Research Explorer

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Researcher

Wim Van Criekinge

Publications & Research Data

Awards & Distinctions

291 Results

2026

Comprehensive analysis of the melanoma DNA methylome identifies LY75 methylation as an independent marker predicting poor clinical outcome

Karin van den HurkKim LommenLouis CoussementDanique van den KerkhofMara BeckersGeert TrooskensLeander Van NesteMarloes OosterhofRemco van DoornJoost J. van den Oord et al.

A1 Journal Article in JOURNAL OF INVESTIGATIVE DERMATOLOGY

Epigenetic age deceleration reflects exercise-induced cardiorespiratory fitness improvements

Menno Van DammeSanne StegenBram SteenwinckelHelene SchroéGustavo A. Reyes del PasoMatias M. PulopulosRudi De RaedtMarie-Anne VanderhasseltWim DeraveFemke Ongenae et al.

A1 Journal Article in GEROSCIENCE

2025

Accelerating neoantigen discovery : a high-throughput approach to immunogenic target identification

Lena PfitzerGitta BoonsLien LybaertWim Van CriekingeCedric BogaertBruno Fant

A1 Journal Article in VACCINES

Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants : a randomized controlled trial

Lishi DengSteff TaelmanMatthew R. OlmLaéticia Céline ToeEva BaliniWend-Benedo Lionel Olivier OuedraogoYuri Bastos MoreiraAlemayehu Argaw AlemayehuKokeb Tesfamariam HadushErica D. Sonnenburg et al.

A1 Journal Article in NATURE COMMUNICATIONS

Population-level allelic dispersion modeling by maelstRom yields genome-wide maps of allele-specific dysregulation during early carcinogenesis

Cedric StroobandtLouis CoussementTine GoovaertsFemke De GraeveJeroen GalleWim Van CriekingeTim De Meyer

A1 Journal Article in GIGASCIENCE

The molecular causes and clinical consequences of dysregulation at the HM13 locus in cancer

Floris VoorthuijzenTim De MeyerWim Van Criekinge

Unravelling the hidden side of laundry : malodour, microbiome and pathogenome

Celia Diez LopezFlorence Van HerreweghenBritta De PessemierYorick MinneboSteff TaelmanKara JudgeKaren RansleyChristopher HammondMatthew BatsonMichiel Stock et al.

A1 Journal Article in BMC BIOLOGY

2024

A genomic urine assay for surveillance of patients with bladder cancer treated with radiotherapy

Florus C. de JongIris G. IfléAngelique C. van der MadeDenise KooperJoep J. de JongMartine FranckenaTahlita C.M. ZuiverloonWim Van CriekingeLuca IncrocciEllen C. Zwarthoff et al.

A1 Journal Article in EUROPEAN UROLOGY OPEN SCIENCE

Beyond correlations : a causal perspective on host-microbiome interactions

Steff TaelmanWim Van CriekingeMichiel StockLiesbeth Ceelen

Development of a novel assay to characterize the HIV-1 reservoir using long-read sequencing

Laurens LambrechtsLinos VandekerckhoveWim Van Criekinge

Hyperdimensional computing : a fast, robust, and interpretable paradigm for biological data

Michiel StockWim Van CriekingeDimitri BoeckaertsSteff TaelmanMaxime Van HaeverbekePieter DewulfBernard De Baets

A1 Journal Article in PLOS COMPUTATIONAL BIOLOGY

Loss-of-imprinting of HM13 leads to poor prognosis in clear cell renal cell carcinoma

Floris VoorthuijzenCedric StroobandtWim Van CriekingeTine GoovaertsTim De Meyer

A1 Journal Article in BIOMOLECULES

Maternal fortified balanced energy-protein supplementation increases diversity of the maternal gut microbiome and the capacity of carbohydrate uptake in infant gut

Lishi DengSteff TaelmanMatthew R OlmLaéticia Céline ToeEva BaliniWend-Benedo Lionel Olivier OuedraogoYuri Bastos MoreiraAlemayehu Argaw AlemayehuKokeb Tesfamariam HadushErica D Sonnenburg et al.

