Research Explorer

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Researcher

Jo Vandesompele

Publications & Research Data

Awards & Distinctions

633 Results

2026

Deconvoluting fibre type proportions from human skeletal muscle transcriptomics and proteomics data using FibeRtypeR

Thibaux Van der StedeRoger Moreno‐JusticiaFreek Van de CasteeleEline LievensAlexia Van de LoockJonas VandecauterPeter MerseburgerJimmy Van den EyndenDelphi Van HaverAn Staes et al.

U Journal Article in JOURNAL OF PHYSIOLOGY-LONDON

PeakPrime : a peak-guided primer design pipeline for target enrichment in 3′-end RNA-seq

Franco Alexander Poma SotoBrecht SoulliaertHanne Van DroogenbroeckPieter MestdaghJo Vandesompele

A2 Journal Article in BIOINFORMATICS ADVANCES

Standardized digital PCR assay validation using PCR-ValiPal, demonstrated in cross-platform quantification of bovine papilloma virus

David GleerupMatthijs VynckLien GysensCindy De BaereWim TrypsteenJo VandesompeleOlivier ThasAnn MartensMaarten HaspeslaghWard De Spiegelaere

A1 Journal Article in ANALYTICA CHIMICA ACTA

2025

Blood collection tube and RNA purification method recommendations for extracellular RNA transcriptome profiling

The exRNAQC ConsortiumJasper AnckaertFrancisco Avila CobosAnneleen DecockPhilippe DecruyenaereJill DeleuKatleen De PreterOlivier De WeverJilke De WildeBert Dhondt et al.

A1 Journal Article in NATURE COMMUNICATIONS

Carriers, cargo, and consequences : analytical strategies to resolve heterogeneity in lipid nanoparticle delivery

Sarah GoddaerKatrien RemautJo VandesompeleKevin Braeckmans

Cellular deconstruction of the human skeletal muscle microenvironment identifies an exercise-induced histaminergic crosstalk

Thibaux Van der StedeAlexia Van de LoockGuillermo TurielCamilla HansenAndrea Tamariz-EllemannMax UllrichEline LievensJan SpaasNurten YigitJasper Anckaert et al.

A1 Journal Article in CELL METABOLISM

Cost-effective multiplex digital PCR quantification using universal Rainbow detection probes

Gertjan WilsEmma JacobsAmber DeclercqPeter Natividad D. CeulemansJan HellemansFrauke CoppietersSteve LefeverJo Vandesompele

U Journal Article in EUROPEAN JOURNAL OF HUMAN GENETICS

Deconvoluting fiber type proportions from human skeletal muscle transcriptomics and proteomics data using FibeRtypeR

Thibaux Van der StedeRoger Moreno-JusticiaFreek Van de CasteeleEline LievensAlexia Van de LoockJonas VandecauterPeter MerseburgerJimmy Van den EyndenDelphi Van HaverAn Staes et al.

Development of a digital PCR TERT/TERRA quantification assay in neuroblastoma

Pinar SafariKimberly VerniersLisa WerrChristoph BartenhagenNickolas Johns RamirezAnneleen DecockBram De WildeMatthias FischerJo Vandesompele

Digital PCR-based gene expression analysis using a highly multiplexed assay with universal detection probes to study induced pluripotent stem cell differentiation into cranial neural crest cells

Gertjan WilsLisa HamerlinckWim TrypsteenCharlotte Van Den EeckhautJonathan WeissAfif Abdel NourSarah VergultJo Vandesompele

Bookchapter in Gene expression analysis : methods and protocols

DNA sample tracking for diagnostic exome sequencing - a 1-year experience

Peter N. D. CeulemansMatthias De SmetTom SanteGertjan WilsThalia Van LaethemMauro Alessio MilazzoJo VandesompeleFrauke CoppietersSteve LefeverBrecht Guillemyn et al.

U Journal Article in EUROPEAN JOURNAL OF HUMAN GENETICS

Exploring the cell-free transcriptome as a biomarker source in non-Hodgkin lymphoma

Philippe DecruyenaereJo VandesompeleFritz Offner

Flexible methods for uncertainty estimation of digital PCR data

Yao ChenWard De SpiegelaereMatthijs VynckWim TrypsteenDavid GleerupJo VandesompeleOlivier Thas

A1 Journal Article in ISCIENCE

Human skeletal muscle fiber heterogeneity beyond myosin heavy chains

Roger Moreno-JusticiaThibaux Van der StedeBen StocksJenni LaitilaRobert A. SeaborneAlexia Van de LoockEline LievensDiana SamodovaLeyre Marín-ArraizaOksana Dmytriyeva et al.

A1 Journal Article in NATURE COMMUNICATIONS

PeakPrime manuscript data

Franco Alexander Poma SotoBrecht SouillaertHanne Van DroogenbroeckPieter MestdaghJo Vandesompele

Polytect : an automatic clustering and labeling method for multicolor digital PCR data

Yao ChenWard De SpiegelaereWim TrypsteenJo VandesompeleGertjan WilsDavid GleerupAntoon LievensOlivier ThasMatthijs Vynck

A2 Journal Article in NAR GENOMICS AND BIOINFORMATICS

Sequential orthogonal assays for longitudinal and endpoint characterization of three-dimensional spheroids

Eva BlondeelSam ErnstFelix De VuystÁkos DiósdiCláudio PinheiroDiogo EstêvãoPekka RappuRobin BoiySandor DedeyneLigia Craciun et al.

A1 Journal Article in NATURE PROTOCOLS

Sequential orthogonal assays for longitudinal and endpoint characterization of three-dimensional spheroids (Apr, 10.1038/s41596-025-01150-y, 2025)

Eva BlondeelSam ErnstFelix De VuystÁkos DiósdiCláudio PinheiroDiogo Miguel Monteiro EstêvãoPekka RappuRobin BoiySandor DedeyneLigia Craciun et al.

Subpar reporting of pre‐analytical variables in RNA‐focused blood plasma studies

Céleste Van Der SchuerenPhilippe DecruyenaereFrancisco Avila CobosJohanna BultJill DeleuLydia DipaloHetty HelsmoortelEva HulstaertAnnelien MorlionElena Ramos Varas et al.

A1 Journal Article in MOLECULAR ONCOLOGY

The development of a custom spatial transcriptomics platform to study cellular heterogeneity induced by targeted therapies in neuroblastoma

Hanne Van DroogenbroeckFranco Alexander Poma SotoBrecht SoulliaertMark SomozaMaya GridharCharlotte ScottRobrecht RaedtNiels VandammeBram De WildeTom Van Maerken et al.

The development of a custom spatial transcriptomics platform to study cellular heterogeneity induced by targeted therapies in neuroblastoma

Hanne Van DroogenbroeckFranco Alexander Poma SotoBrecht SoulliaertMark SomozaMaya GridharCharlotte ScottRobrecht RaedtBram De WildeTom Van MaerkenPieter Mestdagh et al.

2024

Advancing extracellular RNA research through method scrutiny, optimization, and mRNA integrity profiling

Jasper VerwiltJo VandesompelePieter Mestdagh

Benchmarking digital PCR partition classification methods with empirical and simulated duplex data

Yao ChenWard De SpiegelaereWim TrypsteenDavid GleerupJo VandesompeleAntoon LievensMatthijs VynckOlivier Thas

A1 Journal Article in BRIEFINGS IN BIOINFORMATICS

Characterizing the cell-free transcriptome in a humanized diffuse large B-cell lymphoma patient-derived tumor xenograft model for RNA-based liquid biopsy in a preclinical setting

Philippe DecruyenaereWillem DaneelsAnnelien MorlionKimberly VerniersJasper AnckaertJan TavernierFritz OffnerJo Vandesompele

A1 Journal Article in INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Characterizing the cell-free transcriptome in a humanized DLBCL patient-derived tumor xenograft model for RNA-based liquid biopsy in a preclinical setting

Philippe DecruyenaereJo VandesompeleWillem DaneelsFritz Offner

Digital PCR threshold robustness analysis and optimization using dipcensR

Matthijs VynckWim TrypsteenOlivier ThasJo VandesompeleWard De Spiegelaere

A1 Journal Article in BRIEFINGS IN BIOINFORMATICS

Exploring the cell-free transcriptome as biomarker source in IgM gammopathies : new insights from the Fondazione Italiana Linfomi 'BIO-WM' trial

Philippe DecruyenaereDaniela DrandiKimberly VerniersSimone RagainiJasper AnckaertVeronica PeriElisa GenuardiFederica CavalloLuigi MarcheselliIrene Dogliotti et al.

FUSIONprimerXL : scalable PCR primer design for fusion transcript quantification

Annelien MorlionMarieke VrommanEveline Vanden EyndeKimberly VerniersJo VandesompeleAnneleen Decock

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

Identification and validation of extracellular vesicle reference genes for the normalization of RT‐qPCR data

Cláudio PinheiroNiké GuilbertLien LippensQuentin RouxRobin BoiySuzanne FischerSofie Van DorpeBram De CraeneGeert BerxTom Boterberg et al.

A1 Journal Article in JOURNAL OF EXTRACELLULAR VESICLES

Nationwide quality assurance of high-throughput diagnostic molecular testing during the SARS-CoV-2 pandemic : role of the Belgian National Reference Centre

Reile JanssenLize CuypersLies LaenenEls KeyaertsKurt BeuselinckSunita JanssenswillenBram SlechtenJannes BodeElke WollantsKristel Van Laethem et al.

A1 Journal Article in VIROLOGY JOURNAL

Nucleic acid degradation as barrier to gene delivery : a guide to understand and overcome nuclease activity

Heyang ZhangJo VandesompeleKevin BraeckmansStefaan De SmedtKatrien Remaut

A1 Journal Article in CHEMICAL SOCIETY REVIEWS

Subpar reporting of pre-analytical variables in RNA-focused blood plasma studies

Céleste Van Der SchuerenPhilippe DecruyenaereFrancisco Avila CobosJohanna BultJill DeleuLydia DipaloHetty HelsmoortelEva HulstaertAnnelien MorlionElena Ramos Varas et al.

Therapy response monitoring in blood plasma from esophageal adenocarcinoma patients using cell-free DNA methylation profiling

Kathleen SchoofsMaísa Renata Ferro Dos SantosJilke De WildeSofie RoelandtSofie Van de VeldePhilippe DecruyenaereLeander MeurisOlivier ThasAnnouck PhilippronLieven Depypere et al.

A1 Journal Article in SCIENTIFIC REPORTS

Transcriptomic signatures of human single skeletal muscle fibers in response to high-intensity interval exercise

Thibaux Van der StedeAlexia Van de LoockEline LievensNurten YigitJasper AnckaertRuud Van ThienenAnneleen WeynsPieter MestdaghJo VandesompeleWim Derave

A1 Journal Article in AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

Unveiling cancer signals in liquid biopsy cell-free RNA profiles

Annelien MorlionPieter MestdaghJo Vandesompele

2023

Artifacts and biases of the reverse transcription reaction in RNA sequencing

Jasper VerwiltPieter MestdaghJo Vandesompele

A1 Journal Article in RNA

Benchmarking blood collection tubes and processing intervals for extracellular vesicle performance metrics

Bert DhondtCláudio PinheiroEdward GeeurickxJoeri TulkensGlenn VergauwenEdwin Van Der PolRienk NieuwlandAnneleen DecockIlkka MiinalainenPekka Rappu et al.

A1 Journal Article in JOURNAL OF EXTRACELLULAR VESICLES

Benchmarking blood collection tubes and processing intervals for extracellular vesicle performance metrics

Bert DhondtCláudio PinheiroEdward GeeurickxJoeri TulkensGlenn VergauwenEdwin Van Der PolRienk NieuwlandAnneleen DecockIlkka MiinalainenPekka Rappu et al.

Blocking abundant RNA transcripts by high-affinity oligonucleotides during transcriptome library preparation

Celine EveraertJasper VerwiltKimberly VerniersNiels VandammeAlvaro Marcos RubioJo VandesompelePieter Mestdagh

A1 Journal Article in BIOLOGICAL PROCEDURES ONLINE

Blood plasma and FFPE derived total RNA seq dataset from DLBCL and PMBCL patients

Philippe DecruyenaereJo VandesompeleFritz Offner

Chasing circles : developing a toolbox for circRNA detection and validation

Marieke VrommanJo VandesompelePieter-Jan Volders

Circular RNA detection pipelines yield divergent sets of circular RNAs

Marieke VrommanJo Vandesompele

Editorial material

Digital PCR partition classification

Matthijs VynckYao ChenDavid GleerupJo VandesompeleWim TrypsteenAntoon LievensOlivier ThasWard De Spiegelaere

A1 Journal Article in CLINICAL CHEMISTRY

Dramatic impact of blood collection tube and RNA purification method on extracellular RNA transcriptomes

Jasper AnckaertFrancisco Avila CobosAnneleen DecockPhilippe DecruyenaereJill DeleuKatleen De PreterOlivier De WeverJilke De WildeBert DhondtThibaut D'huyvetter et al.

Exploration of neuroblastoma xenograft models for the analysis of tumoral cell-free RNA in murine blood plasma

Jill DeleuHanne Van DroogenbroeckJasper AnckaertJilke De WildeKaat DurinckLiselot MusJustine NuytensMuhammad RishfiKathleen SchoofsFranki Speleman et al.

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

Jill DeleuHanne Van DroogenbroeckJasper AnckaertAnneleen DecockJilke De WildeKaat DurinckLiselot MusJustine NuytensMuhammad RishfiKathleen Schoofs et al.

A2 Journal Article in EXRNA

Exploring the cell-free total RNA transcriptome in diffuse large B-cell lymphoma and primary mediastinal B-cell lymphoma patients as biomarker source in blood plasma liquid biopsies

Philippe DecruyenaereEdoardo GiuiliKimberly VerniersJasper AnckaertKatrien De GroveMalaïka Van der LindenDries DeerenJo Van DorpeFritz OffnerJo Vandesompele

A1 Journal Article in FRONTIERS IN ONCOLOGY

Extracellular RNA in liquid biopsies : entering a new era for cancer treatment monitoring?

Jill DeleuBram De WildeTom Van MaerkenJo Vandesompele

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

Marieke VrommanJasper AnckaertStefania BortoluzziAlessia BuratinChia-Ying ChenQinjie ChuTrees-Juen ChuangRoozbeh DehghannasiriChristoph DieterichXin Dong et al.

A1 Journal Article in NATURE METHODS

Longitudinal evaluation of serum microRNAs as biomarkers for neuroblastoma burden and therapeutic p53 reactivation

Alan Van GoethemJill DeleuNurten YigitCeline EveraertMyrthala Moreno-SmithSanjeev A VasudevanFjoralba ZekaFleur DemuynckEveline BarbieriFranki Speleman et al.

A2 Journal Article in NAR CANCER

Nucleic acid biomarkers in blood from patients with esophageal adenocarcinoma : finding the needle in the haystack

Kathleen SchoofsKatleen De PreterJo VandesompelePiet Pattyn

Pan-cancer blood plasma cell-free RNA profiles reveal cancer type and patient-specific changes

Annelien MorlionPhilippe DecruyenaereKathleen SchoofsJasper AnckaertJustine NuytensEveline Vanden EyndeKimberly VerniersCeline EveraertFritz OffnerJo Van Dorpe et al.

Patient-specific alterations in blood plasma cfRNA profiles enable accurate classification of cancer patients and controls

Annelien MorlionPhilippe DecruyenaereKathleen SchoofsJasper AnckaertJustine NuytensEveline Vanden EyndeKimberly VerniersCeline EveraertFritz OffnerJo Van Dorpe et al.

Performance evaluation of RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study

Anneleen DecockOlivier De WeverCeline EveraertHetty HelsmoortelAn HendrixPieter MestdaghAnnelien MorlionJo VandesompeleRuben Van PaemelFrancisco Avila Cobos et al.

Performance evaluation of RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study

Anneleen DecockOlivier De WeverCeline EveraertHetty HelsmoortelAn HendrixPieter MestdaghAnnelien MorlionJo VandesompeleRuben Van PaemelFrancisco Avila Cobos et al.

Reporting of pre-analytical variables in RNA-focused blood plasma studies : a prerequisite for quality assessment and replication

Céleste Van Der SchuerenPhilippe DecruyenaereFrancisco Avila CobosJill DeleuHetty HelsmoortelEva HulstaertAnnelien MorlionKathleen SchoofsEveline Vanden EyndeKimberly Verniers et al.

RNA extraction method impacts quality metrics and sequencing results in diffuse large B-cell lymphoma formalin-fixed paraffin-embedded tissue samples

Philippe DecruyenaereKimberly VerniersFranco Alexander Poma SotoJo Van DorpeFritz OffnerJo Vandesompele

RNA extraction method impacts quality metrics and sequencing results in formalin-fixed, paraffin-embedded tissue samples

Philippe DecruyenaereKimberly VerniersFranco Alexander Poma SotoJo Van DorpeFritz OffnerJo Vandesompele

A1 Journal Article in LABORATORY INVESTIGATION

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

Blocking unwanted sequences by target specific high-affinity binding oligonucleotides during transcriptome library preparation

Celine EveraertJasper VerwiltKimberly VerniersNiels VandammeAlvaro Marcos RubioJo VandesompelePieter Mestdagh

CiLiQuant : quantification of RNA junction reads based on their circular or linear transcript origin

Annelien MorlionEva HulstaertMarieke VrommanJasper AnckaertCeline EveraertJo VandesompelePieter Mestdagh

A2 Journal Article in FRONTIERS IN BIOINFORMATICS

CIRCprimerXL : convenient and high-throughput PCR primer design for circular RNA quantification

Marieke VrommanJasper AnckaertJo VandesompelePieter-Jan Volders

A2 Journal Article in FRONTIERS IN BIOINFORMATICS

Comprehensive RNA dataset of tissue and plasma from patients with esophageal cancer or precursor lesions

Kathleen SchoofsAnnouck PhilippronFrancisco Avila CobosJan KosterSteve LefeverJasper AnckaertDanny De LoozeJo VandesompelePiet PattynKatleen De Preter

A1 Journal Article in SCIENTIFIC DATA

Digital PCR-based evaluation of nucleic acid extraction kit performance for the co-purification of cell-free DNA and RNA

Jill DeleuKathleen SchoofsAnneleen DecockKimberly VerniersSofie RoelandtAngie DenolfJoke VerrethBram De WildeTom Van MaerkenKatleen De Preter et al.

A1 Journal Article in HUMAN GENOMICS

Evaluation of efficiency and sensitivity of 1D and 2D sample pooling strategies for SARS-CoV-2 RT-qPCR screening purposes

Jasper VerwiltJan HellemansTom SantePieter MestdaghJo Vandesompele

A1 Journal Article in SCIENTIFIC REPORTS

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

Large-scale benchmarking of circular RNA detection tools

Marieke VrommanJo VandesompelePieter-Jan Volders

mRNA capture sequencing and RT-qPCR for the detection of pathognomonic, novel, and secondary fusion transcripts in FFPE tissue : a sarcoma showcase

Anneleen DecockDavid CreytensSteve LefeverJoni Van der MeulenJasper AnckaertAriane De GanckJill DeleuBram De WildeCarolina FierroScott Kuersten et al.

A1 Journal Article in INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

mRNA Capture Sequencing and RT-qPCR for the Detection of Pathognomonic, Novel, and Secondary Fusion Transcripts in FFPE Tissue: A Sarcoma Showcase

Anneleen DecockDavid CreytensSteve LefeverJoni Van der MeulenJasper AnckaertAriane De GanckJill DeleuBram De WildeCarolina FierroScott Kuersten et al.

Nucleic acid biomarkers in Waldenstrom Macroglobulinemia and IgM-MGUS : current insights and clinical relevance

Daniela DrandiPhilippe DecruyenaereMartina FerranteFritz OffnerJo VandesompeleSimone Ferrero

A1 Journal Article in DIAGNOSTICS

Performance evaluation of RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study

Jasper AnckaertFrancisco Avila CobosAnneleen DecockPhilippe DecruyenaereJill DeleuKatleen De PreterOlivier De WeverJilke De WildeBert DhondtThibaut D'huyvetter et al.

