Research Explorer

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Researcher

Bart Mesuere

Publications & Research Data

Awards & Distinctions

67 Results

2025

Are LLMs good at answering student questions in CS1 courses?

Thomas Van MullemBart MesuerePeter Dawyndt

Classification of collagens via peptide ambiguation, in a paleoproteomic LC-MS/MS-based taxonomic pipeline

Ian EngelsAlexandra BurnettPrudence RobertCamille PironneauGrégory AbramsRobbin BouwmeesterPeter Van Der PlaetsenKévin Di ModicaMarcel OtteLawrence Guy Straus et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Direct construction of sparse suffix arrays with Libsais

Simon Van de VyverTibo Vande MoortelePeter DawyndtBart MesuerePieter Verschaffelt

Direct construction of sparse suffix arrays with Libsais

Simon Van de VyverTibo Vande MoortelePeter DawyndtBart MesuerePieter Verschaffelt

A1 Journal Article in BMC BIOINFORMATICS

Dolos : source code similarity detection

Rien MaertensPeter DawyndtBart Mesuere

Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes

Robert HeyerMaximilian WolfDirk BenndorfSergio UzzauJana SeifertLucia GrengaMartin PabstHeike SchmittBart MesuereTim Van Den Bossche et al.

Editorial material

PathwayPilot : a user-friendly tool for visualizing and navigating metabolic pathways

Tibo Vande MoortelePieter VerschaffeltQingyao HuangNadezhda T. DonchevaTanja HolsteinCaroline JachmannPeter DawyndtLennart MartensBart MesuereTim Van Den Bossche

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Source code plagiarism detection as a service with Dolos

Rien MaertensPeter DawyndtBart Mesuere

The microbiologist's guide to metaproteomics

Tim Van Den BosscheJean ArmengaudDirk BenndorfJose Alfredo Blakeley‐RuizMadita BrauerKai ChengMarybeth CreskeyDaniel FigeysLucia GrengaTimothy J. Griffin et al.

A1 Journal Article in IMETA

The microbiologist’s guide to metaproteomics

Tim Van Den BosscheJean ArmengaudDirk BenndorfJose Alfredo Blakeley-RuizMadita BrauerKai ChengMarybeth CreskeyDaniel FigeysLucia GrengaTimothy J Griffin et al.

Unipept in 2024 : expanding metaproteomics analysis with support for missed cleavages and semitryptic and nontryptic peptides

Tibo Vande MoorteleBram DevlaminckSimon Van de VyverTim Van Den BosscheLennart MartensPeter DawyndtBart MesuerePieter Verschaffelt

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2024

Biodiversity analysis of metaproteomics samples with Unipept : a comprehensive tutorial

Tim Van Den BosschePieter VerschaffeltTibo Vande MoortelePeter DawyndtLennart MartensBart Mesuere

Bookchapter in Protein bioinformatics

Blink : an educational software debugger for Scratch

Niko StrijbolRobbe De ProftKlaas GoethalsBart MesuerePeter DawyndtChristophe Scholliers

A1 Journal Article in SOFTWAREX

Discovering and exploring cases of educational source code plagiarism with Dolos

Rien MaertensMaarten Van NeyghemMaxiem GeldhofCharlotte Van PetegemNiko StrijbolPeter DawyndtBart Mesuere

A1 Journal Article in SOFTWAREX

Dodona : improving programming education through automated assessment, learning analytics, and educational data mining

Charlotte Van PetegemPeter DawyndtBart MesuereBram De Wever

Educational software testing for textual and block-based programming languages

Niko StrijbolPeter DawyndtChristophe ScholliersBart Mesuere

Reproducing predictive learning analytics in CS1 : toward generalizable and explainable models for enhancing student retention

Denis ZhidkikhVille HeilalaCharlotte Van PetegemPeter DawyndtMiitta JärvinenSami ViitanenBram De WeverBart MesuereVesa LappalainenLauri Kettunen et al.

