Research Explorer

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Researcher

Gerben Menschaert

Awards & Distinctions

97 Results

2024

Deep learning decodes new sites of RNA translation in medulloblastoma

Jim ClauwaertGerben MenschaertJohn Prensner

Deep learning to decode sites of RNA translation in normal and cancerous tissues

Jim ClauwaertZahra McVeyRamneek GuptaIan YannuzziGerben MenschaertJohn R. Prensner

Multimodal deregulation of imprinted gene HM13 : a pan-cancer study

Floris VoorthuijzenCedric StroobandtJeroen GalleLouis CoussementJim ClauwaertTine GoovaertsRyan EnglanderOlga AnczukowGerben MenschaertWim Van Criekinge et al.

Pre-trained Maldi Transformers improve MALDI-TOF MS-based prediction

Gaetan De WaeleGerben MenschaertPeter VandammeWillem Waegeman

2023

An antimicrobial drug recommender system using MALDI-TOF MS and dual-branch neural networks

Gaetan De WaeleGerben MenschaertWillem Waegeman

An antimicrobial drug recommender system using MALDI-TOF MS and dual-branch neural networks

Gaetan De WaeleGerben MenschaertWillem Waegeman

Multimodal deregulation of imprinted gene HM13 leads to pan-cancer upregulation of putative oncogene MCTS2

Floris VoorthuijzenTine GoovaertsCedric StroobandtJeroen GalleRyan EnglanderOlga AnczukowWim Van CriekingeGerben MenschaertTim De Meyer

RIBO-former: applying attention-based neural networks for precise delineation of translated open reading frames using ribosome profiling data.

Jim ClauwaertZahra McVeyRamneek GuptaJohn PrensnerGerben Menschaert

RIBO-former: leveraging ribosome profiling information to improve the detection of translated open reading frames

Jim ClauwaertZahra McVeyRamneek GuptaGerben Menschaert

TIS transformer : remapping the human proteome using deep learning

Jim ClauwaertZahra McVeyRamneek GuptaGerben Menschaert

A2 Journal Article in NAR GENOMICS AND BIOINFORMATICS

2022

Coelomocytes and immunity in axenic longevity

Lucas MerganBrecht DriesschaertElisabeth DensElke VandewyerLouis CoussementGerben MenschaertBart BraeckmanLiesbet Temmerman

CpG transformer for imputation of single-cell methylomes

Gaetan De WaeleJim ClauwaertGerben MenschaertWillem Waegeman

A1 Journal Article in BIOINFORMATICS

Editorial : sORF encoded peptides in health and disease

Joseph RothnagelHarsha GowdaGerben Menschaert

Editorial material

Identification and characterization of eukaryotic small open reading frames and microproteins

Marlies PeetersGerben MenschaertLiesbet TemmermanWim Van Criekinge

Standardized annotation of translated open reading frames

Jonathan M. MudgeJorge Ruiz-OreraJohn R. PrensnerMarie A. BrunetFerriol CalvetIrwin JungreisJose Manuel GonzalezMichele MagraneThomas F. MartinezJana Felicitas Schulz et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

2021

A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

Jonathan M MudgeJorge Ruiz-OreraJohn R PrensnerMarie A BrunetJose Manuel GonzalezMichele MagraneThomas MartinezJana Felicitas SchulzYucheng T YangM Mar Albà et al.

Downregulation of the FTO m(6)A RNA demethylase promotes EMT-mediated progression of epithelial tumors and sensitivity to Wnt inhibitors

Jana JeschkeEvelyne CollignonClemence Al WardiMohammad KrayemMartin BizetYan JiaSoizic GaraudZena WimanaEmilie CalonneBouchra Hassabi et al.

A1 Journal Article in NATURE CANCER

Explainability in transformer models for functional genomics

Jim ClauwaertGerben MenschaertWillem Waegeman

A1 Journal Article in BRIEFINGS IN BIOINFORMATICS

Identification of non-canonical translation products in C. elegans using tandem mass spectrometry

Bhavesh S. ParmarMarlies PeetersKurt BoonenEllie C. ClarkGeert BaggermanGerben MenschaertLiesbet Temmerman

A1 Journal Article in FRONTIERS IN GENETICS

Ion mobility coupled to a time-of-flight mass analyzer combined with fragment intensity predictions improves identification of classical bioactive peptides and small open reading frame-encoded peptides

Marlies PeetersGeert BaggermanRalf GabrielsElise PepermansGerben MenschaertKurt Boonen

A1 Journal Article in FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY

Role of coelomocytes and immunity in axenic dietary restriction

Lucas MerganBrecht DriesschaertElisabeth DensElke VandewyerLouis CoussementGerben MenschaertBart BraeckmanLiesbet Temmerman

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

A methodology for discovering novel brain-relevant peptides : combination of ribosome profiling and peptidomics

Ravi TharakanSimion KreimerCeereena Ubaida-MohienJoelle LavoieVolodimir OlexioukGerben MenschaertNicholas T. IngoliaRobert N. ColeKoko IshizukaAkira Sawa et al.

