Research Explorer

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Researcher

Pieter Mestdagh

Publications & Research Data

Awards & Distinctions

327 Results

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

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

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.

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

Mapping modulators of T-cell activation and cancer immune evasion through chemical and genetic perturbations using an in-vitro co-culture system

Ramiro MartinezPieter MestdaghEric de Bony de Lavergne

Non-enzymatic isothermal strand displacement and amplification (NISDA) does not enable sensitive nucleic acid quantification

Thijs Van der SnicktScott AillietSimone BassiniAnouk PeymenAhmet ColakerEnrico CadoniAlejandro ValverdeElise DaemsAnnemieke MadderKarolien De Wael et al.

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.

2024

A co-culture model to study modulators of tumor immune evasion through scalable arrayed CRISPR-interference screens

Ramiro MartinezChiara FinocchiaroLouis DelhayeFien GysensJasper AnckaertWim TrypsteenMaarten VerstevenEva LionSandra Van LintKarim Vermaelen et al.

A1 Journal Article in FRONTIERS IN IMMUNOLOGY

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

Jasper VerwiltJo VandesompelePieter Mestdagh

Host lncRNAs and their interplay with the HIV-1 infection cycle

Willem van SnippenbergPieter MestdaghLinos VandekerckhoveWim Trypsteen

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

Interactome of the HIV-1 proteome and human host RNA

Tinus SchynkelWillem van SnippenbergKimberly VerniersGwendolyn M. JangNevan J. KroganPieter MestdaghLinos VandekerckhoveWim Trypsteen

A1 Journal Article in EMBO REPORTS

Selective replacement of cholesterol with cationic amphiphilic drugs enables the design of lipid nanoparticles with improved RNA delivery

Bram BogaertAliona DebisschopThomas EhouarneHannelore Van EeckhoutteJoyceline De VolderAn JacobsEline PottieRiet De RyckeAurélie CrabbéPieter Mestdagh et al.

A1 Journal Article in NANO LETTERS

The unfolded protein sensor IRE1a is essential for homeostatic dendritic cell maturation

Sophie JanssensVictor BosteelsSandra MaréchalEva ClootsLaurien Van HeddegemSimon TavernierSofie RennenClint De NolfSeraja AmstelveenJonathan Maelfait et al.

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

Direct lysis of 3D cell cultures for RT-qPCR gene expression quantification

Fien GysensLisa OstynEllen GoeteynEva BlondeelJustine NuytensOlivier De WeverEric de Bony de LavergneAurélie CrabbéPieter Mestdagh

A1 Journal Article in SCIENTIFIC REPORTS

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.

Exploring HIV-1 protein : host RNA interactions during HIV-1 infection

Tinus SchynkelLinos VandekerckhoveWim TrypsteenPieter Mestdagh

mTOR inhibition enhances delivery and activity of antisense oligonucleotides in uveal melanoma cells

Shanna DewaeleLouis DelhayeBoel De PaepeBram BogaertRamiro MartinezJasper AnckaertNurten YigitJustine NuytensRudy Van CosterSven Eyckerman et al.

A1 Journal Article in NUCLEIC ACID THERAPEUTICS

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.

Unlocking lncRNA functions through high-throughput CRISPR-interference screens in an in vitro airway inflammation model

Fien GysensPieter MestdaghKen BrackeTania Maes

2022

A 3′‐end capture sequencing method for high‐throughput targeted gene expression profiling

Eric de Bony de LavergneFien GysensNurten YigitJasper AnckaertCeline EveraertEveline Vanden EyndeKimberly VerniersWillem van SnippenbergWim TrypsteenPieter Mestdagh

A1 Journal Article in BIOTECHNOLOGY JOURNAL

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

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

IL-10 producing regulatory B cells are decreased in blood from smokers and COPD patients

Merel JacobsSven VerschraegenBihiyga SalhiJasper AnckaertPieter MestdaghGuy BrusselleKen Bracke

A1 Journal Article in RESPIRATORY RESEARCH

MiR-99b-5p, miR-380-3p, and miR-485-3p are novel chemosensitizing miRNAs in high-risk neuroblastoma

Holly HollidayJessica YangEoin DodsonIva NikolicAlvin KamiliMadeleine WheatleyNiantao DengSarah AlexandrouThomas P. DavisMaria Kavallaris et al.

