Sebastian Böcker

发表

Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics

William Stafford Noble, S. Degroeve, Mathias Wilhelm, 2022, Journal of proteome research.

Computational mass spectrometry for small molecules

Sebastian Böcker, Franziska Hufsky, Kerstin Scheubert, 2013, Journal of Cheminformatics.

Comment on: “An Efficient Method to Calculate the Aggregated Isotopic Distribution and Exact Center-Masses” by Jürgen Claesen, Piotr Dittwald, Tomasz Burzykowski, Dirk Valkenborg, J. Am. Soc. Mass Spectrom. 2012, 23, 753–763

Sebastian Böcker, S. Böcker, Sebastian Böcker, 2012, Journal of The American Society for Mass Spectrometry.

Comment on “ An Efficient Method to Calculate the Aggregated Isotopic Distribution and Exact Center-Masses ” by Claesen et al .

Sebastian Böcker, Sebastian Böcker, 2012 .

Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spectrometry: A tool for rapid bacterial identification

Sebastian Böcker, Niels Storm, Friedrich von Wintzingerode, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Current state-of-the-art of separation methods used in LC-MS based metabolomics and lipidomics.

S. Böcker, M. Witting, Eva-Maria Harrieder, 2021, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

S. Böcker, P. Dorrestein, Kai Dührkop, 2019, Nature Methods.

High-confidence structural annotation of metabolites absent from spectral libraries

Emily C. Gentry, Martin A. Hoffmann, S. Böcker, 2021, Nature Biotechnology.

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

Juho Rousu, Sebastian Böcker, Markus Fleischauer, 2020, Nature Biotechnology.

Database-independent molecular formula annotation using Gibbs sampling through ZODIAC

Pieter C. Dorrestein, Sebastian Böcker, Markus Fleischauer, 2020, Nature Machine Intelligence.

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

S. Böcker, Kai Dührkop, Juho Rousu, 2015, Proceedings of the National Academy of Sciences.

Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics

Tim W. Nattkemper, Oliver Kohlbacher, Sebastian Böcker, 2008, BMC Bioinformatics.

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

S. Böcker, M. Sammeth, M. Marz, 2016, PLoS genetics.

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

Kerstin Voigt, Manja Marz, Sebastian Böcker, 2014, PLoS genetics.

Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

Se Jin Song, Luke R. Thompson, James T. Morton, 2022, Nature Microbiology.

UvA-DARE ( Digital Academic Repository ) Unbiased Transcriptional Comparisons of Generalist and Specialist Herbivores Feeding on Progressively Defenseless Nicotiana attenuata Plants

S. Böcker, Thasso Griebel, I. Baldwin, 2010 .

Combinatorial Approaches for Mass Spectra Recalibration

Veli Mäkinen, Sebastian Böcker, S. Böcker, 2005, IEEE ACM Trans. Comput. Biol. Bioinform..

Combinatorial Approaches for Mass Spectra Recalibration

S. Böcker, V. Mäkinen, Sebastian Böcker, 2008, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Computing bond orders in molecule graphs

Sebastian Böcker, Quang Bao Anh Bui, Anke Truß, 2011, Theor. Comput. Sci..

Computing Bond Types in Molecule Graphs

Sebastian Böcker, Quang Bao Anh Bui, Anke Truß, 2009, COCOON.

BERTax: taxonomic classification of DNA sequences with Deep Neural Networks

S. Böcker, M. Marz, Florian Mock, 2021, bioRxiv.

Magnitude-Preserving Ranking for Structured Outputs

Juho Rousu, Eric Bach, Sebastian Böcker, 2017, ACML.

Feature-Based Molecular Networking in the GNPS Analysis Environment

Simon Rogers, Nuno Bandeira, Mingxun Wang, 2019, Nature Methods.

Critical Assessment of Small Molecule Identification 2016: automated methods

Juho Rousu, Martin Krauss, Emma L. Schymanski, 2017, Journal of Cheminformatics.

