Research Explorer

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Researcher

Sven Degroeve

Publications & Research Data

Awards & Distinctions

75 Results

2026

iDeepLC : chemical structure information yields improved retention time prediction of peptides with unseen modifications

Alireza NameniArthur DeclercqRalf GabrielsRobbe DevreeseSven DegroeveAmélie De MaesschalckMaarten DhaenensCristina ChivaEduard SabidóLennart Martens et al.

A1 Journal Article in ANALYTICAL CHEMISTRY

2025

TIMS2Rescore : a data dependent acquisition-parallel accumulation and serial fragmentation-optimized data-driven rescoring pipeline based on MS2Rescore

Arthur DeclercqRobbe DevreeseJonas ScheidCaroline JachmannTim Van Den BosscheAnnica PreikschatDavid Gomez-ZepedaJeewan Babu RijalAurelie HirschlerJonathan R. Krieger et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2024

Bioinformatics pipeline for processing single-cell data

Arthur DeclercqNina DemeulemeesterRalf GabrielsRobbin BouwmeesterSven DegroeveLennart Martens

Bookchapter in Mass spectrometry based single cell proteomics

Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links

Arslan SirajRobbin BouwmeesterArthur DeclercqLuisa WelpAleksandar ChernevAlexander WulfHenning UrlaubLennart MartensSven DegroeveOliver Kohlbacher et al.

A1 Journal Article in PROTEOMICS

MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0

Louise M. BuurArthur DeclercqMarina StroblRobbin BouwmeesterSven DegroeveLennart MartensViktoria DorferRalf Gabriels

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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

Robbin BouwmeesterKeith RichardsonRichard DennyIan D. WilsonSven DegroeveLennart MartensJohannes P.C. Vissers

A1 Journal Article in TALANTA

2023

PhosphoLingo : protein language models for phosphorylation site prediction

Jasper ZuallaertPathmanaban RamasamyRobbin BouwmeesterNico CallewaertSven Degroeve

psm_utils : a high-level python API for parsing and handling peptide-spectrum matches and proteomics search results

Ralf GabrielsArthur DeclercqRobbin BouwmeesterSven DegroeveLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Toward an integrated machine learning model of a proteomics experiment

Benjamin A. NeelyViktoria DorferLennart MartensIsabell BludauRobbin BouwmeesterSven DegroeveEric W. DeutschSiegfried GessulatLukas KaellPawel Palczynski et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Updated MS²PIP web server supports cutting-edge proteomics applications

Arthur DeclercqRobbin BouwmeesterCristina ChivaEduard SabidoAurelie HirschlerChristine CarapitoLennart MartensSven DegroeveRalf Gabriels

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2022

Interpretation of the DOME recommendations for machine learning in proteomics and metabolomics

Magnus PalmbladSebastian BoeckerSven DegroeveOliver KohlbacherLukas KällWilliam Stafford NobleMathias Wilhelm

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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

Sven DegroeveRalf GabrielsKevin VelgheRobbin BouwmeesterNatalia TichshenkoLennart Martens

Machine learning to the rescue : enabling novel proteomics workflows with data-driven bioinformatics methods

Ralf GabrielsLennart MartensSven Degroeve

MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Arthur DeclercqRobbin BouwmeesterAurélie HirschlerChristine CarapitoSven DegroeveLennart MartensRalf Gabriels

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Orthogonal proteomics methods to unravel the HOTAIR interactome

Louis DelhayeEdith De BruyckerPieter-Jan VoldersDaria FijalkowskaDelphine De SutterSven DegroeveLennart MartensPieter MestdaghSven Eyckerman

Orthogonal proteomics methods to unravel the HOTAIR interactome

Louis DelhayeEdith De BruyckerPieter-Jan VoldersDaria FijalkowskaDelphine De SutterSven DegroeveLennart MartensPieter MestdaghSven Eyckerman

A1 Journal Article in SCIENTIFIC REPORTS

Psm_utils : a high level Python API for parsing and handling peptide-spectrum-matches and proteomics search results

Ralf GabrielsArthur DeclercqRobbin BouwmeesterSven DegroeveLennart Martens

2021

Cov-MS : a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients

Bart Van PuyveldeKatleen Van UytfangheOlivier TytgatLaurence Van OudenhoveRalf GabrielsRobbin BouwmeesterSimon DaledTim Van Den BosschePathmanaban RamasamySigrid Verhelst et al.

A2 Journal Article in JACS AU

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

Robbin BouwmeesterRalf GabrielsNiels HulstaertLennart MartensSven Degroeve

A1 Journal Article in NATURE METHODS

Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit

Morgane BoonePathmanaban RamasamyJasper ZuallaertRobbin BouwmeesterBerre Van MoerDavy MaddeleinDemet TuranNiels HulstaertHannah EeckhautElien Vandermarliere et al.

