Research Explorer

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Researcher

Vanessa Vermeirssen

Publications & Research Data

Awards & Distinctions

57 Results

2026

How negative sampling shapes the performance of transcription factor binding site prediction models

Natan TourneGaetan De WaeleVanessa VermeirssenWillem Waegeman

A1 Journal Article in BIOINFORMATICS

2025

A human-specific, concerted repression of microcephaly genes contributes to radiation-induced growth defects in cortical organoids

Jessica Honorato RibeiroEmre EtliogluJasmine BusetAnn JanssenHanne PuypeLisa BerdenAndre Claude Mbouombouo MfossaWinnok H. De VosVanessa VermeirssenSarah Baatout et al.

A1 Journal Article in ISCIENCE

Methodological analysis of network inference and multi-omics data integration to unravel eukaryotic gene regulation

Jens Uwe LoersVanessa Vermeirssen

Repurposing itraconazole and pyrimethamine as a combinatorial treatment for glioblastoma

Thibault LootensAnne-Sophie BamelisJelle VandersteeneHarry PinsonSam ErnstTom BoterbergVanessa VermeirssenOlivier De WeverFrederik De SmetRobrecht Raedt

Repurposing itraconazole and pyrimethamine with temozolomide as a combinatorial treatment for glioblastoma

Thibault LootensJelle VandersteeneHarry PinsonSam ErnstTom BoterbergVanessa VermeirssenOlivier De WeverFrederik De SmetRobrecht Raedt

2024

A single-cell multimodal view on gene regulatory network inference from transcriptomics and chromatin accessibility data

Jens Uwe LoersVanessa Vermeirssen

A1 Journal Article in BRIEFINGS IN BIOINFORMATICS

Evaluation of single-sample network inference methods for precision oncology

Joke DeschildreBoris VandemoorteleJens Uwe LoersKatleen De PreterVanessa Vermeirssen

A1 Journal Article in NPJ SYSTEMS BIOLOGY AND APPLICATIONS

HTSplotter : an end-to-end data processing, analysis and visualisation tool for chemical and genetic in vitro perturbation screening

Carolina de Carvalho NunesJasper AnckaertFanny De VloedJolien De WynKaat DurinckJo VandesompeleFranki SpelemanVanessa Vermeirssen

A1 Journal Article in PLOS ONE

Human iPSC modeling recapitulates in vivo sympathoadrenal development and reveals an aberrant developmental subpopulation in familial neuroblastoma

Stéphane Van HaverYujie FanSarah-Lee BekaertCeline EveraertWouter Van LoockeVittorio ZanzaniJoke DeschildreInes Fernandez MaestreAdrianna AmaroVanessa Vermeirssen et al.

A1 Journal Article in ISCIENCE

NBAtlas : a harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors

Noah BonineVittorio ZanzaniAnnelies Van HemelrykBavo VannesteChristian ZwickerTinne THONESofie RoelandtSarah-Lee BekaertJan KosterIsabelle Janoueix-Lerosey et al.

A1 Journal Article in CELL REPORTS

Proteomics dataset of lysolecithin-induced demyelinated lesions in corpus callosum of Lewis rats, treated with Vagus nerve stimulation or sham treatment

Helen BachmannBoris VandemoorteleVanessa VermeirssenEvelien CarretteKristl VonckPaul BoonRobrecht RaedtGuy Laureys

A2 Journal Article in DATA IN BRIEF

Repurposing itraconazole and pyrimethamine with temozolomide as a combinatorial treatment for glioblastoma

Thibault LootensJelle VandersteeneHarry PinsonTom BoterbergVanessa VermeirssenOlivier De WeverFrederik De SmetRobrecht Raedt

Vagus nerve stimulation enhances remyelination and decreases innate neuroinflammation in lysolecithin-induced demyelination

Helen BachmannBoris VandemoorteleVanessa VermeirssenEvelien CarretteKristl VonckPaul BoonRobrecht RaedtGuy Laureys

A1 Journal Article in BRAIN STIMULATION

2023

A harmonized single-cell transcriptomic atlas of human neuroblastoma

Noah BonineVittorio ZanzaniLiselot MusBavo VannesteChristian ZwickerTinne THONESofie RoelandtCécile ThirantAmira KramdiIsabelle Janoueix-Lerosey et al.

