2024
A. K. P. Shah, A. Walter, F. Ottosson, F. Russo, M. Navarro-Diaz, J. Boldt, J.-C. J. Kalinski, E. E. Kontou, J. Elofson, A. Polyzois, C. González-Marín, S. Farrell, M. R. Aggerbeck, T. Pruksatrakul, N. Chan, Y. Wang, M. Pöchhacker, C. Brungs, B. Cámara, A. M. Caraballo-Rodríguez, A. Cumsille, F. de Oliveira, K. Dührkop, Y. El Abiead, C. Geibel, L. G. Graves, M. Hansen, S. Heuckeroth, S. Knoblauch, A. Kostenko, M. C. M. Kuijpers, K. Mildau, S. Papadopoulos Lambidis, P. Wender Portal Gomes, T. Schramm, K. Steuer-Lodd, P. Stincone, S. Tayyab, G. A. Vitale, B. C. Wagner, S. Xing, M. T. Yazzie, S. Zuffa, M. de Kruijff, C. Beemelmanns, H. Link, C. Mayer, J. J. J. van der Hooft, T. Damiani, T. Pluskal, P. Dorrestein, J. Stanstrup, R. Schmid, M. Wang, A. Aron, M. Ernst and D. Petras
Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data
Nat Protoc, 2024.
[DOI]
F. Kretschmer, E.-M. Harrieder, M. A. Hoffmann, S. Böcker, and M. Witting
RepoRT: a comprehensive repository for small molecule retention times
Nat Methods 21(2):153-155, 2024.
[DOI] [PubMed] [Preprint] [ReadOnly]
2023
R. Schmid, S. Heuckeroth, A. Korf, A. Smirnov, O. Myers, T. S. Dyrlund, R. Bushuiev, K. J. Murray, N. Hoffmann, M. Lu, A. Sarvepalli, Z. Zhang, M. Fleischauer, K. Dührkop, M. Wesner, S. J. Hoogstra, E. Rudt, O. Mokshyna, C. Brungs, K. Ponomarov, L. Mutabdžija, T. Damiani, C. J. Pudney, M. Earll, P. O. Helmer, T. R. Fallon, T. Schulze, A. Rivas-Ubach, A. Bilbao, H. Richter, L.-F. Nothias, M. Wang, M. Orešič, J.-Ke Weng, S. Böcker, A. Jeibmann, H. Hayen, U. Karst, P. C. Dorrestein, D. Petras, X. Du, and T. Pluskal
Integrative analysis of multimodal mass spectrometry data in MZmine 3
Nat Biotechnol 41(4):447-449, 2023.
[DOI] [PubMed]
M. A. Hoffmann, F. Kretschmer, M. Ludwig, and S. Böcker
Mad Hatter correctly annotates 98% of small molecule tandem mass spectra searching in PubChem
Metabolites 13(3):314, 2023
[DOI][PubMed]
E. Karunaratne, D. W. Hill, K. Dührkop, S. Böcker, and D. F. Grant
Combining Experimental with Computational Infrared and Mass Spectra for High-Throughput Nontargeted Chemical Structure Identification
Anal Chem 95(32):11901-11907, 2023
[DOI][PubMed]
S. Böcker, H. Mamitsuka, and J. Rousu
Computational Metabolomics and Machine Learning
NII Shonan Meeting Report 179, 2023
[Link] [PDF]
F. Kretschmer, E.-M. Harrieder, M. Hoffmann, S. Böcker, and M. Witting
RepoRT: A Comprehensive Repository for Small Molecule Retention Times
Preprint, ChemRxiv 2023-1mq73-v2, 2023
[DOI]
F. Kretschmer, J. Seipp, M. Ludwig, G. W. Klau, and S. Böcker
Small molecule machine learning: All models are wrong, some may not even be useful
Preprint, bioRxiv 2023.03.27.534311, 2023
[DOI]
2022
J. P. Shaffer, L.-F. Nothias, L. R. Thompson, J. G. Sanders, R. A. Salido, S. P. Couvillion, A. D. Brejnrod, F. Lejzerowicz, N. Haiminen, S. Huang, H. L. Lutz, Q. Zhu, C. Martino, J. T. Morton, S. Karthikeyan, M. Nothias-Esposito, K. Dührkop, S. Böcker, H. W. Kim, A. A. Aksenov, W. Bittremieux, J. J. Minich, C. Marotz, M. M. Bryant, K. Sanders, T. Schwartz, G. Humphrey, Y. Vásquez-Baeza, A. Tripathi, L. Parida, A. P. Carrieri, K. L. Beck, P. Das, A. González, D. McDonald, J. Ladau, S. M. Karst, M. Albertsen, G. Ackermann, J. DeReus, T. Thomas, D. Petras, A. Shade, J. Stegen, S. J. Song, T. O. Metz, A. D. Swafford, P. C. Dorrestein, J. K. Jansson, J. A. Gilbert, R. Knight and the Earth Microbiome Project 500 (EMP500) Consortium
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
Nat Microbiol 7(12):2128-2150, 2022
[DOI] [PubMed]
E.‑M. Harrieder, F. Kretschmer, W. Dunn, S. Böcker, and M. Witting
Critical assessment of chromatographic metadata in publicly available metabolomics data repositories
Metabolomics 18:97, 2022
[DOI] [PubMed]
I. Koester, Z. A. Quinlan, L.-F. Nothias, M. E. White, A. Rabines, D. Petras, J. K. Brunson, K. Dührkop, M. Ludwig, S. Böcker, F. Azam, A. E. Allen, P. C. Dorrestein, and L. I. Aluwihare
Illuminating the dark metabolome of Pseudo-nitzschia-microbiome associations
Environ Microbiol 24(11):5408-5424, 2022
[DOI] [PubMed]
F. Mock, F. Kretschmer, A. Kriese, S. Böcker, and M. Marz
Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks
Proc Natl Acad Sci U S A 119(35):e2122636119, 2022
[DOI] [PubMed]
M. A. Stravs, K. Dührkop, S. Böcker, and N. Zamboni
MSNovelist: de novo structure generation from mass spectra
Nat Methods 19(7):865–870, 2022
[DOI] [PubMed]
C. Simon, K. Dührkop, D. Petras, V. N. Roth, S. Böcker, P. C. Dorrestein, and G. Gleixner
Mass Difference Matching Unfolds Hidden Molecular Structures of Dissolved Organic Matter
Environ Sci Technol 56(15):11027-11040, 2022
[DOI] [PubMed]
M. A. Hoffmann, L.-F. Nothias, M. Ludwig, M. Fleischauer, E. C. Gentry, M. Witting, P. C. Dorrestein, K. Dührkop, and S. Böcker
High-confidence structural annotation of metabolites absent from spectral libraries
Nat Biotechnol 40(3):411–421, 2022
[DOI] [PubMed]
K. Dührkop
Deep kernel learning improves molecular fingerprint prediction from tandem mass spectra
Bioinformatics, Volume 38:i342–i349, Issue Supplement_1, 2022. Proc. of Intelligent Systems for Molecular Biology (ISMB 2022).
