Works by Böcker, Sebastian

Results: 47

Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 4, p. e38, doi. 10.1093/nar/gni038

By:

Ehrich, Mathias;
Böcker, Sebastian;
van den Boom, Dirk

Publication type:

Article

Design of chromatographic separations on reversed phase.

Published in:

Separation Science & Technology, 2002, v. 37, n. 7, p. 1725

By:

Böcker, Sebastian;
Mazzotti, Marco;
Morbidelli, Massimo;
Fleury, Christian;
Schenkel, Berthold

Publication type:

Article

Significance estimation for large scale metabolomics annotations by spectral matching.

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-01318-5

By:

Scheubert, Kerstin;
Hufsky, Franziska;
Petras, Daniel;
Wang, Mingxun;
Nothias, Louis-Félix;
Dührkop, Kai;
Bandeira, Nuno;
Dorrestein, Pieter C.;
Böcker, Sebastian

Publication type:

Article

Identifying gene clusters by discovering common intervals in indeterminate strings.

Published in:

BMC Genomics, 2014, v. 15, p. 1, doi. 10.1186/1471-2164-15-S6-S2

By:

Doerr, Daniel;
Stoye, Jens;
Böcker, Sebastian;
Jahn, Katharina

Publication type:

Article

Coverage bias in small molecule machine learning.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-024-55462-w

By:

Kretschmer, Fleming;
Seipp, Jan;
Ludwig, Marcus;
Klau, Gunnar W.;
Böcker, Sebastian

Publication type:

Article

Exploring the Limits of the Geometric Copolymerization Model.

Published in:

Polymers (20734360), 2017, v. 9, n. 3, p. 101, doi. 10.3390/polym9030101

By:

Engler, Martin S.;
Scheubert, Kerstin;
Schubert, Ulrich S.;
Böcker, Sebastian

Publication type:

Article

Abundance correction for mass discrimination effects in polymer mass spectra.

Published in:

Rapid Communications in Mass Spectrometry: RCM, 2016, v. 30, n. 10, p. 1233, doi. 10.1002/rcm.7553

By:

Engler, Martin S.;
Crotty, Sarah;
Barthel, Markus J.;
Pietsch, Christian;
Schubert, Ulrich S.;
Böcker, Sebastian

Publication type:

Article

Bad Clade Deletion Supertrees: A Fast and Accurate Supertree Algorithm.

Published in:

Molecular Biology & Evolution, 2017, v. 34, n. 9, p. 2408, doi. 10.1093/molbev/msx191

By:

Fleischauer, Markus;
Böcker, Sebastian

Publication type:

Article

Correcting mass shifts: A lock mass-free recalibration procedure for mass spectrometry imaging data.

Published in:

Analytical & Bioanalytical Chemistry, 2015, v. 407, n. 25, p. 7603, doi. 10.1007/s00216-015-8935-4

By:

Kulkarni, Purva;
Kaftan, Filip;
Kynast, Philipp;
Svatoš, Aleš;
Böcker, Sebastian

Publication type:

Article

Computational mass spectrometry for metabolomics: Identification of metabolites and small molecules.

Published in:

Analytical & Bioanalytical Chemistry, 2010, v. 398, n. 7/8, p. 2779, doi. 10.1007/s00216-010-4142-5

By:

Neumann, Steffen;
Böcker, Sebastian

Publication type:

Article

Drosophila melanogaster chemical ecology revisited: 2-D distribution maps of sex pheromones on whole virgin and mated flies by mass spectrometry imaging.

Published in:

BMC Zoology, 2020, v. 5, n. 1, p. 1, doi. 10.1186/s40850-020-00053-7

By:

Kaftan, Filip;
Kulkarni, Purva;
Knaden, Markus;
Böcker, Sebastian;
Hansson, Bill S.;
Svatoš, Aleš

Publication type:

Article

Correction: Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina).

Published in:

2016

By:

Schwartze, Volker U.;
Winter, Sascha;
Shelest, Ekaterina;
Marcet-Houben, Marina;
Horn, Fabian;
Wehner, Stefanie;
Linde, Jörg;
Valiante, Vito;
Sammeth, Michael;
Riege, Konstantin;
Nowrousian, Minou;
Kaerger, Kerstin;
Jacobsen, Ilse D.;
Marz, Manja;
Brakhage, Axel A.;
Gabaldón, Toni;
Böcker, Sebastian;
Voigt, Kerstin

Publication type:

Correction Notice

De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation.