Performance Evaluation of Three DNA Sample Tracking Tools in a Whole Exome Sequencing Workflow

Gertjan WilsCeline HelsmoortelPieter-Jan VoldersInge VereeckeMauro Alessio MilazzoJo VandesompeleFrauke CoppietersKim De LeeneerSteve Lefever

U Journal Article in MOLECULAR DIAGNOSIS & THERAPY

Reliable and scalable SARS-CoV-2 qPCR testing at a high sample throughput : lessons learned from the Belgian initiative

Steven Van VoorenJames GraysonMarc Van RanstElisabeth DequekerLies LaenenReile JanssenLaurent GilletFabrice BureauWouter CoppietersNathalie Devos et al.

A1 Journal Article in LIFE-BASEL

RNA biomarkers from proximal liquid biopsy for diagnosis of ovarian cancer

Eva HulstaertKeren LevanonAnnelien MorlionStefan Van AelstAnthony-Alexander ChristidisRuben ZamarJasper AnckaertKimberly VerniersKeren Bahar-ShanyStav Sapoznik et al.

A1 Journal Article in NEOPLASIA

The adrenergic-specific long non-coding RNA NESPR controls survival of neuroblastoma cells

Louis DelhayeEric de Bony de LavergneDries RombautLim Fang QiBieke DecaestekerLisa DepestelAmber LouwagieEva D'haenePieter-Jan VoldersNurten Yigit et al.

The dangers of using Cq to quantify nucleic acid in biological samples : a lesson from COVID-19

Daniel EvansSimon CowenMartin KammelDenise M O’SullivanGraham StewartHans-Peter GrunertJacob Moran-GiladJasper VerwiltJiwon InJo Vandesompele et al.

A1 Journal Article in CLINICAL CHEMISTRY

The long non-coding RNA SAMMSON is essential for uveal melanoma cell survival

Shanna DewaeleLouis DelhayeBoel De PaepeEric de Bony de LavergneJilke De WildeKatrien VanderheydenJasper AnckaertNurten YigitJustine NuytensEveline Vanden Eynde et al.

A1 Journal Article in ONCOGENE

The long non-coding RNA SAMMSON is essential for uveal melanoma cell survival (Sept, 10.1038/s41388-021-02006-x, 2021)

Shanna DewaeleLouis DelhayeBoel De PaepeEric James de BonyJilke De WildeKatrien VanderheydenJasper AnckaertNurten YigitJustine NuytensEveline Vanden Eynde et al.

Transient nuclear lamin A/C accretion aids in recovery from vapor nanobubble-induced permeabilisation of the plasma membrane

Gaëlle HouthaeveGerardo García-Díaz BarrigaStephan StremerschHerlinde De KeersmaeckerJuan FraireJo VandesompelePieter MestdaghStefaan De SmedtKevin BraeckmansWinnok De Vos

A1 Journal Article in CELLULAR AND MOLECULAR LIFE SCIENCES

Unraveling the therapeutic potential of SAMMSON lncRNA inhibition in uveal melanoma

Shanna DewaelePieter MestdaghJo Vandesompele

When DNA gets in the way in RNA-seq experiments, a sequel

Jasper VerwiltMaria D. GiraldezWim TrypsteenRuben Van PaemelKatleen De PreterPieter MestdaghJo Vandesompele

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

A G316A polymorphism in the ornithine decarboxylase gene promoter modulates MYCN-driven childhood neuroblastoma

Laura D. GambleStefania PurgatoMichelle J. HendersonSimone Di GiacomoAmanda J. RussellPaolo PiginiJayne MurrayEmanuele ValliGiorgio MilazzoFederico M. Giorgi et al.

A1 Journal Article in CANCERS

Candidate RNA biomarkers in biofluids for early diagnosis of ovarian cancer : a systematic review

Eva HulstaertAnnelien MorlionKeren LevanonJo VandesompelePieter Mestdagh

A1 Journal Article in GYNECOLOGIC ONCOLOGY

Charting regulatory RNAs in the human transcriptome using RNA-sequencing

Lucia LorenziPieter MestdaghJo Vandesompele

Circulating bacterial vesicles : from discovery towards clinical application

Joeri TulkensAn HendrixJo Vandesompele

Circulating RNA biomarkers in diffuse large B-cell lymphoma : a systematic review

Philippe DecruyenaereFritz OffnerJo Vandesompele

A1 Journal Article in EXPERIMENTAL HEMATOLOGY & ONCOLOGY

Closing the circle : current state and perspectives of circular RNA databases

Marieke VrommanJo VandesompelePieter-Jan Volders

A1 Journal Article in BRIEFINGS IN BIOINFORMATICS

Custom long non-coding RNA capture enhances detection sensitivity in different human sample types

Annelien MorlionCeline EveraertJustine NuytensEva HulstaertJo VandesompelePieter Mestdagh

A1 Journal Article in RNA BIOLOGY

Evaluating diagnostic accuracy of saliva sampling methods for severe acute respiratory syndrome coronavirus 2 reveals differential sensitivity and association with viral load

Pieter MestdaghMichel GillardSharonjit K. DhillonJean-Paul PirnayJeroen PoelsJan HellemansVeronik HutseCeline VermeirenMaxime BoutierVeerle De Wever et al.

A1 Journal Article in JOURNAL OF MOLECULAR DIAGNOSTICS

Exploring RNA signatures in human biofluids as novel liquid biopsy tool

Eva HulstaertPieter MestdaghLieve BrochezJo Vandesompele

Exploring the extracellular transcriptome in seminal plasma for non-invasive prostate cancer diagnosis

Eva HulstaertAnnelien MorlionJustine NuytensGiovanni PontiMonia MaccaferriSusan LauEleftherios DiamandisJarvi KeithIoannis PrassasNicolaas Lumen et al.

Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome

Ruben Van PaemelAndries De KokerChrista CaggianoAnnelien MorlionPieter MestdaghBram De WildeJo VandesompeleKatleen De Preter

A1 Journal Article in EPIGENETICS

Large-scale benchmarking of circular RNA detection tools

Marieke VrommanJo VandesompelePieter-Jan Volders

Messenger RNA capture sequencing of extracellular RNA from human biofluids using a comprehensive set of spike-in controls

Eva HulstaertAnneleen DecockAnnelien MorlionCeline EveraertKimberly VerniersJustine NuytensNele NijsGary P SchrothScott KuerstenStephen M Gross et al.

Minimally invasive classification of pediatric solid tumors using reduced representation bisulfite sequencing of cell-free DNA : a proof-of-principle study

Ruben Van PaemelAndries De KokerCharlotte VandeputteLieke van ZogchelTim LammensGenevieve LaureysJo VandesompeleGudrun SchleiermacherMathieu ChicardNadine Van Roy et al.

A1 Journal Article in EPIGENETICS

MISpheroID : a knowledgebase and transparency tool for minimum information in spheroid identity

Arne PeirsmanEva BlondeelTasdiq AhmedJasper AnckaertDominique AudenaertTom BoterbergKrisztina BuzasNeil CarragherGastone CastellaniFlávia Castro et al.

A1 Journal Article in NATURE METHODS

Protocol Messenger RNA capture sequencing of extracellular RNA from human biofluids using a comprehensive set of spike-in controls

Eva HulstaertAnneleen DecockAnnelien MorlionCeline EveraertKimberly VerniersJustine NuytensNele NijsGary P. SchrothScott KuerstenStephen M. Gross et al.

A2 Journal Article in STAR PROTOCOLS

Recurrent chromosomal imbalances provide selective advantage to human embryonic stem cells under enhanced replicative stress conditions

Liselot MusStéphane Van HaverMina PopovicWim TrypsteenSteve LefeverNadja ZeltnerYudelca OgandoEva JacobsGeertrui DeneckerEllen Sanders et al.

A1 Journal Article in GENES CHROMOSOMES & CANCER

Robust sequential biophysical fractionation of blood plasma to study variations in the biomolecular landscape of systemically circulating extracellular vesicles across clinical conditions

Glenn VergauwenJoeri TulkensCláudio PinheiroFrancisco Avila CobosSandor DedeyneMarie-Angélique De ScheerderLinos VandekerckhoveFrancis ImpensIlkka MiinalainenGeert Braems et al.

A1 Journal Article in JOURNAL OF EXTRACELLULAR VESICLES

Selection and validation of reference genes for accurate RT-qPCR gene expression normalization in cacao beans during fermentation

Jocelyn De WeverTibo De ConinckHelena EveraertEmmanuel Ohene AfoakwaFrauke CoppietersHayley RottiersStephen Yaw OpokuSamuel LoworKoen DewettinckJo Vandesompele et al.

A1 Journal Article in TREE GENETICS & GENOMES

Substantial performance differences among RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study

Anneleen DecockOlivier De WeverCeline EveraertHetty HelsmoortelAn HendrixPieter MestdaghAnnelien MorlionJo VandesompeleRuben Van PaemelFrancisco Avila Cobos et al.

Substantial performance differences among RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study

Anneleen DecockOlivier De WeverCeline EveraertHetty HelsmoortelAn HendrixPieter MestdaghAnnelien MorlionJo VandesompeleRuben Van PaemelFrancisco Avila Cobos et al.

Targeted therapy of TERT-rearranged neuroblastoma with BET bromodomain inhibitor and proteasome inhibitor combination therapy

Jingwei ChenChristopher NelsonMatthew WongAndrew E. TeePei Y. LiuTing LaJamie I. FletcherAlvin KamiliChelsea MayohChristoph Bartenhagen et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

The MicroRNA landscape of acute beta cell destruction in type 1 diabetic recipients of intraportal islet grafts

Geert MartensGeert StangéLorenzo PiemontiJasper AnckaertZhidong LingDaniel G. PipeleersFrans K. GorusPieter MestdaghDieter De SmetJo Vandesompele et al.

A1 Journal Article in CELLS

The RNA Atlas expands the catalog of human non-coding RNAs

Lucia LorenziHua-Sheng ChiuFrancisco Avila CobosStephen GrossPieter-Jan VoldersRobrecht CannoodtJustine NuytensKatrien VanderheydenJasper AnckaertSteve Lefever et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

The RNA Atlas expands the catalog of human non-coding RNAs (June, 10.1038/s41587-021-00936-1, 2021)

Lucia LorenziHua-Sheng ChiuFrancisco Avila CobosStephen GrossPieter-Jan VoldersRobrecht CannoodtJustine NuytensKatrien VanderheydenJasper AnckaertSteve Lefever et al.

Validation of circular RNAs using RT‐qPCR after effective removal of linear RNAs by ribonuclease R

Marieke VrommanNurten YigitKimberly VerniersSteve LefeverJo VandesompelePieter-Jan Volders

A2 Journal Article in CURRENT PROTOCOLS

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

Cautionary note on contamination of reagents used for molecular detection of SARS-CoV-2

J. F. HuggettV. BenesS. A. BustinJ. A. GarsonK. HarrisM. KammelM. KubistaT. D. McHughJ. Moran-GiladT. Nolan et al.

Editorial material

Charting extracellular transcriptomes in the human biofluid RNA atlas

Eva HulstaertAnnelien MorlionFrancisco Avila CobosKimberly VerniersJustine NuytensEveline Vanden EyndeNurten YigitJasper AnckaertAnja GeertsPieter Hindryckx et al.

A1 Journal Article in CELL REPORTS

Development of extracellular RNA sequencing technologies and applications for cancer diagnosis and monitoring

Celine EveraertPieter MestdaghJo Vandesompele

Distinct Notch1 and BCL11B requirements mediate human γδ/αβ T cell development

Anne-Catherine DolensKaat DurinckMarieke LavaertJoni Van der MeulenImke VelgheJelle De MedtsKarin WeeningJuliette RoelsKatrien De MulderPieter-Jan Volders et al.

A1 Journal Article in EMBO REPORTS

Increased levels of systemic LPS-positive bacterial extracellular vesicles in patients with intestinal barrier dysfunction

Joeri TulkensGlenn VergauwenJan Van DeunEdward GeeurickxBert DhondtLien LippensMarie-Angélique De ScheerderIlkka MiinalainenPekka RappuBruno De Geest et al.

A1 Journal Article in GUT

Localization and expression of nuclear factor of activated T-cells 5 in myoblasts exposed to pro-inflammatory cytokines or hyperosmolar stress and in biopsies from myositis patients

Sandrine HerbeletElly De VlieghereAmanda GonçalvesBoel De PaepeKarsten SchmidtEline NysLaurens WeynantsJoachim WeisGert Van PeerJo Vandesompele et al.

Bookchapter in Myokines, adipokines, cytokines in muscle pathophysiology

Minimally invasive classification of pediatric solid tumors using reduced representation bisulfite sequencing of cell-free DNA

Ruben Van PaemelAndries De KokerCharlotte VandeputteLieke Van ZogchelTim LammensGenevieve LaureysJo VandesompeleGudrun SchleiermacherMatthieu ChicardNadine Van Roy et al.

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments

Alemu Takele AssefaJo VandesompeleOlivier Thas

A1 Journal Article in BMC GENOMICS

Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles

Celine EveraertHetty HelsmoortelAnneleen DecockEva HulstaertRuben Van PaemelKimberly VerniersJustine NuytensJasper AnckaertNele NijsJoeri Tulkens et al.

SPsimSeq : semi-parametric simulation of bulk and single-cell RNA-sequencing data

Alemu Takele AssefaJo VandesompeleOlivier Thas

A1 Journal Article in BIOINFORMATICS

Statistical methods for testing differential gene expression in bulk and single-cell RNA sequencing data

Alemu Takele AssefaOlivier ThasJo Vandesompele

Substantial performance differences among RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control study-important considerations for liquid biopsies

Anneleen DecockJasper AnckaertCeline EveraertJustine NuytensScott KuerstenAn HendrixJo VandesompelePieter MestdaghBert DhondtRuben Van Paemel et al.

The digital MIQE guidelines update : minimum information for publication of quantitative digital PCR experiments for 2020

Jim F. HuggettAlexandra S. WhaleWard De SpiegelaereWim TrypsteenAfif Abdel NourYoung-Kyung BaeVladimir BenesDaniel BurkeMegan ClevelandPhilippe Corbisier et al.

A1 Journal Article in CLINICAL CHEMISTRY

Vapor nanobubble is the more reliable photothermal mechanism for inducing endosomal escape of siRNA without disturbing cell homeostasis

Juan FraireGaëlle HouthaeveJing LiuLaurens RaesLotte VermeulenStephan StremerschToon BransGerardo Garcia-Diaz BarrigaSarah De KeulenaerFilip Van Nieuwerburgh et al.

A1 Journal Article in JOURNAL OF CONTROLLED RELEASE

When DNA gets in the way : a cautionary note for DNA contamination in extracellular RNA-seq studies

Jasper VerwiltWim TrypsteenRuben Van PaemelKatleen De PreterMD GiraldezPieter MestdaghJo Vandesompele

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

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

Benchmarking the impact of data transformation, pre-processing and choice of method in the computational deconvolution of transcriptomics data

Francisco Avila CobosJosé Alquicira-HernandezJo VandesompeleJoseph PowellPieter MestdaghKatleen De Preter

Cost-effective and robust genotyping using double-mismatch allele-specific quantitative PCR

Steve LefeverAli RihaniJoni Van der MeulenFilip PattynTom Van MaerkenJo Van DorpeJan HellemansJo Vandesompele

A1 Journal Article in SCIENTIFIC REPORTS

Deciphering complete cancer transcriptomes from bulk to single cell level

Karen VerboomFranki SpelemanJo VandesompeleKaat Durinck

Discovery and validation of a serum microRNA signature to characterize oligo- and polymetastatic prostate cancer : not ready for prime time

Bert DhondtElise De BleserTom ClaeysSarah BuelensNicolaas LumenJo VandesompeleAnneleen BeckersValerie FonteyneKim Van der EeckenAurélie De Bruycker et al.

A1 Journal Article in WORLD JOURNAL OF UROLOGY

Dramatic differences in RNA purification kit performance in the extracellular RNA quality control study : important considerations for liquid biopsies

Annelien MorlionJasper AnckaertFrancisco Avila CobosAnneleen DecockOlivier De WeverBert DhondtCeline EveraertCarolina FierroHetty HelsmoortelAn Hendrix et al.

Dramatic differences in RNA purification kit performance in the extracellular RNA quality control study : important considerations for liquid biopsies

Annelien MorlionJasper AnckaertFrancisco Avila CobosAnneleen DecockOlivier De WeverBert DhondtCeline EveraertCarolina FierroHetty HelsmoortelAn Hendrix et al.

Effect of methylprednisolone on NFAT5 in Duchenne muscular dystrophy fibroblasts

Sandrine HerbeletAmanda GonçalvesJo VandesompeleJan De Bleecker

Evaluating the applicability of mouse SINEs as an alternative normalization approach for RT-qPCR in brain tissue of the APP23 model for Alzheimer’s disease

Jana JanssensRené CransKathleen Van CraenenbroeckJo VandesompeleChristophe StoveDebby Van DamPeter P. De Deyn

A1 Journal Article in JOURNAL OF NEUROSCIENCE METHODS

Evaluating the impact of RNA purification kit and blood collection tube in the extracellular RNA quality control study : important considerations for liquid biopsies

Annelien MorlionJasper AnckaertFrancisco Avila CobosAnneleen DecockJill DeleuOlivier De WeverBert DhondtCeline EveraertCarolina FierroHetty Helsmoortel et al.

Integrative analysis identifies lincRNAs up- and downstream of neuroblastoma driver genes

Dries RombautHua-Sheng ChiuBieke DecaestekerCeline EveraertNurten YigitAgathe PelthierIsabelle JanoueixChristophe BartenhagenMatthias FischerStephen Roberts et al.

A1 Journal Article in SCIENTIFIC REPORTS

Lack of adequate reporting of pre-analytical variables in RNA based liquid biopsies studies hampers quality assessment and replication

Pieter MestdaghJo VandesompeleCéleste Van Der SchuerenAnneleen DecockHetty HelsmoortelEva Hulstaert

LNCipedia 5 : towards a reference set of human long non-coding RNAs

Pieter-Jan VoldersJasper AnckaertKenneth VerheggenJustine NuytensLennart MartensPieter MestdaghJo Vandesompele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Long noncoding RNA expression profiling in cancer : challenges and opportunities

Lucia LorenziFrancisco Avila CobosAnneleen DecockCeline EveraertHetty HelsmoortelSteve LefeverKaren VerboomPieter-Jan VoldersFranki SpelemanJo Vandesompele et al.

A1 Journal Article in GENES CHROMOSOMES & CANCER

Minimally invasive classification of pediatric solid tumors using reduced representation bisulfite sequencing of cell-free DNA : a proof-of-principle study

Ruben Van PaemelAndries De KokerCharlotte VandeputteLieke van ZogchelTim LammensGenevieve LaureysJo VandesompeleGudrun SchleiermacherMathieu ChicardNadine Van Roy et al.

Non-invasive classification of pediatric tumor types using reduced representation bisulfite sequencing of cell-free DNA : a proof-of-principle study

Ruben Van PaemelA. De KokerCharlotte VandeputteL. M. J. van ZogchelM. ChicardTim LammensJo VandesompeleNadine Van RoyG. SchleiermacherG. A. M. Tytgat et al.

PCR based target enrichment for variant confirmation, gene panels and multiplex PCR sample tracking in a whole exome sequencing workflow

Frauke CoppietersThalia Van LaethemMatthias De SmetPaul CouckeElfride De BaereKathleen ClaesBjörn MentenJo VandesompeleSteve Lefever

Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles

Celine EveraertHetty HelsmoortelAnneleen DecockEva HulstaertRuben Van PaemelKimberly VerniersJustine NuytensJasper AnckaertNele NijsJoeri Tulkens et al.

A1 Journal Article in SCIENTIFIC REPORTS

Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes

Siebe LoontiensLisa DepestelSuzanne VanhauwaertGivani DewynCharlotte GistelinckKaren VerboomWouter Van LoockeFilip MatthijssensAndy WillaertJo Vandesompele et al.