Correction to 'Illuminating the dark metabolome of Pseudo-nitzschia-microbiome associations'.

S. Böcker, P. Dorrestein, Kai Dührkop, 2023, Environmental microbiology.

High-confidence structural annotation of metabolites absent from spectral libraries

Emily C. Gentry, Martin A. Hoffmann, S. Böcker, 2021, Nature Biotechnology.

Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment

Emily C. Gentry, Allegra T. Aron, Kelly C. Weldon, 2021, Nature Communications.

Novel Mass Spectrometry-Based Tool for Genotypic Identification of Mycobacteria

Sebastian Böcker, Michael Lefmann, Christiane Honisch, 2004, Journal of Clinical Microbiology.

Integrative analysis of multimodal mass spectrometry data in MZmine 3

Timothy R. Fallon, S. Böcker, P. Dorrestein, 2023, Nature Biotechnology.

Predicting the Presence of Uncommon Elements in Unknown Biomolecules from Isotope Patterns.

Sebastian Böcker, Rolf Müller, Franziska Hufsky, 2016, Analytical chemistry.

Fragmentation trees reloaded

Sebastian Böcker, Kai Dührkop, S. Böcker, 2014, Journal of Cheminformatics.

MSNovelist: de novo structure generation from mass spectra

Michael A. Stravs, S. Böcker, Kai Dührkop, 2021, Nature Methods.

Munronia pinnata (Wall.) Theob.: unveiling phytochemistry and dual inhibition of 5-lipoxygenase and microsomal prostaglandin E2 synthase (mPGES)-1.

S. Böcker, O. Werz, A. Koeberle, 2014, Journal of ethnopharmacology.

SIRIUS: decomposing isotope patterns for metabolite identification†

Zsuzsanna Lipták, Sebastian Böcker, Anton Pervukhin, 2008, Bioinform..

Partitioning biological data with transitivity clustering

Dorothea Emig, Mario Albrecht, Jens Stoye, 2010, Nature Methods.

Classes for the masses: Systematic classification of unknowns using fragmentation spectra

Juho Rousu, Pieter C. Dorrestein, Sebastian Böcker, 2020, bioRxiv.

Multi-omics profiling of Earth’s biomes reveals that microbial and metabolite composition are shaped by the environment

Se Jin Song, Luke R. Thompson, James T. Morton, 2021 .

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree

Justin J. J. van der Hooft, Mingxun Wang, Pieter C. Dorrestein, 2020, Nature Chemical Biology.

Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree

Justin J.J. van der Hooft, Jo Handelsman, Mingxun Wang, 2020, bioRxiv.

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

Sebastian Böcker, Markus Fleischauer, S. Böcker, 2018, PeerJ.

Bad Clade Deletion Supertrees: A Fast and Accurate Supertree Algorithm

S. Böcker, M. Fleischauer, Markus Fleischauer, 2017, Molecular biology and evolution.

Simple but fundamental limitations on supertree and consensus tree methods.

M Steel, S. Böcker, M. Steel, 2000, Systematic biology.

Metabolite identification through multiple kernel learning on fragmentation trees

Juho Rousu, Sebastian Böcker, Huibin Shen, 2014, Bioinform..

Identifying the unknowns by aligning fragmentation trees.

Thomas Zichner, Florian Rasche, Sebastian Böcker, 2012, Analytical chemistry.

Towards de novo identification of metabolites by analyzing tandem mass spectra

Florian Rasche, Sebastian Böcker, S. Böcker, 2008, ECCB.

Mass Difference Matching Unfolds Hidden Molecular Structures of Dissolved Organic Matter

S. Böcker, P. Dorrestein, Kai Dührkop, 2022, Environmental science & technology.

Mass difference matching crystallizes hidden molecular structures of dissolved organic matter from ultrahigh-resolution tandem mass spectra

S. Böcker, P. Dorrestein, Kai Dührkop, 2021 .

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

S. Böcker, S. Neumann, Sebastian Böcker, 2010, Analytical and bioanalytical chemistry.

Small molecule machine learning: All models are wrong, some may not even be useful

G. Klau, M. Ludwig, Fleming Kretschmer, 2023, bioRxiv.

De Novo Molecular Formula Annotation and Structure Elucidation Using SIRIUS 4.