A1 Journal Article in NEUROSCIENCE RESEARCH

BRAWNIN: A sORF-encoded Peptide Essential for Vertebrate Mitochondrial Complex III Assembly

Shan ZhangChao LiangCamille MaryBaptiste KerouantonJoel FranciscoNarendra Suhas JagannathanVolodimir OlexioukJih Hou PehClaire TangGio Fidelito et al.

Deep learning techniques for genome processing and annotation tasks in prokaryotes

Jim ClauwaertWillem WaegemanMarjan De MeyGerben Menschaert

Functional role of Tet-mediated RNA hydroxymethylcytosine in mouse ES cells and during differentiation

Jie LanNicholas RajanMartin BizetAudrey PenningNitesh K. SinghDiana GuallarEmilie CalonneAndrea Li GreciElise BonvinRachel Deplus et al.

A1 Journal Article in NATURE COMMUNICATIONS

Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory complex III assembly

Shan ZhangBoris ReljićChao LiangBaptiste KerouantonJoel Celio FranciscoJih Hou PehCamille MaryNarendra Suhas JagannathanVolodimir OlexioukClaire Tang et al.

A1 Journal Article in NATURE COMMUNICATIONS

The hunt for sORFs : a multidisciplinary strategy

Marlies PeetersGerben Menschaert

A1 Journal Article in EXPERIMENTAL CELL RESEARCH

The proteogenomic hunt for new proteoforms using ribosome profiling

Steven VerbruggenWim Van CriekingeGerben MenschaertPetra Van Damme

2019

A combined strategy of neuropeptide prediction and tandem mass spectrometry identifies evolutionarily conserved ancient neuropeptides in the sea anemone Nematostella vectensis

Eisuke HayakawaHiroshi WatanabeGerben MenschaertThomas W HolsteinGeert BaggermanLiliane Schoofs

A1 Journal Article in PLOS ONE

A proteogenomic endeavour investigating the unexplored domain of putatively coding small open reading frames

Volodimir OlexioukWim Van CriekingeGerben Menschaert

Beyond genes : re-identifiability of proteomic data and its implications for personalized medicine

Kurt BoonenKristien HensGerben MenschaertGeert BaggermanDirk ValkenborgGokhan Ertaylan

A1 Journal Article in GENES

DeepRibo : a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns

Jim ClauwaertGerben MenschaertWillem Waegeman

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Multiple solvent elution, a method to counter the effects of coelution and ion suppression in LC-MS analysis in bottom up proteomics

Harshavardhan BudamguntaEvelyne MaesHanny WillemsGerben MenschaertKarin SchildermansAjay Anand KumarKurt BoonenGeert Baggerman

A1 Journal Article in JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

PROTEOFORMER 2.0 : further developments in the ribosome profiling-assisted proteogenomic hunt for new proteoforms

Steven VerbruggenElvis NdahWim Van CriekingeSiegfried GessulatBernhard KusterMathias WilhelmGerben MenschaertPetra Van Damme

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Proteomics Standards Initiative extended FASTA format

Pierre-Alain BinzJim ShofstahlJuan Antonio VizcaínoHarald BarsnesRobert J ChalkleyGerben MenschaertEmanuele AlpiKarl ClauserJimmy K EngLydie Lane et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2018

A gene family coding for salivary proteins (SHOT) of the polyphagous spider mite Tetranychus urticae exhibits fast host-dependent transcriptional plasticity

Wim JonckheereWannes DermauwMousaalreza KhaglighiNena PavlidiWim ReubensGeert BaggermanLuc TirryGerben MenschaertMerijn R KantBartel Vanholme et al.

