Sci, pages 278-289. Springer, Berlin, 2012.
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Lynn Ullmann-Zeunert, Alexander Muck, Natalie Wielsch, Franziska Hufsky, Mariana A. Stanton, Stefan Bartram, Sebastian Böcker, Ian T. Baldwin, Karin Groten and Aleš Svatoš
Determination of 15N-incorporation into plant proteins and their absolute quantitation: a new tool to study nitrogen flux dynamics and protein pool sizes elicited by plant-herbivore interactions.
J Proteome Res, 11(10):4947-4960, 2012.
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Xiao Yang, Florian Sikora, Guillaume Blin, Sylvie Hamel, Romeo Rizzi and Srinivas Aluru
An Algorithmic View on Multi-related-segments: A unifying model for approximate common interval.
In Proc. of Theory and Applications of Models of Computation (TAMC 2012), volume 7287 of Lect Notes Comput Sci, pages 319-329. Springer, Berlin, 2012.
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Sebastian Böcker, Franziska Hufsky, Kerstin Scheubert, Jana Schleicher and Stefan Schuster
German Conference on Bioinformatics 2012.
Volume 26 of OpenAccess Series in Informatics (OASIcs), Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, 2012.
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2011

Sebastian Böcker
A golden ratio parameterized algorithm for Cluster Editing.
In Proc. of International Workshop on Combinatorial Algorithms (IWOCA 2011), volume 7056 of Lect Notes Comput Sci, pages 85-95. Springer, Berlin, 2011.
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Sebastian Böcker
Towards a data reduction for the Minimum-Flip Supertree problem.
Technical report, Cornell University Library, 2011. arXiv:1104.4471v1.
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Sebastian Böcker, Sebastian Briesemeister and Gunnar W. Klau
Exact Algorithms for Cluster Editing: Evaluation and Experiments.
Algorithmica, 60(2):316-334, 2011.
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Sebastian Böcker, Bao Bui, François Nicolas and Anke Truss
Intractability of the Minimum Flip Supertree problem and its variants.
Technical report, Cornell University Library, 2011. arXiv:1112.4536v1.
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Sebastian Böcker, Quang Bao Anh Bui and Anke Truss
Computing Bond Orders in Molecule Graphs.
Theor Comput Sci, 412(12--14):1184-1195, 2011.
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Sebastian Böcker and Peter Damaschke
Even faster parameterized cluster deletion and cluster editing.
Inform Process Lett, 111(14):717-721, 2011.
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Sebastian Böcker, Birte Kehr and Florian Rasche
Determination of glycan structure from tandem mass spectra.
IEEE/ACM Trans Comput Biology Bioinform, 8(4):976-986, 2011.
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Sebastian Böcker and François Nicolas
Various complexity results for computational mass spectrometry problems.
Technical report, Cornell University Library, 2011. arXiv:1109.3367v4.
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Anja Baumgaertel, Kerstin Scheubert, Bernhard Pietsch, Kristian Kempe, Anna C. Crecelius, Sebastian Böcker and Ulrich S. Schubert
Analysis of different synthetic homopolymers by the use of a new calculation software for tandem mass spectra.
Rapid Commun Mass Spectrom, 25(12):1765-1778, 2011.
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Malte Brinkmeyer, Thasso Griebel and Sebastian Böcker
FlipCut Supertrees: Towards Matrix Representation Accuracy in Polynomial Time.
In Proc. of Computing and Combinatorics Conference (COCOON 2011), volume 6842 of Lect Notes Comput Sci, pages 37-48. Springer, Berlin, 2011.
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Malte Brinkmeyer, Thasso Griebel and Sebastian Böcker
Polynomial Supertree Methods Revisited.
Adv Bioinformatics, 2011(Article ID 524182):21 pages, 2011.
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Markus Chimani, Matthias Woste and Sebastian Böcker
A Closer Look at the Closest String and Closest Substring Problem.
In Proc. of Algorithm Engineering & Experiments (ALENEX 2011), pages 13-24. SIAM, 2011.
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Anna Katharina Dehof, Alexander Rurainski, Quang Bao Anh Bui, Sebastian Böcker, Hans-Peter Lenhof and Andreas Hildebrandt
Automated Bond Order Assignment as an Optimization Problem.
Bioinformatics, 27(5):619-625, 2011.
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Konrad Grützmann, Sebastian Böcker and Stefan Schuster
Combinatorics of aliphatic amino acids.
Naturwissenschaften, 98(1):79-86, 2011.
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Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye and Sebastian Böcker
Swiftly computing center strings.
BMC Bioinformatics, 12:106, 2011.
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Florian Rasche, Aleš Svatoš, Ravi Kumar Maddula, Christoph Böttcher and Sebastian Böcker
Computing fragmentation trees from tandem mass spectrometry data.
Anal Chem, 83(4):1243-1251, 2011.
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Kerstin Scheubert, Franziska Hufsky, Florian Rasche and Sebastian Böcker
Computing fragmentation trees from metabolite multiple mass spectrometry data.
In Proc. of Research in Computational Molecular Biology (RECOMB 2011), volume 6577 of Lect Notes Comput Sci, pages 377-391. Springer, Berlin, 2011.
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Kerstin Scheubert, Franziska Hufsky, Florian Rasche and Sebastian Böcker
Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data.
J Comput Biol, 18(11):1383-1397, 2011.
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Tobias Wittkop, Dorothea Emig, Anke Truss, Mario Albrecht, Sebastian Böcker and Jan Baumbach
Comprehensive cluster analysis with Transitivity Clustering.
Nat Protocols, 6:285-295, 2011.
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Tobias Wittkop, Sven Rahmann, Sebastian Böcker and Jan Baumbach
Extension and robustness of Transitivity Clustering for protein-protein interaction network analysis.
Internet Math, 7(4):255-273, 2011.
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2010