Sebastian Böcker, Markus Fleischauer, Kai Dührkop, 2020, Methods in molecular biology.

De novo analysis of electron impact mass spectra using fragmentation trees.

Florian Rasche, Martin Rempt, Sebastian Böcker, 2012, Analytica chimica acta.

Finding Maximum Colorful Subtrees in Practice

Florian Rasche, François Nicolas, Sebastian Böcker, 2012, RECOMB.

Computing fragmentation trees from tandem mass spectrometry data.

Florian Rasche, Sebastian Böcker, S. Böcker, 2011, Analytical chemistry.

Annotating Fragmentation Patterns

Florian Rasche, Tamara Steijger, Sebastian Böcker, 2009, WABI.

Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data

Florian Rasche, Sebastian Böcker, Franziska Hufsky, 2011, RECOMB.

Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints

Sebastian Böcker, Kai Dührkop, Marcus Ludwig, 2018, Bioinform..

Abundance correction for mass discrimination effects in polymer mass spectra.

Martin S. Engler, S. Böcker, U. Schubert, 2016, Rapid communications in mass spectrometry : RCM.

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

Oliver Kohlbacher, Christian G Huber, Sebastian Böcker, 2009, Electrophoresis.

Studying Charge Migration Fragmentation of Sodiated Precursor Ions in Collision-Induced Dissociation at the Library Scale.

Emma L. Schymanski, S. Böcker, P. Dorrestein, 2020, Journal of the American Society for Mass Spectrometry.

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.

S. Böcker, I. Baldwin, K. Groten, 2012, Journal of proteome research.

Collecting reliable clades using the Greedy Strict Consensus Merger

S. Böcker, M. Fleischauer, Markus Fleischauer, 2016, PeerJ Prepr..

Intractability of the Minimum-Flip Supertree problem and its variants pdf

François Nicolas, Sebastian Böcker, Quang Bao Anh Bui, 2011, ArXiv.

FlipCut Supertrees: Towards Matrix Representation Accuracy in Polynomial Time

S. Böcker, Thasso Griebel, Malte Brinkmeyer, 2011, Algorithmica.

Towards a Data Reduction for the Minimum Flip Supertree Problem pdf

Sebastian Böcker, S. Böcker, Sebastian Böcker, 2011, ArXiv.

Polynomial Supertree Methods Revisited

Sebastian Böcker, Malte Brinkmeyer, Thasso Griebel, 2010, PRIB.

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

Martin A. Hoffmann, M. Ludwig, Fleming Kretschmer, 2022, bioRxiv.

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

S. Böcker, M. Ehrich, D. van den Boom, 2005, Nucleic acids research.

Liquid‐chromatography retention order prediction for metabolite identification

Juho Rousu, Eric Bach, Sándor Szedmák, 2018, Bioinform..

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

Sebastian Böcker, Franziska Hufsky, S. Böcker, 2017, Mass spectrometry reviews.

Searching molecular structure databases using tandem MS data: are we there yet?

Sebastian Böcker, S. Böcker, Sebastian Böcker, 2017, Current opinion in chemical biology.

New kids on the block: novel informatics methods for natural product discovery.

Sebastian Böcker, Franziska Hufsky, Kerstin Scheubert, 2014, Natural product reports.

Fast metabolite identification with Input Output Kernel Regression

Juho Rousu, Florence d'Alché-Buc, Sebastian Böcker, 2016, Bioinform..

Molecular Formula Identification Using Isotope Pattern Analysis and Calculation of Fragmentation Trees.