A1 Journal Article in BMC GENOMICS

RNA-based liquid biopsies for better clinical management of Barrett’s esophagus and esophageal adenocarcinoma

Kathleen SchoofsAnnouck PhilippronPhilippe NafteuxLieven DepyperePiet PattynJo VandesompeleKatleen De Preter

RNAcentral : a hub of information for non-coding RNA sequences

Blake A SweeneyAnton I PetrovBoris BurkovRobert D FinnAlex BatemanMaciej SzymanskiWojciech M KarlowskiJan GorodkinStefan E SeemannJamie J Cannone et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Searching for liquid RNA biomarkers for esophageal adenocarcinoma

Kathleen SchoofsAnnouck PhilippronPhilippe NafteuxLieven DepyperePiet PattynJo VandesompeleKatleen De Preter

SMARTer single cell total RNA sequencing

Karen VerboomCeline EveraertNathalie BolducKenneth LivakNurten YigitDries RombautJasper AnckaertMorten VenøJørgen KjemsFranki Speleman et al.

SMARTer single cell total RNA-sequencing

Karen VerboomCeline EveraertNathalie BolducKenneth LivakNurten YigitDries RombautJasper AnckaertSimon LeeMorten VenøJørgen Kjems et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

The generation and use of recombinant extracellular vesicles as biological reference material

Edward GeeurickxJoeri TulkensBert DhondtJan Van DeunLien LippensGlenn VergauwenElisa HeyrmanDelphine De SutterKris GevaertFrancis Impens et al.

A1 Journal Article in NATURE COMMUNICATIONS

The human biofluid RNA atlas : expanding the liquid biopsy field beyond the blood stream

Eva HulstaertKimberly VerniersJustine NuytensEveline Vanden EyndeNurten YigitJasper AnckaertAnja GeertsPeggy JacquesGuy BrusselleTHIERRY DERVEAUX et al.

The long noncoding RNA lncNB1 promotes tumorigenesis by interacting with ribosomal protein RPL35

Pei Y LiuAndrew E TeeGiorgio MilazzoKatherine M HannanJesper MaagSujanna MondalBernard AtmadibrataNenad BartonicekHui PengNicholas Ho et al.

A1 Journal Article in NATURE COMMUNICATIONS

The proliferation of Duchenne muscular dystrophy fibroblasts cultured under inflammatory conditions is reduced by methylprednisolone through modulation of NFAT5 localization in the cell

Sandrine HerbeletAmanda GonçalvesJo VandesompeleJan De Bleecker

The RNA Atlas, a single nucleotide resolution map of the human transcriptome

Lucia LorenziHua-Sheng ChiuFrancisco Avila CobosStephen GrossPieter-Jan VoldersRobrecht CannoodtJustine NuytensKatrien VanderheydenJasper AnckaertSteve Lefever et al.

Therapeutic applications of SAMMSON lncRNA inhibition in uveal melanoma

Shanna DewaeleKatrien VanderheydenBoel De PaepeLouis DelhayeFariba NematiDidier DecaudinSven EyckermanRudy Van CosterJo VandesompelePieter Mestdagh

Therapeutic applications of SAMMSON lncRNA inhibition in uveal melanoma

Shanna DewaeleKatrien VanderheydenBoel De PaepeLouis DelhayeFariba NematiDidier DecaudinSven EyckermanRudy Van CosterJo VandesompelePieter Mestdagh

Therapeutic applications of SAMMSON lncRNA inhibition in uveal melanoma

Shanna DewaeleKatrien VanderheydenBoel De PaepeLouis DelhayeFariba NematiDidier DecaudinSven EyckermanRudy Van CosterJo VandesompelePieter Mestdagh

Variant calling and fusion gene detection in formalin-fixed paraffin-embedded tumor tissue using RNA capture sequencing

Anneleen DecockDavid CreytensJoni Van der MeulenSandra SteyaertCarolina FierroManuel LuypaertSteve LefeverEveline Vanden EyndeKatrien VanderheydenKimberly Verniers 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

A comprehensive inventory of TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia through polyA+ and total RNA sequencing

Karen VerboomWouter Van LoockePieter-Jan VoldersBieke DecaestekerFrancisco Avila CobosSimon BornscheinCharles E de BockZeynep Kalender AtakEmmanuelle ClappierStein Aerts et al.

A1 Journal Article in HAEMATOLOGICA

A high-throughput 3’ UTR reporter screening identifies microRNA interactomes of cancer genes

Gert Van PeerEvelien MetsShana ClaeysInes De PuntSteve LefeverMaté OngenaertPieter RondouFranki SpelemanPieter MestdaghJo Vandesompele

A1 Journal Article in PLOS ONE

A mechanistic classification of clinical phenotypes in neuroblastoma

S AckermannM CartolanoB HeroA RoderwieserC BartenhagenC RosswogF HertwigT SimonA EggertFranki Speleman et al.

A mechanistic classification of clinical phenotypes in neuroblastoma

S AckermannM CartolanoB HeroA RoderwieserC BartenhagenC RosswogF HertwigT SimonA EggertFranki Speleman et al.

A mechanistic classification of clinical phenotypes in neuroblastoma.

Sandra AckermannMaria CartolanoBarbara HeroAnne WelteYvonne KahlertAndrea RoderwieserChristoph BartenhagenEsther WalterJudith GechtLaura Kerschke et al.

A1 Journal Article in SCIENCE

Assessing the biological signal of different RNA fractions for computational deconvolution of healthy tissues

Francisco Avila CobosLucia LorenziJo VandesompeleGary SchrothKatleen De PreterPieter Mestdagh

Assessment of risk refinement strategies for improved clinical outcome of neuroblastoma patients

Fjoralba ZekaJo VandesompelePieter Mestdagh

Circulating microRNA biomarkers for metastatic disease in neuroblastoma patients

Fjoralba ZekaAnneleen DecockAlan Van GoethemKatrien VanderheydenFleur DemuynckTim LammensHetty HelsmoortelJoëlle VermeulenRosa NogueraAna P. Berbegall et al.

A1 Journal Article in JCI INSIGHT

Circulating microRNA biomarkers for metastatic neuroblastoma

Fjoralba ZekaAlan Van GoethemTim LammensAnneleen DecockHetty HelsmoortelGenevieve LaureysMichael HogartyEveline BarbieriJason ShohetFrank Berthold et al.

Comparative analysis of naive, primed and ground state pluripotency in mouse embryonic stem cells originating from the same genetic background

Sabitri GhimireMargot Van der JeughtJitesh NeupaneMatthias S RoostJasper AnckaertMina PopovicFilip Van NieuwerburghPieter MestdaghJo VandesompeleDieter Deforce et al.

A1 Journal Article in SCIENTIFIC REPORTS

Computational deconvolution of transcriptomics data from mixed cell populations

Francisco Avila CobosJo VandesompelePieter MestdaghKatleen De Preter

A1 Journal Article in BIOINFORMATICS

Cross-cohort analysis identifies a TEAD4-MYCN positive-feedback loop as the core regulatory element of high-risk neuroblastoma

Presha RajbhandariGonzalo LopezClaudia CapdevilaBeatrice SalvatoriJiyang YuRuth Rodriguez-BarruecoDaniel MartinezMark YarmarkovichNina Weichert-LeaheyBrian J Abraham et al.

A1 Journal Article in CANCER DISCOVERY

Data analysis methods for digital PCR quantification

Matthijs VynckOlivier ThasJo Vandesompele

Detecting long non-coding RNA biomarkers in prostate cancer liquid biopsies : hype or hope?

Hetty HelsmoortelCeline EveraertNicolaas LumenPiet OstJo Vandesompele

A2 Journal Article in NON-CODING RNA RESEARCH

Differential gene expression analysis of RNA-sequencing data : evaluation of DGE tools for long non-coding RNA-sequencing data

Alemu Takele AssefaJo VandesompeleOlivier Thas

Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

Alemu Takele AssefaKatrijn De PaepeCeline EveraertPieter MestdaghOlivier ThasJo Vandesompele

A1 Journal Article in GENOME BIOLOGY

Expressed repetitive elements are broadly applicable reference targets for normalization of reverse transcription-qPCR data in mice

Marjolijn RenardSuzanne VanhauwaertMarine VanhomwegenAli RihaniNiels VandammeSteven GoossensGeert BerxPieter Van VlierbergheJody J HaighBieke Decaesteker et al.

A1 Journal Article in SCIENTIFIC REPORTS

Fusion gene detection and variant calling in formalin-fixed paraffin-embedded tumor tissue using mRNA capture sequencing

Anneleen DecockDavid CreytensJoni Van der MeulenSandra SteyaertKimberly VerniersKatrien VanderheydenManuel LuypaertThibaut D’huyvetterIsabelle RottiersJo Van Dorpe et al.

In silico discovery of a FOXM1 driven embryonal signaling pathway in therapy resistant neuroblastoma tumors

Suzanne VanhauwaertBieke DecaestekerSara De BrouwerCarina LeonelliKaat DurinckPieter MestdaghJo VandesompeleKaren SermonGeertrui DeneckerChristophe Van Neste et al.

A1 Journal Article in SCIENTIFIC REPORTS

Isolation of high-quality RNA from fluorescent activated cell sorted (FACS) zebrafish cells for RNA sequencing purposes

Siebe LoontiensSuzanne VanhauwaertLisa DepestelGivani DewynCharlotte GistelinckKaren VerboomEls JanssensFilip MatthijssensAndy WillaertJo Vandesompele et al.

Localization and expression of nuclear factor of activated T-cells 5 in myoblasts exposed to pro-inflammatory cytokines or hyperosmolar stress and in biopsies from myositis patients

Sandrine HerbeletElly De VlieghereAmanda GonçalvesBoel De PaepeKarsten SchmidtEline NysLaurens WeynantsJoachim WeisGert Van PeerJo Vandesompele et al.

A1 Journal Article in FRONTIERS IN PHYSIOLOGY

Longitudinal evaluation of murine serum microRNAs as biomarkers for neuroblastoma burden and therapeutic TP53 reactivation

Alan Van GoethemNurten YigitCeline EveraertMyrthala Moreno-SmithSanjeev A VasudevanFjoralba ZekaFleur DemunckEveline BarbieriFranki SpelemanPieter Mestdagh et al.

Non-invasive differential diagnosis of neuroblastoma with other paediatric solid tumors using methylation profiling of circulating cell-free DNA

Ruben Van PaemelAnneleen DecockCharlotte VandeputteTim LammensGenevieve LaureysFranki SpelemanWim Van CriekingeNadine Van RoyJo VandesompeleKatleen De Preter et al.

Non-invasive differential diagnosis of neuroblastoma with other paediatric solid tumors using methylation profiling of circulating cell-free DNA

Ruben Van PaemelAnneleen DecockCharlotte VandeputteTim LammensGenevieve LaureysFranki SpelemanWim Van CriekingeNadine Van RoyJo VandesompeleKatleen De Preter et al.

Non-invasive differential diagnosis of neuroblastoma with other paediatric solid tumors using methylation profiling of circulating cell-free DNA

Ruben Van PaemelAnneleen DecockCharlotte VandeputteTim LammensGenevieve LaureysFranki SpelemanWim Van CriekingeNadine Van RoyJo VandesompeleKatleen De Preter et al.

On determining the power of digital PCR experiments

Matthijs VynckJo VandesompeleOlivier Thas

A1 Journal Article in ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Pharmacological restoration of tumour suppressor protein p53 in neuroblastoma : seeking synergy and non-invasive biomarkers

Alan Van GoethemJo VandesompeleTom Van Maerken

A2 Journal Article in BELGIAN JOURNAL OF MEDICAL ONCOLOGY

Prognostic and therapeutic implications of circulating androgen receptor gene copy number in prostate cancer patients using droplet digital polymerase chain reaction

Sarah BuelensTom ClaeysBert DhondtFilip PoelaertMatthijs VynckNurten YigitOlivier ThasPiet OstJo VandesompeleNicolaas Lumen et al.

A1 Journal Article in CLINICAL GENITOURINARY CANCER

Recombinant extracellular vesicles : biological reference material to standardize extracellular vesicle research

Edward GeeurickxElisa HeyrmanJan Van DeunLien LippensJoeri TulkensBert DhondtGlenn VergauwenKris GevaertFrancis ImpensIlkka Miinalainen et al.

Recombinant extracellular vesicles : biological reference material to standardize extracellular vesicle research

Edward GeeurickxElisa HeyrmanJan Van DeunLien LippensJoeri TulkensBert DhondtGlenn VergauwenKris GevaertFrancis ImpensIlkka Miinalainen et al.

Targeted genomic screen reveals focal long non-coding RNA copy number alterations in cancer cell lines

Pieter-Jan VoldersSteve LefeverShalina BauteJustine NuytensKatrien VanderheydenBjörn MentenPieter MestdaghJo Vandesompele

A2 Journal Article in NON-CODING RNA

The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation

Maria Polycarpou-SchwarzMatthias GroßPieter MestdaghJohanna SchottStefanie E GrundCatherina HildenbrandJoachim RomSebastian AulmannHans-Peter SinnJo Vandesompele et al.

A1 Journal Article in ONCOGENE

The extracellular RNA quality control (exRNAQC) study : controlling pre-analytical variables of RNA sequencing in blood-based precision medicine

Francisco Avila CobosAnneleen DecockKatleen De PreterBert DhondtOlivier De WeverBram De WildeCeline EveraertCarolina FierroHetty HelsmoortelAn Hendrix et al.

The extracellular RNA quality control (exRNAQC) study : controlling pre-analytical variables of RNA sequencing in blood-based precision medicine

Francisco Avila CobosAnneleen DecockKatleen De PreterOlivier De WeverBram De WildeBert DhondtCeline EveraertCarolina FierroHetty HelsmoortelAn Hendrix et al.

The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease

Bram De WildeAnneleen BeckersSven LindnerKristina AlthoffKatleen De PreterPauline DepuydtPieter MestdaghTom SanteSteve LefeverFalk Hertwig et al.

A2 Journal Article in ONCOTARGET

The neuroblastoma-specific lncRNA NESPR activates PHOX2B expression and is essential for neuroblastoma cell survival

Dries RombautTiago França BrazaoLouis DelhayeEva D'haeneGiorgio MilazzoRoberto CiaccioNurten YigitCeline EveraertMatthias FischerThorsten Simon et al.

The ornithine decarboxylase G316A promoter polymorphism impacts neuroblastoma clinical outcome and may identify patients particularly susceptible to polyamine inhibition

Laura GambleStefania PurgatoSimone Di GiacomoAmanda RussellPaolo PiginiEmanuele ValliLesley AshtonTom Van MaerkenJo VandesompeleRogier Versteeg et al.

The potential of methylome sequencing in the diagnostic work : up of pediatric solid tumors

Ruben Van PaemelCharlotte VandeputteBram De WildeKatleen De PreterNadine Van RoyJo VandesompeleTim LammensWim Van CriekingeP. UltzNico Callewaert et al.

The TLX1 oncogene modules the enhancer RNA landscape in T-ALL

Karen VerboomWouter Van LoockeJo VandesompeleNiels VandammeGeert BerxYvan SaeysLiesbet MartensPieter Van VlierbergheFranki SpelemanKaat Durinck

Therapeutic applications of SAMMSON lncRNA inhibition in uveal melanoma

Shanna DewaeleKatrien VanderheydenBoel De PaepeFariba NematiSergio Roman RomanRudy Van CosterJo VandesompelePieter Mestdagh

Therapeutic applications of SAMMSON lncRNA inhibition in uveal melanoma

Shanna DewaeleKatrien VanderheydenBoel De PaepeFariba NematiSergio Roman RomanRudy Van CosterJo VandesompelePieter Mestdagh

TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia

Karen VerboomWouter Van LoockeJo VandesompeleNiels VandammeGeert BerxLiesbet MartensYvan SaeysPieter Van VlierbergheFranki SpelemanKaat Durinck

Zipper plot : visualizing transcriptional activity of genomic regions

Francisco Avila CobosJasper AnckaertPieter-Jan VoldersCeline EveraertDries RombautJo VandesompeleKatleen De PreterPieter Mestdagh

2017

A unified censored normal regression model for qPCR differential gene expression analysis

Peter PipelersLieven ClementMatthijs VynckJan HellemansJo VandesompeleOlivier Thas

A1 Journal Article in PLOS ONE

Androgen receptor gene copy number detection using droplet digital PCR and its therapeutic consequences in prostate cancer patients

Sarah BuelensTom ClaeysCandy KumpsBert DhondtFilip PoelaertNurten YigitMatthijs VynckOlivier ThasPiet OstJo Vandesompele et al.

decodeRNA-predicting non-coding RNA functions using guilt-by-association

Steve LefeverJasper AnckaertPieter-Jan VoldersManuel LuypaertJo VandesompelePieter Mestdagh

A1 Journal Article in DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION

Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay (vol 6, 36111, 2016)

Wim TrypsteenPejman MohammadiClarissa Van HeckePieter MestdaghSteve LefeverYvan SaeysPieter De BleserJo VandesompeleAngela CiuffiLinos Vandekerckhove et al.

Direct comparison of distinct naive pluripotent states in human embryonic stem cells

Sharat WarrierMargot Van der JeughtGalbha DuggalLaurentijn TillemanElla SutherlandJasin TaelmanMina PopovicSylvie LiermanSusana Marina Chuva de Sousa LopesAnn Van Soom et al.

A1 Journal Article in NATURE COMMUNICATIONS

Direct detection of circulating microRNAs unveiled the absence of microRNA-218-5p in smoker subjects : reply

Griet ConickxPieter MestdaghJo VandesompeleGuy BrusselleKen Bracke

A1 Journal Article in AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Dual targeting of MDM2 and BCL2 as a therapeutic strategy in neuroblastoma

Alan Van GoethemNurten YigitMyrthala Moreno-SmithSanjeev A VasudevanEveline BarbieriFranki SpelemanJason ShohetJo VandesompeleTom Van Maerken

A1 Journal Article in ONCOTARGET

EV-TRACK : transparent reporting and centralizing knowledge in extracellular vesicle research

Jan Van DeunPieter MestdaghPatrizia AgostinisÖzden AkaySushma AnandJasper AnckaertZoraida Andreu MartinezTine BaetensEls BegheinLaurence Bertier et al.

A1 Journal Article in NATURE METHODS

Evaluation of relative quantification of alternatively spliced transcripts using droplet digital PCR

Mattias Van HeetveldeWouter Van LoockeWim TrypsteenAnnelot BaertKatrien VanderheydenBrecht CrombezJo VandesompeleKim De LeeneerKathleen Claes

A2 Journal Article in BIOMOLECULAR DETECTION AND QUANTIFICATION

High-throughput PCR assay design for targeted resequencing using primerXL

Steve LefeverFilip PattynBram De WildeFrauke CoppietersSarah De KeulenaerJan HellemansJo Vandesompele

A1 Journal Article in BMC BIOINFORMATICS

Influence of microRNAs and long non-coding RNAs in cancer chemoresistance

Duncan AyersJo Vandesompele

A1 Journal Article in GENES

lncRNA discovery in the HIV replication cycle adds new layer in HIV-host interplay

Wim TrypsteenMohammadi PejmanClarissa Van HeckePieter MestdaghSteve LefeverPieter De BleserJo VandesompeleAngela CiuffiWard De SpiegelaereLinos Vandekerckhove

Long non-coding RNAs in cutaneous melanoma : clinical perspectives

Eva HulstaertLieve BrochezPieter-Jan VoldersJo VandesompelePieter Mestdagh

A1 Journal Article in ONCOTARGET

MicroRNA expression analysis using small RNA sequencing discovery and RT-qPCR-based validation

Alan Van GoethemPieter MestdaghTom Van MaerkenJo Vandesompele

Bookchapter in Functional genomics : methods and protocols

MicroRNA profiling reveals a role for microRNA-218-5p in the pathogenesis of chronic obstructive pulmonary disease

Griet ConickxPieter MestdaghFrancisco Avila CobosFien VerhammeTania MaesBart M VanaudenaerdeLeen SeysLies LahousseRichard Y KimAlan C Hsu et al.

A1 Journal Article in AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

MicroRNA-184 is a downstream effector of albuminuria driving renal fibrosis in rats with diabetic nephropathy

Cristina ZanchiDaniela MacconiPiera TrionfiniSusanna TomasoniDaniela RottoliMonica LocatelliMichael RudnickiJo VandesompelePieter MestdaghGiuseppe Remuzzi et al.