Molecular systems biology approaches to investigate mechanisms of gut-brain communication in neurological diseases

Boris VandemoorteleVanessa Vermeirssen

A1 Journal Article in EUROPEAN JOURNAL OF NEUROLOGY

Preclinical evaluation of targeted therapeutic strategies for high-risk neuroblastoma

Carolina de Carvalho NunesFranki SpelemanKaat DurinckVanessa Vermeirssen

Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models enables specific monitoring of tumour-derived extracellular RNA

Vanessa VermeirssenJill DeleuAnnelien MorlionCeline EveraertJilke De WildeJasper AnckaertKaat DurinckJustine NuytensMuhammad RishfiFranki Speleman et al.

2022

Exploration of neuroblastoma xenograft models for tumor extracellular RNA profiling in murine blood plasma

Vanessa VermeirssenJill DeleuAnnelien MorlionCeline EveraertJilke De WildeJasper AnckaertKaat DurinckJustine NuytensMuhammad RishfiFranki Speleman et al.

HTSplotter : an end-to-end data processing, analysis and visualisation tool for chemical and genetic in vitro perturbation screening

Carolina de Carvalho NunesJasper AnckaertFanny De VloedJolien De WynKaat DurinckJo VandesompeleFranki SpelemanVanessa Vermeirssen

Maximal acyclic subgraph optimization for gene regulatory networks

Kenneth StoopTom MichoelVanessa VermeirssenMario PickavetP. AudenaertDidier Colle

Nearby transposable elements impact plant stress gene regulatory networks : a meta-analysis in A. thaliana and S. lycopersicum

Jan DenewethYves Van de PeerVanessa Vermeirssen

A1 Journal Article in BMC GENOMICS

Opportunities and challenges in interpretable deep learning for drug sensitivity prediction of cancer cells

Bikash Ranjan SamalJens Uwe LoersVanessa VermeirssenKatleen De Preter

A2 Journal Article in FRONTIERS IN BIOINFORMATICS

RRM2 enhances MYCN driven neuroblastoma formation and acts as a synergistic target with CHK1 inhibition

Lisa DepestelCarolina de Carvalho NunesLiselot MusIris NelenLouis DelhayeKaylee KellerVolodimir OlexioukFanny De VloedEllen SandersAline Eggermont et al.

RRM2 enhances MYCN-driven neuroblastoma formation and acts as a synergistic target with CHK1 inhibition

Carolina de Carvalho NunesLisa DepestelLiselot MusKaylee M. KellerLouis DelhayeAmber LouwagieMuhammad RishfiAlex WhaleNeesha KaraSimon R. Andrews et al.

A1 Journal Article in SCIENCE ADVANCES

SUBATOMIC : a SUbgraph BAsed mulTi-OMIcs clustering framework to analyze integrated multi-edge networks

Jens Uwe LoersVanessa Vermeirssen

A1 Journal Article in BMC BIOINFORMATICS

Whole transcriptome profiling of liquid biopsies from tumor xenografted mouse models enables specific monitoring of tumor-derived RNA

Vanessa VermeirssenJill DeleuAnnelien MorlionCeline EveraertKimberly VerniersTom Van MaerkenBram De WildeJo VandesompeleAnneleen Decock

Whole transcriptome profiling of liquid biopsies from tumor xenografted mouse models enables specific monitoring of tumor-derived RNA

Vanessa VermeirssenJill DeleuAnnelien MorlionCeline EveraertKimberly VerniersTom Van MaerkenBram De WildeJo VandesompeleAnneleen Decock

Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models enables specific monitoring of tumour-derived extracellular RNA

Vanessa VermeirssenJill DeleuAnnelien MorlionCeline EveraertJilke De WildeJasper AnckaertKaat DurinckJustine NuytensMuhammad RishfiFranki Speleman et al.