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

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

Quantitative transcriptomic and epigenomic data analysis : a primer

Louis CoussementWim Van CriekingeTim De Meyer

A2 Journal Article in BIOINFORMATICS ADVANCES

The role of Helicobacter suis, Fusobacterium gastrosuis, and the pars oesophageal microbiota in gastric ulceration in slaughter pigs receiving meal or pelleted feed

Emily TaillieuSteff TaelmanSofie De BruyckereEvy GoossensIlias ChantziarasChristophe Van SteenkistePeter YdeSteven HanssensDimitri De MeyerWim Van Criekinge et al.

A1 Journal Article in VETERINARY RESEARCH

2023

A bioinformatics-driven exploration of the evolutionary (dis)advantages of epigenetics

Louis CoussementTim De MeyerWim Van Criekinge

A urine-based genomic assay improves risk stratification for patients with high-risk hematuria stratified according to the American Urological Association guidelines

Joep J. de JongOlga M. PijpersKim. E.M. van KesselJoost. L. BoormansWim Van CriekingeEllen C. ZwarthoffYair Lotan

A1 Journal Article in EUROPEAN UROLOGY ONCOLOGY

Challenges in neoantigen-directed therapeutics

Lien LybaertSteve LefeverBruno FantEvelien SmitsBruno De GeestKarine BreckpotLuc DirixSteven A. FeldmanWim Van CriekingeKris Thielemans et al.

A1 Journal Article in CANCER CELL

Cost-effectiveness of an urinary biomarker panel in combination with MRI for prostate cancer diagnosis

Tim M. GoversMatthew J ResnickArdeshir R. RastinehadLaura CabaJack GroskopfWim Van Criekinge

A1 Journal Article in WORLD JOURNAL OF UROLOGY

HIV-PULSE : a long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization

Laurens LambrechtsNoah BonineRita VerstraetenMarion PardonsYtse NoppeSofie RutsaertFilip Van NieuwerburghWim Van CriekingeBasiel ColeLinos Vandekerckhove

A1 Journal Article in NUCLEIC ACIDS RESEARCH

HIV-PULSE : a long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization

Laurens LambrechtsNoah BonineRita VerstraetenMarion PardonsYtse NoppeSofie RutsaertFilip Van NieuwerburghWim Van CriekingeBasiel ColeLinos Vandekerckhove

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

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

Variational autoencoders to predict DNA-methylation age and provide biological insights in age-related health and disease

Sandra SteyaertAdriaan VerhelleWim Van Criekinge

2022

A genomic urine assay to detect urinary tract recurrences in patients with bladder cancer treated with radiotherapy

Florus C. de JongIris I. IfleDenise KooperAngelique C. J. van der MadeJoep J. De JongTahlita C. M. ZuiverloonLuca IncrocciWim Van CriekingeMartine FranckenaJoost L. Boormans et al.

A urine-based molecular assay refines the risk stratification of the recent American Urological Association guideline on hematuria

Joep de JongOlga PijpersKim van KesselJoost BoormansWim Van CriekingeEllen ZwarthoffYair Lotan

Copy number gain and loss-of-imprinting lead to HM13 intron retention across multiple cancer types

Floris VoorthuijzenTine GoovaertsCedric StroobandtJeroen GalleWim Van CriekingeTim De Meyer

Exploring PhaLP, an open source portal for Phage Lytic Proteins, to engineer modular enzybiotics against vancomycin-resistant Enterococcus faecalis

Bjorn CrielWim Van CriekingeYves Briers

Exploring PhaLP, an open source portal for Phage Lytic Proteins, to engineer modular enzybiotics against vancomycin-resistant Enterococcus faecalis

Bjorn CrielWim Van CriekingeYves Briers

Haplotyping pharmacogenes using TLA combined with Illumina or Nanopore sequencing

Laurentijn TillemanKaat RubbenWim Van CriekingeDieter DeforceFilip Van Nieuwerburgh

A1 Journal Article in SCIENTIFIC REPORTS

Identification and characterization of eukaryotic small open reading frames and microproteins

Marlies PeetersGerben MenschaertLiesbet TemmermanWim Van Criekinge

Machine learning-guided engineering of modular enzybiotics to target vancomycin-resistant Enterococcus faecalis infections of the urinary tract

