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Employment (9)

Ghent University: Ghent, BE

2019-10-01 to present | Professor (Department of Biomolecular Medicine)
Employment
Source: Self-asserted source
Sven Degroeve

Vlaams Instituut voor Biotechnologie: Ghent, BE

2017-03-01 to present | Staff Scientist (VIB-UGent Center for Medical Biotechnology)
Employment
Source: Self-asserted source
Sven Degroeve

Ghent University - VIB: Ghent, BE

2009-07-01 to 2017-02-01 | Post-doctoral researcher / Machine learning scientist
Employment
Source: Self-asserted source
Sven Degroeve

MDCPartners: Antwerp, BE

2008-10-01 to 2009-03-01 | Knowledge Systems Engineer
Employment
Source: Self-asserted source
Sven Degroeve

Pronota: Zwijnaarde, BE

2005-10-01 to 2008-08-31 | Senior Scientist
Employment
Source: Self-asserted source
Sven Degroeve

Ghent University: Ghent, BE

2005-01-01 to 2005-09-30 | Post-doctoral Fellow (Applied Mathematics, Biometrics and Process Control)
Employment
Source: Self-asserted source
Sven Degroeve

Vlaams Instituut voor Biotechnologie: Ghent, BE

2001-01-01 to 2004-12-31 | Doctoral Student (Plant Systems Biology)
Employment
Source: Self-asserted source
Sven Degroeve

Tibotec-Virco Virology BVBA: Mechelen, BE

2001-01-01 to 2001-12-31 | Researcher
Employment
Source: Self-asserted source
Sven Degroeve

Lernout & Hauspie: Ieper, BE

1999-09-01 to 2000-12-31 | Research Assistant (Centre for Evolutionary Language Engineering (CELE))
Employment
Source: Self-asserted source
Sven Degroeve

Works (48)

MS2Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0

Journal of Proteome Research
2024-08-02 | Journal article
DOI: 10.1021/acs.jproteome.3c00785
Contributors: Louise M. Buur; Arthur Declercq; Marina Strobl; Robbin Bouwmeester; Sven Degroeve; Lennart Martens; Viktoria Dorfer; Ralf Gabriels
Source: check_circle
Crossref

Predicting ion mobility collision cross sections and assessing prediction variation by combining conventional and data driven modeling

Talanta
2024-07 | Journal article
DOI: 10.1016/j.talanta.2024.125970
Contributors: Robbin Bouwmeester; Keith Richardson; Richard Denny; Ian D. Wilson; Sven Degroeve; Lennart Martens; Johannes P.C. Vissers
Source: check_circle
Crossref

Updated MS²PIP web server supports cutting-edge proteomics applications

Nucleic Acids Research
2023-07-05 | Journal article
DOI: 10.1093/nar/gkad335
Contributors: Arthur Declercq; Robbin Bouwmeester; Cristina Chiva; Eduard Sabidó; Aurélie Hirschler; Christine Carapito; Lennart Martens; Sven Degroeve; Ralf Gabriels
Source: check_circle
Crossref

Toward an Integrated Machine Learning Model of a Proteomics Experiment

Journal of Proteome Research
2023-03-03 | Journal article
DOI: 10.1021/acs.jproteome.2c00711
Contributors: Benjamin A. Neely; Viktoria Dorfer; Lennart Martens; Isabell Bludau; Robbin Bouwmeester; Sven Degroeve; Eric W. Deutsch; Siegfried Gessulat; Lukas Käll; Pawel Palczynski et al.
Source: check_circle
Crossref

psm_utils: A High-Level Python API for Parsing and Handling Peptide-Spectrum Matches and Proteomics Search Results

Journal of Proteome Research
2023-02-03 | Journal article
DOI: 10.1021/acs.jproteome.2c00609
Contributors: Ralf Gabriels; Arthur Declercq; Robbin Bouwmeester; Sven Degroeve; Lennart Martens
Source: check_circle
Crossref

