List of works - Sebastian Böcker

A virtual “Werkstatt” for digitization in the sciences

scholarly article by Sheeba Samuel et al published 11 May 2020 in Research Ideas and Outcomes

Abundance correction for mass discrimination effects in polymer mass spectra

scientific article

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

scientific article published on June 2011

Automated bond order assignment as an optimization problem

scientific article

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

scientific article published on 8 June 2018

Bad Clade Deletion Supertrees: A Fast and Accurate Supertree Algorithm

scientific article

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

scientific article

Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints.

scientific article published in July 2018

COCONUT—An Efficient Tool for Estimating Copolymer Compositions from Mass Spectra

scientific article

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree

scientific article published on 16 November 2020

Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree

scientific article published on 5 May 2020

Cluster Editing

Collecting reliable clades using the Greedy Strict Consensus Merger

scientific article published on 28 June 2016

Combinatorial approaches for mass spectra recalibration.

scientific article published in January 2008

Combinatorics of aliphatic amino acids

scientific article published in December 2010

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

scientific article published on 07 June 2012

Comprehensive cluster analysis with Transitivity Clustering

scientific article published on 10 February 2011

Computation of median gene clusters

scientific article published in August 2009

Computational Metabolomics: From Cheminformatics to Machine Learning (Dagstuhl Seminar 20051) ⬇️

proceedings

Computational Metabolomics: Identification, Interpretation, Imaging (Dagstuhl Seminar 17491)

proceedings

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

scientific article published on October 9, 2010

Computational mass spectrometry for small molecules

scientific article (publication date: March 2013)

Computational mass spectrometry for small-molecule fragmentation

scientific article published in 2014

Computing fragmentation trees from metabolite multiple mass spectrometry data

scientific article

Computing fragmentation trees from tandem mass spectrometry data

scientific article

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

scientific article

Correction to Computing Fragmentation Trees from Tandem Mass Spectrometry Data

scholarly article published in Analytical Chemistry

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

scientific article published on 5 December 2016

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

scholarly article in RSC Advances, vol. 7 no. 21, 2017

Counting glycans revisited

scientific article published on 23 August 2013

Critical Assessment of Small Molecule Identification 2016: automated methods

scientific article

Critical assessment of chromatographic metadata in publicly available metabolomics data repositories

scientific article published in 2022

Current status of retention time prediction in metabolite identification

scientific article published on 07 March 2020

DECOMP--from interpreting Mass Spectrometry peaks to solving the Money Changing Problem

scientific article published on 2 January 2008

Database-independent molecular formula annotation using Gibbs sampling through ZODIAC

scientific article published in 2020

De Novo Molecular Formula Annotation and Structure Elucidation Using SIRIUS 4

scientific article published on 01 January 2020

De novo analysis of electron impact mass spectra using fragmentation trees

scientific article

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

scientific article published in November 2009

Determination of glycan structure from tandem mass spectra

scientific article published in July 2011

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

scientific article published on 17 September 2012

EPoS: a modular software framework for phylogenetic analysis

scientific article

EXACT AND HEURISTIC ALGORITHMS FOR WEIGHTED CLUSTER EDITING

scholarly article published September 2007

Exact ILP solutions for phylogenetic minimum flip problems

Exact and heuristic algorithms for weighted cluster editing

scientific article published in January 2007

Expanding the use of spectral libraries in proteomics

Exploring the Limits of the Geometric Copolymerization Model.

scientific article published on 13 March 2017

Extension and Robustness of Transitivity Clustering for Protein–Protein Interaction Network Analysis

Fast alignment of fragmentation trees

scientific article published on June 2012

Fast metabolite identification with Input Output Kernel Regression

scientific article published on June 2016

Faster Mass Decomposition

scientific article published in 2013

Feature-based molecular networking in the GNPS analysis environment

scientific article published on 24 August 2020

Finding approximate gene clusters with Gecko 3.

scientific article

Finding maximum colorful subtrees in practice

scientific article published on 19 March 2013

Fragmentation Trees Reloaded

scientific article published in 2015

Fragmentation trees reloaded

scientific article (publication date: 2016)

Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina)

scientific article

High-confidence structural annotation of metabolites absent from spectral libraries

scientific article published on 14 October 2021

High-throughput MALDI-TOF discovery of genomic sequence polymorphisms

scientific article published in January 2004

Identifying gene clusters by discovering common intervals in indeterminate strings

scientific article published on 17 October 2014

Identifying the Unknowns by Aligning Fragmentation Trees

scientific article

Improved Mass Spectrometry Peak Intensity Prediction by Adaptive Feature Weighting

Integrative analysis of multimodal mass spectrometry data in MZmine 3

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

scientific article

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

scientific article published on 5 July 2017

Liquid-chromatography retention order prediction for metabolite identification

scientific article published on 01 September 2018

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

scientific article published in 2023

MSNovelist: de novo structure generation from mass spectra

scientific article published in 2022

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

scholarly article in RSC Advances, vol. 7 no. 15, 2017

Mass Difference Matching Unfolds Hidden Molecular Structures of Dissolved Organic Matter

scientific article published in 2022

Mass spectrometry imaging of surface lipids on intact Drosophila melanogaster flies

scientific article

Metabolite identification through multiple kernel learning on fragmentation trees

scientific article published on June 2014

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

scientific article

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

scientific article published on 18 July 2014

Molecular Formula Identification with SIRIUS.