A2 Journal Article in NAR CANCER

Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models enables specific monitoring of tumour-derived extracellular RNA

Vanessa VermeirssenJill DeleuAnnelien MorlionCeline EveraertJilke De WildeJasper AnckaertKaat DurinckJustine NuytensMuhammad RishfiFranki Speleman et al.

2021

From DNA copy number gains and tumor dependencies to novel therapeutic targets for high-risk neuroblastoma

Bieke DecaestekerKaat DurinckNadine Van RoyBram De WildeChristophe Van NesteStéphane Van HaverStephen RobertsKatleen De PreterVanessa VermeirssenFranki Speleman

A1 Journal Article in JOURNAL OF PERSONALIZED MEDICINE

Whole transcriptome profiling of liquid biopsies from tumor xenografted mouse models enables specific monitoring of tumor-derived RNA

Vanessa VermeirssenJill DeleuAnnelien MorlionCeline EveraertKimberly VerniersTom Van MaerkenBram De WildeJo VandesompeleAnneleen Decock

Whole transcriptome profiling of liquid biopsies from tumor xenografted mouse models enables specific monitoring of tumor-derived RNA

Vanessa VermeirssenJill DeleuCeline EveraertAnnelien MorlionKimberly VerniersJasper AnckaertJo VandesompeleTom Van MaerkenAnneleen DecockBram De Wilde

2020

Whole transcriptome profiling of liquid biopsies from tumor xenografted mouse models enables specific monitoring of tumor-derived RNA

Jill DeleuVanessa VermeirssenCeline EveraertAnnelien MorlionKimberly VerniersJasper AnckaertJo VandesompeleTom Van MaerkenAnneleen DecockBram De Wilde

2019

17q gain provides proliferative advantage to human embryonic stem cells under replicative stress

Liselot MusStéphane Van HaverGeertrui DeneckerNadja ZeltnerYudelca OgandoEllen SandersEva JacobsMina PopovicChristophe Van NesteSuzanne Vanhauwaert et al.

Whole transcriptome profiling of liquid biopsies from patient-derived xenograft (PDX) models

Vanessa VermeirssenAnneleen DecockKimberly VerniersCeline EveraertAnnelien MorlionJill DeleuTom Van MaerkenBram De WildeJo Vandesompele

2018

Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant

Jonas DefoortYves Van de PeerVanessa Vermeirssen

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2014

Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress

Vanessa VermeirssenInge De ClercqThomas Van ParysFrank Van BreusegemYves Van de Peer

A1 Journal Article in PLANT CELL

Reciprocal responses in the interaction between Arabidopsis and the cell-content feeding chelicerate herbivore spider mite

Vladimir ZhurovMarie NavarroKristie A BruinsmaVicent ArbonaM Estrella SantamariaMarc CazauxNicky WybouwEdward J OsborneCherise EnsCristina Rioja et al.

A1 Journal Article in PLANT PHYSIOLOGY

2013

The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis

Inge De ClercqVanessa VermeirssenOlivier Van AkenKlaas VandepoeleMonika W MurchaSimon R LawAnnelies InzéSophia NgAneta IvanovaDebbie Rombaut et al.

A1 Journal Article in PLANT CELL

2012

Identification of cis-regulatory elements specific for different types of reactive oxygen species in Arabidopsis thaliana

Veselin PetrovVanessa VermeirssenInge De ClercqFrank Van BreusegemIvan MinkovKlaas VandepoeleTsanko S Gechev

A1 Journal Article in GENE

2010

Towards system level modeling of functional modules and regulatory pathways using genome-scale data

Tom MichoelAnagha Madhusudan JoshiEric BonnetVanessa VermeirssenYves Van de Peer

2009

Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development

Vanessa VermeirssenAnagha Madhusudan JoshiTom MichoelEric BonnetTine CasneufYves Van de Peer

A1 Journal Article in MOLECULAR BIOSYSTEMS

2007

Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping

Vanessa VermeirssenBart DeplanckeM Inmaculada BarrasaJohn S Reece-HoyesH Efsun ArdaChristian A GroveNatalia J MartinezReynaldo SequerraLynn Doucette-StammMichael R Brent et al.