A1 Journal Article in MOLECULAR PLANT-MICROBE INTERACTIONS

An update on sORFs.org : a repository of small ORFs identified by ribosome profiling

Volodimir OlexioukWim Van CriekingeGerben Menschaert

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Complementary use of ribosome profiling and proteomics for mapping the translation landscape

Elvis NdahPetra Van DammeGerben MenschaertLennart Martens

Comprehensive peptide analysis of mouse brain striatum identifies novel sORF-encoded polypeptides

Harshavardhan BudamguntaVolodimir OlexioukWalter LuytenKarin SchildermansEvelyne MaesKurt BoonenGerben MenschaertGeert Baggerman

A1 Journal Article in PROTEOMICS

DeepRibo : precise gene annotation of prokaryotes using deep learning and ribosome profiling data

Jim ClauwaertGerben MenschaertWillem Waegeman

DeepRibo : precise gene annotation of prokaryotes using deep learning and ribosome profiling data, validated with mass spectrometry data

Jim ClauwaertGerben MenschaertWillem Waegeman

Deletion 6q drives T-cell leukemia progression by ribosome modulation

Stéphanie GachetTiama El-ChaarDavid AvranEulalia GenescaFrédéric CatezSamuel QuentinMarc DelordGabriel ThérizolsDelphine BriotGodelieve Meunier et al.

A1 Journal Article in CANCER DISCOVERY

Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini

Chan Hyun NaMustafa BarbhuiyaMin-Sik KimSteven VerbruggenStephen EackerOlga PletnikovaJuan TroncosoMarc HalushkaGerben MenschaertChristopher Overall et al.

A1 Journal Article in GENOME RESEARCH

Mass spectrometric evidence for neuropeptide-amidating enzymes in Caenorhabditis elegans

Sven Van BaelJan WatteyneKurt BoonenWouter De HaesGerben MenschaertNiels RingstadH. Robert HorvitzLiliane SchoofsSteven J. HussonLiesbet Temmerman

A1 Journal Article in JOURNAL OF BIOLOGICAL CHEMISTRY

Short open reading frames and their encoded peptides

Joseph RothnagelGerben Menschaert

Editorial material

The proBAM and proBed standard formats : enabling a seamless integration of genomics and proteomics data

Gerben MenschaertXiaojing WangAndrew R JonesFawaz GhaliDavid FenyöVolodimir OlexioukBing ZhangEric W DeutschTobias TernentJuan Antonio Vizcaíno

A1 Journal Article in GENOME BIOLOGY

Using the sORFs.org database

Volodimir OlexioukGerben Menschaert

A2 Journal Article in CURRENT PROTOCOLS IN BIOINFORMATICS

mQC : a post-mapping data exploration tool for ribosome profiling

Steven VerbruggenGerben Menschaert

A1 Journal Article in COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

2017

In search of lost small peptides

Serge PlazaGerben MenschaertFrançois Payre

A1 Journal Article in Annual Review of Cell and Developmental Biology

Noncoding after all : biases in proteomics data do not explain observed absence of lncRNA translation products

Kenneth VerheggenPieter-Jan VoldersPieter MestdaghGerben MenschaertPetra Van DammeKris GevaertLennart MartensJo Vandesompele

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Proteogenomics from a bioinformatics angle : a growing field

Gerben MenschaertDavid Fenyö

A1 Journal Article in MASS SPECTROMETRY REVIEWS

Proteomics Standards Initiative : fifteen years of progress and future work

Eric W DeutschSandra OrchardPierre-Alain BinzWout BittremieuxMartin EisenacherHenning HermjakobShin KawanoHenry LamGerhard MayerGerben Menschaert et al.

Editorial material

REPARATION : ribosome profiling assisted (re-)annotation of bacterial genomes

Elvis NdahVeronique JonckheereAdam GiessEivind ValenGerben MenschaertPetra Van Damme

A1 Journal Article in NUCLEIC ACIDS RESEARCH

eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs

Daria FijalkowskaSteven VerbruggenElvis NdahVeronique JonckheereGerben MenschaertPetra Van Damme

A1 Journal Article in NUCLEIC ACIDS RESEARCH

proBAMconvert : a conversion tool for proBAM/proBed

Volodimir OlexioukGerben Menschaert

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2016

A role for human N-alpha acetyltransferase 30 (Naa30) in maintaining mitochondrial integrity

Petra Van DammeThomas V KalvikKristian W StarheimVeronique JonckheereLine M MyklebustGerben MenschaertJan Erik VarhaugKris GevaertThomas Arnesen

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Fast and reliable quantitative peptidomics with labelpepmatch