Bjorn CrielWim Van CriekingeYves Briers

Technical considerations in PCR-based assay design for diagnostic DNA methylation cancer biomarkers

Maartje MassenKim LommenKim A. D. WoutersJohan VandersmissenWim Van CriekingeJames G. HermanVeerle MelotteLeo J. SchoutenManon van EngelandKim M. Smits

A1 Journal Article in CLINICAL EPIGENETICS

Unraveling the molecular framework of de novo shoot organogenesis in Arabidopsis thaliana

Robin LardonDanny GeelenWim Van Criekinge

2021

Clinical use of the SelectMDx urinary-biomarker test with or without mpMRI in prostate cancer diagnosis : a prospective, multicenter study in biopsy-naive men

Rianne J. HendriksMarloes M. G. van der LeestBas IsraelGerjon HanninkAnglita YantiSetiastiErik B. CornelChristina A. Hulsbergen-van de KaaO. Sjoerd KlaverJ. P. Michiel SedelaarWim Van Criekinge et al.

A1 Journal Article in PROSTATE CANCER AND PROSTATIC DISEASES

DNA methylation regulates transcription factor-specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon

Jolien DiddensLouis CoussementCarolina Frankl-VilchesGaurav MajumdarSandra SteyaertSita M. Ter HaarJeroen GalleEllen De MeesterSarah De KeulenaerWim Van Criekinge et al.

A1 Journal Article in FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY

Evaluation of the new American Urological Association guidelines risk classification for hematuria

Solomon L. WolduCasey K. NgRonald K. LooJeff M. SlezakSteven J. JacobsenWei Shen TanJohn D. KellyTony LoughDavid DarlingKim E. M. van Kessel et al.

A1 Journal Article in JOURNAL OF UROLOGY

PhaLP : a database for the study of phage lytic proteins and their evolution

Bjorn CrielSteff TaelmanWim Van CriekingeMichiel StockYves Briers

A1 Journal Article in VIRUSES-BASEL

Single cell epigenetic visualization assay

Sam KintWim Van CriekingeLinos VandekerckhoveWinnok H De VosKarol BomsztykDiane S KrauseOleg Denisenko

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Spectral prediction features as a solution for the search space size problem in proteogenomics

Steven VerbruggenSiegfried GessulatRalf GabrielsAnna MatsarokiHendrik Van de VoordeBernhard KusterSven DegroeveLennart MartensWim Van CriekingeMathias Wilhelm et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

2020

A urine assay to triage patients with hematuria for cystoscopy

Kim E. M. van KesselJoep J. de JongAngelique C. J. Ziel-van der MadeHossain RoshaniStefan M. HaenselJosien H. WolterbeekEgbert R. BoeveEric H. G. M. OomensNiels J. van CasterenManuel Krispin et al.

A urine based genomic assay to triage patients with hematuria for cystoscopy

Kim E. M. van KesselJoep J. de JongAngelique C. J. Ziel-van der MadeHossain RoshaniStefan M. HaenselJosien H. WolterbeekEgbert R. BoeveEric H. G. M. OomensNiels J. van CasterenManuel Krispin et al.

A1 Journal Article in JOURNAL OF UROLOGY

Exploring allele-specific expression mechanisms in health and disease

Tine GoovaertsTim De MeyerWim Van Criekinge

Exploring methods to measure DNA methylation in the context of HIV-1

Sam KintWim Van CriekingeLinos VandekerckhoveWim Trypsteen

The elusive source of HIV-1 rebound after treatment interruption

Laurens LambrechtsBasiel ColeMarie-Angélique De ScheerderZoe BoyerYtse NoppeKatie FisherJohn-Sebastian EdenWim Van CriekingeLisa FrenkelSarah Palmer et al.