A2 Journal Article in JOURNAL OF LEARNING ANALYTICS

The Peptonizer2000 : bringing confidence to metaproteomics

Tanja HolsteinPieter VerschaffeltTim Van Den BosscheSimon Van de VyverLennart MartensBart MesuereThilo Muth

2023

Building the Unipept Ecosystem : empowering high-throughput metaproteomics data analysis for characterizing complex microbial communities

Pieter VerschaffeltPeter DawyndtLennart MartensBart Mesuere

Dodona : learn to code with a virtual co-teacher that supports active learning

Charlotte Van PetegemRien MaertensNiko StrijbolJorg Van RenterghemFelix Van der JeugtBram De WeverPeter DawyndtBart Mesuere

A1 Journal Article in SOFTWAREX

Dodona : learn to code with a virtual co-teacher that supports active learning

Charlotte Van PetegemPeter DawyndtBart Mesuere

Dolos 2.0 : towards seamless source code plagiarism detection in online learning environments

Rien MaertensPeter DawyndtBart Mesuere

Dolos — Source Code Plagiarism Detection System

Rien MaertensCharlotte Van PetegemNiko StrijbolToon BaeyensArne Carla JacobsPeter DawyndtBart Mesuere

Engaging schools to build a regional urban climate monitoring network

Steven CaluwaertsSara TopBart MesuereThomas Vergauwen

TESTed : an educational testing framework with language-agnostic test suites for programming exercises

Niko StrijbolCharlotte Van PetegemRien MaertensBoris SelsChristophe ScholliersPeter DawyndtBart Mesuere

A1 Journal Article in SOFTWAREX

Unipept Desktop 2.0 : construction of targeted reference protein databases for metaproteogenomics analyses

Pieter VerschaffeltAlessandro TancaMarcello AbbondioTim Van Den BosscheTibo Vande MoortelePeter DawyndtLennart MartensBart Mesuere

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2022

Benchmark and improving methods in metaproteomics informatics

Tim Van Den BosscheLennart MartensBart MesuereThilo Muth

Dolos : language‐agnostic plagiarism detection in source code

Rien MaertensCharlotte Van PetegemNiko StrijbolToon BaeyensArne JacobsPeter DawyndtBart Mesuere

A1 Journal Article in JOURNAL OF COMPUTER ASSISTED LEARNING

Engaging schools to explore meteorological observational gaps

Steven CaluwaertsSara TopBart MesuereThomas Vergauwen

FragGeneScanRs : faster gene prediction for short reads

Felix Van der JeugtPeter DawyndtBart Mesuere

A1 Journal Article in BMC BIOINFORMATICS

Pass/fail prediction in programming courses

Charlotte Van PetegemLouise DeconinckDieter MourisseRien MaertensNiko StrijbolBart DhoedtBram De WeverPeter DawyndtBart Mesuere

A1 Journal Article in JOURNAL OF EDUCATIONAL COMPUTING RESEARCH

Pout2Prot : an efficient tool to create protein (sub)groups from Percolator Output Files

Kay SchallertPieter VerschaffeltBart MesuereDirk BenndorfLennart MartensTim Van Den Bossche

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Taming nondeterminism : programming language abstractions and tools for dealing with nondeterministic programs

Robbert Gurdeep SinghChristophe ScholliersBart Mesuere

The unipept metagenomics analysis pipeline

Felix Van der JeugtPeter DawyndtBart Mesuere

UMGAP : the Unipept MetaGenomics analysis pipeline

Felix Van der JeugtRien MaertensAranka SteyaertPieter VerschaffeltCaroline De TenderPeter DawyndtBart Mesuere

A1 Journal Article in BMC GENOMICS

Unipept visualizations : an interactive visualization library for biological data

Pieter VerschaffeltJames CollierAlexander BotzkiLennart MartensPeter DawyndtBart Mesuere

A1 Journal Article in BIOINFORMATICS

2021

Critical assessment of metaproteome investigation (CAMPI) : a multi-lab comparison of established workflows

Tim Van Den BosscheBenoit J. KunathKay SchallertStephanie S. SchäpePaul E. AbrahamJean ArmengaudMagnus Ø. ArntzenAriane BassignaniDirk BenndorfStephan Fuchs et al.