A1 Journal Article in MOLECULAR THERAPY

Open problems in extracellular RNA data analysis : insights from an ERCC online workshop

Roger P. AlexanderRobert R. KitchenJuan Pablo TosarMatthew RothPieter MestdaghKlaas E. A. MaxJoel RozowskyKarolina Elzbieta Kaczor-UrbanowiczJustin ChangLeonora Balaj et al.

A1 Journal Article in FRONTIERS IN GENETICS

Orthogonal proteomics methods to unravel the HOTAIR interactome

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

Orthogonal proteomics methods to unravel the HOTAIR interactome

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

A1 Journal Article in SCIENTIFIC REPORTS

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.

Pinpointing molecular mechanisms of long non-coding RNAs : at the crossroads of biochemistry and genetics

Louis DelhayeSven EyckermanPieter Mestdagh

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 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

Unlocking the secrets of long non-coding RNAs in asthma

Fien GysensPieter MestdaghEric de Bony de LavergneTania Maes

A1 Journal Article in THORAX

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

2021

A microRNA-21–mediated SATB1/S100A9/NF-κB axis promotes chronic obstructive pulmonary disease pathogenesis

Richard Y. KimKrishna P. SunkaraKen R. BrackeAndrew G. JarnickiChantal DonovanAlan C. HsuAntonio IeniEmma L. BeckettIzabela GalvãoSara Wijnant et al.

A1 Journal Article in SCIENCE TRANSLATIONAL MEDICINE

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

Checkpoint inhibition in combination with an immunoboost of external beam radiotherapy in solid tumors (CHEERS) : study protocol for a phase 2, open-label, randomized controlled trial

Mathieu SpaasNora SundahlEva HulstaertVibeke KruseSylvie RotteyDaan De MaeseneerVeerle SurmontAnnabel MeiresonLieve BrochezDries Reynders et al.

A1 Journal Article in BMC CANCER

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

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.

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

RNAcentral 2021 : secondary structure integration, improved sequence search and new member databases

Blake A. SweeneyI Petrov, AntonCarlos E. RibasRobert D. FinnAlex BatemanMaciej SzymanskiWojciech M. KarlowskiStefan E. SeemannJan GorodkinJamie J. Cannone et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

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

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 functional annotation and exploration the SOX11 enhanceosome

Amber LouwagieBieke DecaestekerLouis DelhayeEva D'haeneEric de Bony de LavergneVolodimir OlexioukSarah VergultRogier VersteegJan KosterJohan van Nes et al.

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.

2020

Addressing challenges in transcriptome annotation and cell-type heterogeneity through integration of omics datasets and computational deconvolution

Francisco Avila CobosKatleen De PreterPieter Mestdagh

Benchmarking of cell type deconvolution pipelines for transcriptomics data

Francisco Avila CobosJosé Alquicira-HernandezJoseph E. PowellPieter MestdaghKatleen De Preter

A1 Journal Article in NATURE COMMUNICATIONS

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

Long noncoding RNA SILC1 is an upstream regulator of SOX11 in neuroblastoma

Amber LouwagieBieke DecaestekerEva D'haeneLouis DelhayeEric de Bony de LavergneChristophe Van NesteRogier VersteegSara EkBjörn MentenJan Koster et al.

mTor inhibitor GDC-0349 improves ASO induced SAMMSON knock down resulting in enhanced anti-tumor efficacy in uveal melanoma

Shanna DewaeleBoel De PaepeLouis DelhayeEric de Bony de LavergneJilke De WildeKatrien VanderheydenJasper AnckaertNurten YigitEveline Vanden EyndeFariba Nemati et al.

mTor inhibitor GDC-0349 improves ASO induced SAMMSON knock down resulting in enhanced anti-tumor efficacy in uveal melanoma

Shanna DewaeleBoel De PaepeLouis DelhayeEric de Bony de LavergneJilke De WildeKatrien VanderheydenJasper AnckaertNurten YigitEveline Vanden EyndeFariba Nemati et al.

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.