Published in:

Electrophoresis, 2009, v. 30, n. 21, p. 3736, doi. 10.1002/elps.200900332

By:

Bertsch, Andreas;
Leinenbach, Andreas;
Pervukhin, Anton;
Lubeck, Markus;
Hartmer, Ralf;
Baessmann, Carsten;
Elnakady, Yasser Abbas;
Müller, Rolf;
Böcker, Sebastian;
Huber, Christian G.;
Kohlbacher, Oliver

Publication type:

Article

Critical Assessment of Small Molecule Identification 2016: automated methods.

Published in:

Journal of Cheminformatics, 2017, v. 9, n. 1, p. 1, doi. 10.1186/s13321-017-0207-1

By:

Schymanski, Emma;
Ruttkies, Christoph;
Krauss, Martin;
Brouard, Céline;
Kind, Tobias;
Dührkop, Kai;
Allen, Felicity;
Vaniya, Arpana;
Verdegem, Dries;
Böcker, Sebastian;
Rousu, Juho;
Shen, Huibin;
Tsugawa, Hiroshi;
Sajed, Tanvir;
Fiehn, Oliver;
Ghesquière, Bart;
Neumann, Steffen

Publication type:

Article

Fragmentation trees reloaded.

Published in:

Journal of Cheminformatics, 2016, v. 8, n. 1, p. 1, doi. 10.1186/s13321-016-0116-8

By:

Böcker, Sebastian;
Dührkop, Kai

Publication type:

Article

Computational mass spectrometry for small molecules.

Published in:

Journal of Cheminformatics, 2013, v. 5, n. 1, p. 1, doi. 10.1186/1758-2946-5-12

By:

Scheubert, Kerstin;
Hufsky, Franziska;
Böcker, Sebastian

Publication type:

Article

Sequencing from Compomers: The Puzzle.

Published in:

Theory of Computing Systems, 2006, v. 39, n. 3, p. 455, doi. 10.1007/s00224-005-1238-y

By:

Böcker, Sebastian

Publication type:

Article

Metabolite identification through multiple kernel learning on fragmentation trees.

Published in:

Bioinformatics, 2014, v. 30, n. 12, p. i157, doi. 10.1093/bioinformatics/btu275

By:

Shen, Huibin;
Dührkop, Kai;
Böcker, Sebastian;
Rousu, Juho

Publication type:

Article

Fast alignment of fragmentation trees.

Published in:

Bioinformatics, 2012, v. 28, n. 12, p. i265, doi. 10.1093/bioinformatics/bts207

By:

Hufsky, Franziska;
Dührkop, Kai;
Rasche, Florian;
Chimani, Markus;
Böcker, Sebastian

Publication type:

Article

Automated bond order assignment as an optimization problem.

Published in:

Bioinformatics, 2011, v. 27, n. 5, p. 619, doi. 10.1093/bioinformatics/btq718

By:

Dehof, Anna Katharina;
Rurainski, Alexander;
Bui, Quang Bao Anh;
Böcker, Sebastian;
Lenhof, Hans-Peter;
Hildebrandt, Andreas

Publication type:

Article

EPoS: a modular software framework for phylogenetic analysis.

Published in:

Bioinformatics, 2008, v. 24, n. 20, p. 2399, doi. 10.1093/bioinformatics/btn364

By:

Thasso Griebel;
Malte Brinkmeyer;
Sebastian Böcker

Publication type:

Article

Towards de novo identification of metabolites by analyzing tandem mass spectra.

Published in:

Bioinformatics, 2008, v. 24, n. 16, p. i49, doi. 10.1093/bioinformatics/btn270

By:

Sebastian Böcker;
Florian Rasche

Publication type:

Article

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

Published in:

Bioinformatics, 2007, v. 23, n. 2, p. e5, doi. 10.1093/bioinformatics/btl291

By:

Sebastian Böcker

Publication type:

Article

Illuminating the dark metabolome of Pseudo‐nitzschia–microbiome associations.

Published in:

Environmental Microbiology, 2022, v. 24, n. 11, p. 5408, doi. 10.1111/1462-2920.16242

By:

Koester, Irina;
Quinlan, Zachary A.;
Nothias, Louis‐Félix;
White, Margot E.;
Rabines, Ariel;
Petras, Daniel;
Brunson, John K.;
Dührkop, Kai;
Ludwig, Marcus;
Böcker, Sebastian;
Azam, Farooq;
Allen, Andrew E.;
Dorrestein, Pieter C.;
Aluwihare, Lihini I.