Critical Assessment of MetaProteome Investigation (CAMPI) : a multi-laboratory comparison of established workflows

Tim Van Den BosscheBenoit J. KunathKay SchallertStephanie S. SchäpePaul E. AbrahamJean ArmengaudMagnus Ø. ArntzenAriane BassignaniDirk BenndorfStephan Fuchs et al.

A1 Journal Article in NATURE COMMUNICATIONS

Engaging schools to explore meteorological observational gaps

Steven CaluwaertsSara TopThomas VergauwenGuy WautersKoen De RidderRafiq HamdiBart MesuereBert Van SchaeybroeckHendrik WoutersPiet Termonia

A1 Journal Article in BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY

Het VLINDER-project

Steven CaluwaertsThomas VergauwenSara TopHerwig DejongheBart MesuerePiet TermoniaGuy Wauters

Bookchapter in Jaarboek De Aardrijkskunde 2020

MegaGO : a fast yet powerful approach to assess functional gene ontology similarity across meta-omics data sets

Pieter VerschaffeltTim Van Den BosscheWassim GabrielMichał BurdukiewiczAlessio SoggiuLennart MartensBernhard Y. RenardHenning SchiebenhoeferBart Mesuere

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Pout2Prot : an efficient tool to create protein (sub)groups from Percolator output files

Tim Van Den BosscheKay SchallertPieter VerschaffeltBart MesuereDirk BenndorfLennart Martens

The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes

Tim Van Den BosscheMagnus Ø. ArntzenDörte BecherDirk BenndorfVincent G. H. EijsinkCéline HenryPratik D. JagtapNico JehmlichCatherine JusteBenoit J. Kunath et al.

A1 Journal Article in MICROBIOME

Unipept Desktop : a faster, more powerful metaproteomics results analysis tool

Pieter VerschaffeltTim Van Den BosscheLennart MartensPeter DawyndtBart Mesuere

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2020

Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for seamless end-to-end metaproteomics data analysis

Tim Van Den BosschePieter VerschaffeltKay SchallertHarald BarsnesPeter DawyndtDirk BenndorfBernhard Y. RenardBart MesuereLennart MartensThilo Muth

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Proceedings of the EuBIC-MS 2020 Developers’ Meeting

Christopher AshwoodWout BittremieuxEric W. DeutschNadezhda T. DonchevaViktoria DorferRalf GabrielsVladimir GorshkovSurya GuptaAndrew R. JonesLukas Käll et al.

A2 Journal Article in EUPA OPEN PROTEOMICS

Survey of metaproteomics software tools for functional microbiome analysis

Ray SajulgaCaleb EasterlyMichael RiffleBart MesuereThilo MuthSubina MehtaPraveen KumarJames JohnsonBjoern Andreas GrueningHenning Schiebenhoefer et al.

A1 Journal Article in PLOS ONE

Unipept CLI 2.0 : adding support for visualizations and functional annotations

Pieter VerschaffeltPhilippe Van ThienenTim Van Den BosscheFelix Van der JeugtCaroline De TenderLennart MartensPeter DawyndtBart Mesuere

A1 Journal Article in BIOINFORMATICS

2019

A method for comprehensive proteomic analysis of human faecal samples to investigate gut dysbiosis in patients with cystic fibrosis

Griet DebyserMaarten AertsPieter Van HeckeBart MesuereGwen DuytschaeverPeter DawyndtKris De BoeckPeter VandammeBart Devreese

A1 Journal Article in ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY

Het is tijd voor één aanmeldsysteem voor alle Vlaamse scholen

Wouter RogiestBart Mesuere

Article in a magazine

metaQuantome : an integrated, quantitative metaproteomics approach reveals connections between taxonomy and protein function in complex microbiomes