scientific article

Multi-omics profiling of Earth’s biomes reveals patterns of diversity and co-occurrence in microbial and metabolite composition across environments

scientific article published on 6 June 2021

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

scientific article

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

scientific article published on 4 December 2013

Neural Network Approach for Mass Spectrometry Prediction by Peptide Prototyping

New Statistical Models for Copolymerization

scientific article published on 22 June 2016

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

scientific article

Novel mass spectrometry-based tool for genotypic identification of mycobacteria

scientific article

On optimal comparability editing with applications to molecular diagnostics

scientific article

Partitioning biological data with transitivity clustering

scientific article

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

scientific article

Polynomial supertree methods revisited

scientific article published on 21 December 2011

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

scientific article published on 11 July 2016

Publisher Correction: Database-independent molecular formula annotation using Gibbs sampling through ZODIAC

correction of a scholarly article

RNase T1 mediated base-specific cleavage and MALDI-TOF MS for high-throughput comparative sequence analysis

scientific article

SAMPI: protein identification with mass spectra alignments

scientific article

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

scientific article published on 18 March 2019

SIRIUS: decomposing isotope patterns for metabolite identification

scientific article published on 17 November 2008

SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry

scientific article

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

scientific article

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

scientific article published on 21 September 2015

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

scientific article

Sequencing from compomers: using mass spectrometry for DNA de novo sequencing of 200+ nt.

scientific article published in January 2004

Significance estimation for large scale metabolomics annotations by spectral matching

scientific article published on 14 November 2017

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

scientific article published in January 2007

Speedy Colorful Subtrees

scientific article published in 2015

Statistics for approximate gene clusters

scientific article

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

scientific article published on 13 November 2020

Swiftly computing center strings ⬇️

scientific article

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

scientific article published on 23 November 2020

Towards de novo identification of metabolites by analyzing tandem mass spectra

scientific article published in August 2008

Unbiased transcriptional comparisons of generalist and specialist herbivores feeding on progressively defenseless Nicotiana attenuata plants

scientific article

List of works by Sebastian Böcker

A virtual “Werkstatt” for digitization in the sciences

Abundance correction for mass discrimination effects in polymer mass spectra

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

Automated bond order assignment as an optimization problem

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

Bad Clade Deletion Supertrees: A Fast and Accurate Supertree Algorithm

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

Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints.

COCONUT—An Efficient Tool for Estimating Copolymer Compositions from Mass Spectra

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree

Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree

Cluster Editing

Collecting reliable clades using the Greedy Strict Consensus Merger

Combinatorial approaches for mass spectra recalibration.

Combinatorics of aliphatic amino acids

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

Comprehensive cluster analysis with Transitivity Clustering

Computation of median gene clusters

Computational Metabolomics: From Cheminformatics to Machine Learning (Dagstuhl Seminar 20051) ⬇️

Computational Metabolomics: Identification, Interpretation, Imaging (Dagstuhl Seminar 17491)

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

Computational mass spectrometry for small molecules

Computational mass spectrometry for small-molecule fragmentation

Computing fragmentation trees from metabolite multiple mass spectrometry data

Computing fragmentation trees from tandem mass spectrometry data

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

Correction to Computing Fragmentation Trees from Tandem Mass Spectrometry Data

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

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

Counting glycans revisited

Critical Assessment of Small Molecule Identification 2016: automated methods

Critical assessment of chromatographic metadata in publicly available metabolomics data repositories

Current status of retention time prediction in metabolite identification

DECOMP--from interpreting Mass Spectrometry peaks to solving the Money Changing Problem

Database-independent molecular formula annotation using Gibbs sampling through ZODIAC

De Novo Molecular Formula Annotation and Structure Elucidation Using SIRIUS 4

De novo analysis of electron impact mass spectra using fragmentation trees

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

Determination of glycan structure from tandem mass spectra

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

EPoS: a modular software framework for phylogenetic analysis

EXACT AND HEURISTIC ALGORITHMS FOR WEIGHTED CLUSTER EDITING

Exact ILP solutions for phylogenetic minimum flip problems

Exact and heuristic algorithms for weighted cluster editing

Expanding the use of spectral libraries in proteomics

Exploring the Limits of the Geometric Copolymerization Model.

Extension and Robustness of Transitivity Clustering for Protein–Protein Interaction Network Analysis

Fast alignment of fragmentation trees

Fast metabolite identification with Input Output Kernel Regression

Faster Mass Decomposition

Feature-based molecular networking in the GNPS analysis environment

Finding approximate gene clusters with Gecko 3.

Finding maximum colorful subtrees in practice

Fragmentation Trees Reloaded

Fragmentation trees reloaded

Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina)

High-confidence structural annotation of metabolites absent from spectral libraries

High-throughput MALDI-TOF discovery of genomic sequence polymorphisms

Identifying gene clusters by discovering common intervals in indeterminate strings

Identifying the Unknowns by Aligning Fragmentation Trees

Improved Mass Spectrometry Peak Intensity Prediction by Adaptive Feature Weighting

Integrative analysis of multimodal mass spectrometry data in MZmine 3

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

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

Liquid-chromatography retention order prediction for metabolite identification

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

MSNovelist: de novo structure generation from mass spectra

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

Mass Difference Matching Unfolds Hidden Molecular Structures of Dissolved Organic Matter

Mass spectrometry imaging of surface lipids on intact Drosophila melanogaster flies

Metabolite identification through multiple kernel learning on fragmentation trees

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

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

Molecular Formula Identification with SIRIUS.

Multi-omics profiling of Earth’s biomes reveals patterns of diversity and co-occurrence in microbial and metabolite composition across environments

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

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

Neural Network Approach for Mass Spectrometry Prediction by Peptide Prototyping

New Statistical Models for Copolymerization