The potential influence of human Y-chromosome haplogroup on COVID-19 prevalence and mortality

Joris DelangheMarc De BuyzereSander De BruyneWim Van CriekingeMarijn Speeckaert

A1 Journal Article in ANNALS OF ONCOLOGY

The proteogenomic hunt for new proteoforms using ribosome profiling

Steven VerbruggenWim Van CriekingeGerben MenschaertPetra Van Damme

The SelectMDx urinary-biomarker test : role in the detection of high-grade prostate cancer and in combination with multi-parametric magnetic resonance imaging in a contemporary prospective cohort of biopsy-naive men

Rianne HendriksMarloes van der LeestBas IsraelGerjon HanninkAnglita Yanti SetiastiErik CornelChristina Hulsbergen-van de KaaSjoerd KlaverMichiel SedelaarWim Van Criekinge et al.

Underestimated effect of intragenic HIV-1 DNA methylation on viral transcription in infected individuals

Sam KintWim TrypsteenWard De SpiegelaereEva MalatinkováSabine Kinloch-de LoesTim De MeyerWim Van CriekingeLinos Vandekerckhove

A1 Journal Article in CLINICAL EPIGENETICS

Validation of a 2-gene mRNA urine test for the detection of >= GG2 prostate cancer in an opportunistic screening population

Jose Rubio-BrionesAngel Borque-FernandoLuis M. EstebanJuan M. MascarosMiguel Ramirez-BackhausJuan CasanovaArgimiro ColladoCarmen MirAlvaro Gomez-FerrerAugusto Wong et al.

A1 Journal Article in PROSTATE

2019

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

Volodimir OlexioukWim Van CriekingeGerben Menschaert

Clinical utility of ConfirmMDx for prostate cancer in a community urology practice

Paul YonoverSandra SteyaertJustin CohenCeleste RuizKarolina GrafczynskaElizabeth GarciaJessica DeHartMichael BrawerJack GroskopfWim Van Criekinge

Clinical utility study of confirms mdx for prostate cancer in a community urology practice

Paul YonoverSandra SteyaertJustin J. CohenCeleste RuizKarolina GrafczynskaElizabeth GarciaJessica DeHartMichael BrawerJack GroskopfWim Van Criekinge

Clinically significant prostate cancer diagnosed using a urinary molecular biomarker-based risk score : two case reports

Pieter MinneeDaphne HesselsJack A SchalkenWim Van Criekinge

A1 Journal Article in BMC UROLOGY

Cost-effectiveness of a two-gene urine biomarker assay in MRI strategies for the initial detection of prostate cancer

Tim GoversMatthew J. ResnickGeert TrooskensWim Van CriekingeJack A. Schalken

Cost-effectiveness of SelectMDx for prostate cancer in four European countries : a comparative modeling study

Tim M. GoversDaphne HesselsVirginie Vlaeminck-GuillemBernd J. Schmitz-DraegerChristian G. StiefClaudio Martinez-BallesterosMatteo FerroAngel Borque-FernandoJose Rubio-BrionesJ. P. Michiel Sedelaarll et al.

A1 Journal Article in PROSTATE CANCER AND PROSTATIC DISEASES

Evaluation of an epigenetic assay for predicting repeat prostate biopsy outcome in African American men

Robert L, Jr WaterhouseLeander Van NesteKelvin A MosesCarlton BarnswellJonathan L SilbersteinMark JalkutRonald TutroneJames SyloraRonald AngladeMyron Murdock et al.

A1 Journal Article in UROLOGY

MEXPRESS update 2019

Alexander KochJana JeschkeWim Van CriekingeManon van EngelandTim De Meyer

A1 Journal Article in NUCLEIC ACIDS RESEARCH

MGMT promoter methylation cutoff with safety margin for selecting glioblastoma patients into trials omitting temozolomide : a pooled analysis of four clinical trials

Monika E HegiEls GenbruggeThierry GorliaRoger StuppMark R GilbertOlivier L ChinotL Burt NaborsGreg JonesWim Van CriekingeJosef Straub et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

Multicenter optimization and validation of a 2-gene mRNA urine test for detection of clinically significant prostate cancer before initial prostate biopsy

Alexander HaeseGeert TrooskensSandra SteyaertDaphne HesselsMichael BrawerVirginie Vlaeminck-GuillemAlain RuffionDerya TilkiJack SchalkenJack Groskopf et al.