Rik VerdonckWouter De HaesDries CardoenGerben MenschaertThomas HuhnBart LanduytGeert BaggermanKurt BoonenTom WenseleersLiliane Schoofs

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Identification of small novel coding sequences, a proteogenomic endeavor

Volodimir OlexioukGerben Menschaert

Bookchapter in Proteogenomics

The salivary protein repertoire of the polyphagous spider mite Tetranychus urticae: a quest for effectors

Wim JonckheereWannes DermauwVladimir ZhurovNicky WybouwJan Van den BulckeCarlos A VillarroelRobert GreenhalghMike GrbićRob C SchuurinkLuc Tirry et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

2015

An update on LNCipedia : a database for annotated human lncRNA sequences

Pieter-Jan VoldersKenneth VerheggenGerben MenschaertKlaas VandepoeleLennart MartensJo VandesompelePieter Mestdagh

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Different approaches to measuring gene expression and DNA methylation and their application in cancer research

Alexander KochWim Van CriekingeTim De MeyerGerben Menschaert

Micropeptides as non-classical bioactive peptides in Eukaryotes, a ribosome profiling centered approach

Jeroen CrappéWim Van CriekingeGerben MenschaertGeert Baggerman

PROTEOFORMER : deep proteome coverage through ribosome profiling and MS integration

Jeroen CrappéElvis NdahAlexander KochSandra SteyaertDaria FijalkowskaSarah De KeulenaerEllen De MeesterTim De MeyerWim Van CriekingePetra Van Damme et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

sORFs.org : a repository of small ORFs identified by ribosome profiling

Volodimir OlexioukJeroen CrappéSteven VerbruggenKenneth VerheggenLennart MartensGerben Menschaert

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2014

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

Alexander KochDaria FijalkowskaSandra SteyaertElvis NdahJeroen CrappéSarah De KeulenaerEllen De MeesterMing MaBen ShenKris Gevaert et al.

A1 Journal Article in PROTEOMICS

Little things make big things happen : a summary of micropeptide encoding genes

Jeroen CrappéWim Van CriekingeGerben Menschaert

A2 Journal Article in EUPA OPEN PROTEOMICS

N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men

Petra Van DammeDaria FijalkowskaWim Van CriekingeGerben Menschaert

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

2013

Colorado potato beetle (Coleoptera) gut transcriptome analysis: expression of RNA interference-related genes

L SweversHanneke HuvenneGerben MenschaertD KontogiannatosA KourtiY PauchetR Ffrench-ConstantGuy Smagghe

A1 Journal Article in INSECT MOLECULAR BIOLOGY

Combining endogenous peptide prediction and MS/MS peptide search: an application to search for the most primitive neuropeptides

Eisuke HayakawaHiroshi WatanabeGerben MenschaertThomas HolsteinGeert BaggermanLiliane Schoofs

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs

Jeroen CrappéWim Van CriekingeGeert TrooskensEisuke HayakawaWalter LuytenGeert BaggermanGerben Menschaert

A1 Journal Article in BMC GENOMICS

Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events

Gerben MenschaertWim Van CriekingeTineke NotelaersAlexander KochJeroen CrappéKris GevaertPetra Van Damme

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Improving the identification rate of endogenous peptides using electron transfer dissociation and collision-induced dissociation

Eisuke HayakawaGerben MenschaertPieter-Jan De BockWalter LuytenKris GevaertGeert BaggermanLiliane Schoofs

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Mass spectrometry and ribosome profiling, a perfect combination towards a more comprehensive identification strategy of true in vivo protein forms

Jeroen CrappéAlexander KochSandra SteyaertWim Van CriekingePetra Van DammeGerben Menschaert

Micropeptides, the next best thing after micro-RNA?: combining in silico prediction and ribosome profiling in a genome-wide search for novel micropeptides

Jeroen CrappéGeert TrooskensEisuke HayakawaWalter LuytenGeert BaggermanWim Van CriekingeGerben Menschaert

PIUS: peptide identification by unbiased search

Eduardo P CostaGerben MenschaertWalter LuytenKurt De GraveJan Ramon

A1 Journal Article in BIOINFORMATICS

PROTEIN IDENTIFICATION BASED ON RIBOSOME TARGETED MRNA FRAGMENTS.