Sebastian Böcker, Kai Dührkop, Franziska Hufsky, 2014, Mass spectrometry.

Expanding the Use of Spectral Libraries in Proteomics.

Johannes Griss, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2018, Journal of proteome research.

A golden ratio parameterized algorithm for Cluster Editing

Sebastian Böcker, Sebastian Böcker, 2011, J. Discrete Algorithms.

Even faster parameterized cluster deletion and cluster editing

Peter Damaschke, Sebastian Böcker, P. Damaschke, 2011, Inf. Process. Lett..

Going weighted: Parameterized algorithms for cluster editing

Sebastian Böcker, Quang Bao Anh Bui, Anke Truß, 2008, Theor. Comput. Sci..

Exact Algorithms for Cluster Editing: Evaluation and Experiments

Sebastian Böcker, Gunnar W. Klau, Sebastian Briesemeister, 2008, Algorithmica.

Exploring the Limits of the Geometric Copolymerization Model

Martin S. Engler, S. Böcker, U. Schubert, 2017, Polymers.

Faster Mass Decomposition

Sebastian Böcker, Kai Dührkop, Marcus Ludwig, 2013, WABI.

Algorithmic Aspects of Tree Amalgamation

Mike A. Steel, David Bryant, Andreas W. M. Dress, 2000, J. Algorithms.

Limitations , traps , and phylogenetic patchworks

S. Böcker, Sebastian Böcker, 2004 .

A Fixed-Parameter Approach for Weighted Cluster Editing

Sebastian Böcker, Quang Bao Anh Bui, Anke Truß, 2007, APBC.

Current status of retention time prediction in metabolite identification.

S. Böcker, M. Witting, Sebastian Böcker, 2020, Journal of separation science.

Multiple Mass Spectrometry Fragmentation Trees Revisited: Boosting Performance and Quality

Sebastian Böcker, Franziska Hufsky, Kerstin Scheubert, 2014, WABI.

Comparing Fragmentation Trees from Electron Impact Mass Spectra with Annotated Fragmentation Pathways

Sebastian Böcker, Franziska Hufsky, S. Böcker, 2012, GCB.

Finding Characteristic Substructures for Metabolite Classes

Sebastian Böcker, Samy Elshamy, Marcus Ludwig, 2012, GCB.

Computational mass spectrometry for small-molecule fragmentation

Sebastian Böcker, Franziska Hufsky, Kerstin Scheubert, 2014 .

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

S. Böcker, A. Svatoš, Purva Kulkarni, 2015, Analytical and Bioanalytical Chemistry.

Improved Fixed-Parameter Algorithms for Minimum-Flip Consensus Trees

Quang Bao Anh Bui, A. Truß, Sebastian Böcker, 2012, ACM Trans. Algorithms.

Exact ILP solutions for phylogenetic minimum flip problems

Markus Chimani, Sven Rahmann, Sebastian Böcker, 2010, BCB '10.

An Improved Fixed-Parameter Algorithm for Minimum-Flip Consensus Trees

Sebastian Böcker, Quang Bao Anh Bui, Anke Truß, 2008, IWPEC.

A Note on Maximal Hierarchies

Andreas W. M. Dress, Sebastian Böcker, S. Böcker, 2000 .

Patching upX-trees

Mike Steel, Andreas W. M. Dress, Sebastian Böcker, 1999 .

Patching Up X-Trees

Mike Steel, Andreas W. M. Dress, Sebastian Böcker, 1999 .

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

Sebastian Böcker, S. Böcker, Sebastian Böcker, 2007, Bioinform..

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

Hon Wai Leong, Veli Mäkinen, Sebastian Böcker, 2014, NII Shonan Meet. Rep..

Combinatorics of aliphatic amino acids

S. Schuster, S. Böcker, Konrad Grützmann, 2010, Naturwissenschaften.

EPoS: a modular software framework for phylogenetic analysis

Sebastian Böcker, Malte Brinkmeyer, Thasso Griebel, 2008, Bioinform..