SPECS: a non-parametric method to identify tissue-specific molecular features for unbalanced sample groups

Celine EveraertPieter-Jan VoldersAnnelien MorlionOlivier ThasPieter Mestdagh

A1 Journal Article in BMC Bioinformatics

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 role of miR-155 in cigarette smoke-induced pulmonary inflammation and COPD

Elise De SmetHannelore Van EeckhoutteFrancisco Avila CobosEvy BlommeFien VerhammeSharen ProvoostSTIJN VERLEDENKoen VenkenTania MaesGuy Joos et al.

A1 Journal Article in MUCOSAL IMMUNOLOGY

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

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

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.

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

LncRNAs as novel players in neuroblastoma tumor biology

Dries RombautPieter MestdaghSteve Lefever

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

Orthogonal proteomic methods to decipher the RNA-protein interactome of the long non-coding RNA HOTAIR

Louis DelhayeEdith De BruyckerEric de Bony de LavergneDelphine De SutterPieter MestdaghSven Eyckerman

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

Plasma miRNAs as biomarkers for endometriosis

A. VanhieD. PeterseA. BeckersA. CuellarA. FassbenderC. MeulemanPieter MestdaghT. D'Hooghe

A1 Journal Article in HUMAN REPRODUCTION

RNA-directed proteomics to explore the interactome of the melanoma-specific lncRNA SAMMSON

Louis DelhayeShanna DewaeleDelphine De SutterPieter MestdaghSven Eyckerman

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 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.

2018

A comprehensive pan-cancer molecular study of gynecologic and breast cancers

Ashton C BergerAnil KorkutRupa S KanchiApurva M HegdeWalter LenoirWenbin LiuYuexin LiuHuihui FanHui ShenVisweswaran Ravikumar et al.

A1 Journal Article in CANCER CELL

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

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

Contribution of lncRNAs in establishment of HIV latency in central memory CD4 T cells

Wim TrypsteenCory WhiteAlberto BosquePieter MestdaghSteve LefeverCelsa A SpinaLinos VandekerckhoveNadejd Beliakova-Bethell

Contribution of lncRNAs in the establishment of HIV latency in CD4+ T cell models

Wim TrypsteenClarissa Van HeckeTinus SchynkelCory H WhiteChristopher WoelkAlberto BosqueCelsa SpinaSteve LefeverPieter MestdaghLinos Vandekerckhove et al.

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

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

How long noncoding RNAs enforce their will on mitochondrial activity : regulation of mitochondrial respiration, reactive oxygen species production, apoptosis, and metabolic reprogramming in cancer

Boel De PaepeSteve LefeverPieter Mestdagh

A1 Journal Article in CURRENT GENETICS

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

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.

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.

SAMMSON fosters cancer cell fitness by concertedly enhancing mitochondrial and cytosolic translation

Roberto VendraminYvessa VerheydenHideaki IshikawaLucas GoedertEmilien NicolasKritika SarafAlexandros ArmaosRiccardo Delli PontiKeichi IzumikawaPieter Mestdagh et al.

A1 Journal Article in NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

TBX2 is a neuroblastoma core regulatory circuitry component enhancing MYCN/FOXM1 reactivation of DREAM targets

Bieke DecaestekerGeertrui DeneckerChristophe Van NesteEmmy M DolmanWouter Van LoockeMoritz GartlgruberCarolina de Carvalho NunesFanny De VloedPauline DepuydtKaren Verboom et al.

A1 Journal Article in NATURE COMMUNICATIONS

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 role of microRNA-155 in cigarette smoke-induced inflammation

Elise De SmetPieter MestdaghFrancisco Avila CobosEvy BlommeFien VerhammeSharen ProvoostTania MaesGuy JoosGuy BrusselleKen Bracke

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

Zipper plot : visualizing transcriptional activity of genomic regions

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

2017

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

Celine EveraertManuel LuypaertJesper LV MaagQuek Xiu ChengMarcel E DingerJan HellemansPieter Mestdagh

A1 Journal Article in SCIENTIFIC REPORTS

Contribution of lncRNAs in establishment of HIV latency in central memory CD4 T cells

Wim TrypsteenCory WhiteAlberto BosqueCelsa SpinaSteve LefeverPieter MestdaghLinos VandekerckhoveNadejd Beliakova-Bethell