A1 Journal Article in DIABETOLOGIA

miSTAR : miRNA target prediction through modeling quantitative and qualitative miRNA binding site information in a stacked model structure

Gert Van PeerAyla De PaepeMichiel StockJasper AnckaertPieter-Jan VoldersJo VandesompeleBernard De BaetsWillem Waegeman

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Model-based classification for digital PCR : your Umbrella for rain

Bart JacobsEls GoetghebeurJo VandesompeleAriane De GanckNele NijsAnneleen BeckersNina PapazovaNancy H RoosensLieven Clement

A1 Journal Article in ANALYTICAL CHEMISTRY

mRNA capture sequencing enabled liquid biopsy screening

Anneleen DecockOlivier De WeverBert DhondtCarolina FierroAn HendrixHetty HelsmoortelScott KuerstenPieter MestdaghNele NijsPiet Ost et al.

mRNA capture sequencing enabled liquid biopsy screening

Jo Vandesompele

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

Nonparametric simulation to evaluate the performance of statistical methods for differential gene expression analysis of long non-coding RNA-seq data in cancer studies

Alemu Takele AssefaOlivier ThasJo VandesompeleKatrijn De Paepe

PAN-cancer identification of ncRNAs with a high therapeutic and diagnostic potential

Celine EveraertJo VandesompelePieter Mestdagh

Pancreatic cancer : hope to improve prognosis through thorough analysis of DNA and RNA biomarkers for detection and therapy monitoring in liquid biopsies

Greet WiemeFrederik BerrevoetAude VanlanderMarc De ManKaren GeboesJo Van DorpeAnne HoorensMalaïka Van der LindenJurgen van LimmenANN DE BRUYNE et al.

Quality control of digital PCR assays and platforms

Matthijs VynckJo VandesompeleOlivier Thas

A1 Journal Article in ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Restoration of p53 in neuroblastoma : seeking synergy and non-invasive biomakers

Alan Van GoethemTom Van MaerkenJo Vandesompele

Second hit landscape in BRCA-associated breast cancer

Mattias Van HeetveldeMieke Van BockstalTrees LepezSteve LefeverLeen PietersKathleen LambeinMarleen PraetIvo Van Den BergheFrauke CoppietersNadine Van Roy et al.

Secretome analysis of breast cancer-associated adipose tissue to identify paracrine regulators of breast cancer growth

Lore LapeireAn HendrixEvelyne LecoutereMieke Van BockstalJo VandesompeleDawn MaynardGeert BraemsRudy Van den BroeckeCathérine MüllerMarc Bracke et al.

A1 Journal Article in ONCOTARGET

Stage 4S neuroblastoma tumors show a characteristic DNA methylation portrait

Anneleen DecockMaté OngenaertBram De WildeBénédicte BrichardRosa NogueraFranki SpelemanJo Vandesompele

The extracellular RNA quality control (exRNAQC) study : testing and controlling pre-analytical variables of RNA sequencing on liquid biopsies

Anneleen DecockOlivier De WeverBert DhondtThibaut D'huyvetterHetty HelsmoortelAn HendrixAnnouck PhilippronKimberly VerniersPieter MestdaghJo Vandesompele

The occurrence and therapeutic consequences of androgen receptor copy number gain in prostate cancer patients using Droplet Digital PCR

Sarah BuelensTom ClaeysCandy KumpsBert DhondtFilip PoelaertY NurtenMatthijs VynckOlivier ThasPiet OstJo Vandesompele et al.

The transcriptome of lung tumor-infiltrating dendritic cells reveals a tumor-supporting phenotype and a microRNA signature with negative impact on clinical outcome

Lotte PyfferoenElisabeth BrabantsCeline EveraertNancy De CabooterKelly HeynsKim DeswarteManon VanheerswynghelsSofie De PrijckGlenn WaegemansMelissa Dullaers et al.

A1 Journal Article in ONCOIMMUNOLOGY

Therapeutic applications of SAMMSON lncRNA inhibition in uveal melanoma

Shanna DewaeleKatrien VanderheydenBoel De PaepeFariba NematiSergio Roman RomanRudy Van CosterJo VandesompelePieter Mestdagh

Therapeutic applications of SAMMSON lncRNA inhibition in uveal melanoma

Shanna DewaeleKatrien VanderheydenJo VandesompelePieter Mestdagh

Thermodynamic framework to assess low abundance DNA mutation detection by hybridization

Hanny WillemsAn JacobsWahyu Wijaya HadiwikartaTom VenkenDirk ValkenborgNadine Van RoyJo VandesompeleJef Hooyberghs

A1 Journal Article in PLOS ONE

Zipper plot : visualizing transcriptional activity of genomic regions

Francisco Avila CobosJasper AnckaertPieter-Jan VoldersCeline EveraertDries RombautJo VandesompeleKatleen De PreterPieter Mestdagh

A1 Journal Article in BMC BIOINFORMATICS

2016

An embryonic stem cell activated FOXM1 transcriptional program marks ultra-high-risk primary neuroblastoma patients for FDI-6 small molecule inhibition

Suzanne VanhauwaertCarina LeonelliSara De BrouwerJolien De WynAnneleen BeckersKaren SermonJo VandesompeleFranki SpelemanKatleen De Preter

Asthma inflammatory phenotypes show differential microRNA expression in sputum

Tania MaesFrancisco Avila CobosFlorence SchleichValentina SorbelloMonique HenketKatleen De PreterKen BrackeGriet ConickxClaire MesnilJo Vandesompele et al.

A1 Journal Article in JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data

Celine EveraertAriane De GanckJan HellemansJo VandesompelePieter Mestdagh

Decoding cancer transcriptomes using public RNA sequencing data

Celine EveraertJo VandesompelePieter Mestdagh

Decoding cancer transcriptomes using public RNA sequencing data

Celine EveraertJo VandesompelePieter Mestdagh

Decoding cancer transcriptomes using public RNA sequencing data

Celine EveraertJo VandesompelePieter Mestdagh

Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples

Alan Van GoethemNurten YigitCeline EveraertMyrthala Moreno-SmithLiselot MusEveline BarbieriFranki SpelemanPieter MestdaghJason ShohetTom Van Maerken et al.

A1 Journal Article in SCIENTIFIC REPORTS

Differential expression of lncRNAs during the HIV replication cycle : an underestimated layer in the HIV-host interplay

Wim TrypsteenPejman MohammadiClarissa Van HeckePieter MestdaghSteve LefeverYvan SaeysPieter De BleserJo VandesompeleAngela CiuffiLinos Vandekerckhove et al.

A1 Journal Article in SCIENTIFIC REPORTS

Dissecting the NOTCH1 driven transcriptional landscape in T-cell acute lymphoblastic leukemia at single cell level

Karen VerboomKaat DurinckCeline EveraertRobrecht CannoodtPieter Van VlierbergheJo VandesompeleFranki Speleman

DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing

Anneleen DecockMaté OngenaertWim Van CriekingeFranki SpelemanJo Vandesompele

A1 Journal Article in SCIENTIFIC DATA

Endogenous controls for miRNA analysis in renal cells and tissue

Michael RudnickiNinella SchweibertAnneleen BeckersStefan SchneebergerAlfred KoenigsrainerGeorg BoehmigJo VandesompeleGert MayerJohannes Leierer

Eradication of neuroblastoma by suppressing the expression of a single long noncoding RNA

Pei Y LiuAndrew E TeeBernard AtmadibrataPieter MestdaghJo VandesompeleMarcel DingerTao Liu

EV-TRAQ: tracking transparent reporting and quality to boost standardized extracellular vesicle research

Jan Van DeunPieter MestdaghJasper AnckaertJo VandesompeleOlivier De WeverAn Hendrix

Expanding the TLX1 regulome in T-cell acute lymphoblastic leukemia towards long noncoding RNAs

Kaat DurinckWouter Van LoockeInge Van de WalleJoni Van der MeulenPieter-Jan VoldersNadine Van RoyYves BenoitBruce PoppePieter MestdaghJo Vandesompele et al.

Exploring the neuroblastoma DNA methylome: from biology to biomarker

Anneleen DecockJo VandesompeleFranki SpelemanMaté Ongenaert

Flexible analysis of digital PCR experiments using generalized linear mixed models

Matthijs VynckJo VandesompeleNele NijsBjörn MentenAriane De GanckOlivier Thas

A2 Journal Article in BIOMOLECULAR DETECTION AND QUANTIFICATION

Identification of non-invasive biomarkers for treatment response in neuroblastoma by circulating miRNA profiling

Alan Van GoethemNurten YigitMythala Moreno-SmithCeline EveraertOlivier DelattrePieter MestdaghSaurabh AgarwalEveline BarbieriIsabelle Janoueix-LeroseyJason Shohet et al.

LncRNAs in the context of Chronic Obstructive Pulmonary Disease (COPD) are associated to immune response and metabolism of xenobiotics

Francisco Avila CobosKen BrackeJo VandesompeleKimberly VerniersGuy JoosKatleen De PreterGuy BrussellePieter Mestdagh

Long non-coding RNA expression profiling in the NCI60 cancer cell line panel using high-throughput RT-qPCR

Pieter MestdaghSteve LefeverPieter-Jan VoldersStefaan DerveauxJan HellemansJo Vandesompele

A1 Journal Article in SCIENTIFIC DATA

Long non-coding RNAs as novel components in the TP53 pathway

Dries RombautSteve LefeverJan KosterJohannes SchulteRogier VersteegPeter van SluisJo VandesompelePieter Mestdagh

Long non-coding RNAs as novel components in the TP53 pathway

Dries RombautSteve LefeverJan KosterSven LindnerJohannes SchulteRogier VersteegPeter van SluisJo VandesompelePieter Mestdagh

Long noncoding RNA signatures define oncogenic subtypes in T-cell acute lymphoblastic leukemia

Annelynn WallaertKaat DurinckWouter Van LoockeInge Van de WalleFilip MatthijssensPieter-Jan VoldersFrancisco Avila CobosDries RombautPieter RondouPieter Mestdagh et al.

A1 Journal Article in LEUKEMIA

Mapping the methodological diversity of EV isolation and characterization

Jan Van DeunPieter MestdaghJo VandesompeleOlivier De WeverAn Hendrix

Melanoma addiction to the long non-coding RNA SAMMSON

Eleonora LeucciRoberto VendraminMarco SpinazziPatrick LauretteMark FiersJasper WoutersEnrico RadaelliSven EyckermanCarina LeonelliKatrien Vanderheyden et al.

A1 Journal Article in NATURE

Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma

Anneleen DecockMaté OngenaertRobrecht CannoodtKimberly VerniersBram De WildeGenevieve LaureysNadine Van RoyAna Pilar BerbegallJulie Bienertova-VaskuNick Bown et al.

A1 Journal Article in ONCOTARGET

Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma

Anneleen DecockMaté OngenaertRobrecht CannoodtKimberly VerniersBram De WildeGenevieve LaureysNadine Van RoyAna Pilar BerbegallJulie Bienertova-VaskuNick Bown et al.

Microrna-218-5p is implicated in the pathogenesis of chronic obstructive pulmonary disease

Griet ConickxPieter MestdaghFrancisco Avila CobosFien VerhammeTania MaesBM VanaudenaerdeLies LahousseGuy JoosJo VandesompeleKen Bracke et al.

NFAT5 in Duchenne muscular dystrophy cultured myoblasts after exposure to hyperosmolar salt conditions

Sandrine HerbeletAmanda GonçalvesElly De VlieghereGert Van PeerBoel De PaepeChris GuerinJo VandesompeleOlivier De WeverJan De Bleecker

PAN-cancer identification of ncRNAs with a high therapeutic and diagnostic potential

Celine EveraertJo VandesompelePieter Mestdagh

PAN-cancer identification of ncRNAs with a high therapeutic and diagnostic potential

Celine EveraertJo VandesompelePieter Mestdagh

PAN-cancer therapeutic target identification by omics data integration

Celine EveraertJo VandesompelePieter Mestdagh

Quantitative and functional requirements for bioluminescent cancer models

Lynn FeysBenedicte DescampsChristian VanhoveStefan VermeulenJo VandesompeleKatrien VanderheydenKathy Messensmarc brackeOlivier De Wever

A1 Journal Article in IN VIVO

Rol van microRNA in neutrofiel astma

Tania MaesFrancisco Avila CobosFlorence SchleichValentina SorbelloMonique HenketKatleen De PreterKen BrackeGriet ConickxClaire MesnilJo Vandesompele et al.

A4 Journal Article in BLOEDVATEN HART LONGEN

RT-qPCR gene expression analysis in zebrafish : preanalytical precautions and use of expressed repetitive elements for normalization

Suzanne VanhauwaertSteve LefeverPaul CouckeFranki SpelemanAnne De PaepeJo VandesompeleAndy Willaert

A1 Journal Article in Methods in Cell Biology

Selective cross-cohort discovery of transcriptional mechanisms presiding over high-risk neuroblastoma subtype state maintenance

Presha RajbhandariGonzalo LopezJiyang YuRuth Rodriguez-BarruecoMariano AlvarezDaniel MartinezMark YarmarkovichJo VandesompelePieter MestdaghJose M Silva et al.

Stage 4S neuroblastoma tumors show a characteristic DNA methylation portrait

Anneleen DecockMaté OngenaertBram De WildeBénédicte BrichardRosa NogueraFranki SpelemanJo Vandesompele

A1 Journal Article in EPIGENETICS

Straightforward and sensitive RT-qPCR based gene expression analysis of FFPE samples

Fjoralba ZekaKatrien VanderheydenEls De SmetClaude CuvelierPieter MestdaghJo Vandesompele

A1 Journal Article in SCIENTIFIC REPORTS

Targeted resequencing and variant validation using pxlence PCR assays

Frauke CoppietersKimberly VerniersKim De LeeneerJo VandesompeleSteve Lefever

A2 Journal Article in BIOMOLECULAR DETECTION AND QUANTIFICATION

The core protein to myogenesis NFAT5 forms aggresomes in normal and Duchenne muscular dystrophy myotubes exposed to cell stressors

Sandrine HerbeletElly De VlieghereGert Van PeerBoel De PaepeEline NysLaurens WeynantsJo VandesompeleOlivier De WeverJens SchmidtJan De Bleecker

The T-ALL oncogene TLX1 controls enhancer lncRNA expression

Karen VerboomKaat DurinckWouter Van LoockeFilip MatthijssensInge Van de WalleAnnelynn WallaertPieter-Jan VoldersNadine Van RoyYves BenoitBruce Poppe et al.

Thorough second hit analysis in BRCA1/2 associated breast cancer

Mattias Van HeetveldeTrees LepezLeen PietersSteve LefeverJo Van DorpeKathleen LambeinMarleen Praetivo Van Den BergheFrauke CoppietersJo Vandesompele et al.

Thorough second-hit analysis in BRCA1/2-associated breast cancer

Mattias Van HeetveldeTrees LepezLeen PietersSteve LefeverJo Van DorpeKathleen LambeinMarleen PraetIvo Van Den BergheFrauke CoppietersJo Vandesompele et al.

2015

Alternative routes to induce naive pluripotency in human embryonic stem cells

Galbha DuggalSharat WarrierSabitri GhimireDorien BroekaertMargot Van der JeughtSylvie LiermanTom DerooLuc PeelmanAnn Van SoomMaria Cornelissen et al.

A1 Journal Article in STEM CELLS

An embryonic stem cell activated FOXM1 transcriptional program marks ultra-high-risk primary neuroblastoma patients for FDI-6 small molecule inhibition

Suzanne VanhauwaertCarina LeonelliSara De BrouwerJolien De WynAnneleen BeckersNeuroblastoma Research consortiumJo VandesompeleKaren SermonFranki SpelemanKatleen De Preter

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

Best-in-class PCR based target enrichment for NGS panels and Sanger variant confirmation

Steve LefeverFrauke CoppietersJo Vandesompele

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction

Wenqian ZhangYing YuFalk HertwigJean Thierry-MiegWenwei ZhangDanielle Thierry-MiegJian WangCesare FurlanelloViswanath DevanarayanJie Cheng et al.

A1 Journal Article in GENOME BIOLOGY

Data analysis of droplet digital PCR with generalized linear mixed models

Olivier ThasMatthijs VynckJo Vandesompele

Exploring lncRNAs in cancer : tools for discovery and characterization of cancer associated lncRNAs

Pieter-Jan VoldersJo VandesompeleKris Gevaert

Flexible, scalable, and efficient targeted resequencing on a benchtop sequencer for variant detection in clinical practice

Kim De LeeneerJan HellemansWouter SteyaertSteve LefeverInge VereeckeEveline DebalsBrecht CrombezMachteld BaetensMattias Van HeetveldeFrauke Coppieters et al.

A1 Journal Article in HUMAN MUTATION

Genome wide expression profiling of p53 regulated miRNAs in neuroblastoma

Ali RihaniAlan Van GoethemMaté OngenaertSara De BrouwerPieter-Jan VoldersSaurabh AgarwalKatleen De PreterPieter MestdaghJason ShohetFranki Speleman et al.

A1 Journal Article in SCIENTIFIC REPORTS

GLMMs for nucleic acid concentration estimation in digital droplet PCR

Matthijs VynckJo VandesompeleOlivier Thas

Identification of miRNAs contributing to neuroblastoma chemoresistance

Duncan AyersPieter MestdaghTom Van MaerkenJo Vandesompele

A1 Journal Article in COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL

Improving accuracy and precision of dPCR experiments by relying on multiple reference genes

Matthijs VynckJo VandesompeleOlivier Thas

Individual patient risk stratification of high-risk neuroblastomas using a two-gene score suited for clinical use

Kristoffer von StedingkKatleen De PreterJo VandesompeleRosa NogueraIngrid ØraJan KosterRogier VersteegSven PåhlmanDavid LindgrenHåkan Axelson

A1 Journal Article in INTERNATIONAL JOURNAL OF CANCER

Inhibition of CDK4/6 as a novel therapeutic option for neuroblastoma

Ali RihaniJo VandesompeleFranki SpelemanTom Van Maerken

A1 Journal Article in CANCER CELL INTERNATIONAL

Integrated and cross-species omics analyses identify the DNA damage response pathway as an important vulnerable pathway in aggressive neuroblastoma tumors

Katleen De PreterAnneleen BeckersSuzanne VanhauwaertAnnelies FieuwSara De BrouwerPieter MestdaghJo VandesompeleFranki Speleman

lncRNAs as upstream regulators and downstream effectors of TP53 in neuroblastoma

Dries RombautSteve LefeverPieter-Jan VoldersJan KosterSven LindnerJohannes SchulteAlan Van GoethemRogier VersteegPeter van SluisJo Vandesompele et al.

Long non-coding RNAs as upstream regulators and downstream effectors of TP53 activity in neuroblastoma

Dries RombautSteve LefeverJan KosterJohannes SchulteRogier VersteegPeter van SluisJo VandesompelePieter Mestdagh

Massively parallel sequencing technologies in neuroblastoma research

Bram De WildeJo VandesompeleFranki Speleman

Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma

Anneleen DecockMaté OngenaertRobrecht CannoodtKimberly VerniersBram De WildeGenevieve LaureysNadine Van RoyAna Pilar BerbegallJulie Bienertova-VaskuNick Bown et al.

MicroRNA-193b-3p acts as a tumor suppressor by targeting the MYB oncogene in T-cell acute lymphoblastic leukemia

Evelien MetsJoni Van der MeulenGert Van PeerMichael BoicePieter MestdaghInge Van de WalleTim LammensSteven GoossensBarbara De MoerlooseYves Benoit et al.

A1 Journal Article in LEUKEMIA

MiR-34a deficiency accelerates medulloblastoma formation in vivo

Theresa ThorAnnette KünkeleKristian W PajtlerAnnika K WefersHarald StephanPieter MestdaghLukas HeukampWolfgang HartmannJo VandesompeleNatalie Sadowski et al.

A1 Journal Article in INTERNATIONAL JOURNAL OF CANCER

miR-542-3p exerts tumor suppressive functions in neuroblastoma by downregulating Survivin

Kristina AlthoffSven LindnerAndrea OderskyPieter MestdaghAnneleen BeckersSarah KarczewskiJan J MolenaarAnna BohrerShirley KnauerFranki Speleman et al.

A1 Journal Article in INTERNATIONAL JOURNAL OF CANCER

miRNome-wide high-throughput microRNA target identification

Gert Van PeerJo VandesompelePieter Mestdagh

MYCN-driven regulatory mechanisms controlling LIN28B in neuroblastoma

Anneleen BeckersGert Van PeerDaniel R CarterMoritz GartlgruberCarl HerrmannSaurabh AgarwalHetty HelsmoortelKristina AlthoffJan J MolenaarBelamy B Cheung et al.