A1 Journal Article in NATURE METHODS

Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network

Vanessa VermeirssenM Inmaculada BarrasaCesar A HidalgoJenny Aurielle B BabonReynaldo SequerraLynn Doucette-StammAlbert-Laszlo BarabasiAlbertha JM Walhout

A1 Journal Article in GENOME RESEARCH

2006

Gateway-compatible yeast one-hybrid screens

Bart DeplanckeVanessa VermeirssenHatice Efsun ArdaNatalia J MartinezAlberta J Walhout

A4 Journal Article in COLD SPRING HARBOR PROTOCOLS

2005

ACE inhibitor captopril reduces ecdysteroids and oviposition in moths

Lieselot VercruysseD GelmanSANDRIEN VAN DE VELDEElke RaesB HoogheVanessa VermeirssenJohn Van CampGuy Smagghe

A1 Journal Article in Annals of the New York Academy of Sciences

Fractionation of angiotensin I converting enzyme inhibitory activity from pea and whey protein in vitro gastrointestinal digests

Vanessa VermeirssenJohn Van CampWilly Verstraete

A1 Journal Article in JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

In vitro intestinal transport and antihypertensive activity of ACE inhibitory pea and whey digests

Vanessa VermeirssenPatrick AugustijnsNicole MorelJohn Van CampAnne OpsomerWilly Verstraete

A1 Journal Article in INTERNATIONAL JOURNAL OF FOOD SCIENCES AND NUTRITION

2004

A quantitative in silico analysis calculates the angiotensin I converting enzyme (ACE) inhibitory activity in pea and whey protein digests

Vanessa VermeirssenArie van der BentJohn Van CampAart van AmerongenWilly Verstraete

A1 Journal Article in BIOCHIMIE

Influence of the lactokinin Ala-Leu-Pro-Met-His-Ile-Arg (ALPMHIR) on the release of endothelin-1 by endothelial cells

Wim MaesJohn Van CampVanessa VermeirssenMattias HemeryckJean Marie KetelslegersJürgen SchrezenmeirPatric Van OostveldtAndré Huyghebaert

A1 Journal Article in REGULATORY PEPTIDES

The angiotensin converting enzyme inhibitor captopril reduces oviposition and ecdysteroid levels in Lepidoptera

Lieselot VercruysseD GelmanElke RaesB HoogheVanessa VermeirssenJohn Van CampGuy Smagghe

A1 Journal Article in ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY

2003

Release and activity of ACE inhibitory peptides from pea and whey protein

Vanessa VermeirssenJohn Van CampWilly Verstraete

Release of angiotensin I converting enzyme (ACE) inhibitory activity during in vitro gastrointestinal digestion: from batch experiment to semicontinuous model

Vanessa VermeirssenJohn Van CampLiesbeth DevosWilly Verstraete

A1 Journal Article in JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

The impact of fermentation and in vitro digestion on the formation of angiotensin-I-converting enzyme inhibitory activity from pea and whey protein

Vanessa VermeirssenJohn Van CampKarel DecroosL Van WijmelbekeWilly Verstraete

A1 Journal Article in JOURNAL OF DAIRY SCIENCE

2002

Intestinal transport of the lactokinin Ala-Leu-Pro-Met-His-Ile-Arg through a Caco-2 Bbe monolayer

Vanessa VermeirssenB DeplanckeKA TappendenJohn Van CampHR GaskinsWilly Verstraete

A1 Journal Article in JOURNAL OF PEPTIDE SCIENCE

Optimisation and validation of an angiotensin-converting enzyme inhibition assay for the screening of bioactive peptides

Vanessa VermeirssenJohn Van CampWilly Verstraete

A1 Journal Article in JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS

2001

Development of a six-stage culture system for simulating the gastrointestinal microbiota of weaned infants

Patrick De BoeverRoel WoutersVanessa VermeirssenNico BoonWilly Verstraete

A2 Journal Article in MICROBIAL ECOLOGY IN HEALTH AND DISEASE