Contribution of lncRNAs in the establishment of HIV latency in central memory CD4 T cells

Wim TrypsteenCory WhiteAlberto BosqueSteve LefeverPieter MestdaghLinos VandekerckhoveChristopher Woelk

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

Discovering cancer vulnerabilities using high-throughput micro-RNA screening

Iva NikolicBenjamin ElsworthEoin DodsonSunny Z WuCathryn M GouldPieter MestdaghGlenn M MarshallLisa G HorvathKaylene J SimpsonAlexander Swarbrick

A1 Journal Article in NUCLEIC ACIDS RESEARCH

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

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 in lung tissue and bronchoalveolar lavage of cigarette smoke-exposed mice and in COPD patients : a translational approach

Griet ConickxFrancisco Avila CobosMaarten van den BergeAlen FaizWim TimensPieter S. HiemstraGuy JoosGuy BrussellePieter MestdaghKen Bracke

A1 Journal Article in SCIENTIFIC REPORTS

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

MicroRNAs as future therapeutic targets in COPD?

Ken BrackePieter Mestdagh

Editorial material

mRNA capture sequencing enabled liquid biopsy screening

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

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

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

Celine EveraertJo VandesompelePieter Mestdagh

RNAcentral : a comprehensive database of non-coding RNA sequences

Anton I PetrovSimon JE KayIoanna KalvariKevin L HoweKristian A GrayElspeth A BrufordPaul J KerseyGuy CochraneRobert D FinnAlex Bateman et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

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 long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states

Guy BarryJames A BriggsDo Won HwangSam P NaylerPatrick RJ FortunaNicky JonkhoutFabien DachetJesper LV MaagPieter MestdaghErin M Singh et al.

A1 Journal Article in SCIENTIFIC REPORTS

The role of dicer in alveolar macrophages and dendritic cells in smoke-induced inflammation

Elise De SmetPieter MestdaghS ProvoostLeen SeysGuy JoosKarim VermaelenGuy BrusselleKen Bracke

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

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

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

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.

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 expression profiling in normal B-cell subsets and Hodgkin lymphoma reveals Hodgkin and Reed-Sternberg cell-specific long noncoding RNAs

Mina Masoumeh TayariMelanie WinkleGertrud KortmanJantine SietzemaDebora de JongMartijn TerpstraPieter MestdaghFrans GM KroeseLydia VisserArjan Diepstra et al.

A1 Journal Article in AMERICAN JOURNAL OF PATHOLOGY

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

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.

Next generation sequencing of microRNAs from isogenic neuroblastoma cell lines isolated before and after treatment

Sarah Andrea RothErik KnutsenTonje FiskaaPeter UtnesSwapnil BhavsarØyvind H HaldCecilie LøkkePieter MestdaghSteinar D JohansenTrond Flægstad et al.

A1 Journal Article in CANCER LETTERS

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

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

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.

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

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.

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 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

Determining differentially expressed miRNAs and validating miRNA-target relationships using the SPRET/Ei mouse strain

Steven TimmermansFilip Van HauwermeirenLeen PuimègeLien DejagerElien Van WonterghemValerie VanhoorenPieter MestdaghClaude LibertRoosmarijn Vandenbroucke

A1 Journal Article in MAMMALIAN GENOME

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

Identification of differentially expressed microRNAs in neutrophilic asthma

Tania MaesKatleen De PreterFN SchleichM HenketKen BrackeLies LahoussePieter MestdaghGuy JoosGuy BrusselleR Louis

Identification of miRNAs contributing to neuroblastoma chemoresistance

Duncan AyersPieter MestdaghTom Van MaerkenJo Vandesompele

A1 Journal Article in COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL

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

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-135a inhibits cancer stem cell-driven medulloblastoma development by directly repressing Arhgef6 expression

Katayoun HemmesiMario Leonardo SquadritoPieter MestdaghValentina ContiManuela CominelliIgnazio S PirasLucia Sergi SergiSara PiccininRoberta MaestroPietro L Poliani et al.

A1 Journal Article in STEM CELLS

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-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.

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

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

Fjoralba ZekaPieter MestdaghJo Vandesompele

Bookchapter in Small non-coding RNAs : methods and protocols

2014

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.