Elvis NdahJeroen CrappéAlexander KochGerben MenschaertSandra SteyaertPetra Van Damme

Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing

Tim De MeyerEvi MampaeyMichaël VlemmixSimon DenilGeert TrooskensJean-Pierre RenardSarah De KeulenaerPierre DehanGerben MenschaertWim Van Criekinge

A1 Journal Article in PLOS ONE

Reviving nuclear translation

Petra Van DammeGerben Menschaert

2012

Micropeptides, the next best thing after micro-RNA?: combining in silico prediction and ribosome profiling in a genome-wide search for novel micropeptides

Jeroen CrappéGeert TrooskensEisuke HayakawaWalter LuytenGeert BaggermanWim Van CriekingeGerben Menschaert

Spectral clustering in peptidomics studies allows homology searching and modification profiling: HomClus, a versatile tool

Gerben MenschaertEisuke HayakawaLiliane SchoofsWim Van CriekingeGeert Baggerman

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2011

A novel endogenous peptide identified in the pancreas enhances learning behavior and inhibits neuro degeneration

Bart LanduytMelissa PaulussenGerben MenschaertGeert BaggermanA Van DijckP De DeynT WahleC DottiLut ArckensWalter Luyten et al.

Diversity in protein glycosylation among insect species

Gianni VandenborreGuy SmaggheBart GhesquièreGerben MenschaertNagender RaoKris GevaertEls Van Damme

A1 Journal Article in PLOS ONE

Interaction of the tobacco lectin with histone proteins

Dieter SchouppeBart GhesquièreGerben MenschaertWinnok De VosStéphanie BourqueGeert TrooskensPaul ProostKris GevaertEls Van Damme

A1 Journal Article in PLANT PHYSIOLOGY

Linking mass spectrometric imaging and traditional peptidomics: a validation in the obese mouse model

Laurens MinervaKurt BoonenGerben MenschaertBart LanduytGeert BaggermanLut Arckens

A1 Journal Article in ANALYTICAL CHEMISTRY

Micro peptides as a new class of bio-active peptides in Eukaryotes

Jeroen CrappéGerben MenschaertGeert TrooskensJoachim De SchrijverGeert BaggermanWim Van Criekinge

2010

A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome

Gerben MenschaertTom VandekerckhoveGeert BaggermanBart LanduytJonathan V SweedlerLiliane SchoofsWalter LuytenWim Van Criekinge

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Bioinformatics solutions for MS/MS data interpretation tailored to the peptidomics field

Gerben MenschaertWim Van Criekinge

Glycosylation signatures in Drosophila : fishing with lectins

Gianni VandenborreEls Van DammeBart GhesquièreGerben MenschaertMohamad HamshouRameshwaram Nagender RaoKris GevaertGuy Smagghe

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Mining cleavage sites of the mouse peptidome

Kurt De GraveTias GunsTom VandekerckhoveBart LanduytGerben MenschaertWim Van CriekingeLiliane SchoofsWalter Luyten

Peptidomics coming of age : a review of contributions from a bioinformatics angle

Gerben MenschaertTom VandekerckhoveGeert BaggermanLiliane SchoofsWalter LuytenWim Van Criekinge

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2009

Bioinformatics solutions for MS/MS interpretation tailored to the peptidomics field

Gerben MenschaertTom VandekerckhoveGeert BaggermanBart LanduytLiliane SchoofsWalter LuytenWim Van Criekinge

A4 Journal Article in COMMUNICATIONS IN AGRICULTURAL AND APPLIED BIOLOGICAL SCIENCES

Spectral clustering in peptidomics studies helps to unravel modification profile of biologically active peptides and enhances peptide identification rate

Gerben MenschaertTom VandekerckhoveBart LanduytEisuke HayakawaLiliane SchoofsWalter LuytenWim Van Criekinge

A1 Journal Article in PROTEOMICS

2008

PubMeth: a cancer methylation database combining text-mining and expert annotation

Maté OngenaertLeander Van NesteTim De MeyerGerben MenschaertSofie BekaertWim Van Criekinge

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Pubmeth: reviewed methylation database in cancer based on text-mining

Maté OngenaertLeander Van NesteTim De MeyerGerben MenschaertSofie BekaertWim Van Criekinge

2007

SOS MS: Enhancements for Mascot Search Engine and Other Mass Spectrometry Software

Tom TM VandekerckhoveGerben MenschaertBart LanduytKurt BoonenWim Van Criekinge

2000

Maturation performance, offspring quality and lipid composition of Macrobrachium rosenbergii females fed increasing levels of dietary phospholipids.

RO CAVALLIGerben MenschaertPatrick LavensPatrick Sorgeloos

A1 Journal Article in AQUACULTURE INTERNATIONAL