Publication type:

Article

High-confidence structural annotation of metabolites absent from spectral libraries.

Published in:

Nature Biotechnology, 2022, v. 40, n. 3, p. 411, doi. 10.1038/s41587-021-01045-9

By:

Hoffmann, Martin A.;
Nothias, Louis-Félix;
Ludwig, Marcus;
Fleischauer, Markus;
Gentry, Emily C.;
Witting, Michael;
Dorrestein, Pieter C.;
Dührkop, Kai;
Böcker, Sebastian

Publication type:

Article

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra.

Published in:

Nature Biotechnology, 2021, v. 39, n. 4, p. 462, doi. 10.1038/s41587-020-0740-8

By:

Dührkop, Kai;
Nothias, Louis-Félix;
Fleischauer, Markus;
Reher, Raphael;
Ludwig, Marcus;
Hoffmann, Martin A.;
Petras, Daniel;
Gerwick, William H.;
Rousu, Juho;
Dorrestein, Pieter C.;
Böcker, Sebastian

Publication type:

Article

Statistics for approximate gene clusters.

Published in:

BMC Bioinformatics, 2013, v. 14, n. Suppl 15, p. 1, doi. 10.1186/1471-2105-14-S15-S14

By:

Jahn, Katharina;
Winter, Sascha;
Stoye, Jens;
Böcker, Sebastian

Publication type:

Article

Swiftly Computing Center Strings.

Published in:

BMC Bioinformatics, 2011, v. 12, n. 1, p. 106, doi. 10.1186/1471-2105-12-106

By:

Hufsky, Franziska;
Kuchenbecker, Léon;
Jahn, Katharina;
Stoye, Jens;
Böcker, Sebastian

Publication type:

Article

On optimal comparability editing with applications to molecular diagnostics.

Published in:

BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-S1-S61

By:

Böcker, Sebastian;
Briesemeister, Sebastian;
Klau, Gunnar W.

Publication type:

Article

Current status of retention time prediction in metabolite identification.

Published in:

Journal of Separation Science, 2020, v. 43, n. 9/10, p. 1746, doi. 10.1002/jssc.202000060

By:

Witting, Michael;
Böcker, Sebastian

Publication type:

Article

Counting glycans revisited.

Published in:

Journal of Mathematical Biology, 2014, v. 69, n. 4, p. 799, doi. 10.1007/s00285-013-0721-3

By:

Böcker, Sebastian;
Wagner, Stephan

Publication type:

Article

Liquid-chromatography retention order prediction for metabolite identification.

Published in:

Bioinformatics, 2018, v. 34, n. 17, p. i875, doi. 10.1093/bioinformatics/bty590

By:

Bach, Eric;
Szedmak, Sandor;
Brouard, Céline;
Böcker, Sebastian;
Rousu, Juho

Publication type:

Article

Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints.

Published in:

Bioinformatics, 2018, v. 34, n. 13, p. i333, doi. 10.1093/bioinformatics/bty245

By:

Ludwig, Marcus;
Dührkop, Kai;
Böcker, Sebastian

Publication type:

Article

Fast metabolite identification with Input Output Kernel Regression.

Published in:

Bioinformatics, 2016, v. 32, n. 12, p. i28, doi. 10.1093/bioinformatics/btw246

By:

Brouard, Céline;
Shen, Huibin;
Dührkop, Kai;
d'Alché-Buc, Florence;
Böcker, Sebastian;
Rousu, Juho

Publication type:

Article

MAD HATTER Correctly Annotates 98% of Small Molecule Tandem Mass Spectra Searching in PubChem.

Published in:

Metabolites (2218-1989), 2023, v. 13, n. 3, p. 314, doi. 10.3390/metabo13030314

By:

Hoffmann, Martin A.;
Kretschmer, Fleming;
Ludwig, Marcus;
Böcker, Sebastian

Publication type:

Article

Finding approximate gene clusters with GECKO 3.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 20, p. 9600, doi. 10.1093/nar/gkw843

By:

Winter, Sascha;
Jahn, Katharina;
Wehner, Stefanie;
Kuchenbecker, Leon;
Marz, Manja;
Stoye, Jens;
Böcker, Sebastian

Publication type:

Article

New Statistical Models for Copolymerization.

Published in:

Polymers (20734360), 2016, v. 8, n. 6, p. 240, doi. 10.3390/polym8060240

By:

Engler, Martin S.;
Scheubert, Kerstin;
Schubert, Ulrich S.;
Böcker, Sebastian

Publication type:

Article

Polynomial Supertree Methods Revisited.