A study on experimental bias in post-translational modification predictors

2022-11-28 | Preprint
DOI: 10.1101/2022.11.28.518163
Contributors: Jasper Zuallaert; Pathmanaban Ramasamy; Robbin Bouwmeester; Nico Callewaert; Sven Degroeve
Source: check_circle
Crossref

MS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates

Molecular & Cellular Proteomics
2022-08 | Journal article
DOI: 10.1016/j.mcpro.2022.100266
Contributors: Arthur Declercq; Robbin Bouwmeester; Aurélie Hirschler; Christine Carapito; Sven Degroeve; Lennart Martens; Ralf Gabriels
Source: check_circle
Crossref

Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics

Molecular & Cellular Proteomics
2021 | Journal article
DOI: 10.1016/j.mcpro.2021.100076
Part of ISSN: 1535-9476
Source: Self-asserted source
Sven Degroeve

MS2Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates

2021-11-04 | Preprint
DOI: 10.1101/2021.11.02.466886
Contributors: Arthur Declercq; Robbin Bouwmeester; Aurélie Hirschler; Christine Carapito; Sven Degroeve; Lennart Martens; Ralf Gabriels
Source: check_circle
Crossref

DeepLC can predict retention times for peptides that carry as-yet unseen modifications

Nature Methods
2021-09-01 | Preprint
DOI: 10.1101/2020.03.28.013003
Source: Self-asserted source
Sven Degroeve
grade
Preferred source (of 2)‎

ionbot: a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identification

2021-08-19 | Preprint
DOI: 10.21203/rs.3.rs-691927/v1
Contributors: Sven Degroeve; Ralf Gabriels; Kevin Velghe; Robbin Bouwmeester; Natalia Tichshenko; Lennart Martens
Source: check_circle
Crossref

ionbot: a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identification

2021-07-02 | Preprint
DOI: 10.1101/2021.07.02.450686
Contributors: Sven Degroeve; Ralf Gabriels; Kevin Velghe; Robbin Bouwmeester; Natalia Tichshenko; Lennart Martens
Source: check_circle
Crossref

Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients

JACS Au
2021-06-28 | Journal article
DOI: 10.1021/jacsau.1c00048
Part of ISSN: 2691-3704
Source: Self-asserted source
Sven Degroeve

Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection

Journal of Proteome Research
2021-06-04 | Journal article
DOI: 10.1021/acs.jproteome.1c00264
Part of ISSN: 1535-3893
Part of ISSN: 1535-3907
Source: Self-asserted source
Sven Degroeve

The Age of Data‐Driven Proteomics: How Machine Learning Enables Novel Workflows

PROTEOMICS
2020-11 | Journal article
DOI: 10.1002/pmic.201900351
Part of ISSN: 1615-9853
Part of ISSN: 1615-9861
Source: Self-asserted source
Sven Degroeve

Generalized Calibration Across Liquid Chromatography Setups for Generic Prediction of Small-Molecule Retention Times

Analytical Chemistry
2020-05-05 | Journal article
DOI: 10.1021/acs.analchem.0c00233
Part of ISSN: 0003-2700
Part of ISSN: 1520-6882
Source: Self-asserted source
Sven Degroeve

Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries

PROTEOMICS
2020-02 | Journal article
DOI: 10.1002/pmic.201900306
DOI: 10.1101/681429
Part of ISSN: 1615-9853
Part of ISSN: 1615-9861
Source: Self-asserted source
Sven Degroeve
grade
Preferred source (of 2)‎

Generalized calibration across LC-setups for generic prediction of small molecule retention times

Analytical Chemistry
2020-01-14 | Journal article
DOI: 10.1101/2020.01.14.905844
Source: Self-asserted source
Sven Degroeve
grade
Preferred source (of 2)‎

Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions

Bioinformatics
2019-12-15 | Journal article
DOI: 10.1093/bioinformatics/btz383
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Source: Self-asserted source
Sven Degroeve

Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

Nucleic Acids Research
2019-07-02 | Journal article
DOI: 10.1093/nar/gkz299
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Source: Self-asserted source
Sven Degroeve
grade
Preferred source (of 2)‎