A1 Journal Article in CANCER LETTERS

MYCN-targeting miRNAs are predominantly downregulated during MYCN-driven neuroblastoma tumor formation

Anneleen BeckersGert Van PeerDaniel R CarterKristina AlthoffBelamy B CheungJohannes H SchultePieter MestdaghJo VandesompeleGlenn M MarshallKatleen De Preter et al.

A1 Journal Article in ONCOTARGET

Non-coding RNAs and respiratory disease

Pieter MestdaghJo VandesompeleGuy BrusselleKarim Vermaelen

A1 Journal Article in THORAX

Non-coding RNAs in the pathogenesis of COPD

Elise De SmetPieter MestdaghJo VandesompeleGuy BrusselleKen Bracke

A1 Journal Article in THORAX

Oncogenic dysregulations in neuroblastoma are associated with distal large chromosomal aberrations

Gonzalo LopezMariano AlvarezJames ChenPresha RajbhandariKristina A ColeEdward F AttiyehSharon DiskinPieter MestdaghJo VandesompeleJohn M Maris et al.

RDML-Ninja and RDMLdb for standardized exchange of qPCR data

Jan M RuijterSteve LefeverJasper AnckaertJan HellemansMichael W PfafflVladimir BenesStephen A BustinJo VandesompeleAndreas Untergasser

A1 Journal Article in BMC BIOINFORMATICS

Renal microRNA- and RNA-profiles in progressive chronic kidney disease

Michael RudnickiPaul PercoBarbara D′haeneJohannes LeiererAndreas HeinzelIrmgard MühlbergerNinella SchweibertJudith SunzenauerHeinz RegeleAndreas Kronbichler et al.

A1 Journal Article in EUROPEAN JOURNAL OF CLINICAL INVESTIGATION

Revised risk estimation and treatment stratification of low- and intermediate-risk neuroblastoma patients by integrating clinical and molecular prognostic markers

André OberthuerDilafruz JuraevaBarbara HeroRuth VollandCarolina SterzRene SchmidtAndreas FaldumYvonne KahlertAnne EngesserShahab Asgharzadeh et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

RNA expression signatures and posttranscriptional regulation in diabetic nephropathy

Michael RudnickiAnneleen BeckersHannes NeuwirtJo Vandesompele

A1 Journal Article in NEPHROLOGY DIALYSIS TRANSPLANTATION

RT-qPCR-based quantification of small non-coding RNAs

Fjoralba ZekaPieter MestdaghJo Vandesompele

Bookchapter in Small non-coding RNAs : methods and protocols

2014

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

Zhenqiang SuPawel P LabajSheng LiJean Thierry-MiegDanielle Thierry-MiegWei ShiCharles WangGary P SchrothRobert A SetterquistJohn F Thompson et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

Cancer-associated adipose tissue promotes breast cancer progression by paracrine Oncostatin M and Jak/STAT3 signaling

Lore LapeireAn HendrixKathleen LambeinMieke Van BockstalGeert BraemsRudy Van den BroeckeRIDHA LIMAMEPieter MestdaghJo VandesompeleChristian Vanhove et al.

A1 Journal Article in CANCER RESEARCH

Cancer-associated adipose tissue promotes breast cancer progression by paracrine Oncostatin M and JAK3/STAT3 signaling

Lore LapeireAn HendrixKathleen LambeinMieke Van BockstalGeert BraemsRudy Van den BroeckeRidha LimamePieter MestdaghJo VandesompeleChristian Vanhove et al.

CASP8 SNP D302H (rs1045485) is associated with worse survival in MYCN-amplified neuroblastoma patients

Ali RihaniBram De WildeFjorabla ZekaGenevieve LaureysNadine FrancotteGian Paolo ToniniSimona CocoRogier VersteegRosa NogueraJohannes H Schulte et al.

A1 Journal Article in PLOS ONE

CASP8 SNP D302H (rs1045485) is associated with worse survival in MYCN-amplified neuroblastoma patients

Ali RihaniBram De WildeFjoralba ZekaGenevieve LaureysNadine FrancotteGian Paolo ToniniSimona CocoRogier VersteegRosa NogueraJohannes Schulte et al.

CASP8 SNP D302H (rs1045485) is associated with worse survival in MYCN-amplified neuroblastoma patients

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Early targets of miR-34a in neuroblastoma

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A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

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A1 Journal Article in PLOS ONE

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A1 Journal Article in NATURE METHODS

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Evaluation of targeted drugs in combination with the MDM2 antagonist RG7388 in neuroblastoma

Alan Van GoethemGwen NicholsFranki SpelemanJo VandesompeleTom Van Maerken

Evaluation of targeted drugs in combination with the MDM2 antagonist RG7388 in neuroblastoma

Alan Van GoethemGwen NicholsFranki SpelemanJo VandesompeleTom Van Maerken

Evaluation of targeted drugs in combination with the MDM2 antagonist RG7388 in neuroblastoma

Alan Van GoethemGwen NicholsFranki SpelemanJo VandesompeleTom Van Maerken

Expressed repeat elements improve RT-qPCR normalization across a wide range of zebrafish gene expression studies

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A1 Journal Article in PLOS ONE

Genetisch geïnspireerde toekomstperspectieven voor de therapie van het neuroblastoom

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A2 Journal Article in TIJDSCHRIFT VOOR GENEESKUNDE

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Illumina sequencing of 15 deafness genes using fragmented amplicons

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A2 Journal Article in BMC RESEARCH NOTES

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A1 Journal Article in PEDIATRIC BLOOD & CANCER

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A1 Journal Article in INTERNATIONAL JOURNAL OF CANCER

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A1 Journal Article in HAEMATOLOGICA

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A1 Journal Article in DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION

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Pharmacologic activation of wild-type p53 by nutlin therapy in childhood cancer

Tom Van MaerkenAli RihaniAlan Van GoethemAnne De PaepeFranki SpelemanJo Vandesompele

A1 Journal Article in CANCER LETTERS

Promoter DNA-methylation in the TH-MYCN neuroblastoma mouse model

Anneleen BeckersWouter Van LoockeAnneleen DecockMaté OngenaertJo VandesompeleFranki SpelemanKatleen De Preter

Reduced DICER1 functionality in neuroblastoma through reduced expression levels or somatic mutations

Bram De WildeJohannes H SchulteAnneleen BeckersAlexander SchrammAnnelies FieuwDaniel CarterBelamy CheungGlenn MarshallAngelika EggertKatleen De Preter et al.

Selecting potent antisense oligonucleotides for lncRNA knockdown using generalized additive models

Pieter-Jan VoldersJo VandesompelePieter Mestdagh

Selecting potent antisense oligonucleotides for lncRNA silencing in vitro using thermodynamic properties and target RNA structure

Pieter-Jan VoldersPieter MestdaghJo Vandesompele

Selection of reliable reference genes for RT-qPCR analysis

Jan HellemansJo Vandesompele

Bookchapter in Qualntitative real-time PCR : methods and protocols

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Jo VandesompelePieter Mestdagh

Editorial material

Target enrichment using parallel nanoliter quantitative PCR amplification

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A1 Journal Article in BMC GENOMICS

Targeted analysis of TP53 pathway SNPs in neuroblastoma patients

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The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling

Jan Van DeunPieter MestdaghRaija SormunenVeronique CocquytKarim VermaelenJo VandesompeleMarc BrackeOlivier De WeverAn Hendrix

A2 Journal Article in JOURNAL OF EXTRACELLULAR VESICLES

The MYCN/miR-26a-5p/LIN28B regulatory axis controls MYCN-driven LIN28B upregulation in neuroblastoma

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Anneleen BeckersDaniel CarterAndrew LudwigGert Van PeerBelamy CheungJo VandesompeleGlenn MarshallJason ShohetKatleen De PreterFranki Speleman

The Notch driven long non-coding RNA repertoire in T-cell acute lymphoblastic leukemia

Kaat DurinckAnnelynn WallaertInge Van de WalleWouter Van LoockePieter-Jan VoldersSuzanne VanhauwaertEllen GeerdensYves BenoitNadine Van RoyBruce Poppe et al.

A1 Journal Article in HAEMATOLOGICA

The NOTCH1 driven long non-coding RNA repertoire in T-cell acute lymphoblastic leukemia

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Time-resolved transcriptome analysis of TH-MYCN driven hyperplastic ganglia and tumors marks BRD3 as a novel candidate oncogene

Anneleen BeckersDaniel CarterCheung BelamyJo VandesompeleGlen MarshallKatleen De PreterFranki Speleman

Unique lncRNA signatures mark the major T-ALL genetic subgroups

Annelynn WallaertKaat DurinckWouter Van LoockePieter-Jan VoldersYves BenoitBruce PoppePieter MestdaghJo VandesompeleJean SoulierJan Cools et al.

2013

A bioinformatics analysis of renal miRNA- and mRNA-expression signatures in progressive chronic kidney disease

Michael RudnickiPaul PercoBarbara D'haeneJohannes LeiererJudith SunzenauerRaul FecheteAndreas HeinzelPieter MestdaghJo VandesompeleBernd Mayer et al.

CLL cells respond to B-cell receptor stimulation with a microRNA/mRNA signature associated with MYC activation and cell cycle progression

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A1 Journal Article in PLOS ONE

DNA methylation silences miR-132 in prostate cancer

A FormosaAM LenaEK MarkertS CortelliR MianoA MaurielloN CroceJo VandesompelePieter MestdaghE Finazzi-Agrò et al.

A1 Journal Article in ONCOGENE

Dynamic regulation of miRNAs implicated in the MYCN-EZH2 regulatory axis during neuroblastoma tumor initiation and progression in a MYCN mouse model

Anneleen BeckersKatleen De PreterBelamy CheungDaniel CarterGert Van PeerSara De BrouwerPieter MestdaghGenevieve LaureysJo VandesompeleGlenn Marshall et al.

Effective Alu repeat based RT-qPCR normalization in cancer cell perturbation experiments

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A1 Journal Article in PLOS ONE

Evaluation of qPCR curve analysis methods for reliable biomarker discovery: bias, resolution, precision, and implications

Jan M RuijterMichael W PfafflSheng ZhaoAndrej N SpiessGregory BoggyJochen BlomRobert G RutledgeDavide SistiAntoon LievensKatleen De Preter et al.

A1 Journal Article in METHODS

Expanding the TLX1 regulate in T-cell acute lymphoblastic leukemia towards long non-coding RNAs

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Expanding the TLX1-regulome in T cell acute lymphoblastic leukemia towards long non-coding RNAs

Kaat DurinckJoni Van der MeulenMaté OngenaertPieter-Jan VoldersAnnelynn WallaertNadine Van RoyYves BenoitBruce PoppePieter MestdaghJo Vandesompele et al.

Focal DNA copy number changes in neuroblastoma target MYCN regulated genes

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A1 Journal Article in PLOS ONE

Genome wide expression, mutation and methylation analysis validates three new mouse models for neuroblastoma targeting MYCN, ALK and LIN28B for pre-clinical studies

Anneleen BeckersBram De WildeMaté OngenaertCandy KumpsJohannes H SchulteJo VandesompeleKatleen De PreterFranki Speleman

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers

Anneleen DecockMaté OngenaertJasmien HoebeeckKatleen De PreterGert Van PeerWim Van CriekingeRuth LadensteinJohannes H. SchulteRosa NogueraRaymond L. Stallings et al.

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers

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Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers

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Pieter MestdaghSteve LefeverKristina AlthoffCarina LeonelliJan HellemansJean-Christophe MarineJohannes SchulteJo Vandesompele

Identification and functional characterization of lncRNAs in cancer

Pieter MestdaghSteve LefeverKristina AlthoffCarina LeonelliJan HellemansJean-Christophe MarineJohannes SchulteJo Vandesompele

Identification of miR-145 as a key regulator of the pigmentary process

Peter DynoodtPieter MestdaghGert Van PeerJo VandesompeleKaren GoossensLuc PeelmanBarbara GeusensReinhart SpeeckaertJo LambertMireille Van Gele

A1 Journal Article in JOURNAL OF INVESTIGATIVE DERMATOLOGY

Identification of miRNAs implicated in neuroblastoma tumor initiation and progression through cross-species integrated genomic analysis

Anneleen BeckersKatleen De PreterBelamy CheungSara De BrouwerGert Van PeerPieter MestdaghGenevieve LaureysJo VandesompeleGlenn MarshallFranki Speleman

Identifying and validating DNA methylation biomarkers: the example of neuroblastoma

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Improved outcome prediction of children with neuroblastoma using an integrated miRNA and DNA methylation signature

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LNCipedia 2.0: a database for annotated human lncRNA transcript sequences and structures

Pieter-Jan VoldersKenny HelsensXiaowei WangLennart MartensKris GevaertJo VandesompelePieter Mestdagh

LNCipedia 2.0: a database for annotated human lncRNA transcript sequences and structures

Pieter-Jan VoldersKenny HelsensXiaowei WangLennart MartensKris GevaertJo VandesompelePieter Mestdagh

LNCipedia : a database for annotated human lncRNA transcript sequences and structures

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A1 Journal Article in NUCLEIC ACIDS RESEARCH

LNCipedia: a database for annotated human lncRNA transcript sequences and structures

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MiR-128 is a novel PHF6 targeting regulatory non-coding RNA acting as a T-ALL oncogene

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miR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A

Kristina AlthoffAnneleen BeckersAndrea OderskyPieter MestdaghJohannes KösterIsabella BrayKenneth BryanJo VandesompeleFranki SpelemanRaymond Stallings et al.

A1 Journal Article in INTERNATIONAL JOURNAL OF CANCER

miRNAs distinguish children with myelodysplastic syndrome from healthy donors

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miRNAs distinguish children with myelodysplastic syndrome from healthy donors

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Modulation of neuroblastoma disease pathogenesis by an extensive network of epigenetically regulated microRNAs

S DasK BryanPG BuckleyO PiskarevaIM BrayN FoleyJ RyanJ LynchL CreeveyJ Fay et al.

A1 Journal Article in ONCOGENE

MYCN and ALKF1174L are sufficient to drive neuroblastoma development from neural crest progenitor cells

JH SchulteS LindnerA BohrerJ MaurerKatleen De PreterSteve LefeverL HeukampS SchulteJ MolenaarR Versteeg et al.

A1 Journal Article in ONCOGENE

Of flies, mice and men : a systematic approach to understanding the early life origins of chronic lung disease

Susanne Krauss-EtschmannAndrew BushSaverio BellusciGuy BrusselleSven Erik K DahlénStefan DehmelOliver EickelbergGreg GibsonMachteld N HylkemaPetra Knaus et al.

A1 Journal Article in THORAX

Reference loci for RT-qPCR analysis of differentiating human embryonic stem cells

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A1 Journal Article in BMC MOLECULAR BIOLOGY

Regulatory microRNA network identification in bovine blastocyst development

Karen GoossensPieter MestdaghSteve LefeverMario Van PouckeAlex Van ZeverenAnn Van SoomJo VandesompeleLuc Peelman

A1 Journal Article in STEM CELLS AND DEVELOPMENT

Selective inhibition of the p53–MDM2 interaction by nutlin drugs: a new therapeutic perspective for neuroblastoma

Tom Van MaerkenAli RihaniAlan Van GoethemAnne De PaepeFranki SpelemanJo Vandesompele

A2 Journal Article in PROCEEDINGS OF THE BELGIAN ROYAL ACADEMIES OF MEDICINE

Single-nucleotide polymorphisms and other mismatches reduce performance of quantitative PCR assays

Steve LefeverFilip PattynJan HellemansJo Vandesompele

A1 Journal Article in CLINICAL CHEMISTRY

The digital MIQE guidelines : minimum information for publication of quantitative digital PCR experiments

Jim F HuggettCarole A FoyVladimir BenesKerry EmslieJeremy A GarsonRoss HaynesJan HellemansMikael KubistaReinhold D MuellerTania Nolan et al.

A1 Journal Article in CLINICAL CHEMISTRY

The MYCN driven murine and human neuroblastoma methylome and dynamic regulation of chromatin regulators as a guide for epigenetic therapy

Anneleen BeckersAnneleen DecockBelamy CheungDaniel CarterGert Van PeerSara De BrouwerGenevieve LaureysJo VandesompeleJohannes H SchulteGlenn Marshall et al.

The need for transparency and good practices in the qPCR literature

Stephen A BustinVladimir BenesJeremy GarsonJan HellemansJim HuggettMikael KubistaReinhold MuellerTania NolanMichael W PfafflGregory Shipley et al.

A1 Journal Article in NATURE METHODS

2012

Accurate RT-qPCR gene expression analysis on cell culture lysates

Gert Van PeerPieter MestdaghJo Vandesompele

A1 Journal Article in SCIENTIFIC REPORTS

ALK(F1174L) is a driving oncogene of neuroblastoma in transgenic mice

Johannes SchulteLukas HeukampTheresa ThorCandy KumpsKatleen De PreterBram De WildeJo VandesompeleFranki SpelemanAlexander SchrammAngelika Eggert

Cancer gene prioritization for targeted resequencing using fitSNP scores

Annelies FieuwBram De WildeFranki SpelemanJo VandesompeleKatleen De Preter

A1 Journal Article in PLOS ONE

Development of bioinformatics tools for high-throughput PCR applications

Steve LefeverJo Vandesompele

Dickkopf-3 is regulated by the MYCN-induced miR-17-92 cluster in neuroblastoma

Sara De BrouwerPieter MestdaghIrina LambertzFilip PattynAnne De PaepeFrank WestermannChristina SchroederJohannes H SchulteAlexander SchrammKatleen De Preter et al.

A1 Journal Article in INTERNATIONAL JOURNAL OF CANCER

Exon-level expression analyses identify MYCN and NTRK1 as major determinants of alternative exon usage and robustly predict primary neuroblastoma outcome

A SchrammB SchoweK FielitzM HeilmannM MartinT MarschallJ KösterJo VandesompeleJoëlle VermeulenKatleen De Preter et al.

A1 Journal Article in BRITISH JOURNAL OF CANCER

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers.

Anneleen DecockMaté OngenaertJasmien HoebeeckKatleen De PreterGert Van PeerWim Van CriekingeRuth LadensteinJohannes H SchulteRosa NogueraRaymond L Stallings et al.

A1 Journal Article in GENOME BIOLOGY

Genomic profiling of MYCN and ALKF1174L transgenic neuroblastoma mouse models provides insights into the dynamic process of tumor formation

Katleen De PreterAnneleen BeckersCandy KumpsPieter MestdaghAngelika EggertJo VandesompeleFranki SpelemanJohannes H Schulte

Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas

Annelies FieuwCandy KumpsAlexander SchrammFilip PattynBjörn MentenFrancesca AntonacciPeter SudmantJohannes H SchulteNadine Van RoySarah Vergult et al.

A1 Journal Article in INTERNATIONAL JOURNAL OF CANCER

Improved risk stratification and outcome prediction in children with average risk 1 precursor-B acute lymphoblastic leukemia using a 19-microRNA signature

Farzaneh GhazaviTim LammensStefan SuciuGenevieve LaureysMarleen BakkusAlina FersterAnne UyttebroeckPatrick LutzHélène CavéGeneviève Plat et al.

Improved risk-stratification and outcome prediction in children with average risk precursor-B acute lymphoblastic leukemia using a 19-microRNA signature

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Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer

Martin PeiferLynnette Fernández-CuestaMartin L SosJulie GeorgeDanila SeidelLawryn H KasperDennis PlenkerFrauke LeendersRuping SunThomas Zander et al.

A1 Journal Article in NATURE GENETICS

Large-scale and targeted genomic screen reveals focal lncRNA copy number alterations in cancer cells

Pieter-Jan VoldersPieter MestdaghBjörn MentenJo Vandesompele

LIN28B induces neuroblastoma and enhances MYCN levels via let-7 suppression

Jan J MolenaarRaquel Domingo-FernándezMarli E EbusSven LindnerJan KosterKsenjia DrabekPieter MestdaghPeter van SluisLinda J ValentijnJohan van Nes et al.