A1 Journal Article in JOURNAL OF UROLOGY

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

Steven VerbruggenElvis NdahWim Van CriekingeSiegfried GessulatBernhard KusterMathias WilhelmGerben MenschaertPetra Van Damme

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Urinary molecular biomarker test impacts prostate biopsy decision making in clinical practice

Neal ShoreJason HafronTimothy LangfordMarshall SteinJessica DeHartMichael BrawerDaphne HesselsJack SchalkenWim Van CriekingeJack Groskopf et al.

A2 Journal Article in UROLOGY PRACTICE

Validation of a two-gene mRNA urine test for detection of high-grade prostate cancer in German men

Derya TilkiDaphne HesselsGeert TrooskensSusan MuldersMichael BrawerWim Van CriekingeJack GroskopfAlexander Haese

2018

A comprehensive overview of genomic imprinting in breast and its deregulation in cancer

Tine GoovaertsSandra SteyaertChari VandenbusscheJeroen GalleOlivier ThasWim Van CriekingeTim De Meyer

A1 Journal Article in NATURE COMMUNICATIONS

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

Volodimir OlexioukWim Van CriekingeGerben Menschaert

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Analysis of DNA methylation in cancer : location revisited

Alexander KochSophie C JoostenZheng FengTim C de RuijterMuriel X DrahtVeerle MelotteKim M SmitsJurgen VeeckJames G HermanLeander Van Neste et al.

A1 Journal Article in NATURE REVIEWS CLINICAL ONCOLOGY

Cost-effectiveness of SelectMDX for prostate cancer in four European countries : a modelling study

Daphne HesselsTim GoversWim Van CriekingeVirginie Vlaeminck-GuillemBernd Schmitz-dragerChristian StiefJack Schalken

Epigenetic markers in circulating cell-free DNA as prognostic markers for survival of castration-resistant prostate cancer patients

Rianne J HendriksSiebren DijkstraFrank P SmitJohan VandersmissenHendrik Van de VoordePeter FA MuldersInge M van OortWim Van CriekingeJack A Schalken

A1 Journal Article in PROSTATE

Evaluation of bisulfite kits for DNA methylation profiling in terms of DNA fragmentation and DNA recovery using digital PCR

Sam KintWard De SpiegelaereJonas De KeselLinos VandekerckhoveWim Van Criekinge

A1 Journal Article in PLOS ONE

Evaluation of two urinary RNA biomarker tests with an epigenetic DNA assay for the identification of men with high-grade prostate cancer

Geert TrooskensAnglita YantisetiastiRianne HendriksInge Van OortPeter MuldersChristina Hulsbergen-van de KaaWim Van CriekingeJack Schalken

Exploratory analysis of the human breast DNA methylation profile upon soymilk exposure

Louis CoussementSelin BolcaWim Van CriekingeGeert TrooskensKlaas MensaertKatrien PoelsNathalie RochePhillip BlondeelLode GodderisHerman Depypere et al.

A1 Journal Article in SCIENTIFIC REPORTS

Integrated transcriptomic and epigenomic analysis of ovarian cancer reveals epigenetically silenced GULP1

Leonel MaldonadoMariana BraitEvgeny IzumchenkoShahnaz BegumAditi ChatterjeeTanusree SenMyriam LoyoAlvaro BarbosaMaria Luana PoetaEugene Makarev et al.

A1 Journal Article in CANCER LETTERS

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

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

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

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

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

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

Prospective validation of a diagnostic urine test for bladder cancer : the Hematuria study

Kim van KesselJoep de JongAngelique Ziel-van der MadeHossain RoshaniStefan HaenselJosien van Montfrans-WolterbeekEgbert BoeveEric OomensNiels van CasterenJoost Boormans et al.

Stable oxidative cytosine modifications accumulate in cardiac mesenchymal cells from type2 diabetes patients : rescue by α-ketoglutarate and TET-TDG functional reactivation

Francesco SpallottaChiara CencioniSandra AtlanteDavide GarellaMattia CoccoMattia MoriRaffaella MastrocolaCarsten KuenneStefan GuentherSimona Nanni et al.