[DOI] [PubMed]
E.-M. Harrieder, F. Kretschmer, S. Böcker, and M. Witting
Current state-of-the-art of separation methods used in LC-MS based metabolomics and lipidomics
J Chromatography B 1188:123069, 2022
[DOI] [PubMed] [reprint]
M. Palmblad, S. Böcker, S. Degroeve, O. Kohlbacher, L. Käll, W. S. Noble, and M. Wilhelm
Interpretation of the DOME recommendations for machine learning in proteomics and metabolomics
J Proteome Res 21(4):1204–1207, 2022
[DOI] [PubMed]
2021
R. Schmid, D. Petras, L.-F. Nothias, M. Wang, A. T. Aron, A. Jagels, H. Tsugawa, J. Rainer, M. Garcia-Aloy, K. Dührkop, A. Korf, T. Pluskal, Z. Kameník, A. K. Jarmusch, A. M. Caraballo-Rodríguez, K. C. Weldon, M. Nothias-Esposito, A. A. Aksenov, A. Bauermeister, A. Albarracin Orio, C. O. Grundmann, F. Vargas, I. Koester, J. M. Gauglitz, E. C. Gentry, Y. Hövelmann, S. A. Kalinina, M. A. Pendergraft, M. Panitchpakdi, R. Tehan, A. Le Gouellec, G. Aleti, H. Mannochio Russo, B. Arndt, F. Hübner, H. Hayen, H. Zhi, M. Raffatellu, K. A. Prather, L. I. Aluwihare, S. Böcker, K. L. McPhail, H.-U. Humpf, U. Karst, and P. C. Dorrestein
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment
Nat Commun 12:3832, 2021
[DOI] [PubMed]
K. Dührkop, L. F. Nothias, M. Fleischauer, R. Reher, M. Ludwig, M. A. Hoffmann, D. Petras, W. H. Gerwick, J. Rousu, P. C. Dorrestein, and S. Böcker
Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
Nat Biotechnol 39(4):462–471, 2021
[DOI] [ReadOnly] [PubMed]
A. Tripathi, Y. Vázquez-Baeza, J. M. Gauglitz, M. Wang, K. Dührkop, M. Nothias-Esposito, D. D. Acharya, M. Ernst, J. J. van der Hooft, Q. Zhu, D. McDonald, A. Gonzalez, J. Handelsman, M. Fleischauer, M. Ludwig, S. Böcker, L.-F. Nothias, R. Knight, and P. C. Dorrestein
Chemically-informed analyses of metabolomics mass spectrometry data with Qemistree
Nat Chem Biol 17(2):146–151, 2021
[DOI] [PubMed]
M. Ludwig, C. D. Broeckling, P. C. Dorrestein, K. Dührkop, E. L. Schymanski, S. Böcker, and L.-F. Nothias
Studying charge migration fragmentation of sodiated precursor ions in collision-induced dissociation at the library scale
J Am Soc Mass Spectrom 32(1):180–186, 2021
[DOI] [PubMed] [Reprint]
M. A. Hoffmann, L.-F. Nothias, M. Ludwig, M. Fleischauer, E. C. Gentry, M. Witting, P. C. Dorrestein, K. Dührkop, and S. Böcker
Assigning confidence to structural annotations from mass spectra with COSMIC
Preprint, bioRxiv:2021.03.18.435634, 2021
[DOI]
2020
M. Witting and S. Böcker
Current status of retention time prediction in metabolite identification
J Sep Sci 43(9–10):1746–1754, 2020
[DOI] [PubMed]
L.-F. Nothias, D. Petras, R. Schmid, K. Dührkop, J. Rainer, A. Sarvepalli, I. Protsyuk, M. Ernst, H. Tsugawa, M. Fleischauer, F. Aicheler, A. A. Aksenov, O. Alka, P.-M. Allard, A. Barsch, X. Cachet, A. M. Caraballo-Rodriguez, R. R. Da Silva, T. Dang, N. Garg, J. M. Gauglitz, A. Gurevich, G. Isaac, A. K. Jarmusch, Z. Kamenık, K. B. Kang, N. Kessler, I. Koester, A. Korf, A. Le Gouellec, M. Ludwig, C. Martin H, L.-I. McCall, J. McSayles, S. W. Meyer, H. Mohimani, M. Morsy, O. Moyne, S. Neumann, H. Neuweger, N. H. Nguyen, M. Nothias-Esposito, J. Paolini, V. V. Phelan, T. Pluskal, R. A. Quinn, S. Rogers, B. Shrestha, A. Tripathi, J. J. J. van der Hooft, F. Vargas, K. C. Weldon, M. Witting, H. Yang, Z. Zhang, F. Zubeil, O. Kohlbacher, S. Böcker, T. Alexandrov, N. Bandeira, M. Wang, and P. C. Dorrestein
Feature-based molecular networking in the GNPS analysis environment
Nat Methods 17(9):905–908, 2020
[DOI] [PubMed]
M. Ludwig, L.-F. Nothias, K. Dührkop, I. Koester, M. Fleischauer, M. A. Hoffmann, D. Petras, F. Vargas, M. Morsy, L. Aluwihare, P. C. Dorrestein, and S. Böcker
Database-independent molecular formula annotation using Gibbs sampling through ZODIAC
Nat Mach Intell 2(10):629–641, 2020
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F. Kaftan, P. Kulkarni, M. Knaden, S. Böcker, B. S. Hansson, and A. Svatoš
Drosophila melanogaster chemical ecology revisited: 2-D distribution maps of sex pheromones on whole virgin and mated flies by mass spectrometry imaging
BMC Zoology 5(1):4, 2020
[DOI]
M. Ludwig, M. Fleischauer, K. Dührkop, M. A. Hoffmann, and S. Böcker
De novo molecular formula annotation and structure elucidation using SIRIUS 4
In S. Li, editor, Computational Methods and Data Analysis for Metabolomics. Volume 2104, Pages 185–207. Springer US, New York, NY, 2020
[DOI] [Reprint] [PubMed]
M. Ludwig
Bayesian methods for small molecule identification
PhD thesis, Friedrich-Schiller-Universität Jena, Jena, Germany, 2020
[DOI]
K. Dührkop, L. F. Nothias, M. Fleischauer, M. Ludwig, M. A. Hoffmann, J. Rousu, P. C. Dorrestein, and S. Böcker
Classes for the masses: systematic classification of unknowns using fragmentation spectra
Preprint, bioRxiv:2020.04.17.046672, 2020
[DOI]
S. Böcker, C. Broeckling, E. Schymanski, and N. Zamboni
Computational metabolomics: from cheminformatics to machine learning (Dagstuhl Seminar 20051)
Dagstuhl Reports 10(1):144–159, 2020