Published in:

Advances in Bioinformatics, 2011, p. 1, doi. 10.1155/2011/524182

By:

Brinkmeyer, Malte;
Griebel, Thasso;
Böcker, Sebastian

Publication type:

Article

Unbiased Transcriptional Comparisons of Generalist and Specialist Herbivores Feeding on Progressively Defenseless Nicotiana attenuata Plants.

Published in:

PLoS ONE, 2010, v. 5, n. 1, p. 1, doi. 10.1371/journal.pone.0008735

By:

Govind, Geetha;
Mittapalli, Omprakash;
Griebel, Thasso;
Allmann, Silke;
Böcker, Sebastian;
Baldwin, Ian Thomas

Publication type:

Article

Critical assessment of chromatographic metadata in publicly available metabolomics data repositories.

Published in:

Metabolomics, 2022, v. 18, n. 12, p. 1, doi. 10.1007/s11306-022-01956-x

By:

Harrieder, Eva-Maria;
Kretschmer, Fleming;
Dunn, Warwick;
Böcker, Sebastian;
Witting, Michael

Publication type:

Article

Gene Expansion Shapes Genome Architecture in the Human Pathogen <i>Lichtheimia corymbifera</i>: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina).

Published in:

PLoS Genetics, 2014, v. 10, n. 8, p. 1, doi. 10.1371/journal.pgen.1004496

By:

Schwartze, Volker U.;
Winter, Sascha;
Shelest, Ekaterina;
Marcet-Houben, Marina;
Horn, Fabian;
Wehner, Stefanie;
Linde, Jörg;
Valiante, Vito;
Sammeth, Michael;
Riege, Konstantin;
Nowrousian, Minou;
Kaerger, Kerstin;
Jacobsen, Ilse D.;
Marz, Manja;
Brakhage, Axel A.;
Gabaldón, Toni;
Böcker, Sebastian;
Voigt, Kerstin

Publication type:

Article

BCD Beam Search: considering suboptimal partial solutions in Bad Clade Deletion supertrees.

Published in:

PeerJ, 2018, p. 1, doi. 10.7717/peerj.4987

By:

Fleischauer, Markus;
Böcker, Sebastian

Publication type:

Article

Secondary ion mass spectrometry imaging and multivariate data analysis reveal co-aggregation patterns of Populus trichocarpa leaf surface compounds on a micrometer scale.

Published in:

Plant Journal, 2018, v. 93, n. 1, p. 193, doi. 10.1111/tpj.13763

By:

Kulkarni, Purva;
Dost, Mina;
Bulut, Özgül Demir;
Welle, Alexander;
Böcker, Sebastian;
Boland, Wilhelm;
Svatoš, Aleš

Publication type:

Article

Mining molecular structure databases: Identification of small molecules based on fragmentation mass spectrometry data.

Published in:

Mass Spectrometry Reviews, 2017, v. 36, n. 5, p. 624, doi. 10.1002/mas.21489

By:

Hufsky, Franziska;
Böcker, Sebastian

Publication type:

Article

Mass spectrometry imaging of surface lipids on intact Drosophila melanogaster flies.

Published in:

Journal of Mass Spectrometry, 2014, v. 49, n. 3, p. 223, doi. 10.1002/jms.3331

By:

Kaftan, Filip;
Vrkoslav, Vladimír;
Kynast, Philipp;
Kulkarni, Purva;
Böcker, Sebastian;
Cvačka, Josef;
Knaden, Markus;
Svatoš, Aleš

Publication type:

Article

Analysis of different synthetic homopolymers by the use of a new calculation software for tandem mass spectra.

Published in:

Rapid Communications in Mass Spectrometry: RCM, 2011, v. 25, n. 12, p. 1765, doi. 10.1002/rcm.5019

By:

Baumgaertel, Anja;
Scheubert, Kerstin;
Pietsch, Bernhard;
Kempe, Kristian;
Crecelius, Anna C.;
Böcker, Sebastian;
Schubert, Ulrich S.

Publication type:

Article

Partitioning biological data with transitivity clustering.

Published in:

2010

By:

Wittkop, Tobias;
Emig, Dorothea;
Lange, Sita;
Rahmann, Sven;
Albrecht, Mario;
Morris, John H.;
Böcker, Sebastian;
Stoye, Jens;
Baumbach, Jan

Publication type:

Letter