Malte Brinkmeyer, Thasso Griebel and Sebastian Böcker
Polynomial Supertree Methods Revisited.
In Proc. of Pattern Recognition in Bioinformatics (PRIB 2010), volume 6282 of Lect Notes Comput Sci, pages 183-194. Springer, Berlin, 2010.
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Markus Chimani, Sven Rahmann and Sebastian Böcker
Exact ILP Solutions for Phylogenetic Minimum Flip Problems.
In Proc. of ACM Conf. on Bioinformatics and Computational Biology (ACM-BCB 2010), pages 147-153. ACM press, New York, 2010.
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Michael Dom, Jiong Guo, Falk Hüffner, Rolf Niedermeier and Anke Truss
Fixed-parameter tractability results for feedback set problems in tournaments.
J Discrete Algorithms, 8(1):76-86, 2010.
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Geetha Govind, Omprakash Mittapalli, Thasso Griebel, Silke Allmann, Sebastian Böcker and Ian Thomas Baldwin
Unbiased Transcriptional Comparisons of Generalist and Specialist Herbivores Feeding on Progressively Defenseless Nicotiana attenuata Plants.
PLoS One, 5(1):e8735, 2010.
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Sylvain Guillemot and Matthias Mnich
Kernel and Fast Algorithm for Dense Triplet Inconsistency.
In Proc. of Theory and Applications of Models of Computation (TAMC 2010), volume 6108 of Lect Notes Comput Sci, pages 247-257. Springer, Berlin, 2010.
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Sylvain Guillemot and Florian Sikora
Finding and counting vertex-colored subtrees.
In Proc. of Mathematical Foundations of Computer Science (MFCS 2010), volume 6281 of Lect Notes Comput Sci, pages 405-416. Springer, Berlin, 2010.
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Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye and Sebastian Böcker
Swiftly computing center strings.
In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2010), volume 6293 of Lect Notes Comput Sci, pages 325-336. Springer, Berlin, 2010.
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Steffen Neumann and Sebastian Böcker
Computational Mass Spectrometry for Metabolomics -- A Review.
Anal Bioanal Chem, 398(7):2779-2788, 2010.
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Tobias Wittkop, Dorothea Emig, Sita Lange, Sven Rahmann, Mario Albrecht, John H. Morris, Sebastian Böcker, Jens Stoye and Jan Baumbach
Partitioning biological data with transitivity clustering.
Nat Methods, 7(6):419-420, 2010.
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2009

Sebastian Böcker, Sebastian Briesemeister, Quang Bao Anh Bui and Anke Truss
Going Weighted: Parameterized Algorithms for Cluster Editing.
Theor Comput Sci, 410(52):5467-5480, 2009.
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Sebastian Böcker, Sebastian Briesemeister and Gunnar W. Klau
On optimal comparability editing with applications to molecular diagnostics.
BMC Bioinformatics, 10(Suppl 1):S61, 2009. Proc. of Asia-Pacific Bioinformatics Conference (APBC 2009).
[ bib | doi | pmid | url | abstract ]