[DOI]
2019
K. Dührkop, M. Fleischauer, M. Ludwig, A. A. Aksenov, A. V. Melnik, M. Meusel, P. C. Dorrestein, J. Rousu, and S. Böcker
SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information
Nat Methods 16(4):299–302, 2019
[DOI] [ReadOnly] [Reprint] [PubMed]
M. Ludwig, L.-F. Nothias, K. Dührkop, I. Koester, M. Fleischauer, M. A. Hoffmann, D. Petras, F. Vargas, M. Morsy, L. Aluwihare, P. C. Dorrestein, and S. Böcker
ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules
Preprint, bioRxiv:842740, 2019
[DOI]
S. Böcker
Algorithmic Mass Spectrometry: From molecules to masses and back again
https://bio.informatik.uni-jena.de/textbook-algoms/. Version 0.8.2.
Friedrich-Schiller-Universität Jena, Jena, Germany, 2019
2018
K. Peters, A. Worrich, A. Weinhold, O. Alka, G. Balcke, C. Birkemeyer, H. Bruelheide, O. W. Calf, S. Dietz, K. Dührkop, E. Gaquerel, U. Heinig, M. Kücklich, M. Macel, C. Müller, Y. Poeschl, G. Pohnert, C. Ristok, V. M. Rodrıguez, C. Ruttkies, M. Schuman, R. Schweiger, N. Shahaf, C. Steinbeck, Tortosa, H. Treutler, N. Ueberschaar, P. Velasco, B. M. Weiß, A. Widdig, S. Neumann, and N. M. van Dam
Current challenges in plant eco-metabolomics
Int J Mol Sci 19(5):1385, 2018
[DOI] [PubMed]
P. Kulkarni, M. Dost, Ö. D. Bulut, A. Welle, S. Böcker, W. Boland, and A. Svatoš
Secondary ion mass spectrometry imaging and multivariate data analysis reveal co-aggregation patterns of populus trichocarpa leaf surface compounds on a micrometer scale
The Plant Journal 93(1):193–206, 2018
[DOI] [PubMed]
M. Fleischauer and S. Böcker
BCD Beam Search: considering suboptimal partial solutions in Bad Clade Deletion supertrees
PeerJ 6:e4987, 2018
[DOI] [PubMed]
E. W. Deutsch, Y. Perez-Riverol, R. J. Chalkley, M. Wilhelm, S. Tate, T. Sachsenberg, M. Walzer, L. Käll, B. Delanghe, S. Böcker, E. L. Schymanski, P. Wilmes, V. Dorfer, B. Kuster, P.-J. Volders, N. Jehmlich, J. P. C. Vissers, D. W. Wolan, A. Y. Wang, L. Mendoza, J. Shofstahl, A. W. Dowsey, J. Griss, R. M. Salek, S. Neumann, P.-A. Binz, H. Lam, J. A. Vizcaıno, N. Bandeira, and H. Röst
Expanding the use of spectral libraries in proteomics
J Proteome Res 17(12):4051–4060, 2018
[DOI] [PubMed]
M. Ludwig, K. Dührkop, and S. Böcker
Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints
Bioinformatics 34(13):i333–i340, 2018. Proc. of Intelligent Systems for Molecular Biology (ISMB 2018)
[DOI] [PubMed]
E. Bach, S. Szedmak, C. Brouard, S. Böcker, and J. Rousu
Liquid-chromatography retention order prediction for metabolite identification
Bioinformatics 34(17):i875–i883, 2018. Proc. of European Conference on Computational Biology (ECCB 2018)
[DOI] [PubMed]
K. Dührkop, M. A. Lataretu, W. T. J. White, and S. Böcker
Heuristic algorithms for the maximum colorful subtree problem
In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2018), volume 113 of Leibniz International Proceedings in Informatics (LIPIcs), 23:1–23:14, Dagstuhl, Germany. Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, 2018
[DOI]
P. Kulkarni
Computational Methods for the Analysis of Mass Spectrometry Imaging Data
PhD thesis, Friedrich-Schiller-Universität Jena, Jena, Germany, 2018
[DOI]
M. Fleischauer
Fast and accurate supertrees: towards large scale phylogenies
PhD thesis, Friedrich-Schiller-Universität Jena, Jena, Germany, 2018
[DOI]
K. Dührkop
Computational Methods for Small Molecule Identification
PhD thesis, Friedrich-Schiller-Universität Jena, Jena, Germany, 2018
[DOI]
Martin S. Engler
Computational Mass Spectrometry of Linear Binary Synthetic Copolymers
PhD thesis, Friedrich-Schiller-Universität Jena, Jena, Germany, 2018
[DOI]
K. Dührkop, M. A. Lataretu, W. T. J. White, and S. Böcker
Heuristic algorithms for the Maximum Colorful Subtree problem
Technical report arXiv:1801.07456, arXiv, 2018
[Link]
T. Alexandrov, S. Böcker, P. Dorrestein, and E. Schymanski
Computational metabolomics: identification, interpretation, imaging (Dagstuhl Seminar 17491)
Dagstuhl Reports 7(12):1–17, 2018
[DOI]
2017
K. Scheubert, F. Hufsky, D. Petras, M. Wang, L.-F. Nothias, K. Dührkop, N. Bandeira, P. C. Dorrestein, and S. Böcker
Significance estimation for large scale metabolomics annotations by spectral matching
Nat Commun 8:1494, 2017
[DOI] [PubMed]
E. L. Schymanski, C. Ruttkies, M. Krauss, C. Brouard, T. Kind, K. Dührkop, F. R. Allen, A. Vaniya, D. Verdegem, S. Böcker, J. Rousu, H. Shen, H. Tsugawa, T. Sajed, O. Fiehn, B. Ghesquière, and S. Neumann
Critical Assessment of Small Molecule Identification 2016: automated methods
J Cheminformatics 9:22, 2017
[DOI] [PubMed]
M. Fleischauer and S. Böcker
Bad Clade Deletion supertrees: a fast and accurate supertree algorithm
Mol Biol Evol 34(9):2408–2421, 2017
[DOI] [PubMed]
M. S. Engler, K. Scheubert, U. S. Schubert, and S. Böcker
Exploring the limits of the geometric copolymerization model
Polymers 9(3):101, 2017
[DOI]
S. Böcker
Searching molecular structure databases using tandem MS data: are we there yet?