A1 Journal Article in NATURE GENETICS

Lncipedia: a novel database for annotated lncRNA sequences and structures

Pieter-Jan VoldersKenny HelsensXiaowei WangLennart MartensKris GevaertJo VandesompelePieter Mestdagh

LNCipedia: a novel databse for annotated lncRNA sequences and structures

Pieter-Jan VoldersPieter MestdaghJo Vandesompele

Lysine-specific demethylase 1 restricts hematopoietic progenitor proliferation and is essential for terminal differentiation

A SprüsselJH SchulteS WeberM NeckeK HändschkeT ThorKW PajtlerA SchrammK KönigL Diehl et al.

A1 Journal Article in LEUKEMIA

Mapping the neuroblastoma epigenome

Maté OngenaertAnneleen DecockJo VandesompeleFranki Speleman

Mapping the neuroblastoma epigenome: perspectives for improved prognostic biomarkers

Maté OngenaertAnneleen DecockGenevieve LaureysJo VandesompeleFranki Speleman

Mapping the neuroblastoma epigenome: perspectives for improved prognostic biomarkers

Maté OngenaertAnneleen DecockJo VandesompeleFranki Speleman

Massively parallel sequencing for early molecular diagnosis in Leber congenital amaurosis

Frauke CoppietersBram De WildeSteve LefeverEllen De MeesterNina De RockerCaroline Van CauwenberghFilip PattynFrançoise MeireBart LeroyJan Hellemans et al.

A1 Journal Article in GENETICS IN MEDICINE

microRNAs in colon cancer : a roadmap for discovery

Simona RossiAntonio Fabio Di NarzoPieter MestdaghBart JacobsFredrik T BosmanBengt GustavssonBernard MajoieArnaud RothJo VandesompeleIsidore Rigoutsos et al.

A1 Journal Article in FEBS LETTERS

miRNA expression profiling: from reference genes to global mean normalization

Barbara D'haenePieter MestdaghJan HellemansJo Vandesompele

Bookchapter in Next-generation microRNA expression profiling technology : methods and protocols

Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform

Sarah De KeulenaerJan HellemansSteve LefeverJean-Pierre RenardJoachim De SchrijverHendrik Van de VoordeMohammad Amin TabatabaiefarFilip Van NieuwerburghDaisy FlamezFilip Pattyn et al.

A1 Journal Article in BMC MEDICAL GENOMICS

MYCN directly regulates long non-coding RNA expression in neuroblastoma

Pieter MestdaghJohannes SchulteFilip PattynFrank WestermannGenevieve LaureysFranki SpelemanJo Vandesompele

N-Cadherin in neuroblastoma disease : expression and clinical significance

Tim LammensKatrien SwertsLara DeryckeANNEMIE DE CRAEMERSara De BrouwerKatleen De PreterNadine Van RoyJo VandesompeleFranki SpelemanJan Philippé et al.

A1 Journal Article in PLOS ONE

Oncogenic activation of FOXR1 by 11q23 intrachromosomal deletion-fusions in neuroblastoma

EE SantoME EbusJ KosterJH SchulteA LakemanP van SluisJ VermeulenD GisselssonI ØraS Lindner et al.

A1 Journal Article in ONCOGENE

Promoter methylation analysis identifies prognostic methylation biomarkers in neuroblastoma

Anneleen DecockMaté OngenaertJasmien HoebeeckKatleen De PreterGert Van PeerWim Van CriekingeRuth LadensteinJohannes H SchulteRosa NogueraRaymond L Stallings et al.

Semi-high-throughput epigenetic validation using MSP on a real-time qPCR platform

Anneleen DecockMaté OngenaertJo VandesompeleFranki Speleman

Synthetic lethality between Rb, p53 and Dicer or miR-17-92 in retinal progenitors suppresses retinoblastoma formation

David NittnerIrina LambertzFrederic ClermontPieter MestdaghCorinna KöhlerSøren Jensby NielsenAart JochemsenFranki SpelemanJo VandesompeleMichael A Dyer et al.

A1 Journal Article in NATURE CELL BIOLOGY

Targeted expression of mutated ALK induces neuroblastoma in transgenic mice

Lukas C HeukampTheresa ThorAlexander SchrammKatleen De PreterCandy KumpsBram De WildeAndrea OderskyMartin PeiferSven LindnerAnnika Spruessel et al.

A1 Journal Article in SCIENCE TRANSLATIONAL MEDICINE

Whole-genome RT-qPCR microRNA expression profiling

Pieter MestdaghStefaan DerveauxJo Vandesompele

Bookchapter in Functional genomics : methods and protocols

2011

EVI1-mediated down regulation of MIR449A is essential for the survival of EVI1 positive leukaemic cells

An De WeerJoni Van der MeulenPieter RondouTom TaghonTorsten A KonradKatleen De PreterPieter MestdaghTom Van MaerkenNadine Van RoyMarta Jeison et al.

A1 Journal Article in BRITISH JOURNAL OF HAEMATOLOGY

Ewings sarcoma and prostate cancer: different yet similar

Heinrich KovarStephan NiedanSven BilkeRaphaela SchwentnerJozef BanMaximilian KauerPieter MestdaghJo VandesompelePaul Meltzer

Exploring the neuroblastoma methylome using MBD2-seq

Maté OngenaertAnneleen DecockJo VandesompeleFranki Speleman

Functional analysis of the p53 pathway in neuroblastoma cells using the small-molecule MDM2 antagonist Nutlin-3

Tom Van MaerkenAli RihaniDaniel DreidaxSarah De ClercqNurten YigitJean-Christophe MarineFrank WestermannAnne De PaepeJo VandesompeleFranki Speleman

A1 Journal Article in MOLECULAR CANCER THERAPEUTICS

High ALK receptor tyrosine kinase expression supersedes ALK mutation as a determining factor of an unfavorable phenotype in primary neuroblastoma

Johannes H SchulteHagen S BachmannBent BrockmeyerKatleen De PreterAndré OberthürSandra AckermannYvonne KahlertKristian PajtlerJessica TheissenFrank Westermann et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

Hsa-mir-145 is the top EWS-FLI1-repressed microRNA involved in a positive feedback loop in Ewing's sarcoma

J BanG JugPieter MestdaghR SchwentnerM KauerDNT AryeeK-L SchaeferF NakataniK ScotlandiM Reiter et al.

A1 Journal Article in ONCOGENE

Identification of a new rare recurrent 1q42.2-qter deletion in neuroblastoma

Annelies FieuwCandy KumpsAlexander SchrammBjörn MentenJohannes SchulteNadine Van RoySarah VergultRosa NogueraRogier VersteegR Stallings et al.

Mapping the neuroblastoma epigenome

Maté OngenaertAnneleen DecockJo VandesompeleFranki Speleman

Measurable impact of RNA quality on gene expression results from quantitative PCR

Joëlle VermeulenKatleen De PreterSteve LefeverJustine NuytensFanny De VloedStefaan DerveauxJan HellemansFranki SpelemanJo Vandesompele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

MicroRNA expression in induced sputum of smokers and patients with chronic obstructive pulmonary disease

Geert Van PottelbergePieter MestdaghKen BrackeOlivier ThasYANNICK VAN DURMEGuy JoosJo VandesompeleGuy Brusselle

A1 Journal Article in AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

MicroRNA miR-885-5p targets CDK2 and MCM5, activates p53 and inhibits proliferation and survival

EA AfanasyevaPieter MestdaghCandy KumpsJo VandesompeleV EhemannJ TheissenMark ZapatkaBenedikt BrorsL SavelyevaV Sagulenko et al.

A1 Journal Article in CELL DEATH AND DIFFERENTIATION

miRNA Expression profiling enables risk stratification in archived and fresh neuroblastoma tumor samples

Katleen De PreterPieter MestdaghJoëlle VermeulenFjoralba ZekaAlene NaranjoIsabella BrayVictoria CastelCaifu ChenElzbieta DrozynskaAngelika Eggert et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

Molecular portraits of non-coding RNAs in neuroblastoma

Pieter MestdaghJo VandesompeleFranki Speleman

Neuroblastoma epigenetics : from candidate gene approaches to genome-wide screenings

Anneleen DecockMaté OngenaertJo VandesompeleFranki Speleman

A1 Journal Article in EPIGENETICS

Neuroblastoma genetics and phenotype: a tale of heterogeneity

Franki SpelemanKatleen De PreterJo Vandesompele

A1 Journal Article in SEMINARS IN CANCER BIOLOGY

New options for molecular therapy of neuroblastoma: from p53 to gene therapy

Tom Van MaerkenFranki SpelemanJo Vandesompele

Pharmacological activation of p53 and gene therapy as emerging treatment options for neuroblastoma

Tom Van MaerkenAli RihaniAnne De PaepeJo VandesompeleFranki Speleman

A2 Journal Article in BELGIAN JOURNAL OF MEDICAL ONCOLOGY

Pharmacological activation of the p53 pathway by nutlin-3 inhibits medulloblastoma cell proliferation in vitro and in vivo

Annette KünkeleKatleen De PreterJo VandesompeleTheresa ThorKristian PajtlerWolfgang HartmannLukas HeukampAlexander SchrammAngelika EggertJohannes H Schulte

Practical tools to implement massive parallel pyrosequencing of PCR products in next generation molecular diagnostics

Kim De LeeneerJoachim De SchrijverLieven ClementMachteld BaetensSteve LefeverSarah De KeulenaerWim Van CriekingeDieter DeforceFilip Van NieuwerburghSofie Bekaert et al.

A1 Journal Article in PLOS ONE

Primer sequence disclosure : a clarification of the MIQE guidelines

Stephen A BustinVladimir BenesJeremy A GarsonJan HellemansJim HuggettMikael KubistaReinhold MuellerTania NolanMichael W PfafflGregory L Shipley et al.

A1 Journal Article in CLINICAL CHEMISTRY

Regulatory networks governed by microRNAs in T-ALL oncogenesis and normal T-cell development

Joni Van der MeulenEvelien MetsPieter MestdaghPeter PipelersTom TaghonDavid Camacho TrujilloDavid AvranGert Van PeerNadine Van RoyOlivier Thas et al.

Selectieve inhibitie van de p53–MDM2 interactie door nutlin-3 als een nieuwe therapeutische strategie voor neuroblastoom

Tom Van MaerkenAli RihaniAnne De PaepeJo VandesompeleFranki Speleman

A2 Journal Article in TIJDSCHRIFT VAN DE BELGISCHE KINDERARTS = JOURNAL DU PEDIATRE BELGE

Semi-high throughput epigenetic validation using MSP on a real-time qPCR platform

Anneleen DecockMaté OngenaertJo VandesompeleFranki Speleman

Semi-high throughput epigenetic validation using MSP on a real-time qPCR platform

Anneleen DecockMaté OngenaertJo VandesompeleFranki Speleman

The microRNA body map : dissecting microRNA function through integrative genomics

Pieter MestdaghSteve LefeverFilip PattynDana RidzonErik FredlundAnnelies FieuwMaté OngenaertJoëlle VermeulenAnne De PaepeLinda Wong et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

The miR-17-92 microRNA cluster regulates multiple components of the TGF-β pathway in neuroblastoma

Pieter MestdaghAna-Karin BostromFrancis ImpensErik FredlundGert Van PeerPaquito De AntonelisKristoffer Von StedingkBart GhesquièreStefanie SchulteMichael Dews et al.

2010

Accurate and objective copy number profiling using real-time quantitative PCR

B D'haeneJo VandesompeleJan Hellemans

A1 Journal Article in METHODS

Accurate Outcome Prediction in Neuroblastoma across Independent Data Sets Using a Multigene Signature

Katleen De PreterJoëlle VermeulenB BrorsO DelattreA EggertM FischerI Janoueix-LeroseyC LavarinoJM MarisJ Mora et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

Accurate prediction of neuroblastoma outcome based on miRNA expression profiles

Johannes SchulteBenjamin SchowePieter MestdaghLars KaderaliPrabhav KalaghatgiStefanie SchlierfJoëlle VermeulenBent BrockmeyerKristian PajtlerTheresa Thor et al.

Accurate prediction of neuroblastoma outcome based on miRNA expression profiles

Johannes H SchulteBenjamin SchowePieter MestdaghLars KaderaliPrabhav KalaghatgiStefanie SchlierfJoëlle VermeulenBent BrockmeyerKristian PajtlerTheresa Thor et al.

A1 Journal Article in INTERNATIONAL JOURNAL OF CANCER

An integrated genomics approach unravels a role for micro-RNAs in EWS-FLI1 driven Ewings sarcoma pathogenesis

Heinrich KovarPieter MestdaghMax KauerJozef BanSven BilkeRaphaela SchwentnerFranki SpelemanPaul MeltzerJo Vandesompele

An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours

Pieter MestdaghErik FredlundFilip PattynAli RihaniTom Van MaerkenJoëlle VermeulenCandy KumpsBjörn MentenKatleen De PreterAlexander Schramm et al.

An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours

Pieter MestdaghE FredlundFilip PattynAli RihaniTom Van MaerkenJoëlle VermeulenCandy KumpsBjörn MentenKatleen De PreterA Schramm et al.

A1 Journal Article in ONCOGENE

Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline

Joachim De SchrijverKim De LeeneerSteve LefeverNick SabbeFilip PattynFilip Van NieuwerburghPaul CouckeDieter DeforceJo VandesompeleSofie Bekaert et al.

A1 Journal Article in BMC BIOINFORMATICS

Chromosomal and microRNA expression patterns reveal biologically distinct subgroups of 11q- neuroblastoma

Patrick G BuckleyLeah AlcockKenneth BryanIsabella BrayJohannes H SchulteAlexander SchrammAngelika EggertPieter MestdaghKatleen De PreterJo Vandesompele et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma

Johannes H SchulteTobias MarschallMarcel MartinPhilipp RosenstielPieter MestdaghStefanie SchlierfTheresa ThorJo VandesompeleAngelika EggertStefan Schreiber et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Deep sequencing reveals differential expression of microRNAs in favourable versus unfavourable neuroblastoma

Johannes SchulteTobias MarshallMarcel MartinPhilipp RosenstielPieter MestdaghStefanie SchlierfTheresa ThorJo VandesompeleAngelika EggertStefan Schreiber et al.

Different mucosal expression of Th17 related genes in the small and large bowel of IBD patients

Sarah BogaertDebby LaukensHarald PeetersLode MelisKim OlievierNico BoonJo VandesompeleDirk ElewautMartine De Vos

Differential mucosal expression of Th17-related genes between the inflamed colon and ileum of patients with inflammatory bowel disease

Sara BogaertDebby LaukensHarald PeetersLode MelisKim OlievierNico BoonAugust VerbruggenJo VandesompeleDirk ElewautMartine De Vos

A1 Journal Article in BMC IMMUNOLOGY

Exploring 3D pooled next-generation sequencing using SNP-Cub^3

Joachim De SchrijverBram De WildeGeert TrooskensJo VandesompeleWim Van Criekinge

High expression of the ALK receptor tyrosine kinase precedes mutation as a determining factor of unfavourable phenotype in primary neuroblastoma

Johannes SchulteHagen BachmannBent BrockmeyerSandra NowackiYvonne KahlertAndre OberthurKatleen De PreterKristian PajtlerJessica TheissenFrank Westermann et al.

How to do successful gene expression analysis using real-time PCR

Stefaan DerveauxJo VandesompeleJan Hellemans

A1 Journal Article in METHODS

Improved Molecular Diagnostics of Idiopathic Short Stature and Allied Disorders: Quantitative Polymerase Chain Reaction-Based Copy Number Profiling of SHOX and Pseudoautosomal Region 1

B D'haeneJan HellemansMargarita CraenJean De SchepperK DevriendtJP FrynsK KeymolenEveline DebalsA de KleinEM de Jong et al.

A1 Journal Article in JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Meta-analysis of neuroblastomas reveals a skewed ALK mutation spectrum in tumors with MYCN amplification

Sara De BrouwerKatleen De PreterCandy KumpsPiotr ZabrockiMichael PorcuEllen M WesterhoutArjan LakemanJo VandesompeleJasmien HoebeeckTom Van Maerken et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

methGraph: A genome visualization tool for PCR-based methylation assays

Steve LefeverJasmien HoebeeckFilip PattynGábor TusnádyAnne De PaepeFranki SpelemanTamás ArányiJo Vandesompele

A1 Journal Article in EPIGENETICS

MicroRNA expression profiling to identify and validate reference genes for relative quantification in colorectal cancer

KH ChangPieter MestdaghJo VandesompeleMJ KerinN Miller

A1 Journal Article in BMC CANCER

mir-17-92 is a master regulator of TGFβ-pathway activity in neuroblastoma

Pieter MestdaghAnna-Karin BöstromFrancis ImpensErik FredlundKris Von StedingkBart GhesquièreStefanie SchlierfJohannes SchulteAlexander SchrammKris Gevaert et al.

miR-9, a MYC/MYCN-activated microRNA, regulates E-cadherin and cancer metastasis

L MaJ YoungH PrabhalaE PanPieter MestdaghD MuthJ Teruya-FeldsteinF ReinhardtTT OnderS Valastyan et al.

A1 Journal Article in NATURE CELL BIOLOGY

Monoallelic but not biallelic loss of Dicer1 promotes tumorigenesis in vivo

Irina LambertzDavid NittnerPieter MestdaghGeertrui DeneckerJo VandesompeleMA DyerJean-Christophe Marine

A1 Journal Article in CELL DEATH AND DIFFERENTIATION

Multiplex Amplicon Quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma

Candy KumpsNadine Van RoyL HeyrmanD GoossensJ Del-FaveroR NogueraJo VandesompeleFranki SpelemanKatleen De Preter

A1 Journal Article in BMC GENOMICS

MYCN/c-MYC-induced microRNAs repress coding gene networks associated with poor outcome in MYCN/c-MYC-activated tumors

Pieter MestdaghE FredlundFilip PattynJH SchulteD MuthJoëlle VermeulenCandy KumpsS SchlierfKatleen De PreterNadine Van Roy et al.

A1 Journal Article in ONCOGENE

Next generation sequencing: (r)evolutie in DNA sequenering en haar rol in de moderne geneeskunde

Jan HellemansSofie BekaertJo VandesompelePaul CouckeAnne De Paepe

A2 Journal Article in TIJDSCHRIFT VOOR GENEESKUNDE

Pharmacologic activation of the P53 pathway by Nutlin-3 inhibits medulloblastoma cell proliferation in vitro

Annette KuenkeleKatleen De PreterJo VandesompeleKristian PajtlerLukas HeukampMichael GrotzerAlexander SchrammAngelika EggertJohannes Schulte

Predicting outcomes for children with neuroblastoma

Joëlle VermeulenKatleen De PreterPieter MestdaghGenevieve LaureysFranki SpelemanJo Vandesompele

A1 Journal Article in DISCOVERY MEDICINE

Prognostic impact of gene expression-based classification for neuroblastoma

Andre OberthuerBarbara HeroFrank BertholdDilafruz JuraevaAndreas FaldumYvonne KahlertShahab AsgharzadehRobert SeegerPaola ScaruffiGian Paolo Tonini et al.

A1 Journal Article in JOURNAL OF CLINICAL ONCOLOGY

The miR-17-92 MicroRNA Cluster regulates multiple components of the TGF-beta Pathway in neuroblastoma

Pieter MestdaghAnna-Karin BostromFrancis ImpensErik FredlundGert Van PeerPasqualino De AntonellisKristoffer von StedingkBart GhesquièreStefanie SchulteMichael Dews et al.

A1 Journal Article in MOLECULAR CELL

The miRNA body map: dissecting miRNA function through integrative genomics

Pieter MestdaghSteve LefeverFilip PattynDana RidzonErik FredlundAnnelies FieuwJoëlle VermeulenAnne De PaepeLinda WongFranki Speleman et al.

2009

59-gene prognostic signature sub-stratifies high-risk neuroblastoma patients

Joëlle VermeulenKatleen De PreterGenevieve LaureysFranki SpelemanJo Vandesompele

Editorial material

A novel and universal method for microRNA RT-qPCR data normalization

Pieter MestdaghPieter Van VlierbergheAn De WeerDaniel MuthFrank WestermannFranki SpelemanJo Vandesompele

A1 Journal Article in GENOME BIOLOGY

Aberrant methylation of candidate tumor suppressor genes in neuroblastoma

Jasmien HoebeeckEvi MichelsFilip PattynValerie CombaretJoelle VermeulenNurten YigitClaire HoyouxGenevieve LaureysAnne De PaepeFranki Speleman et al.