Sebastian Böcker, Quang Bao Anh Bui, Patrick Seeber and Anke Truss
Computing Bond Types in Molecule Graphs.
In Proc. of Computing and Combinatorics Conference (COCOON 2009), volume 5609 of Lect Notes Comput Sci, pages 297-306. Springer, Berlin, 2009.
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Sebastian Böcker, Falk Hüffner, Anke Truss and Magnus Wahlström
A faster fixed-parameter approach to drawing binary tanglegrams.
In Proc. of International Workshop on Parameterized and Exact Computation (IWPEC 2009), volume 5917 of Lect Notes Comput Sci, pages 38-49. Springer, Berlin, 2009.
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Sebastian Böcker, Katharina Jahn, Julia Mixtacki and Jens Stoye
Computation of median gene clusters.
J Comput Biol, 16(8):1085-1099, 2009.
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Sebastian Böcker, Birte Kehr and Florian Rasche
Determination of glycan structure from tandem mass spectra.
In Proc. of Computing and Combinatorics Conference (COCOON 2009), volume 5609 of Lect Notes Comput Sci, pages 258-267. Springer, Berlin, 2009.
[ bib | doi | pdf | abstract ]

Sebastian Böcker, Matthias Letzel, Zsuzsanna Lipták and Anton Pervukhin
SIRIUS: Decomposing isotope patterns for metabolite identification.
Bioinformatics, 25(2):218-224, 2009.
[ bib | doi | pmid | pdf | url | abstract ]

Sebastian Böcker and Anton Pervukhin
Inferring peptide composition from molecular formulas.
In Proc. of Computing and Combinatorics Conference (COCOON 2009), volume 5609 of Lect Notes Comput Sci, pages 277-286. Springer, Berlin, 2009.
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Sebastian Böcker, Florian Rasche and Tamara Steijger
Annotating fragmentation patterns.
In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2009), volume 5724 of Lect Notes Comput Sci, pages 13-24. Springer, Berlin, 2009.
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Andreas Bertsch, Andreas Leinenbach, Anton Pervukhin, Markus Lubeck, Ralf Hartmer, Carsten Baessmann, Yasser Abbas Elnakady, Rolf Müller, Sebastian Böcker, Christian G Huber and Oliver Kohlbacher
De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation.
Electrophoresis, 30(21):3736-3747, 2009.
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Michael Dondrup, Stefan P Albaum, Thasso Griebel, Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane K Kleindt, Helge Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger, Kai J Runte, Andreas Tauch, Felix Tille, Alfred Pühler and Alexander Goesmann
EMMA 2 - A MAGE-compliant system for the collaborative analysis and integration of microarray data.
BMC Bioinformatics, 10:50, 2009.
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Alexandra Scherbart, Wiebke Timm, Sebastian Böcker and Tim W. Nattkemper
Improved Mass Spectrometry Peak Intensity Prediction by Adaptive Feature Weighting.
In Proc. of International Conference on Neural Information Processing of the Asia-Pacific Neural Network Assembly (ICONIP 2008), volume 5506 of Lect Notes Comput Sci, pages 513-520. Springer, Berlin, 2009.
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2008

Sebastian Böcker, Sebastian Briesemeister, Quang Bao Anh Bui and Anke Truss
A fixed-parameter approach for Weighted Cluster Editing.
In Proc. of Asia-Pacific Bioinformatics Conference (APBC 2008), volume 5 of Series on Advances in Bioinformatics and Computational Biology, pages 211-220. Imperial College Press, 2008.
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Sebastian Böcker, Sebastian Briesemeister, Quang Bao Anh Bui and Anke Truss
Going Weighted: Parameterized Algorithms for Cluster Editing.
In Proc. of Conference on Combinatorial Optimization and Applications (COCOA 2008), volume 5165 of Lect Notes Comput Sci, pages 1-12. Springer, Berlin, 2008.
[ bib | doi | pdf | abstract | data ]

Sebastian Böcker, Sebastian Briesemeister and Gunnar W. Klau
Exact Algorithms for Cluster Editing: Evaluation and Experiments.
In Proc. of Workshop on Experimental Algorithms (WEA 2008), volume 5038 of Lect Notes Comput Sci, pages 289-302. Springer, Berlin, 2008.
[ bib | doi | pdf | abstract | data ]

Sebastian Böcker, Quang Bao Anh Bui and Anke Truss
An Improved Fixed-Parameter Algorithm for Minimum-Flip Consensus Trees.
In Proc. of International Workshop on Parameterized and Exact Computation (IWPEC 2008), volume 5018 of Lect Notes Comput Sci, pages 43-54. Springer-Verlag, 2008.
[ bib | doi | pdf | abstract ]