Curr Opin Chem Biol 36:1–6, 2017
[DOI] [PubMed]
B. Bartels, P. Kulkarni, N. Danz, S. Böcker, H. P. Saluz, and A. Svatoš
Mapping metabolites from rough terrain: laser ablation electrospray ionization on non-flat samples
RSC Adv 7(15):9045–9050, 2017
[DOI]
E. Barbosa, R. Röttger, A.-C. Hauschild, S. de Castro Soares, S. Böcker, V. Azevedo, and J. Baumbach
Lifestyle-specific-islands (LiSSI): integrated bioinformatics platform for genomic island analysis
J Integr Bioinform 14(2):2017–0010, 2017
[DOI] [PubMed]
C. Brouard, E. Bach, S. Böcker, and J. Rousu
Magnitude-preserving ranking for structured outputs
In Proc. of Asian Conference on Machine Learning, volume 77 of Proceedings of Machine Learning Research, pages 407–422. PMLR, 2017
[Link]
W. T. J. White, M. Ludwig, and S. Böcker
Exact and heuristic algorithms for Cograph Editing
Technical report arXiv:1711.05839, arXiv, 2017
[Link]
M. Arita, S. Böcker, and S. Neumann
Computational Metabolomics (NII Shonan Meeting Report 2017-3)
NII Shonan Meeting Report 2017-3, 2017
[Link] [PDF]
2016
S. Winter, K. Jahn, S. Wehner, L. Kuchenbecker, M. Marz, J. Stoye, and S. Böcker
Finding approximate gene clusters with Gecko 3
Nucleic Acids Res, 44(20):9600–9610, 2016
[DOI] [PubMed]
M. Meusel, F. Hufsky, F. Panter, D. Krug, R. Müller, and S. Böcker
Predicting the presence of uncommon elements in unknown biomolecules from isotope patterns
Anal Chem, 88(15):7556–7566, 2016
[DOI] [PubMed] [Preprint]
M. Fleischauer and S. Böcker
Collecting reliable clades using the greedy strict consensus merger
PeerJ, 4:e2172, 2016
[DOI] [PubMed]
M. S. Engler, K. Scheubert, U. S. Schubert, and S. Böcker
New statistical models for copolymerization
Polymers, 8(6):240, 2016
[DOI]
M. S. Engler, S. Crotty, M. J. Barthel, C. Pietsch, U. S. Schubert, and S. Böcker
Abundance correction for mass discrimination effects in polymer mass spectra
Rapid Commun Mass Spectrom, 30:1233–1241, 2016
[DOI]
S. Böcker and K. Dührkop
Fragmentation trees reloaded
J Cheminformatics, 8:5, 2016
[DOI] [PubMed]
C. Brouard, H. Shen, K. Dührkop, F. d’Alché-Buc, S. Böcker, and J. Rousu
Fast metabolite identification with input output kernel regression
Bioinformatics, 32(12):i28–i36, 2016. Proc. of Intelligent Systems for Molecular Biology (ISMB 2016)
[DOI] [PubMed]
K. Scheubert
Small Molecules: From Mass Spectral Fragmentation Data to Structural Elucidation
PhD thesis, Friedrich-Schiller-Universität Jena, Jena, Germany, 2016
S. Böcker, J. Rousu, and E. Schymanski
Computational Metabolomics (Dagstuhl Seminar 15492)
Dagstuhl Reports, 5(11):180–192, 2016
[DOI]
2015
M. S. Engler, S. Crotty, M. J. Barthel, C. Pietsch, K. Knop, U. S. Schubert, and S. Böcker
COCONUT – an efficient tool for estimating copolymer compositions from mass spectra
Anal Chem, 87(10):5223–5231, 2015
[DOI] [Preprint] [PubMed]
K. Dührkop, H. Shen, M. Meusel, J. Rousu, and S. Böcker
Searching molecular structure databases with tandem mass spectra using CSI:FingerID
Proc Natl Acad Sci U S A, 112(41):12580–12585, 2015
[DOI] [PubMed]
S. Böcker
Ten times eighteen
J Inform Process Jpn, 23(3):258–264, 2015
[DOI]
W. T. J. White, S. Beyer, K. Dührkop, M. Chimani, and S. Böcker
Speedy colorful subtrees
In Proc. of Computing and Combinatorics Conference (COCOON 2015), volume 9198 of Lect Notes Comput Sci, pages 310–322. Springer, Berlin, 2015
[DOI] [Preprint]
M. Fleischauer and S. Böcker
Collecting reliable clades using the greedy strict consensus merger
In Proc. of German Conference on Bioinformatics (GCB 2015), volume 3 of PeerJ PrePrints, e1595. PeerJ Inc. San Francisco, USA, 2015
[DOI]
K. Dührkop and S. Böcker
Fragmentation trees reloaded
In Proc. of Research in Computational Molecular Biology (RECOMB 2015), volume 9029 of Lect Notes Comput Sci, pages 65–79. Springer, Berlin, 2015
[DOI]
2014
V. U. Schwartze, S. Winter, E. Shelest, M. Marcet-Houben, F. Horn, S. Wehner, J. Linde, V. Valiante, M. Sammeth, K. Riege, M. Nowrousian, K. Kaerger, I. D. Jacobsen, M. Marz, A. A. Brakhage, T. Gabaldón, S. Böcker, and K. Voigt
Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial Mucorales (Mucoromycotina)
PLos Genet, 10(8):e1004496, 2014
[DOI] [PubMed]
M. Napagoda, J. Gerstmeier, A. Koeberle, S. Wesely, S. Popella, S. Lorenz, K. Scheubert, S. Böcker, A. Svatoš, and O. Werz
Munronia pinnata (Wall.) Theob.: unveiling phytochemistry and dual inhibition of 5-lipoxygenase and microsomal prostaglandin E2 synthase (mPGES)-1
J Ethnopharmacol, 151(2):882–890, 2014
[DOI] [PubMed]
F. Kaftan, V. Vrkoslav, P. Kynast, P. Kulkarni, S. Böcker, J. Cvačka, M. Knaden, and A. Svatoš
Mass spectrometry imaging of surface lipids on intact Drosophila melanogaster flies