Early targets of miR-34a in neuroblastoma

Pasqualino De AntonellisMarianeve CarotenutoJonathan VandenbusscheGennaro De VitaVeronica FerrucciChiara MedagliaIolanda BoffaAlessandra GalieroSarah Di SommaDaniela Magliulo et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Ectopic microRNA-150-5p transcription sensitizes glucocorticoid therapy response in MM1S multiple myeloma cells but fails to overcome hormone therapy resistance in MM1R cells

Ajay PalaganiKen Op de BeeckStefan NaulaertsJolien DiddensChandra Sekhar ChirumamillaGuy Van CampKris LaukensKaren HeyninckSarah GerloPieter Mestdagh et al.

A1 Journal Article in PLOS ONE

Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study

Pieter MestdaghNicole HartmannLukas BaeriswyDitte AndreasenNathalie BernardCaifu ChenDavid CheoPetula D'AndradeMike DeMayoLucas Dennis et al.

A1 Journal Article in NATURE METHODS

LncRNA profiling in T-cell acute lymphoblastic leukemia predicts a functional connection between lncRNAs and the major T-ALL genetic subgroups

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

Lung tumours reprogram pulmonary dendritic cell immunogenicity at the microRNA level

Lotte PyfferoenPieter MestdaghKarl VergoteNancy De CabooterJo VandesompeleBart LambrechtKarim Vermaelen

A1 Journal Article in INTERNATIONAL JOURNAL OF CANCER

MicroRNA-128-3p is a novel oncomiR targeting PHF6 in T-cell acute lymphoblastic leukemia

Evelien MetsGert Van PeerJoni Van der MeulenMichael BoiceTom TaghonSteven GoossensPieter MestdaghYves BenoitBarbara De MoerlooseNadine Van Roy et al.

A1 Journal Article in HAEMATOLOGICA

miRBase Tracker : keeping track of microRNA annotation changes

Gert Van PeerSteve LefeverJasper AnckaertAnneleen BeckersAli RihaniAlan Van GoethemPieter-Jan VoldersFjoralba ZekaMaté OngenaertPieter Mestdagh et al.

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

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.

Robust selection of cancer survival signatures from high-throughput genomic data using two-fold subsampling

Sangkyun LeeJörg RahnenführerMichel LangKatleen De PreterPieter MestdaghJan KosterRogier VersteegRaymond L StallingsLuigi VaresioShahab Asgharzadeh et al.

A1 Journal Article in PLOS ONE

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

Some cautionary notes on the petite 'Holy Grail' of molecular diagnostics

Jo VandesompelePieter Mestdagh

Editorial material

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

Jan Van DeunPieter MestdaghRaija SormunenLotte PyfferoenKarim VermaelenVeronique CocquytJo VandesompeleMarc BrackeOlivier De WeverAn Hendrix

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

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

Valerie PedeAns RomboutJOLIEN VERMEIREEvelien NaessensPieter MestdaghNore RobberechtHanne VanderstraetenNadine Van RoyJo VandesompeleFranki Speleman et al.

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 activity of miR-125b and miR-93 during murine neural stem cell differentiation in vitro and in the subventricular zone neurogenic niche

Annalisa LattanziBernhard GentnerDaniela CornoTiziano Di TomasoPieter MestdaghFranki SpelemanLuigi NaldiniAngela Gritt

A1 Journal Article in PLOS ONE

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

Ali RihaniTom Van MaerkenFilip PattynGert Van PeerAnneleen BeckersSara De BrouwerCandy KumpsEvelien MetsJoni Van der MeulenPieter Rondou et al.

A1 Journal Article in PLOS ONE

Expanding the TLX1 regulate 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.

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

Candy KumpsAnnelies FieuwPieter MestdaghBjörn MentenSteve LefeverFilip PattynSara De BrouwerTom SanteJohannes Hubertus SchulteAlexander Schramm et al.