Sebastian Böcker, Katharina Jahn, Julia Mixtacki and Jens Stoye
Computation of Median Gene Clusters.
In Proc. of Research in Computational Molecular Biology (RECOMB 2008), volume 4955 of Lect Notes Comput Sci, pages 331-345. Springer, Berlin, 2008.
[ bib | doi | pdf | abstract ]

Sebastian Böcker, Zsuzsanna Lipták, Marcel Martin, Anton Pervukhin and Henner Sudek
DECOMP--from interpreting Mass Spectrometry peaks to solving the Money Changing Problem.
Bioinformatics, 24(4):591-593, 2008.
[ bib | doi | pmid | pdf | url | abstract ]

Sebastian Böcker and Veli Mäkinen
Combinatorial Approaches for Mass Spectra Recalibration.
IEEE/ACM Trans Comput Biology Bioinform, 5(1):91-100, 2008.
[ bib | doi | pmid | pdf | abstract ]

Sebastian Böcker and Florian Rasche
Towards de novo identification of metabolites by analyzing tandem mass spectra.
Bioinformatics, 24:I49-I55, 2008. Proc. of European Conference on Computational Biology (ECCB 2008).
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Thasso Griebel, Malte Brinkmeyer and Sebastian Böcker
EPoS: A modular software framework for phylogenetic analysis.
Bioinformatics, 24(20):2399-2400, 2008.
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Wiebke Timm, Alexandra Scherbart, Sebastian Böcker, Oliver Kohlbacher and Tim W. Nattkemper
Peak Intensity Prediction in MALDI-TOF Mass Spectrometry: A Machine Learning Study to Support Quantitative Proteomics.
BMC Bioinformatics, 9:443, 2008.
[ bib | doi | pmid | url | abstract ]

2007

Sebastian Böcker
Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry.
Bioinformatics, 23(2):e5-e12, 2007. Proc. of European Conference on Computational Biology (ECCB 2006).
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Sebastian Böcker and Hans-Michael Kaltenbach
Mass Spectra Alignments and Their Significance.
J Discrete Algorithms, 5(4):714-728, 2007.
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Sebastian Böcker and Zsuzsanna Lipták
A fast and simple algorithm for the Money Changing Problem.
Algorithmica, 48(4):413-432, 2007.
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Hans-Michael Kaltenbach, Andreas Wilke and Sebastian Böcker
SAMPI: Protein identification with Mass Spectra Alignments.
BMC Bioinformatics, 8:102, 2007.
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Michael Kaltenbach, Sebastian Böcker and Sven Rahmann
Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting.
In Proc. of RECOMB Satellite Conference on Systems Biology and Computational Proteomics 2006, volume 4532 of Lect Notes Comput Sci, pages 29-41. Springer, Berlin, 2007.
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Sven Rahmann, Tobias Wittkop, Jan Baumbach, Marcel Martin, Anke Truss and Sebastian Böcker
Exact and Heuristic Algorithms for Weighted Cluster Editing.
In Proc. of Computational Systems Bioinformatics (CSB 2007), volume 6 pages 391-401. 2007.
[ bib | pmid | pdf | url | abstract | data ]

Alexandra Scherbart, Wiebke Timm, Sebastian Böcker and Tim W. Nattkemper
Neural network approach for mass spectrometry prediction by peptide prototyping.
In Proc. of International Conference on Artificial Neural Networks (ICANN 2007), volume 4669 of Lect Notes Comput Sci, pages 90-99. Springer, Berlin, 2007.
[ bib | doi | pdf | abstract ]

Alexandra Scherbart, Wiebke Timm, Sebastian Böcker and Tim W. Nattkemper
SOM-based peptide prototyping for mass spectrometry peak intensity prediction.
In Proc. of Workshop on Self-Organizing Maps (WSOM 2007), 2007. Doi 10.2390/biecoll-wsom2007-157.
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Sebastian Wernicke and Florian Rasche
Simple and fast alignment of metabolic pathways by exploiting local diversity.
In Proc. of Asia-Pacific Bioinformatic Conference (APBC 2007), of Advances in Bioinformatics and Computational Biology, pages 353-362. Imperial College Press, 2007.
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Sebastian Wernicke and Florian Rasche
Simple and fast alignment of metabolic pathways by exploiting local diversity.
Bioinformatics, 23(15):1978-1985, 2007.
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2006