J Mass Spectrom, 49(3):223–232, 2014
[DOI] [PubMed]
F. Hufsky, K. Scheubert, and S. Böcker
New kids on the block: Novel informatics methods for natural product discovery
Nat Prod Rep, 31(6):807–817, 2014
[DOI] [Preprint] [PubMed]
F. Hufsky, K. Scheubert, and S. Böcker
Computational mass spectrometry for small molecule fragmentation
Trends Anal Chem, 53:41–48, 2014
[DOI] [Preprint]
K. Dührkop, F. Hufsky, and S. Böcker
Molecular formula identification using isotope pattern analysis and calculation of fragmentation trees
Mass Spectrom, 3(special issue 2):S0037, 2014
[DOI]
S. Böcker and S. Wagner
Counting glycans revisited
J Math Biol, 69(4):799–816, 2014
[DOI] [PubMed]
H. Shen, K. Dührkop, S. Böcker, and J. 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)
[DOI] [PubMed]
D. Doerr, J. Stoye, S. Böcker, and K. 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)
[DOI] [PubMed]
K. Scheubert, F. Hufsky, and S. 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
[DOI] [Preprint]
C. Beckstein, S. Böcker, M. Bogdan, H. Bruelheide, H. M. Bücker, J. Denzler, P. Dittrich, I. Große, A. Hinneburg, B. König-Ries, F. Löffler, M. Marz, M. Müller-Hannemann, M. Winter, and W. 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
[DOI]
F. Hufsky
Novel Methods for the Analysis of Small Molecule Fragmentation Mass Spectra
PhD thesis, Friedrich-Schiller-Universität Jena, Jena, Germany, 2014
[Link]
S. Böcker, G. W. Klau, and H. W. Leong
Towards the ground truth: Exact algorithms for bioinformatics research (NII Shonan Meeting Report 2014-2)
NII Shonan Meeting Report 2014-2, 2014
[Link] [PDF]
2013
K. Scheubert, F. Hufsky, and S. Böcker
Computational mass spectrometry for small molecules
J Cheminformatics, 5:12, 2013
[DOI] [PubMed]
M. Brinkmeyer
Polynomial supertree methods in phylogenomics: algorithms, simulations and software
PhD thesis, Friedrich-Schiller-Universität Jena, Jena, Germany, 2013
[Link]
I. Rauf, F. Rasche, F. Nicolas, and S. Böcker
Finding maximum colorful subtrees in practice
J Comput Biol, 20(4):1–11, 2013
[DOI] [PubMed]
S. Guillemot and F. Sikora
Finding and counting vertex-colored subtrees
Algorithmica, 65(4):828–844, 2013
[DOI]
K. Dührkop, K. Scheubert, and S. Böcker
Molecular formula identification with SIRIUS
Metabolites, 3:506–516, 2013
[DOI] [PubMed]
M. Brinkmeyer, T. Griebel, and S. Böcker
FlipCut supertrees: towards matrix representation accuracy in polynomial time
Algorithmica, 67(2):142–160, 2013
[DOI]
G. Blin, R. Rizzi, F. Sikora, and S. Vialette
Minimum mosaic inference of a set of recombinants
Int J Found Comput S, 24(1):51, 2013
[DOI]
K. Jahn, S. Winter, J. Stoye, and S. Böcker
Statistics for approximate gene clusters
BMC Bioinformatics, 14(Suppl 15):S14, 2013. Proc. of RECOMB Satelite Workshop on Comparative Genomics (RECOMB-CG 2013)
[DOI] [PubMed]
K. Dührkop, M. Ludwig, M. Meusel, and S. 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
[DOI]
S. Böcker, S. Canzar, and G. 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
[DOI]
S. Böcker and J. Baumbach
Cluster editing
In Proc. of Computability in Europe (CIE 2013), volume 7921 of Lect Notes Comput Sci, pages 33–44. Springer, Berlin, 2013
[DOI]
F. Rasche
Identification of Small Molecules using Mass Spectrometry: A fully automated pipeline proposing similar molecules and compound classes
PhD thesis, Friedrich-Schiller-Universität Jena, Jena, Germany, 2013
[Preprint]
2012
L. Ullmann-Zeunert, A. Muck, N. Wielsch, F. Hufsky, M. A. Stanton, S. Bartram, S. Böcker, I. T. Baldwin, K. Groten, and A. 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
[DOI] [PubMed]
F. Rasche, K. Scheubert, F. Hufsky, T. Zichner, M. Kai, A. Svatoš, and S. Böcker
Identifying the unknowns by aligning fragmentation trees
Anal Chem, 84(7):3417–3426, 2012
[DOI] [Preprint] [PubMed]
F. Hufsky, M. Rempt, F. Rasche, G. Pohnert, and S. Böcker
De novo analysis of electron impact mass spectra using fragmentation trees
Anal Chim Acta, 739:67–76, 2012
[DOI] [PubMed]
S. Böcker and P. Damaschke
A note on the parameterized complexity of unordered maximum tree orientation
Discrete Appl Math, 160(10-11):1634–1638, 2012
[DOI] [Preprint]
S. Böcker, Q. B. A. Bui, and A. Truss
Improved fixed-parameter algorithms for minimum-flip consensus trees
ACM Trans Algorithms, 8(1):17 pages, 2012
[DOI]
S. Böcker
A golden ratio parameterized algorithm for cluster editing
J Discrete Algorithms, 16:79–89, 2012
[DOI] [Preprint]
S. 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
[DOI] [Preprint] [PubMed]
G. Blin, P. Bonizzoni, R. Dondi, and F. Sikora
On the parameterized complexity of the repetition free longest common subsequence problem
