Research Explorer

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Researcher

Pieter-Jan Volders

70 Results

2022

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

Large-scale benchmarking of circular RNA detection tools

Marieke VrommanJo VandesompelePieter-Jan Volders

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

Sensitive and specific spectral library searching with CompOmics Spectral library Searching tool and Percolator

Genet Abay ShiferawRalf GabrielsRobbin BouwmeesterTim Van Den BosscheElien VandermarliereLennart MartensPieter-Jan Volders

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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.

2021

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

Marieke VrommanJo VandesompelePieter-Jan Volders

A1 Journal Article in BRIEFINGS IN BIOINFORMATICS

Large-scale benchmarking of circular RNA detection tools

Marieke VrommanJo VandesompelePieter-Jan Volders

MEIS2 is an adrenergic core regulatory transcription factor involved in early initiation of TH-MYCN-driven neuroblastoma formation

Jolien De WynMark W. ZimmermanNina Weichert-LeaheyCarolina de Carvalho NunesBelamy B. CheungBrian J. AbrahamAnneleen BeckersPieter-Jan VoldersBieke DecaestekerDaniel R. Carter et al.

A1 Journal Article in CANCERS

Personalized proteome : comparing proteogenomics and open variant search approaches for single amino acid variant detection

Renee SalzRobbin BouwmeesterRalf GabrielsSven DegroeveLennart MartensPieter-Jan VoldersPeter A.C. ’t Hoen

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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

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.

The RNA landscape of the human placenta in health and disease

Sungsam GongFrancesca GaccioliJustyna DopieralaUlla SovioEmma CookPieter-Jan VoldersLennart MartensPaul D. W. KirkSylvia RichardsonGordon C. S. Smith et al.

A1 Journal Article in NATURE COMMUNICATIONS

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

2020

A novel TLX1-driven T-ALL zebrafish model : comparative genomic analysis with other leukemia models

Siebe LoontiensSuzanne VanhauwaertLisa DepestelGivani DewynWouter Van LoockeFinola E. MooreElaine G. GarciaLance BatchelorChiara BorgaBarbara Squiban et al.

A1 Journal Article in LEUKEMIA

COSS : a fast and user-friendly tool for spectral library searching

Genet Abay ShiferawElien VandermarliereNiels HulstaertRalf GabrielsLennart MartensPieter-Jan Volders

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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

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

2019

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue-specificity

Kaia MattioliPieter-Jan VoldersChiara GerhardingerJames C LeePhilipp G MaassMarta MeléJohn L Rinn

A1 Journal Article in GENOME RESEARCH

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

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

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.

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

CRISPR/Cas9-mediated genome editing in naïve human embryonic stem cells

Eva JacobsSharat WarrierPieter-Jan VoldersEva D'haeneEva VanlombergenLies VantommeMargot Van der JeughtBjörn HeindryckxBjörn MentenSarah Vergult

CRISPR/Cas9-mediated genome editing in naïve human embryonic stem cells

Eva JacobsSharat WarrierPieter-Jan VoldersEva D'haeneEva VanlombergenLies VantommeMargot Van der JeughtBjörn HeindryckxBjörn MentenSarah Vergult

Expanding the use of spectral libraries in proteomics

Eric W DeutschYasset Perez-RiverolRobert J ChalkleyMathias WilhelmStephen TateTimo SachsenbergMathias WalzerLukas KällBernard DelangheSebastian Böcker et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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

Zipper plot : visualizing transcriptional activity of genomic regions

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

2017

CRISPR/Cas9-mediated genome editing in naïve human embryonic stem cells

Eva JacobsSharat WarrierPieter-Jan VoldersEva D'haeneEva Van LombergenLies VantommeMargot Van der JeughtBjörn HeindryckxBjörn MentenSarah Vergult

A1 Journal Article in SCIENTIFIC REPORTS

Long non-coding RNAs in cutaneous melanoma : clinical perspectives

Eva HulstaertLieve BrochezPieter-Jan VoldersJo VandesompelePieter Mestdagh

A1 Journal Article in ONCOTARGET

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

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

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

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

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

2016

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 lncRNAs involved in neuronal differentiation and intellectual disability

Eva D'haeneEva JacobsPieter-Jan VoldersBjörn MentenSarah Vergult

Identification of long non-coding RNAs in neuronal development and intellectual disability

Eva D'haeneEva JacobsPieter-Jan VoldersBjörn MentenSarah Vergult

Identification of long non-coding RNAs involved in neuronal development and intellectual disability

Eva D'haeneEva JacobsPieter-Jan VoldersTim De MeyerBjörn MentenSarah Vergult

Identification of long non-coding RNAs involved in neuronal development and intellectual disability

Eva D'haeneEva JacobsPieter-Jan VoldersTim De MeyerBjörn MentenSarah Vergult

A1 Journal Article in SCIENTIFIC REPORTS

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 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

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.

The genomic region encompassing the overlapping SOX11 and Lnc-SOX11-1:1 loci exhibits a complex DNA copy number and mRNA expression pattern

Bieke DecaestekerSara De BrouwerRobrecht CannoodtDries RombautWouter Van LoockeAnnelies FieuwFanny De VloedPieter-Jan VoldersBjörn MentenRogier Versteeg et al.

2015

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

Pieter-Jan VoldersKenneth VerheggenGerben MenschaertKlaas VandepoeleLennart MartensJo VandesompelePieter Mestdagh

A1 Journal Article in NUCLEIC ACIDS RESEARCH

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

Pieter-Jan VoldersJo VandesompeleKris Gevaert

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

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.

2014

Integrative analysis of the NOTCH1 regulatory network identifies key downstream lncRNAs in acute T-cell lymphoblastic leukemia and normal T-cell development

Annelynn WallaertKaat DurinckPieter RondouInge Van de WalleWouter Van LoockePieter-Jan VoldersMaté OngenaertNadine Van RoyBruce PoppeYves Benoit et al.

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.

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

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

Annelynn WallaertKaat DurinckPieter RondouInge Van de WalleWouter VanloockePieter-Jan VoldersSuzanne VanhauwaertEllen GeerdensMaté OngenaertNadine Van Roy et al.

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 first lncRNA landscape of major genetic T-ALL subsets and guilt-by-association analysis for ETP-ALL specific lncRNAs

Annelynn WallaertKaat DurinckWouter Van LoockePieter-Jan VoldersInge Van de WalleYves BenoitBruce PoppeJo VandesompeleTom TaghonJean Soulier et al.

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.

ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation

Tom SanteSarah VergultPieter-Jan VoldersWigard P KloostermanGeert TrooskensKatleen De PreterAnnelies DheedeneFranki SpelemanTim De MeyerBjörn Menten

A1 Journal Article in PLOS ONE

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

2013

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.

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

2012

LNCipedia: a novel databse for annotated lncRNA sequences and structures

Pieter-Jan VoldersPieter MestdaghJo Vandesompele

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

Pieter-Jan VoldersPieter MestdaghBjörn MentenJo Vandesompele

Lncipedia: a novel database for annotated lncRNA sequences and structures

Pieter-Jan VoldersKenny HelsensXiaowei WangLennart MartensKris GevaertJo VandesompelePieter Mestdagh

2011

PROKAR‐SEQ: an analysis and visualization framework for next‐generation sequencing based quantification of prokaryotic communities

Joachim De SchrijverPieter-Jan VoldersFrederiek-Maarten KerckhofDagmar ObbelsElie VerleyenWim VyvermanTim De MeyerWim Van Criekinge