Sebastian Böcker
Sequencing from Compomers: The Puzzle.
Theory Comput Syst, 39(3):455-471, 2006.
[ bib | doi | pdf | abstract ]

Sebastian Böcker, Matthias Letzel, Zsuzsanna Lipták and Anton Pervukhin
Decomposing metabolomic isotope patterns.
In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2006), volume 4175 of Lect Notes Comput Sci, pages 12-23. Springer, Berlin, 2006.
[ bib | pdf | abstract ]

Sebastian Böcker and Veli Mäkinen
Combinatorial Approaches for Mass Spectra Recalibration.
In Computational Proteomics, (05471) of Dagstuhl Seminar Proceedings, Internationales Begegnungs- und Forschungszentrum (IBFI), Schloss Dagstuhl, Germany, 2006.
[ bib ]

Michael Dom, Jiong Guo, Falk Hüffner, Rolf Niedermeier and Anke Truss
Fixed-parameter tractability results for feedback set problems in tournaments.
In Proc. of Conference on Algorithms and Complexity (CIAC 2006), volume 3998 of Lect Notes Comput Sci, pages 320-331. Springer, Berlin, 2006.
[ bib | pdf | abstract ]

Michael Sammeth, Thasso Griebel, Felix Tille and Jens Stoye
Panta rhei (QAlign2): An open graphical environment for sequence analysis.
Bioinformatics, 22(7):889-890, 2006.
[ bib | doi | pmid | url | abstract ]

Wiebke Timm, Sebastian Böcker, Thorsten Twellmann and Tim W. Nattkemper
Peak Intensity Prediction for PMF Mass Spectra using Support Vector Regression.
In Proc. of International FLINS Conference on Applied Artificial Intelligence (FLINS 2006), pages 565-572. 2006.
[ bib | pdf ]

Sebastian Wernicke and Florian Rasche
FANMOD: a tool for fast network motif detection.
Bioinformatics, 22(9):1152-1153, 2006.
[ bib | pmid | url ]

2005

Sebastian Böcker and Hans-Michael Kaltenbach
Mass Spectra Alignments and Their Significance.
In Proc. of Combinatorial Pattern Matching Symposium (CPM 2005), volume 3537 of Lect Notes Comput Sci, pages 429-441. Springer, Berlin, 2005.
[ bib | pdf ]

Sebastian Böcker and Zsuzsanna Lipták
Efficient Mass Decomposition.
In Proc. of ACM Symposium on Applied Computing (ACM SAC 2005), pages 151-157. ACM press, New York, 2005.
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Sebastian Böcker and Zsuzsanna Lipták
The Money Changing Problem revisited: Computing the Frobenius number in time $O(k \, a_1)$.
In Proc. of Conf. on Computing and Combinatorics (COCOON 2005), volume 3595 of Lect Notes Comput Sci, pages 965-974. Springer, Berlin, 2005.
[ bib | pdf ]

Sebastian Böcker and Veli Mäkinen
Maximum Line-Pair Stabbing Problem and its Variations.
In Proc. of European Workshop on Computational Geometry (EWCG 2005), pages 183-186. Eindhoven, Netherlands, 2005.
[ bib | url ]

Sebastian Böcker and Jens Stoye
Informatische Methoden zur Protein- und Metaboliten-Identifikation mittels Massenspektrometrie.
LaborPraxis, 10:24-26, 2005. German.
[ bib ]

Mathias Ehrich, Sebastian Böcker and Dirk van den Boom
Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS.
Nucleic Acids Res, 33(4):e38, 2005.
[ bib | doi | pmid | pdf | url ]

Hans-Michael Kaltenbach, Henner Sudek, Sebastian Böcker and Sven Rahmann
Statistics of cleavage fragments in random weighted strings.
Technical report, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2005.
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2004

Sebastian Böcker
Unrooted Supertrees: Limitations, Traps, and Phylogenetic Patchworks.
In Phylogenetic supertrees: Combining information to reveal the Tree of Life, volume 4 of Computational Biology Book Series, chapter 15, pages 331-351. Kluwer Academic, 2004.
[ bib | pdf ]

Sebastian Böcker
Sequencing from compomers: Using mass spectrometry for DNA de-novo sequencing of 200+ nt.
J Comput Biol, 11(6):1110-1134, 2004.
[ bib | doi | pmid | pdf ]

Sebastian Böcker
Sequencing from compomers: The puzzle.
In Proc. of FUN with Algorithms 2004, pages 132-146. Tuscany, Italy, 2004.
[ bib | pdf ]