Inform Process Lett, 112(7):272–276, 2012
[DOI]
F. Hufsky, K. Dührkop, F. Rasche, M. Chimani, and S. Böcker
Fast alignment of fragmentation trees
Bioinformatics, 28(12):i265–i273, 2012. Proc. of Intelligent Systems for Molecular Biology (ISMB 2012)
[DOI] [PubMed]
X. Yang, F. Sikora, G. Blin, S. Hamel, R. Rizzi, and S. 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
[DOI]
R. Rizzi and F. 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
[DOI]
I. Rauf, F. Rasche, F. Nicolas, and S. 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
[DOI]
M. Ludwig, F. Hufsky, S. Elshamy, and S. 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
[DOI]
F. Hufsky and S. 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
[DOI]
G. Blin, P. Bonizzoni, R. Dondi, R. Rizzi, and F. 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
[DOI]
S. Böcker
Ten times eighteen
Technical report, arXiv:1209.1977, arXiv, 2012
2011
T. Wittkop, S. Rahmann, S. Böcker, and J. Baumbach
Extension and robustness of transitivity clustering for protein-protein interaction network analysis
Internet Math, 7(4):255–273, 2011
[DOI]
T. Wittkop, D. Emig, A. Truss, M. Albrecht, S. Böcker, and J. Baumbach
Comprehensive cluster analysis with transitivity clustering
Nat Protocols, 6:285–295, 2011
[DOI] [PubMed]
K. Scheubert, F. Hufsky, F. Rasche, and S. Böcker
Computing fragmentation trees from metabolite multiple mass spectrometry data
J Comput Biol, 18(11):1383–1397, 2011
[DOI] [PubMed]
F. Rasche, A. Svatoš, R. K. Maddula, C. Böttcher, and S. Böcker
Computing fragmentation trees from tandem mass spectrometry data
Anal Chem, 83(4):1243–1251, 2011
[DOI] [PubMed]
F. Hufsky, L. Kuchenbecker, K. Jahn, J. Stoye, and S. Böcker
Swiftly computing center strings
BMC Bioinformatics, 12:106, 2011
[DOI] [PubMed]
K. Grützmann, S. Böcker, and S. Schuster
Combinatorics of aliphatic amino acids
Naturwissenschaften, 98(1):79–86, 2011
[DOI] [PubMed]
A. K. Dehof, A. Rurainski, Q. B. A. Bui, S. Böcker, H.-P. Lenhof, and A. Hildebrandt
Automated bond order assignment as an optimization problem
Bioinformatics, 27(5):619–625, 2011
[DOI] [PubMed]
M. Brinkmeyer, T. Griebel, and S. Böcker
Polynomial supertree methods revisited
Adv Bioinformatics, 2011(Article ID 524182):21 pages, 2011
[DOI] [PubMed]
S. Böcker, S. Briesemeister, and G. W. Klau
Exact algorithms for cluster editing: evaluation and experiments
Algorithmica, 60(2):316–334, 2011
[DOI] [Preprint]
S. Böcker and P. Damaschke
Even faster parameterized cluster deletion and cluster editing
Inform Process Lett, 111(14):717–721, 2011
[DOI] [Preprint]
S. Böcker, B. Kehr, and F. Rasche
Determination of glycan structure from tandem mass spectra
IEEE/ACM Trans Comput Biology Bioinform, 8(4):976–986, 2011
[DOI] [PubMed]
S. Böcker, Q. B. A. Bui, and A. Truss
Computing bond orders in molecule graphs
Theor Comput Sci, 412(12–14):1184–1195, 2011
[DOI] [Preprint]
A. Baumgaertel, K. Scheubert, B. Pietsch, K. Kempe, A. C. Crecelius, S. Böcker, and U. 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
[DOI] [PubMed]
K. Scheubert, F. Hufsky, F. Rasche, and S. 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
[DOI] [Preprint]
M. Chimani, M. Woste, and S. 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
M. Brinkmeyer, T. Griebel, and S. 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
[DOI] [Preprint]
S. 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
[DOI] [Preprint]
S. Böcker and F. Nicolas
Various complexity results for computational mass spectrometry problems
Technical report, 2011
S. Böcker
Towards a data reduction for the Minimum-Flip Supertree problem
Technical report, 2011
S. Böcker, B. Bui, F. Nicolas, and A. Truss
Intractability of the Minimum Flip Supertree problem and its variants
Technical report, arXiv:1112.4536, arXiv, 2011
2010
T. Wittkop, D. Emig, S. Lange, S. Rahmann, M. Albrecht, J. H. Morris, S. Böcker, J. Stoye, and J. Baumbach
Partitioning biological data with transitivity clustering
Nat Methods, 7(6):419–420, 2010
[DOI] [PubMed]
S. Neumann and S. Böcker
Computational mass spectrometry for metabolomics – a review
Anal Bioanal Chem, 398(7):2779–2788, 2010
[DOI] [Preprint] [PubMed]
G. Govind, O. Mittapalli, T. Griebel, S. Allmann, S. Böcker, and I. T. Baldwin
Unbiased transcriptional comparisons of generalist and specialist herbivores feeding on progressively defenseless Nicotiana attenuata plants
PLoS One, 5(1):e8735, 2010
[DOI] [PubMed]
M. Dom, J. Guo, F. Hüffner, R. Niedermeier, and A. Truss
Fixed-parameter tractability results for feedback set problems in tournaments