A1 Journal Article in CANCER LETTERS

ALK Mutation Analysis in Patients of the German Neuroblastoma Study

B BrockmeyerJH SchulteA OberthuerPieter MestdaghK PajtlerJ TheissenH BachmannB HeroJo VandesompeleF Berthold et al.

Amphiregulin and Epiregulin mRNA expression in primary tumors predicts outcome in metastatic colorectal cancer treated with Cetuximab

Bart JacobsWendy De RoockHubert PiessevauxRobin Van OirbeekBart BiesmansJef De SchutterSteffen FieuwsJo VandesompeleMarc PeetersJean-Luc Van Laethem et al.

A1 Journal Article in JOURNAL OF CLINICAL ONCOLOGY

An assessment of air as a source of DNA contamination encountered when performing PCR

N WittG RodgerJo VandesompeleV BenesA ZumlaGA RookJF Huggett

A2 Journal Article in Journal of biomolecular techniques

Antitumor Activity of the Selective MDM2 Antagonist Nutlin-3 Against Chemoresistant Neuroblastoma With Wild-Type p53

Tom Van MaerkenLiesbeth FerdinandeJasmien TaildemanIrina LambertzNurten YigitLiesbeth VercruysseAli RihaniMartin MichaelisJindrich CinatlClaude Cuvelier et al.

A1 Journal Article in JOURNAL OF THE NATIONAL CANCER INSTITUTE

Chromosome 3p microsatellite allelotyping in neuroblastoma: a report on the technical hurdles

Jasmien HoebeeckBram De WildeEvi MichelsValerie CombaretNurten YigitEls De SmetNadine Van RoyEric StanbridgeNing RuGenevieve Laureys et al.

A1 Journal Article in CANCER INVESTIGATION

Comparison of miRNA profiles of microdissected Hodgkin/Reed-Sternberg cells and Hodgkin cell lines versus CD77+ B-cells reveals a distinct subset of differentially expressed miRNAs

Pieter Van VlierbergheAn De WeerPieter MestdaghTom FeysKatleen De PreterAnne De PaepeKathleen LambeinJo VandesompeleNadine Van RoyBruno Verhasselt et al.

A1 Journal Article in BRITISH JOURNAL OF HAEMATOLOGY

Correlation between porcine PPARGC1A mRNA expression and its downstream target genes in backfat and longissimus dorsi muscle

Tim ErkensJo VandesompeleAlex Van ZeverenLuc Peelman

A1 Journal Article in JOURNAL OF APPLIED GENETICS

Downregulation of miR-449a is essential for the survival of EVI1 positive leukemic cells through modulation of NOTCH1 and BCL2

An De WeerPieter MestdaghKatleen De PreterJoni Van der MeulenPieter Van VlierbergheTom Van MaerkenNadine Van RoyMarta JeisonIsaac YanivBarbara Cauwelier et al.

EFFECT OF ZAP-70 ON MIRNA EXPRESSION PROFILE IN CHRONIC LYMPHOCYTIC LEUKEMIA

Valerie PedeJan PhilippéPieter MestdaghJo VandesompeleBruno Verhasselt

Escape from p53-mediated tumor surveillance in neuroblastoma: switching off the p14(ARF)-MDM2-p53 axis

Tom Van MaerkenJo VandesompeleAli RihaniAnne De PaepeFranki Speleman

A1 Journal Article in Cell Death & Differentiation

External oligonucleotide standards enable cross laboratory comparison and exchange of real-time quantitative PCR data

Joëlle VermeulenFilip PattynKatleen De PreterLiesbeth VercruysseStefaan DerveauxPieter MestdaghSteve LefeverJan HellemansFranki SpelemanJo Vandesompele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Gebruik van genexpresieanalyse in de aanpak van neuroblastoom bij kinderen

Joëlle VermeulenKatleen De PreterPieter MestdaghFilip PattynAnne De PaepeNadine Van RoyGenevieve LaureysFranki SpelemanJo Vandesompele

A4 Journal Article in ONCO (NEDERLANDSE ED.)

Gene expression of PPARGC1A and several downstream target genes in porcine backfat and longissimus dorsi muscle

Tim ErkensJo VandesompeleMario Van PouckeAlex Van ZeverenLuc Peelman

Genetic analysis of PRNP, SPRN and RPSA in relation to prion disease resistance in sheep

Mario Van PouckeEvelyne LampoAlice Van den BroekeNicolas WilemarckDominique Vander DoncktCarolien RogiersTim ErkensKaren GoossensJo VandesompeleAlex Van Zeveren et al.

Improved outcome prediction of children with neuroblastoma using a multigene expression signature

Joëlle VermeulenJo VandesompeleFranki Speleman

Meta-mining of Neuroblastoma and Neuroblast Gene Expression Profiles Reveals Candidate Therapeutic Compounds

Katleen De PreterSara De BrouwerTom Van MaerkenFilip PattynA SchrammA EggertJo VandesompeleFranki Speleman

A1 Journal Article in CLINICAL CANCER RESEARCH

MICRORNA SIGNATURES IN GENETIC SUBTYPES OF T-CELL ACUTE LYMPHOBLASTIC LEUKEMIA

Joni Van der MeulenPieter Van VlierberghePieter MestdaghJo VandesompeleBruce PoppeNadine Van RoyTom TaghonJean PlumB. CauwelierDLD Selleslag et al.

Modeling neuroblastomagenesis from neural crest stem cells in vitro and in vivo

J SchulteA BohrerE MahlowJ MaurerH SchorleKatleen De PreterJo VandesompeleFranki SpelemanS SchlierfK Pajtler et al.

MODULATION OF MIR-449A EXPRESSION DECREASES CELL VIABILITY, INCREASES APOPTOSIS AND INDUCES DIFFERENTIATION IN EVI1 DEREGULATED LEUKEMIA CELLS

An De WeerBruce PoppePieter MestdaghKatleen De PreterPieter Van VlierbergheNadine Van RoyM JeisonB CauwelierBruno VerhasseltJan Philippé et al.

Positive correlation between relative mRNA expression of PRNP and SPRN in cerebral and cerebellar cortex of sheep

Evelyne LampoMario Van PouckeJo VandesompeleTim ErkensAlex Van ZeverenLuc Peelman

A1 Journal Article in Molecular and Cellular Probes

Predicting outcomes for children with neuroblastoma using a multigene-expression signature: a retrospective SIOPEN/COG/GPOH study

Joëlle VermeulenKatleen De PreterArlene NaranjoLiesbeth VercruysseNadine Van RoyJan HellemansKatrien SwertsSophie BravoPaolo ScaruffiGian Paolo Tonini et al.

A1 Journal Article in LANCET ONCOLOGY

Prognostic role and functional analyses of miRNA expression in neuroblastoma

S SchlierfPieter MestdaghT ThorKatleen De PreterM BaumannA EggertJo VandesompeleA SchrammJH Schulte

RDML : structured language and reporting guidelines for real-time quantitative PCR data

Steve LefeverJan HellemansFilip PattynDaniel R PrzybylskiChris TaylorRené GeurtsAndreas UntergasserJo Vandesompele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Risk estimation of neuroblastoma patients by gene expression based classification

M FischerA OberthuerB BrorsF WestermannJ TheissenS AsgharzadehR SeegerP ScaruffiGP ToniniI Janoueix-Lerosey et al.

RNA pre-amplification enables large-scale RT-qPCR gene-expression studies on limiting sample amounts

Joëlle VermeulenStefaan DerveauxSteve LefeverEls De SmetKatleen De PreterNurten YigitAnne De PaepeFilip PattynFranki SpelemanJo Vandesompele

A2 Journal Article in BMC RESEARCH NOTES

RTPrimerDB : the portal for real-time PCR primers and probes

Steve LefeverJo VandesompeleFranki SpelemanFilip Pattyn

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Selection of reference genes for quantitative real-time PCR in equine in vivo and in vitro blastocysts

Katrien SmitsKaren GoossensAnn Van SoomJan GovaereMaarten HoogewijsEmilie VanhaesebrouckCesare GalliSilvia ColleoniJo VandesompeleLuc Peelman

A2 Journal Article in BMC RESEARCH NOTES

Standardization of qPCR and RT-qPCR

SA BustinJo VandesompeleMW Pfaffl

A1 Journal Article in GENETIC ENGINEERING & BIOTECHNOLOGY NEWS

The emerging molecular pathogenesis of neuroblastoma : implications for improved risk assessment and targeted therapy

Nadine Van RoyKatleen De PreterJasmien HoebeeckTom Van MaerkenFilip PattynPieter MestdaghJoëlle VermeulenJo VandesompeleFranki Speleman

A1 Journal Article in GENOME MEDICINE

The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments

SA BustinV BenesJA GarsonJan HellemansJ HuggettM KubistaR MuellerT NolanMW PfafflGL Shipley et al.

A1 Journal Article in CLINICAL CHEMISTRY

The miR-17-92 gene cluster is amplified and overexpressed in retinoblastoma

E BiewaldPieter MestdaghH StephanKatleen De PreterT ThorM BaumannD LohmannA EggertFranki SpelemanA Schramm et al.

The miR-17-92 gene cluster is amplified and overexpressed in retinoblastoma

J SchulteE BiewaldPieter MestdaghH StephanKatleen De PreterD LohmannFranki SpelemanA SchrammJo VandesompeleA Eggert

Unreliable Real-Time PCR Analysis of Human Endogenous Retrovirus-W (HERV-W) RNA Expression and DNA Copy Number in Multiple Sclerosis

JA GarsonJF HuggettSA BustinMW PfafflV BenesJo VandesompeleGL Shipley

A1 Journal Article in AIDS RESEARCH AND HUMAN RETROVIRUSES

Using real-time qPCR to evaluate RNAi-mediated gene silencing

Tom Van MaerkenPieter MestdaghS De ClercqFilip PattynNurten YigitAnne De PaepeJ C MarineFranki SpelemanJo Vandesompele

A2 Journal Article in BioTechniques Protocol Guide

Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival

I. BrayK. BryanS. PrenterP. G. BuckleyN. H. FoleyD. M. MurphyL. AlcockPieter MestdaghJo VandesompeleFranki Speleman et al.

A1 Journal Article in PLoS One

2008

A constitutional translocation t(1;17)(p36.2;q11.2) in a neuroblastoma patient disrupts the human NBPF1 and ACCN1 genes

Karl VandepoeleVanessa AndriesNadine Van RoyKatrien StaesJo VandesompeleGenevieve LaureysEls De SmetGeert BerxFranki SpelemanFrans Van Roy

A1 Journal Article in PLOS ONE

A constitutional translocation t(1;17)(p36.2;q11.2) in a neuroblastoma patient disrupts the the human NBPF1 and ACCN1 genes

Frans Van RoyKlaas VandepoeleNadine Van RoyVanessa AndriesKatrien StaesJo VandesompeleGenevieve LaureysEls De SmetGeert BerxFranki Speleman

Aberrant splicing of the PTPRD gene mimics microdeletions identified at this locus in neuroblastomas (vol 47, pg 197, 2008)

Prakash NairKatleen De PreterJo VandesompeleFranki SpelemanRaymond L Stallings

Aberrant splicing of the PTPRD gene mimics microdeletions identified-at locus this in neuroblastomas

Prakash NairKatleen De PreterJo VandesompeleFranki SpelemanRaymond L Stallings

A1 Journal Article in GENES CHROMOSOMES & CANCER

CADM1 is a strong neuroblastoma candidate gene that maps within a 3.72 Mb critical region of loss on 11q23

Evi MichelsJasmien HoebeeckKatleen De PreterAlexander SchrammBénédicte BrichardAnne De PaepeAngelika EggertGenevieve LaureysJo VandesompeleFranki Speleman

A1 Journal Article in BMC CANCER

Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas

F WestermannD MuthA BennerT BauerKO HenrichA OberthuerB BrorsT BeissbarthJo VandesompeleFilip Pattyn et al.

A1 Journal Article in GENOME BIOLOGY

Expression profiling of a new class of non-coding RNAs in human neuroblastoma

Pieter MestdaghFilip PattynKatleen De PreterJoëlle VermeulenAnne De PaepeFranki SpelemanJo Vandesompele

Gene sets enrichment analysis of chromosomal regions

Katleen De PreterRoland BarriotFranki SpelemanJo VandesompeleYves Moreau

High resolution genome analysis for improved prognostic stratification and candidate gene selection in neuroblastoma

Evi MichelsFranki SpelemanJo Vandesompele

High throughput stem-loop RT-PCR miRNA expression profiling using minute amounts of input RNA reveals new insights in neuroblastoma pathogenesis

Pieter MestdaghJoëlle VermeulenKatleen De PreterFilip PattynGenevieve LaureysRosa NogueraMarta PiquerasFranki SpelemanJo Vandesompele

High-throughput stem-loop RT-PCR miRNA expression profiling using minute amounts of input RNA

Pieter MestdaghTom FeysNathalie BernardSimone GuentherCaifu ChenVladimir BenesFranki SpelemanJo Vandesompele

High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA

Pieter MestdaghTom FeysNathalie BernardSimone GuentherCaifu ChenFranki SpelemanJo Vandesompele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Identification of 2 putative critical segments of 17q gain in neuroblastoma through integrative genomics

Jo VandesompeleEvi MichelsKatleen De PreterBjörn MentenAlexander SchrammAngelika EggertPeter F AmbrosValérie CombaretNadine FrancotteFrancesca Antonacci et al.

A1 Journal Article in INTERNATIONAL JOURNAL OF CANCER

Low-cost dedicated mini-arrays for high-throughput analysis of DNA copy-number alterations in neuroblastoma

Katleen De PreterBjörn MentenSara De BrouwerCandy KumpsEvi MichelsNadine Van RoyJo VandesompeleFranki Speleman

A1 Journal Article in CANCER LETTERS

MICRORNA PROFILING OF EVI1 DEREGULATED MYELOID LEUKEMIA

An De WeerBruce PoppePieter MestdaghPieter Van VlierbergheNadine Van RoyAnne De PaepeBruno VerhasseltJo VandesompeleFranki Speleman

MYCN regulates oncogenic and tumour suppressor miRNA networks in neuroblastoma

Pieter MestdaghJoëlle VermeulenFilip PattynLiesbeth VercruysseAnne De PaepeGenevieve LaureysFranki SpelemanJo Vandesompele

Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions

Katleen De PreterRoland BarriotFranki SpelemanJo VandesompeleYves Moreau

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Positive correlation between relative mRNA expression of PRNP and SPRN in cerebral cortex of sheep

Evelyne LampoMario Van PouckeJo VandesompeleTim ErkensAlex Van ZeverenLuc Peelman

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

Chris F TaylorDawn FieldSusanna-Assunta SansoneJan AertsRolf ApweilerMichael AshburnerCatherine A BallPierre-Alain BinzMolly BogueTim Booth et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

Real-time qPCR as a tool for evaluating RNAi-mediated gene silencing

Tom Van MaerkenPieter MestdaghSarah De ClercqFilip PattynNurten YigitAnne De PaepeJean-Christophe MarineFranki SpelemanJo Vandesompele

A2 Journal Article in Bioradiations

Selection and validation of a set of reliable reference genes for quantitative sod gene expression analysis in C-elegans

David HoogewijsKoen HouthoofdFilip MatthijssensJo VandesompeleJacques Vanfleteren

A1 Journal Article in BMC MOLECULAR BIOLOGY

Standardization of real-time PCR gene expression data from independent biological replicates

Erik WillemsLuc LeynsJo Vandesompele

Editorial material

Unmasking of epigenetically silenced microRNAs in neuroblastoma

Jasmien HoebeeckGeert DeclerckPieter MestdaghFilip PattynKatleen De PreterJoëlle VermeulenNurten YigitAnne De PaepeFranki SpelemanJo Vandesompele

2007

Array CGH analysis of subnanogram quantities of DNA using whole genome amplification: opportunities for detection of copy number alterations in Hodgkin's lymphoma

Tom FeysBart PoppeBruno VerhasseltPascale De PaepeBjörn MentenJo VandesompeleNadine Van RoyAnne De PaepeFranki Speleman

ArrayCGH based classification of neuroblastoma into genomic subgroups

Sara De BrouwerEvi MichelsJo VandesompeleKatleen De PreterJasmien HoebeeckJoëlle VermeulenAlexander SchrammJan J MolenaarBjörn MentenBarbara Marques et al.

ArrayCGH-based classification of neuroblastoma into genomic subgroups

Evi MichelsJo VandesompeleKatleen De PreterJasmien HoebeeckJoëlle VermeulenAlexander SchrammJan J MolenaarBjörn MentenBarbara MarquesRaymond L Stallings et al.

A1 Journal Article in GENES CHROMOSOMES & CANCER

Genome wide promoter methylation analysis in neuroblastoma with perspectives for integrated molecular profiling

Jasmien HoebeeckMaté OngenaertEvi MichelsKatleen De PreterJoëlle VermeulenNurten YigitAnne De PaepeWim Van CriekingeFranki SpelemanJo Vandesompele

Genomic classification according to numerical and segmental chromosome instabilities is of strong prognostic relevance in neuroblastoma

Gudrun SchleiermacherIsabelle Janoueix-LeroseyEvi MichelsVeronique MosseriAgnes RibeiroDelphine LequinJoëlle VermeulenJo VandesompeleGaelle PierronJerome Couturier et al.

High resolution tiling-path BAC array deletion mapping suggests commonly involved 3p21-p22 tumor suppressor genes in neuroblastoma and more frequent tumors

Jasmien HoebeeckEvi MichelsBjörn MentenNadine Van RoyAngelika EggertAlexander SchrammKatleen De PreterNurten YigitEls De SmetAnne De Paepe et al.

A1 Journal Article in INTERNATIONAL JOURNAL OF CANCER

Identification and expression analysis of genes associated with bovine blastocyst formation

Karen GoossensAnn Van SoomMario Van PouckeLeen VandaeleJo VandesompeleAlex Van ZeverenLuc Peelman

A1 Journal Article in BMC DEVELOPMENTAL BIOLOGY

Integrative genomics in neuroblastoma research

Franki SpelemanKatleen De PreterEvi MichelsJasmien HoebeeckFilip PattynJoëlle VermeulenNadine Van RoyAnne De PaepeGenevieve LaureysJo Vandesompele

MicroRNA profiling of EVI1 deregulated myeloid leukemia

An De WeerBruce PoppePieter MestdaghNadine Van RoyAnne De PaepeBruno VerhasseltJo VandesompeleFranki Speleman

Molecular dissection of isolated disease features in mosaic neurofibromatosis type 1

Ophélia MaertensSofie De SchepperJo VandesompeleHilde BremsIne HeynsSandra JanssensFranki SpelemanEric LegiusLudwine Messiaen

A1 Journal Article in AMERICAN JOURNAL OF HUMAN GENETICS

New insights into the genetic basis of neuroblastoma

Franki SpelemanKatleen De PreterJasmien HoebeeckNadine Van RoyJo Vandesompele

A4 Journal Article in VERHANDELINGEN VAN DE KONINKLIJKE ACADEMIE VOOR GENEESKUNDE VAN BELGIË

qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data

Jan HellemansGeert MortierAnne De PaepeFranki SpelemanJo Vandesompele

A1 Journal Article in GENOME BIOLOGY

Rapid and easy prenatal diagnosis of sickle cell anemia using double-dye LNA probe technology

Hakim E. HousniJo VandesompelePascal VannuffelBeatrice GulbisJasmine ParmaPascale Cochaux

A1 Journal Article in BRITISH JOURNAL OF HAEMATOLOGY

Real-time PCR quality control for gene expression profiling on the LightCycler 480 System

Jasmien HoebeeckFilip PattynY NURTENE DE SMETFranki SpelemanJo Vandesompele

A3 Journal Article in Biochemica

Real-time quantitative PCR as an alternative to Southern blot or fluorescence in situ hybridization for detection of gene copy number changes.