Comprehensive and Empirical Evaluation of Machine Learning Algorithms for Small Molecule LC Retention Time Prediction

Analytical Chemistry
2019-03-05 | Journal article
DOI: 10.1021/acs.analchem.8b05820
Part of ISSN: 0003-2700
Part of ISSN: 1520-6882
Source: Self-asserted source
Sven Degroeve

Data-Driven Rescoring of Metabolite Annotations Significantly Improves Sensitivity

Analytical Chemistry
2018-10-02 | Journal article
DOI: 10.1021/acs.analchem.8b03224
Part of ISSN: 0003-2700
Part of ISSN: 1520-6882
Source: Self-asserted source
Sven Degroeve

MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform

Bioinformatics
2017-01-18 | Journal article
DOI: 10.1093/bioinformatics/btx014
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Source: Self-asserted source
Sven Degroeve

A Pipeline for Differential Proteomics in Unsequenced Species

Journal of Proteome Research
2016-06-03 | Journal article
DOI: 10.1021/acs.jproteome.6b00140
Part of ISSN: 1535-3893
Part of ISSN: 1535-3907
Source: Self-asserted source
Sven Degroeve

Identification of Quantitative Proteomic Differences between Mycobacterium tuberculosis Lineages with Altered Virulence

Frontiers in Microbiology
2016-05-31 | Journal article
DOI: 10.3389/fmicb.2016.00813
Part of ISSN: 1664-302X
Source: Self-asserted source
Sven Degroeve

Designing biomedical proteomics experiments: state-of-the-art and future perspectives

Expert Review of Proteomics
2016-05-03 | Journal article
DOI: 10.1586/14789450.2016.1172967
Part of ISSN: 1478-9450
Part of ISSN: 1744-8387
Source: Self-asserted source
Sven Degroeve

MS2PIP prediction server: compute and visualize MS2peak intensity predictions for CID and HCD fragmentation

Nucleic Acids Research
2015-07-01 | Journal article
DOI: 10.1093/nar/gkv542
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Source: Self-asserted source
Sven Degroeve

A Decoy-Free Approach to the Identification of Peptides

Journal of Proteome Research
2015-04-03 | Journal article
DOI: 10.1021/pr501164r
Part of ISSN: 1535-3893
Part of ISSN: 1535-3907
Source: Self-asserted source
Sven Degroeve

Machine learning applications in proteomics research: How the past can boost the future

PROTEOMICS
2014-03 | Journal article
DOI: 10.1002/pmic.201300289
Part of ISSN: 1615-9853
Source: Self-asserted source
Sven Degroeve

MS2PIP: a tool for MS/MS peak intensity prediction

Bioinformatics
2013-12-15 | Journal article
DOI: 10.1093/bioinformatics/btt544
Part of ISSN: 1460-2059
Part of ISSN: 1367-4803
Source: Self-asserted source
Sven Degroeve

Asn3, a Reliable, Robust, and Universal Lock Mass for Improved Accuracy in LC–MS and LC–MS/MS

Analytical Chemistry
2013-11-19 | Journal article
DOI: 10.1021/ac4027093
Part of ISSN: 0003-2700
Part of ISSN: 1520-6882
Source: Self-asserted source
Sven Degroeve

Proteome-derived Peptide Libraries to Study the Substrate Specificity Profiles of Carboxypeptidases

Molecular & Cellular Proteomics
2013-08 | Journal article
DOI: 10.1074/mcp.m112.023234
Part of ISSN: 1535-9476
Source: Self-asserted source
Sven Degroeve

Predicting Tryptic Cleavage from Proteomics Data Using Decision Tree Ensembles

Journal of Proteome Research
2013-05-03 | Journal article
DOI: 10.1021/pr4001114
Part of ISSN: 1535-3893
Part of ISSN: 1535-3907
Source: Self-asserted source
Sven Degroeve

The Effect of Peptide Identification Search Algorithms on MS2-Based Label-Free Protein Quantification