J Discrete Algorithms, 8(1):76–86, 2010
[DOI]
F. Hufsky, L. Kuchenbecker, K. Jahn, J. Stoye, and S. 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
[DOI]
S. Guillemot and F. 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
[DOI]
M. Chimani, S. Rahmann, and S. 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
[DOI]
M. Brinkmeyer, T. Griebel, and S. 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
[DOI]
S. Guillemot, C. Paul, and A. Perez
On the (non-)existence of polynomial kernels for Pl -free edge modification problems
Technical report, 2010
2009
S. Böcker, M. C. Letzel, Z. Liptak, A. Pervukhin
SIRIUS: decomposing isotope patterns for metabolite identification
Bioinformatics, 25(2):218-224, 2009
[DOI] [PubMed]
A. Bertsch, A. Leinenbach, A. Pervukhin, M. Lubeck, R. Hartmer, C. Baessmann, Y. A. Elnakady, R. Müller, S. Böcker, C. G. Huber, and O. Kohlbacher
De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation
Electrophoresis, 30:3736–3747, 2009
[DOI][PubMed]
M. Dondrup, S. P. Albaum, T. Griebel, K. Henckel, S. Jünemann, T. Kahlke, C. K. Kleindt, H. Küster, B. Linke, D. Mertens, V. Mittard-Runte, H. Neuweger, K. J. Runte, A. Tauch, F. Tille, A. Pühler, and A. Goesmann
EMMA 2 – a MAGE-compliant system for the collaborative analysis and integration of microarray data
BMC Bioinformatics, 10:50, 2009
[DOI] [PubMed]
S. Böcker, S. Briesemeister, and G. 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)
[DOI] [PubMed]
S. Böcker, S. Briesemeister, Q. B. A. Bui, and A. Truss
Going weighted: parameterized algorithms for cluster editing
Theor Comput Sci, 410(52):5467–5480, 2009
[DOI]
S. Böcker, K. Jahn, J. Mixtacki, and J. Stoye
Computation of median gene clusters
J Comput Biol, 16(8):1085–1099, 2009
[DOI] [PubMed]
A. Scherbart, W. Timm, S. Böcker, and T. 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
[DOI]
S. Böcker and A. 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
[DOI] [Preprint]
S. Böcker, F. Hüffner, A. Truss, and M. 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
[DOI]
S. Böcker, B. Kehr, and F. 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
[DOI]
S. Böcker, Q. B. A. Bui, P. Seeber, and A. 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
[DOI]
S. Böcker, F. Rasche, and T. 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
[DOI]
A. Pervukhin
Molecular Formula Identification using High Resolution Mass Spectrometry
PhD thesis, Friedrich-Schiller-Universität Jena, Jena, Germany, 2009
[Preprint]
2008
W. Timm, A. Scherbart, S. Böcker, O. Kohlbacher, and T. W. Nattkemper
Peak intensity prediction in MALDI-TOF mass spectrometry: a machine learning study to support quantitative proteomics
BMC Bioinformatics, 9:443, 2008
[DOI] [PubMed]
T. Griebel, M. Brinkmeyer, and S. Böcker
EPoS: a modular software framework for phylogenetic analysis
Bioinformatics, 24(20):2399–2400, 2008
[DOI] [PubMed]
S. Böcker, Z. Lipták, M. Martin, A. Pervukhin, and H. Sudek
DECOMP–from interpreting mass spectrometry peaks to solving the Money Changing Problem
Bioinformatics, 24(4):591–593, 2008
[DOI] [PubMed]
S. Böcker and V. Mäkinen
Combinatorial approaches for mass spectra recalibration
IEEE/ACM Trans Comput Biology Bioinform, 5(1):91–100, 2008
[DOI] [PubMed]
S. Böcker and F. 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)
[DOI] [PubMed]
S. Böcker, Q. B. A. Bui, and A. Truss
An improved fixed-parameter algorithm for minimum-flip consensus trees
In M. Grohe and R. Niedermeier, editors, Proc. of International Workshop on Parameterized and Exact Computation (IWPEC 2008), volume 5018 of Lect Notes Comput Sci, pages 43–54. Springer-Verlag, 2008
[DOI]
S. Böcker, S. Briesemeister, Q. B. A. Bui, and A. 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
[DOI]
S. Böcker, S. Briesemeister, Q. B. A. Bui, and A. 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
[DOI] [Preprint]
S. Böcker, S. Briesemeister, and G. 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
[DOI]
S. Böcker, K. Jahn, J. Mixtacki, and J. 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
[DOI]
2007
S. Wernicke and F. Rasche
Simple and fast alignment of metabolic pathways by exploiting local diversity
Bioinformatics, 23(15):1978–1985, 2007
[DOI] [PubMed]
H.-M. Kaltenbach, A. Wilke, and S. Böcker
SAMPI: protein identification with mass spectra alignments
BMC Bioinformatics, 8:102, 2007
[DOI] [PubMed]
S. Böcker and H.-M. Kaltenbach
Mass spectra alignments and their significance
J Discrete Algorithms, 5(4):714–728, 2007
[DOI]
S. Böcker and Z. Lipták
A fast and simple algorithm for the Money Changing Problem
Algorithmica, 48(4):413–432, 2007
[DOI] [Reprint]