A1 Journal Article in PLOS ONE

High-throughput lncRNA expression profiling identifies candidate cancer lncRNAs

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

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

Pieter-Jan VoldersKenny HelsensXiaowei WangBjörn MentenLennart MartensKris GevaertJo VandesompelePieter Mestdagh

A1 Journal Article in NUCLEIC ACIDS RESEARCH

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

Pieter-Jan VoldersKenny HelsensXiaowei WangLennart MartensKris GevaertJo VandesompelePieter Mestdagh

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

Evelien MetsJoni Van der MeulenGert Van PeerMichael BoicePieter MestdaghTom TaghonDavid AvranBarbara De MoerlooseYves BenoitBruce Poppe et al.

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

Hetty HelsmoortelTim LammensPieter MestdaghNadine Van RoyAnne UyttebroeckAlina FersterYves BenoitJo VandesompeleFranki SpelemanPieter Van Vlierberghe et al.

miRNAs distinguish children with myelodysplastic syndrome from healthy donors

Hetty HelsmoortelTim LammensPieter MestdaghNadine Van RoyAnne UyttebroeckAlina FersterYves BenoitJo VandesompeleFranki SpelemanPieter Van Vlierberghe et al.

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

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

2012

Accurate RT-qPCR gene expression analysis on cell culture lysates

Gert Van PeerPieter MestdaghJo Vandesompele

A1 Journal Article in SCIENTIFIC REPORTS

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

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

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

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

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

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

MiR-137 is epigenetically silenced in MYCN amplified neuroblastoma and targets the polycomb repressive complex 2 (PRC2) component EZH2

Anneleen BeckersMaté OngenaertAnneleen DecockCandy KumpsFilip PattynPieter MestdaghJohannes H. SchulteFranki SpelemanKatleen De Preter

MiR-137 is epigenetically silenced in MYCN amplified neuroblastomas and targets the polycomb repressive complex 2 (PRC2) component EZH2

Anneleen BeckersMaté OngenaertAnneleen DecockCandy KumpsFilip Pattynthe Neuroblastoma Research Consortium (NRC)Pieter MestdaghJohannes H SchulteFranki SpelemanKatleen De Preter

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

MYCN directly regulates long non-coding RNA expression in neuroblastoma

Pieter MestdaghJohannes SchulteFilip PattynFrank WestermannGenevieve LaureysFranki SpelemanJo Vandesompele

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

A genome-wide search for promoters that respond to increased MYCN reveals both new oncogenic and tumor suppressor microRNAs associated with aggressive neuroblastoma

Jason M ShohetRajib GhoshCristian CoarfaAndrew LudwigAshley L BenhamZaoWen ChenDanielle M PattersonEveline BarbieriPieter MestdaghDenae N Sikorski et al.

A1 Journal Article in CANCER RESEARCH

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

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

IL-1 beta potently stabilizes IL-6 mRNA in human astrocytes

Anneleen SpoorenPieter MestdaghPieter RondouKrzysztof KolmusGuy HaegemanSarah Gerlo

A1 Journal Article in BIOCHEMICAL PHARMACOLOGY

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

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.

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 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

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.

Microrna expression in pediatric precursor-B acute lymphoblastic leukemia: biology, classification and prognosis

Tim LammensBarbara De MoerlooseJonas Van BaelenJoni Van der MeulenPieter MestdaghBruno VerhasseltJan PhilippéFranki SpelemanYves Benoit

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

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

Predicting outcomes for children with neuroblastoma

Joëlle VermeulenKatleen De PreterPieter MestdaghGenevieve LaureysFranki SpelemanJo Vandesompele

A1 Journal Article in DISCOVERY MEDICINE

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.

The neuroblastoma miRNA map, prioritization and functional evaluation of candidate miRNAs

Pieter Mestdagh

2009

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

ALK Mutation Analysis in Patients of the German Neuroblastoma Study

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

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

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

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.)

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.

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.

Prognostic role and functional analyses of miRNA expression in neuroblastoma

S SchlierfPieter MestdaghT ThorKatleen De PreterM BaumannA EggertJo VandesompeleA SchrammJH Schulte

Stem-loop RT-qPCR miRNA profling: about single cells, normalization and biomarkers

Pieter Mestdagh

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 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

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

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

Pieter MestdaghFilip PattynKatleen De PreterJoëlle VermeulenAnne De PaepeFranki 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

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

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

Unmasking of epigenetically silenced microRNAs in neuroblastoma

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

2007

MicroRNA profiling of EVI1 deregulated myeloid leukemia

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