OMICS: A Journal of Integrative Biology
2012-09 | Journal article
DOI: 10.1089/omi.2011.0137
Part of ISSN: 1536-2310
Part of ISSN: 1557-8100
Source: Self-asserted source
Sven Degroeve

Analysis of the Resolution Limitations of Peptide Identification Algorithms

Journal of Proteome Research
2011-12-02 | Journal article
DOI: 10.1021/pr200913a
Part of ISSN: 1535-3893
Part of ISSN: 1535-3907
Source: Self-asserted source
Sven Degroeve

Bioinformatics Analysis of a Saccharomyces cerevisiae N-Terminal Proteome Provides Evidence of Alternative Translation Initiation and Post-Translational N-Terminal Acetylation

Journal of Proteome Research
2011-08-05 | Journal article
DOI: 10.1021/pr2002325
Part of ISSN: 1535-3893
Part of ISSN: 1535-3907
Source: Self-asserted source
Sven Degroeve

A posteriori quality control for the curation and reuse of public proteomics data

PROTEOMICS
2011-06 | Journal article
DOI: 10.1002/pmic.201000602
Part of ISSN: 1615-9853
Source: Self-asserted source
Sven Degroeve

Combining quantitative proteomics data processing workflows for greater sensitivity

Nature Methods
2011-06 | Journal article
DOI: 10.1038/nmeth.1604
Part of ISSN: 1548-7091
Part of ISSN: 1548-7105
Source: Self-asserted source
Sven Degroeve

A reproducibility-based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methods

PROTEOMICS
2011-03 | Journal article
DOI: 10.1002/pmic.201000605
Part of ISSN: 1615-9853
Source: Self-asserted source
Sven Degroeve

Random forests as a tool for ecohydrological distribution modelling

Ecological Modelling
2007-10 | Journal article
DOI: 10.1016/j.ecolmodel.2007.05.011
Part of ISSN: 0304-3800
Source: Self-asserted source
Sven Degroeve

Translation initiation site prediction on a genomic scale: beauty in simplicity

Bioinformatics
2007-07-01 | Journal article
DOI: 10.1093/bioinformatics/btm177
Part of ISSN: 1460-2059
Part of ISSN: 1367-4803
Source: Self-asserted source
Sven Degroeve

The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)

Science
2006-09-15 | Journal article
DOI: 10.1126/science.1128691
Part of ISSN: 0036-8075
Part of ISSN: 1095-9203
Source: Self-asserted source
Sven Degroeve

Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features

Proceedings of the National Academy of Sciences
2006-08-01 | Journal article
DOI: 10.1073/pnas.0604795103
Part of ISSN: 0027-8424
Part of ISSN: 1091-6490
Source: Self-asserted source
Sven Degroeve

SpliceMachine: predicting splice sites from high-dimensional local context representations

Bioinformatics
2005-04-15 | Journal article
DOI: 10.1093/bioinformatics/bti166
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Source: Self-asserted source
Sven Degroeve

Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction

Bioinformatics
2003-09-27 | Journal article
DOI: 10.1093/bioinformatics/btg1076
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Source: Self-asserted source
Sven Degroeve

Feature subset selection for splice site prediction

Bioinformatics
2002-10-01 | Journal article
DOI: 10.1093/bioinformatics/18.suppl_2.s75
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Source: Self-asserted source
Sven Degroeve

Classification of Percussive Sounds using Support Vector Machines

Proceedings of Annual Machine Learning Conference of Belgium and The Netherlands, BENELEARN 2004
Conference paper
Source: Self-asserted source
Sven Degroeve

Large-scale structural analysis of the core promoter in mammalian and plant genomes

Proceedings of the 7th International EMBL PhD Symposium, Heidelberg, Germany
Conference paper
DOI: 10.1093/nar/gki737
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Source: Self-asserted source
Sven Degroeve
grade
Preferred source (of 2)‎

Peer review (10 reviews for 3 publications/grants)

Review activity for Analytical chemistry. (3)
Review activity for Journal of proteome research. (6)
Review activity for Nature communications (1)
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