S. 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).
[DOI] [PubMed]
S. Wernicke and F. Rasche
Simple and fast alignment of metabolic pathways by exploiting local diversity
In Proc. of Asia-Pacific Bioinformatic Conference (APBC 2007), Advances in Bioinformatics and Computational Biology, pages 353–362. Imperial College Press, 2007
[DOI]
A. Scherbart, W. Timm, S. Böcker, and T. W. Nattkemper
SOM-based peptide prototyping for mass spectrometry peak intensity prediction
In Proc. of Workshop on Self-Organizing Maps (WSOM 2007), 2007
[DOI]
A. Scherbart, W. Timm, S. Böcker, and T. 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
[DOI]
S. Rahmann, T. Wittkop, J. Baumbach, M. Martin, A. Truss, and S. Böcker
Exact and heuristic algorithms for weighted cluster editing
In Proc. of Computational Systems Bioinformatics (CSB 2007), volume 6, pages 391–401, 2007
[PubMed]
M. Kaltenbach, S. Böcker, and S. 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
[DOI]
2006
S. Wernicke and F. Rasche
FANMOD: a tool for fast network motif detection
Bioinformatics, 22(9):1152–1153, 2006
[DOI] [PubMed]
S. Böcker
Sequencing from compomers: the puzzle
Theory Comput Syst, 39(3):455–471, 2006
[DOI] [Reprint]
W. Timm, S. Böcker, T. Twellmann, and T. 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
M. Dom, J. Guo, F. Hüffner, R. Niedermeier, and A. 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
S. Böcker, M. Letzel, Z. Lipták, and A. 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
[DOI]
S. Böcker and V. Mäkinen
Combinatorial approaches for mass spectra recalibration
In C. Huber, O. Kohlbacher, and K. Reinert, editors, Computational Proteomics, number 05471 in Dagstuhl Seminar Proceedings. Internationales Begegnungs- und Forschungszentrum (IBFI), Schloss Dagstuhl, Germany, 2006
2005
M. Ehrich, S. Böcker, and D. van den Boom
Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS
Nucleic Acids Res, 33(4):e38, 2005
[DOI] [PubMed]
S. Böcker and J. Stoye
Informatische Methoden zur Protein- und Metaboliten-Identifikation mittels Massenspektrometrie
LaborPraxis, 10:24–26, 2005. German
S. Böcker and Z. Lipták
The Money Changing Problem revisited: computing the Frobenius number in time O(k a1)
In Proc. of Computing and Combinatorics Conference (COCOON 2005), volume 3595 of Lect Notes Comput Sci, pages 965–974. Springer, Berlin, 2005
S. Böcker and V. 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
S. Böcker and H.-M. 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
S. Böcker and Z. Lipták
Efficient mass decomposition
In Proc. of ACM Symposium on Applied Computing (ACM SAC 2005), pages 151–157. ACM press, New York, 2005
H.-M. Kaltenbach, H. Sudek, S. Böcker, and S. Rahmann
Statistics of cleavage fragments in random weighted strings
Technical report TR-2005-06, 2005
[Preprint]
2004
P. Stanssens, M. Zabeau, G. Meersseman, G. Remes, Y. Gansemans, N. Storm, R. Hartmer, C. Honisch, C. P. Rodi, S. Böcker, and D. van den Boom
High-throughput MALDI-TOF discovery of genomic sequence polymorphisms
Genome Res, 14:126–133, 2004
M. Lefmann, C. Honisch, S. Böcker, N. Storm, F. von Wintzingerode, C. Schlötelburg, A. Moter, D. van den Boom, and U. B. Göbel
A novel mass spectrometry based tool for genotypic identification of mycobacteria
J Clin Microbiol, 42(1):339–346, 2004. [DOI]
[PubMed]
S. Böcker
Sequencing from compomers: using mass spectrometry for DNA de-novo sequencing of 200+ nt
J Comput Biol, 11(6):1110–1134, 2004
[DOI] [PubMed]
S. 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
S. Böcker
Sequencing from compomers: the puzzle
In Proc. of FUN with Algorithms 2004, pages 132–146, Tuscany, Italy, 2004
S. Böcker
Unrooted supertrees: limitations, traps, and phylogenetic patchworks
In O. R. Bininda-Emonds, editor, Phylogenetic supertrees: Combining information to reveal the Tree of Life. Volume 4, Computational Biology Book Series, Chapter 15, pages 331–351. Kluwer Academic, 2004
[Preprint]
S. Böcker
Sequencing From Compomers is NP-hard
Technical report TR-2004-01, 2004
S. Böcker and Z. Lipták
The Money Changing Problem Revisited: Computing the Frobenius Number in Time O(ka1). Technical Report TR-2004-02, 2004
2003
R. Hartmer, N. Storm, S. Boecker, C. P. Rodi, F. Hillenkamp, C. Jurinke, and D. 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
[DOI] [PubMed]
S. 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)
[DOI] [PubMed]
S. 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
[DOI]
S. Böcker
SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry
Technical report TR-2003-02, 2003
[Preprint]
S. Böcker
Sequencing from compomers: Using mass spectrometry for DNA de-novo sequencing of 200+ nt
Technical report TR-2003-04, 2003
[Preprint]
S. Böcker
Sequencing from compomers in the presence of false negative peaks
Technical report TR-2003-07, 2003
[Preprint]
2002
F. von Wintzingerode, S. Böcker, C. Schlötelburg, N. H. Chiu, N. Storm, C. Jurinke, C. R. Cantor, U. B. Göbel, and D. 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
[DOI]
S. Böcker
Exponentially many supertrees
Appl Math Let, 15(7):861–865, 2002
[DOI]
2001
S. Böcker and A. W. Dress
Patchworks
Adv Math, 157(1):1–21, 2001
[DOI]
2000
M. A. Steel, A. W. Dress, and S. Böcker
Simple but fundamental limitations on supertree and consensus tree methods
Syst Biol, 49(2):363–368, 2000
[PubMed]
S. Böcker and A. W. Dress
A note on maximal hierarchies
Adv Math, 151(2):270–282, 2000
[DOI]
S. Böcker, D. Bryant, A. W. Dress, and M. A. Steel
Algorithmic aspects of tree amalgamation
J Algorithms, 37:522–537, 2000
[DOI]
1999
S. Böcker, A. W. Dress, and M. A. Steel
Patching up X -trees
Ann Comb, 3:1–12, 1999
1998
S. Böcker and A. W. Dress
Recovering symbolically dated, rooted trees from symbolic ultrametrics
Adv Math, 138(1):105–125, 1998
[DOI]