A1 Journal Article in NATURE COMMUNICATIONS

MS²DIP : highly accurate MS2 spectrum prediction for modified peptides & MS²Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Ralf GabrielsRobbin BouwmeesterJasper ZuallaertLennart MartensSven Degroeve

Personalized proteome : comparing proteogenomics and open variant search approaches for single amino acid variant detection

Renee SalzRobbin BouwmeesterRalf GabrielsSven DegroeveLennart MartensPieter-Jan VoldersPeter A.C. ’t Hoen

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Spectral prediction features as a solution for the search space size problem in proteogenomics

Steven VerbruggenSiegfried GessulatRalf GabrielsAnna MatsarokiHendrik Van de VoordeBernhard KusterSven DegroeveLennart MartensWim Van CriekingeMathias Wilhelm et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

2020

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

Robbin BouwmeesterLennart MartensSven Degroeve

A1 Journal Article in ANALYTICAL CHEMISTRY

Removing the hidden data dependency of DIA with predicted spectral libraries

Bart Van PuyveldeSander WillemsRalf GabrielsSimon DaledLaura De ClerckSofie Vande CasteeleAn StaesFrancis ImpensDieter DeforceLennart Martens et al.

A1 Journal Article in PROTEOMICS

The age of data-driven proteomics : how machine learning enables novel workflows

Robbin BouwmeesterRalf GabrielsTim Van Den BosscheLennart MartensSven Degroeve

A1 Journal Article in PROTEOMICS

The difference is in the details : predicting the LC-IM-MS behaviour of metabolites and peptides

Robbin BouwmeesterLennart MartensSven Degroeve

2019

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

Ana Sílvia Ferreira Diamantino Coelho e SilvaRobbin BouwmeesterLennart MartensSven Degroeve

A1 Journal Article in BIOINFORMATICS

Comprehensive and empirical evaluation of machine learning algorithms for small molecule LC retention time prediction

Robbin BouwmeesterLennart MartensSven Degroeve

A1 Journal Article in ANALYTICAL CHEMISTRY

Data-driven approaches for improved mass spectrometry-based analyte identification

Ana Sílvia Ferreira Diamantino Coelho e SilvaLennart MartensSven Degroeve

Fast and accurate MS² peak intensity predictions for multiple fragmentation methods, instruments and labeling techniques

Ralf GabrielsLennart MartensSven Degroeve

MS²PIP : fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

Ralf GabrielsLennart MartensSven Degroeve

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

Ralf GabrielsLennart MartensSven Degroeve

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2018

Data-driven rescoring of metabolite annotations significantly improves sensitivity

Ana Sílvia Ferreira Diamantino Coelho e SilvaAndrew PalmerVitaly KovalevArtem TarasovTheodore AlexandrovLennart MartensSven Degroeve

A1 Journal Article in ANALYTICAL CHEMISTRY

2017

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

Surya GuptaVeronic De PuysseleyrJosé Van Der HeydenDavy MaddeleinIrma LemmensSam LievensSven DegroeveJan TavernierLennart Martens

A1 Journal Article in BIOINFORMATICS

2016

A pipeline for differential proteomics in unsequenced species

Sule Yilmaz-RumpfBjorn VictorNiels HulstaertElien VandermarliereHarald BarsnesSven DegroeveSurya GuptaAdriaan StickerSarah GabriëlPierre Dorny et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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

Evelyne MaesPieter KelchtermansWout BittremieuxKurt De GraveSven DegroeveJef HooyberghsInge MertensGeert BaggermanJan RamonKris Laukens et al.

A1 Journal Article in EXPERT REVIEW OF PROTEOMICS

Identification of quantitative proteomic differences between Mycobacterium tuberculosis lineages with altered virulence

Julian S PetersBridget CalderGiulia GonnelliSven DegroeveElinambinina RajaonarifaraNicola MulderNelson C SoaresLennart MartensJonathan M Blackburn

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

2015

A decoy-free approach to the identification of peptides

Giulia GonnelliMichiel StockJan VerwaerenDavy MaddeleinBernard De BaetsLennart MartensSven Degroeve

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

MS²PIP prediction server : compute and visualize MS² peak intensity predictions for CID and HCD fragmentation

Sven DegroeveDavy MaddeleinLennart Martens

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2014

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

Pieter KelchtermansWout BittremieuxKurt De GraveSven DegroeveJan RamonKris LaukensDirk ValkenborgHarald BarsnesLennart Martens

A1 Journal Article in PROTEOMICS

2013

Asn₃, a reliable, robust, and universal lock mass for improved accuracy in LC-MS and LC-MS/MS

An StaesJonathan VandenbusscheHans DemolMarc GoethalsSule Yilmaz-RumpfNiels HulstaertSven DegroevePieter KelchtermansLennart MartensKris Gevaert

A1 Journal Article in ANALYTICAL CHEMISTRY

MS²PIP: a tool for MS/MS peak intensity prediction

Sven DegroeveLennart Martens

A1 Journal Article in BIOINFORMATICS

Predicting tryptic cleavage from proteomics data using decision tree ensembles

Thomas FannesElien VandermarliereLeander SchietgatSven DegroeveLennart MartensJan Ramon

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Proteome-derived peptide libraries to study the substrate specificity profiles of carboxypeptidases

Sebastian TancoJulia LorenzoJavier Garcia-PardoSven DegroeveLennart MartensFrancesc Xavier AvilesKris GevaertPetra Van Damme