The Money Changing Problem Revisited: Computing the Frobenius Number in Time O(k a1)

Zsuzsanna Lipták, Sebastian Böcker, Z. Lipták, 2005, COCOON.

A virtual “Werkstatt” for digitization in the sciences

Joachim Denzler, Birgitta König-Ries, Mirco Migliavacca, 2020, Research Ideas and Outcomes.

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

Juho Rousu, Sebastian Böcker, Markus Fleischauer, 2019, Nature Methods.

Bioinformatics Analysis of Heterogeneous Data Reveals Characteristic Mutational Landscapes of Neuroblastoma Relapses

Christian W. Remmele, D. Marquard, P. Lindner, 2015 .

Inferring Peptide Composition from Molecular Formulas

Sebastian Böcker, Anton Pervukhin, A. Pervukhin, 2009, COCOON.

Decomposing Metabolomic Isotope Patterns

Zsuzsanna Lipták, Sebastian Böcker, Anton Pervukhin, 2006, WABI.

Efficient mass decomposition

Zsuzsanna Lipták, Sebastian Böcker, Z. Lipták, 2005, SAC '05.

Exact and heuristic algorithms for weighted cluster editing.

Sven Rahmann, Sebastian Böcker, Marcel Martin, 2007, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.

Ion Identity Molecular Networking in the GNPS Environment

Uwe Karst, Kelly Weldon, Mingxun Wang, 2020, bioRxiv.

SIRIUS 4: Turning tandem mass spectra into metabolite structure information

S. Böcker, P. Dorrestein, Kai Dührkop, 2018 .

High-throughput MALDI-TOF discovery of genomic sequence polymorphisms.

Sebastian Böcker, Christiane Honisch, Niels Storm, 2003, Genome research.

Sequencing from Compomers: The Puzzle

Sebastian Böcker, S. Böcker, Sebastian Böcker, 2006, Theory of Computing Systems.

Predicting the Presence of Uncommon Elements in Unknown Biomolecules from Isotope Patterns.

R. Müller, Marvin Meusel, Franziska Hufsky, 2016, Analytical chemistry.

Illuminating the dark metabolome of Pseudo-nitzschia-microbiome associations.

S. Böcker, P. Dorrestein, Kai Dührkop, 2022, Environmental microbiology.

Finding approximate gene clusters with Gecko 3

Jens Stoye, Katharina Jahn, Manja Marz, 2016, Nucleic acids research.

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

S. Böcker, M. Knaden, B. Hansson, 2020, BMC Zoology.

Mapping metabolites from rough terrain: laser ablation electrospray ionization on non-flat samples

S. Böcker, H. Saluz, A. Svatoš, 2017 .

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

S. Böcker, M. Knaden, A. Svatoš, 2014, Journal of mass spectrometry : JMS.

Significance estimation for large scale metabolomics annotations by spectral matching

S. Böcker, P. Dorrestein, Kai Dührkop, 2017, Nature Communications.

LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis

Anne-Christin Hauschild, Sebastian Böcker, Vasco Azevedo, 2017, J. Integr. Bioinform..

Sequencing from Compomers: Using Mass Spectrometry for DNA De-Novo Sequencing of 200+ nt

Sebastian Böcker, S. Böcker, Sebastian Böcker, 2003, WABI.

Counting glycans revisited

Stephan G. Wagner, S. Böcker, S. Wagner, 2014, Journal of mathematical biology.

Counting glycans revisited

S. Böcker, Stephan Wagner, Sebastian Böcker, 2013, Journal of Mathematical Biology.

Towards de novo identification of metabolites by analyzing tandem mass spectra

Sebastian Böcker, Florian Rasche, 2008, ECCB.

Determination of Glycan Structure from Tandem Mass Spectra

Birte Kehr, Sebastian Böcker, Florian Rasche, 2009, IEEE/ACM Transactions on Computational Biology and Bioinformatics.