Caleb W EasterlyRay SajulgaSubina MehtaJames JohnsonPraveen KumarShane HublerBart MesuereJoel RudneyTimothy J GriffinPratik D Jagtap

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome

Caroline De TenderBart MesuereFelix Van der JeugtA HaegemanTom RuttinkB VandecasteelePeter DawyndtJ DebodeEE Kuramae

A1 Journal Article in SCIENTIFIC REPORTS

Unipept 4.0 : functional analysis of metaproteome data

Robbert Gurdeep SinghAlessandro TancaAntonio PalombaFelix Van der JeugtPieter VerschaffeltSergio UzzauLennart MartensPeter DawyndtBart Mesuere

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2018

Disseminating metaproteomic informatics capabilities and knowledge using the Galaxy-P framework

Clemens BlankCaleb EasterlyBjoern GrueningJames JohnsonCarolin A KolmederPraveen KumarDamon MaySubina MehtaBart MesuereZachary Brown et al.

A2 Journal Article in PROTEOMES

High-throughput metaproteomics data analysis with Unipept : a tutorial

Bart MesuereFelix Van der JeugtToon WillemsTom NaessensBart DevreeseLennart MartensPeter Dawyndt

A1 Journal Article in JOURNAL OF PROTEOMICS

Hoe het algoritme achter het aanmeldsysteem voor het onderwijs verbeterd kan worden

2016

Faecal proteomics : a tool to investigate dysbiosis and inflammation in patients with cystic fibrosis

Griet DebyserBart MesuereLieven ClementJens Van de WeygaertPieter Van HeckeGwen DuytschaeverMaarten AertsPeter DawyndtKris De BoeckPeter Vandamme et al.

A1 Journal Article in JOURNAL OF CYSTIC FIBROSIS

The unique peptidome : taxon-specific tryptic peptides as biomarkers for targeted metaproteomics

Bart MesuereFelix Van der JeugtBart DevreesePeter VandammePeter Dawyndt

A1 Journal Article in PROTEOMICS

Unipept web services for metaproteomics analysis

Bart MesuereToon WillemsFelix Van der JeugtBart DevreesePeter VandammePeter Dawyndt

A1 Journal Article in BIOINFORMATICS

Unipept: computational exploration of metaproteome data

Bart MesuerePeter Dawyndt

2015

A cross-sectional and longitudinal metaproteomics approach reveals intestinal dysbiosis, and the presence of markers of chronic inflammation and mucus-related proteins in faecal samples of patients with cystic fibrosis

Griet DebyserBart MesuereJens Van de WeygaertLieven ClementMaarten AertsGwen DuytschaeverPeter DawyndtK De BoeckPeter VandammeBart Devreese

The Unipept metaproteomics analysis pipeline

Bart MesuereGriet DebyserMaarten AertsBart DevreesePeter VandammePeter Dawyndt

A1 Journal Article in PROTEOMICS

2012

A shotgun metaproteomics approach to study the microbiome of cystic fibrosis (CF) patients

Griet DebyserBart MesuerePeter DawyndtPeter VandammeBart Devreese

A shotgun metaproteomics approach to study the microbiome of cystic fibrosis (CF) patients

Griet DebyserBart MesuerePeter DawyndtPeter VandammeBart Devreese

Application of MALDI-TOF mass spectrometry for the detection of enterotoxins produced by pathogenic strains of the Bacillus cereus group

Varvara TsiliaBart DevreeseIlse de BaenstBart MesuereAndreja RajkovicMieke UyttendaeleTom Van de WieleMarc Heyndrickx

A1 Journal Article in ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Unipept: tryptic peptide-based biodiversity analysis of metaproteome samples

Bart MesuereBart DevreeseGriet DebyserMaarten AertsPeter VandammePeter Dawyndt

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2010

Screening for taxon-specific peptides using dynamic index structures

Bart MesuereGriet DebyserPeter VandammeBart DevreesePeter Dawyndt