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

2012

The effect of peptide identification search algorithms on MS2-based label-free protein quantification

Sven DegroeveAn StaesPieter-Jan De BockLennart Martens

A1 Journal Article in OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Towards a human proteomics atlas

Giulia GonnelliNiels HulstaertSven DegroeveLennart Martens

A1 Journal Article in ANALYTICAL AND BIOANALYTICAL CHEMISTRY

2011

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

Joseph M FosterSven DegroeveLaurent GattoMatthieu VisserRui WangJohannes GrissRolf ApweilerLennart Martens

A1 Journal Article in PROTEOMICS

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

Sven DegroeveNiklaas ColaertJoël VandekerckhoveKris GevaertLennart Martens

A1 Journal Article in PROTEOMICS

Analysis of the resolution limitations of peptide identification algorithms

Niklaas ColaertSven DegroeveKenny HelsensLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation

Kenny HelsensPetra Van DammeSven DegroeveLennart MartensThomas ArnesenJoël VandekerckhoveKris Gevaert

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Combining quantitative proteomics data processing workflows for greater sensitivity

Niklaas ColaertChristophe Van HueleSven DegroeveAn StaesJoël VandekerckhoveKris GevaertLennart Martens

A1 Journal Article in NATURE METHODS

2007

Random forests as a tool for ecohydrological distribution modelling.

Jan PetersBernard De BaetsNiko VerhoestRoeland SamsonSven DegroeveP DE BECKERW HUYBRECHTS

A1 Journal Article in ECOLOGICAL MODELLING

2006

Feature ranking using an EDA-based wrapper approach

Yvan SaeysSven DegroeveYves Van de Peer

Bookchapter in Towards a new evolutionary computation : advances in estimation of distribution algorithms

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

Evelyne DerelleConchita FerrazStephane RombautsPierre RouzéAlexandra Z WordenSteven RobbensFrédéric PartenskySven DegroeveSophie EcheyniéRichard Cooke et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

GA TuskanS DiFazioS JanssonJ BohlmannI GrigorievU HellstenN PutnamS RalphStephane RombautsA Salamov et al.

A1 Journal Article in SCIENCE

2005

A simulated annealing optimization of audio features for drum classification

Sven DegroeveKoen TangheBernard De BaetsMarc LemanJean-Pierre Martens

An algorithm for detecting and labeling drum events in polyphonic music

Koen TangheSven DegroeveBernard De Baets

Collecting ground truth annotations for drum detection in polyphonic music

Koen TangheMicheline LesaffreSven DegroeveMarc LemanBernard De BaetsJean-Pierre Martens

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

Kobe FlorquinYvan SaeysSven DegroeveYves Van de Peer

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

Kobe FlorquinYvan SaeysSven DegroevePierre RouzéYves Van de Peer

A1 Journal Article in NUCLEIC ACIDS RESEARCH

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

Sven DegroeveYvan SaeysBernard De BaetsPierre RouzéYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Support Vector Machines for Bass and Snare Drum Recognition

Dirk Van SteelantKoen TangheSven DegroeveBernard De BaetsMarc LemanJean-Pierre Martens

2004

Classification of Percussive Sounds using Support Vector Machines

Dirk Van SteelantKoen TangheSven DegroeveBernard De BaetsMarc LemanJean-Pierre Martens

Design and evaluation of a linear classification strategy for gene structural element recognition

Sven DegroeveBernard, de BaetsYves Van de Peer

Digging into acceptor splice site prediction : an iterative feature selection approach

Yvan SaeysSven DegroeveYves Van de Peer

A1 Journal Article in LECTURE NOTES IN ARTIFICIAL INTELLIGENCE

Feature selection for splice site prediction: A new method using EDA-based feature ranking

Yvan SaeysSven DegroeveDirk AeyelsPierre RouzéYves Van de Peer

A1 Journal Article in BMC BIOINFORMATICS

Selecting relevant features for gene structure prediction

Yvan SaeysSven DegroeveDirk AeyelsPierre RouzéYves Van de Peer

Splice site prediction in eukaryote genome sequences : the algorithmic issues

Sven DegroeveYvan SaeysBernard De BaetsYves Van de PeerPierre Rouzé

Bookchapter in The new avenues in bioinformatics

The role of non-linear DNA structures in transcription

Kobe FlorquinSven DegroeveYvan SaeysYves Van de Peer

2003

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

Yvan SaeysSven DegroeveDirk AeyelsYves Van de PeerPierre Rouzé

A1 Journal Article in BIOINFORMATICS

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

Yvan SaeysSven DegroeveDirk AeyelsYves Van de PeerPierre Rouzé

2002

Feature subset selection for splice site prediction

Sven DegroeveBernard De BaetsYves Van de PeerPierre Rouzé

A1 Journal Article in BIOINFORMATICS

Feature subset selection for splice site prediction by estimation of distribution algorithms

Yvan SaeysSven DegroeveDirk AeyelsYves Van de PeerPierre Rouzé

Selecting Relevant Features for Splice Site Prediction by Estimation of Distribution Algorithms.

Yvan SaeysSven DegroeveDirk AeyelsYves Van de PeerPierre Rouzé