Jasmien HoebeeckFranki SpelemanJo Vandesompele

Bookchapter in Methods in Molecular Biology

Report of a female patient with mental retardation and tall stature due to a chromosomal rearrangement disrupting the OPHN1 gene on Xq12

Björn MentenKaren BuysseStefan VermeulenVALERIE MEERSSCHAUTJo VandesompeleBL NGNP CARTERGeert MortierFranki Speleman

A1 Journal Article in EUROPEAN JOURNAL OF MEDICAL GENETICS

Translating expression profiling into a clinically feasible test to predict neuroblastoma outcome

A SCHRAMMJo VandesompeleJH SCHULTES DREESMANNL KADERALIB BRORSR EILSFranki SpelemanA EGGERT

A1 Journal Article in CLINICAL CANCER RESEARCH

2006

Comprehensive NF1 screening on cultured Schwann cells from neurofibromas: towards an extensive study of the somatic mutation spectrum in neurofibromatosis type 1

Ophélia MaertensHilde BremsJo VandesompeleThomas De RaedtIne HeynsThorsten RosenbaumSofie De SchepperAnne De PaepeGeert MortierSandra Janssens et al.

A1 Journal Article in Human Mutation

Development of a new set of reference genes for normalization of real-time RT-PCR data of porcine backfat and Longissimus dorsi muscle, and evaluation with PPARGC1A

Tim ErkensMario Van PouckeJo VandesompeleKaren GoossensAlex Van ZeverenLuc Peelman

A1 Journal Article in BMC BIOTECHNOLOGY

Differential prion protein mRNA expression in sheep blood

Mario Van PouckeJo VandesompeleAdelheid De KetelaereKaren GoossensMarc MattheeuwsAlex Van ZeverenLuc Peelman

Emerging patterns of cryptic chromosomal imbalance in patients with idiopathic mental retardation and multiple congenital anomalies: a new series of 140 patients and review of published reports

Björn MentenN MAASB THIENPONTKaren BuysseJo VandesompeleC MELOTTET DE RAVELS VAN VOORENI BALIKOVAL BACKX et al.

A1 Journal Article in JOURNAL OF MEDICAL GENETICS

EVII is consistently expressed as principal transcript in common and rare recurrent 3q26 rearrangements

Bruce PoppeN DASTUGUEJo VandesompeleBarbara CauwelierB DE SMETNurten YigitAnne De PaepeJ CERVERAC RECHERV DE MAS et al.

A1 Journal Article in GENES CHROMOSOMES & CANCER

Expression profiling suggests underexpression of the GABA(A) receptor subunit delta in the fragile X knockout mouse model

I GANTOISJo VandesompeleFranki SpelemanE REYNIERSR D'HOOGELA SEVERIJNENR WILLEMSENF TASSONERF KOOY

A1 Journal Article in NEUROBIOLOGY OF DISEASE

Genome wide measurement of DNA copy number changes in neuroblastoma: dissecting amplicons and mapping losses, gains and breakpoints

Evi MichelsJo VandesompeleJasmien HoebeeckBjörn MentenKatleen De PreterGenevieve LaureysNadine Van RoyFranki Speleman

A1 Journal Article in CYTOGENETIC AND GENOME RESEARCH

High throughput analyses for assessment of DNA copy number and methylation status for chromosome 3p genes in high-risk neuroblastoma

Jasmien HoebeeckFranki SpelemanJo Vandesompele

Human fetal neuroblast and neuroblastoma transcriptome analysis confirms neuroblast origin and highlights neuroblastoma candidate genes

Katleen De PreterJo VandesompelePierre HeimannNurten YigitSiv BeckmanAlexander SchrammAngelika EggertRaymond L StallingsYves BenoitMarleen Renard et al.

A1 Journal Article in GENOME BIOLOGY

Identification of MYCN transcriptional target genes in neuroblastoma

Filip PattynFranki SpelemanJo Vandesompele

MethBLAST and methPrimerDB: web-tools for PCR based methylation analysis

Filip PattynJasmien HoebeeckPiet RobbrechtEvi MichelsAnne De PaepeG BOTTUD COORNAERTR HERZOGFranki SpelemanJo Vandesompele

A1 Journal Article in BMC BIOINFORMATICS

Murine m cells express annexin V specifically

Phebe VerbruggheWim WaelputBirger DieriksAnouk WaeytensJo VandesompeleClaude Cuvelier

A1 Journal Article in JOURNAL OF PATHOLOGY

Potential application of ELAVL4 real-time quantitative reverse transcription-PCR for detection of disseminated neuroblastoma cells

Katrien SwertsBarbara De MoerlooseCatharina DhoogeJo VandesompeleC HOYOUXK BEISKEYves BenoitGenevieve LaureysJan Philippé

A1 Journal Article in CLINICAL CHEMISTRY

PPARGC1A mRNA expression in backfat and longissimus dorsi muscle in the pig

Tim ErkensMario Van PouckeJo VandesompeleKaren GoossensAlex Van ZeverenLuc Peelman

PRNP polymorphisms in sheep with differential PRNP mRNA expression in blood

Mario Van PouckeJo VandesompeleAdelheid De KetelaereKaren GoossensAlex Van ZeverenLuc Peelman

Real-time quantitative allele discrimination assay using 3 ' locked nucleic acid primers for detection of low-percentage mosaic mutations

Ophélia MaertensE LEGIUSFranki SpelemanL MESSIAENJo Vandesompele

Editorial material

RTPrimerDB : the real-time PCR primer and probe database, major update 2006

Filip PattynPiet RobbrechtAnne De PaepeFranki SpelemanJo Vandesompele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Small-molecule MDM2 antagonists as a new therapy concept for neuroblastoma

Tom Van MaerkenFranki SpelemanJ VERMEULENIrina LambertzSarah De ClercqEls De SmetNurten YigitV COPPENSJan PhilippéAnne De Paepe et al.

A1 Journal Article in CANCER RESEARCH

The potential (radio-)biological impact of launch vibration

Philippe BaertTim Van CleynenbreugelJo VandesompeleSofie De SchynkelJos Vander SlotenPatric Van Oostveldt

A1 Journal Article in ACTA ASTRONAUTICA

The von Hippel-Lindau tumor suppressor gene expression level has prognostic value in neuroblastoma

Jasmien HoebeeckJo VandesompeleHelén NissonKatleen De PreterNadine Van RoyEls De SmetNurten YigitAnne De PaepeGenevieve LaureysSven Påhlman et al.

A1 Journal Article in INTERNATIONAL JOURNAL OF CANCER

Translocation-excision-deletion-amplification mechanism leading to nonsyntenic coamplification of MYC and ATBF1

Nadine Van RoyJo VandesompeleBjörn MentenH NILSSONEls De SmetM ROCCHIAnne De PaepeS PAHLMANFranki Speleman

A1 Journal Article in GENES CHROMOSOMES & CANCER

2005

A dual fluorescent multiprobe assay for prion protein genotyping in sheep

Mario Van PouckeJo VandesompeleMarc MattheeuwsAlex Van ZeverenLuc Peelman

A1 Journal Article in BMC INFECTIOUS DISEASES

A dual fluorescent multiprobe assay for prion protein genotyping in sheep

Mario Van PouckeJo VandesompeleMarc MattheeuwsAlex Van ZeverenLuc Peelman

A new recurrent inversion, inv(7)(p15q34), leads to transcriptional activation of HOXA10 and HOXA11 in a subset of T-cell acute lymphoblastic leukemias

Franki SpelemanBarbara CauwelierN DASTUGUEJ COOLSBruno VerhasseltBruce PoppeNadine Van RoyJo VandesompeleC GRAUXA UYTTEBROECK et al.

A1 Journal Article in LEUKEMIA

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

Björn MentenFilip PattynKatleen De PreterPiet RobbrechtEvi MichelsKaren BuysseGeert MortierAnne De PaepeSteven van VoorenJoris Vermeesch et al.

A1 Journal Article in BMC BIOINFORMATICS

Differential polyadenylation of ribosomal RNA during post-transcriptional processing in Leishmania

S DECUYPEREJo VandesompeleV YARDLEYS DE DONCKERT LAURENTS RIJALA LLANOS-CUENTASF CHAPPUISJ AREVALOJC DUJARDIN

A1 Journal Article in PARASITOLOGY

Identification of an unbalanced X-autosome translocation by array CGH in a boy with a syndromic form of chondrodysplasia punctata brachytelephalangic type

Björn MentenKaren BuysseJo VandesompeleEls De SmetAnne De PaepeFranki SpelemanGeert Mortier

A1 Journal Article in EUROPEAN JOURNAL OF MEDICAL GENETICS

Impact of RNA quality on reference gene expression stability

Claudina Perez NovoCindy ClaeysFranki SpelemanPaul Van CauwenbergeClaus BachertJo Vandesompele

A1 Journal Article in BIOTECHNIQUES

No evidence for correlation of DDX1 gene amplification with improved survival probability in patients with MYCN-amplified neuroblastomas

Katleen De PreterFranki SpelemanValérie CombaretJohn LunecJulien BoardAndy PearsonAnne De PaepeNadine Van RoyGenevieve LaureysJo Vandesompele

A1 Journal Article in JOURNAL OF CLINICAL ONCOLOGY

Positional and functional mapping of a neuroblastoma differentiation gene on chromosome 11

Katleen De PreterJo VandesompeleBjörn MentenPhilippa CarrHeike FieglerAnders EdsjöNigel P CarterNurten YigitWim WaelputNadine Van Roy et al.

A1 Journal Article in BMC GENOMICS

Rapid detection of VHL exon deletions using real-time quantitative PCR

Jasmien HoebeeckR VAN DER LUIJTBruce PoppeEls De SmetNurten YigitKathleen ClaesR ZEWALDGJ DE JONGAnne De PaepeFranki Speleman et al.

A1 Journal Article in LABORATORY INVESTIGATION

Selection of reference genes for quantitative real-time PCR in bovine preimplantation embryos

Karen GoossensMario Van PouckeAnn Van SoomJo VandesompeleAlex Van ZeverenLuc Peelman

A1 Journal Article in BMC DEVELOPMENTAL BIOLOGY

Unequivocal delineation of clinicogenetic subgroups and development of a new model for improved outcome prediction in neuroblastoma

Jo VandesompeleM BAUDISKatleen De PreterNadine Van RoyP AMBROSN BOWNC BRINKSCHMIDTH CHRISTIANSENV COMBARETM LASTOWSKA et al.

A1 Journal Article in JOURNAL OF CLINICAL ONCOLOGY

2004

Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons

Katleen De PreterFilip PattynGeert BerxKristin StrumaneBjörn MentenFrans Van RoyAnne De PaepeFranki SpelemanJo Vandesompele

A1 Journal Article in BMC GENOMICS

Expression analyses identify MLL as a prominent target of 11q23 amplification and support an etiologic role for MLL gain of function in myeloid malignancies

Bruce PoppeJo VandesompeleC SCHOCHC LINDVALLK MROZEKCD BLOOMFIELDHB BEVERLOOL MICHAUXN DASTUGUEC HERENS et al.

A1 Journal Article in BLOOD

Gene-expression profiling reveals distinct expression patterns for classic versus variant Merkel cell phenotypes and new classifier genes to distinguish Merkel cell from small-cell lung carcinoma

M VAN GELEGM BOYLEAL COOKJo VandesompeleTom BoonefaesPieter RottiersNadine Van RoyAnne De PaepePG PARSONSJH LEONARD et al.

A1 Journal Article in ONCOGENE

Loss-of-function mutations in LEMD3 result in osteopoikilosis, Buschke-Ollendorff syndrome and melorheostosis

Jan HellemansO PREOBRAZHENSKAAndy WillaertP DEBEERPETER VERDONKT COSTAK JANSSENSBjörn MentenNadine Van RoyStefan Vermeulen et al.

A1 Journal Article in NATURE GENETICS

Neuroblastoma cells with overexpressed MYCN retain their capacity to undergo neuronal differentiation

A EDSJOH NILSSONJo VandesompeleJ KARLSSONFilip PattynLA CULPFranki SpelemanS PAHLMAN

A1 Journal Article in LABORATORY INVESTIGATION

No evidence for involvement of SDHD in neuroblastoma pathogenesis

Katleen De PreterJo VandesompeleJasmien HoebeeckCaroline VandenbroeckeJoél SmetAnnick NuytsGenevieve LaureysValérie CombaretNadine Van RoyFrank Roels et al.

A1 Journal Article in BMC CANCER

The human FOXL2 mutation database

DIANE BEYSENJo VandesompeleL MESSIAENAnne De PaepeElfride De Baere

A1 Journal Article in HUMAN MUTATION

2003

Application of laser capture microdissection in genetic analysis of neuroblastoma and neuroblastoma precursor cells

Katleen De PreterJo VandesompelePierre HeimannMark M KockxMireille Van GeleJasmien HoebeeckEls De SmetMartine DemarcheGenevieve LaureysNadine Van Roy et al.

A1 Journal Article in CANCER LETTERS

Evidence for involvement of a tumor suppressor gene on 1p in malignant peripheral nerve sheath tumors

Nadine Van RoyM VAN GELEJo VandesompeleLudwine MessiaenSimon Van BelleR SCIOTK MORTELEJ GYSELINCKE MICHIELSRamses Forsyth et al.

A1 Journal Article in CANCER GENETICS AND CYTOGENETICS

Expression profiling reveals involvement of the GABA(A) receptor subunit delta in the fragile X syndrome

I GANTOISJo VandesompeleFranki SpelemanR D'HOOGEL SEVERIJNENR WILLEMSENF TASSONER KOOY

ID2 expression in neuroblastoma does not correlate to MYCN levels and lacks prognostic value

Jo VandesompeleAnders EdsjöKatleen De PreterHåkan AxelsonFranki SpelemanSven Påhlman

A1 Journal Article in ONCOGENE

More than 125 FOXL2 mutations and variants in BPES and POF patients in the human FOXL2 allelic variant database

DIANE BEYSENJo VandesompeleFilip PattynAnne De PaepeLudwine MessiaenElfride De Baere

Quantitative real time polymerase chain reaction for measurement of human interleukin-5 receptor alpha spliced isoforms mRNA

Claudina Perez NovoJo VandesompeleGabriële HoltappelsFranki SpelemanPhilippe GevaertPaul Van CauwenbergeClaus Bachert

A1 Journal Article in BMC BIOTECHNOLOGY

Regulation of peroxisomal genes by DHEA and vitamin D

M DEPRETERJo VandesompeleS FERDINANDUSSEFranki SpelemanFrank Roels

A1 Journal Article in PEROXISOMAL DISORDERS AND REGULATION OF GENES

RTPrimerDB : the Real-Time PCR primer and probe database

Filip PattynFranki SpelemanAnne De PaepeJo Vandesompele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2002

A brief commentary on "Chromosomal aberrations in neuroblastoma cell lines identified by cross species color banding and chromosome painting".

Jo VandesompeleFranki Speleman

A1 Journal Article in CANCER GENETICS AND CYTOGENETICS

Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes

Jo VandesompeleKatleen De PreterFilip PattynBruce PoppeNadine Van RoyAnne De PaepeFranki Speleman

A1 Journal Article in GENOME BIOLOGY

Delineation of the heterogeneous pattern of genomic changes and identifacation of differentially expressed genes in neuroblastoma

Jo Vandesompele

Elimination of primer-dimer artifacts and genomic coamplification using a two-step SYBR green I real time RT-PCR.

Jo VandesompeleAnne De PaepeFranki Speleman

A1 Journal Article in ANALYTICAL BIOCHEMISTRY

Localization of the 17q breakpoint of a constitutional 1;17 translocation in a patient with neuroblastoma within a 25-kb segment located between the ACCN1 and TLK2 genes and near the distal breakpoints of two microdeletions in neurofibromatosis type I patients.

Nadine Van RoyJo VandesompeleGeert BerxK STAESMireille Van GeleEls De SmetAnne De PaepeGenevieve LaureysP VAN DER DRIFTR VERSTEEG et al.

A1 Journal Article in GENES CHROMOSOMES & CANCER

Modulation of the peroxisomal gene expression pattern by dehydroepiandrosterone and vitamin D : therapeutic implications

Marianne DepreterJo VandesompeleMarc EspeelFranki SpelemanFrank Roels

A1 Journal Article in JOURNAL OF ENDOCRINOLOGY

Pathological splice mutations outside the invariant AG/GT splice sites of BRCA1 exon 5 increase alternative transcript levels in the 5 ' end of the BRCA1 gene.

Kathleen ClaesJo VandesompeleBruce PoppeK DAHANI COENEAnne De PaepeLudwine Messiaen

A1 Journal Article in ONCOGENE

Quantification of MYCN, DDX1, and NAG gene copy number in neuroblastoma using a real-time quantitative PCR assay.

Katleen De PreterFranki SpelemanV COMBARETJ LUNECGenevieve LaureysB EUSSENN FRANCOTTEJ BOARDA PEARSONAnne De Paepe et al.

A1 Journal Article in MODERN PATHOLOGY

Quantification of NF1 transcripts reveals novel highly expressed splice variants.

Ina VandenbrouckeJo VandesompeleAnne De PaepeLudwine Messiaen

A1 Journal Article in FEBS LETTERS

Quantification of soluble and membrane anchored isoforms of IL-5R alpha using real-time PCR

CP NOVOJo VandesompeleI VANDENBROUCKEG HOLTAPPELSPhilippe GevaertPaul Van CauwenbergeClaus Bachert

2001

Combined M-FISH and CGH analysis allows comprehensive description of genetic alterations in neuroblastoma cell lines.

Nadine Van RoyHeidi Van LimbergenJo VandesompeleMireille Van GeleBruce PoppeH SALWENGenevieve LaureysN MANOELAnne De PaepeFranki Speleman

A1 Journal Article in GENES CHROMOSOMES & CANCER

Comparative genomic hybridization (CGH) analysis of stage 4 neuroblastoma reveals high frequency of 11Q deletion in tumors lacking MYCN amplification.

D PLANTAZJo VandesompeleNadine Van RoyM LASTOWSKAN BOWNV COMBARETMC FAVROTO DELATTREJ MICHONJ BENARD et al.

A1 Journal Article in INTERNATIONAL JOURNAL OF CANCER

Multicentre analysis of patterns of DNA gains and losses in 204 neuroblastoma tumors: How many genetic subgroups are there?

Jo VandesompeleFranki SpelemanNadine Van RoyGenevieve LaureysC BRINKSCHMIDTH CHRISTIANSENF LAMPERTM LASTOWSKAN BOWNA PEARSON et al.

A1 Journal Article in MEDICAL AND PEDIATRIC ONCOLOGY

Quantification of splice variants using real-time PCR

Ina VandenbrouckeJo VandesompeleAnne De PaepeLudwine Messiaen

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2000

Chromosome 2 short arm translocations revealed by M-FISH analysis of neuroblastoma cell lines.

Nadine Van RoyHeidi Van LimbergenJo VandesompeleMireille Van GeleBruce PoppeGenevieve LaureysAnne De PaepeFranki Speleman

A1 Journal Article in MEDICAL AND PEDIATRIC ONCOLOGY

Structure and mutation analysis of the gene encoding DNA fragmentation factor 40 (caspase-activated nuclease), a candidate neuroblastoma tumour suppressor gene.

H JUDSONNadine Van RoyL STRAINJo VandesompeleMireille Van GeleFranki SpelemanDT BONTHRON

A1 Journal Article in HUMAN GENETICS

1999

Neuroblastoma: from molecular cytogenetics to gene expression profiling

Jo VandesompeleNadine Van RoyGeert BerxD PLANTAZAnne De PaepeGenevieve LaureysFrans Van RoyFranki Speleman

1998

Characteristic pattern of chromosomal gains and losses in Merkel cell carcinoma detected by comparative genomic hybridization

Mireille Van GeleFranki SpelemanJo VandesompeleNadine Van RoyJH Leonard

A1 Journal Article in CANCER RESEARCH

Genetic heterogeneity of neuroblastoma studied by comparative genomic hybridization.

Jo VandesompeleNadine Van RoyMireille Van GeleGenevieve LaureysP AMBROSP HEIMANNC DEVALCKE SCHUURINGP BROCKJ OTTEN et al.

A1 Journal Article in GENES CHROMOSOMES & CANCER

Molecular analysis of lp36 breakpoints in two Merkel cell carcinomas.

Mireille Van GeleNadine Van RoySG RONANLudwine MessiaenJo VandesompeleMarie GeertsM NAEYAERTE BLENNOWI BAR-AMTK DAS GUPTA et al.

A1 Journal Article in GENES CHROMOSOMES & CANCER