Sebastian Böcker
Sequencing From Compomers is NP-hard.
Technical report, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2004.
[ bib ]

Sebastian Böcker
Weighted Sequencing from Compomers: DNA de-novo sequencing from mass spectrometry data in the presence of false negative peaks.
In Proc. of German Conference on Bioinformatics (GCB 2004), volume P-53 of Lecture Notes in Informatics, pages 13-23. 2004.
[ bib | pdf | url ]

Sebastian Böcker and Zsuzsanna Lipták
The Money Changing Problem Revisited: Computing the Frobenius Number in Time $O(ka_1)$.
Technical report, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2004.
[ bib ]

Michael Lefmann, Christiane Honisch, Sebastian Böcker, Niels Storm, Friedrich von Wintzingerode, Cord Schlötelburg, Annette Moter, Dirk van den Boom and Ulf B. Göbel
A novel mass spectrometry based tool for genotypic identification of mycobacteria.
J Clin Microbiol, 42(1):339-346, 2004.
[ bib | doi | pmid ]

Patrick Stanssens, Marc Zabeau, Geert Meersseman, Gwen Remes, Yannick Gansemans, Niels Storm, Ralf Hartmer, Christiane Honisch, Charles P. Rodi, Sebastian Böcker and Dirk van den Boom
High-throughput MALDI-TOF Discovery of Genomic Sequence Polymorphisms.
Genome Res, 14:126-133, 2004.
[ bib | url ]

2003

Sebastian Böcker
Sequencing from compomers: Using mass spectrometry for DNA de-novo sequencing of 200+ nt (extended abstract).
In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2003), volume 2812 of Lect Notes Comput Sci, pages 476-497. Springer, Berlin, 2003.
[ bib | doi | pdf ]

Sebastian Böcker
Sequencing from compomers in the presence of false negative peaks.
Technical report, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2003.
[ bib | pdf ]

Sebastian Böcker
Sequencing from compomers: Using mass spectrometry for DNA de-novo sequencing of 200+ nt.
Technical report, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2003.
[ bib | pdf ]

Sebastian Böcker
SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry.
Bioinformatics, 19:i44-i53, 2003. Proc. of Intelligent Systems for Molecular Biology (ISMB 2003).
[ bib | doi | pmid | url ]

Sebastian Böcker
SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry.
Technical report, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2003.
[ bib | pdf ]

Ralf Hartmer, Niels Storm, Sebastian Boecker, Charles P. Rodi, Franz Hillenkamp, Christian Jurinke and Dirk van den Boom
RNAse T1 mediated base-specific cleavage and MALDI-TOF MS for high-throughput comparative sequence analysis.
Nucleic Acids Res, 31(9):e47, 2003.
[ bib | doi | pmid | pdf ]

2002

Sebastian Böcker
Exponentially many supertrees.
Appl Math Let, 15(7):861-865, 2002.
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Friedrich von Wintzingerode, Sebastian Böcker, Cord Schlötelburg, Norman H.L. Chiu, Niels Storm, Christian Jurinke, Charles R. Cantor, Ulf B. Göbel and Dirk van den Boom
Base-specific fragmentation of amplified 16S rRNA genes and mass spectrometry analysis: A novel tool for rapid bacterial identification.
Proc Natl Acad Sci U S A, 99(10):7039-7044, 2002.
[ bib | doi | pdf ]

2001

Sebastian Böcker and Andreas W.M. Dress
Patchworks.
Adv Math, 157(1):1-21, 2001.
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2000

Sebastian Böcker, David Bryant, Andreas W.M. Dress and Michael A. Steel
Algorithmic aspects of tree amalgamation.
J Algorithms, 37:522-537, 2000.
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Sebastian Böcker and Andreas W.M. Dress
A Note on Maximal Hierarchies.
Adv Math, 151(2):270-282, 2000.
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Michael A. Steel, Andreas W.M. Dress and Sebastian Böcker
Simple but fundamental limitations on supertree and consensus tree methods.
Syst Biol, 49(2):363-368, 2000.
[ bib | pmid | pdf ]

1999

Sebastian Böcker, Andreas W.M. Dress and Michael A. Steel
Patching up $X$-Trees.
Ann Comb, 3:1-12, 1999.
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1998

Sebastian Böcker and Andreas W.M. Dress
Recovering Symbolically Dated, Rooted Trees from Symbolic Ultrametrics.
Adv Math, 138(1):105-125, 1998.
[ bib | doi | pdf ]