A1 Journal Article in CIRCULATION RESEARCH

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

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

2017

A four-gene promoter methylation marker panel consisting of GREM1, NEURL, LAD1, and NEFH predicts survival of clear cell renal cell cancer patients

Iris JH van VlodropSophie C JoostenTim De MeyerKim M SmitsLeander Van NesteVeerle MelotteMarcella MLL BaldewijnsLeo J SchoutenPiet A van den BrandtJana Jeschke et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

A urinary biomarker-based risk score correlates with multiparametric MRI for prostate cancer detection

Rianne J HendriksMarloes MG van der LeestSiebren DijkstraJelle O BarentszWim Van CriekingeChristina A Hulsbergen-van de KaaJack A SchalkenPeter FA MuldersInge M van Oort

A1 Journal Article in PROSTATE

Clinical performance of an epigenetic assay to identify occult high-grade prostate cancer in African American men

Leander Van NesteCarlton BarnswellMark JalkutRonald TutroneJames SyloraRonald AngladeMyron MurdockKelvin A MosesZvi ShiffmanTodd Vandenberg et al.

Cost-effectiveness of a new urinary biomarker-based risk score compared to standard of care in prostate cancer diagnostics : a decision analytical model

Siebren DijkstraTim M GoversRianne J HendriksJack A SchalkenWim Van CriekingeLeander Van NesteJanneke PC GruttersJohn P Michiel SedelaarInge M van Oort

A1 Journal Article in BJU INTERNATIONAL

Decoy receptor 1 (DCR1) promoter hypermethylation and response to irinotecan in metastatic colorectal cancer

Linda JW BoschGeert TrooskensPetur SnaebjornssonVeerle MH CoupéSandra MongeraJosien C HaanSusan D RichmanMiriam KoopmanJolien TolTim De Meyer et al.

A1 Journal Article in ONCOTARGET

Differential analysis of genome-wide methylation and gene expression in mesenchymal stem cells of patients with fractures and osteoarthritis

Alvaro del RealFlor M Pérez-CampoAgustín F FernándezCarolina SañudoCarmen G IbarbiaMaría I Pérez-NúñezWim Van CriekingeMaarten BraspenningMaría A AlonsoMario F Fraga et al.

A1 Journal Article in EPIGENETICS

Epigenetic profiling in cancer

Geert TrooskensWim Van CriekingeTim De Meyer

Epigenetic risk score improves prostate cancer risk assessment

Leander Van NesteJack GroskopfWilliam E GrizzleGeorge W AdamsMark S DeGuentherPeter N KolettisJames E BryantGary P KearneyMichael C KearneyWim Van Criekinge et al.

A1 Journal Article in PROSTATE

Epigenetic sampling effects : nephrectomy modifies the clear cell renal cell cancer methylome

Christophe Van NesteAlexander LairdFiach O’MahonyWim Van CriekingeDieter DeforceFilip Van NieuwerburghThomas PowlesDavid J HarrisonGrant D StewartTim De Meyer

A1 Journal Article in CELLULAR ONCOLOGY

Genome-wide DNA methylation profiling reveals methylation markers associated with 3q gain for detection of cervical precancer and cancer

Wina VerlaatPeter JF SnijdersPutri W NoviantiSaskia M WiltingLise MA De StrooperGeert TrooskensJohan VandersmissenWim Van CriekingeG Bea A WismanChris JLM Meijer et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

Immune cell profiling of melanoma metastases from patients treated with TriMixDC-MEL dendritic cell therapy in combination with ipilimumab

Kelly SchatsEmily A Van VreIsolde DebyserArno VandenbroeckYanina JansenTeofila SeremetKoen MarienErik FransenDorien SchrijversWim Van Criekinge et al.

Methylome analysis of extreme chemoresponsive patients identifies novel markers of platinum sensitivity in high-grade serous ovarian cancer

Tushar TomarNicolette G AlkemaLeroy SchreuderGert Jan MeersmaTim De MeyerWim Van CriekingeHarry G KlipHeidi FieglEls van NieuwenhuysenIgnace Vergote et al.

A1 Journal Article in BMC MEDICINE

Novel stool-based protein biomarkers for improved colorectal cancer screening : a case-control study

Linda JW BoschMeike de WitThang V PhamVeerle MH CoupeAnnemieke C HiemstraSander R PiersmaGideon OudgenoegGeorge L SchefferSandra MongeraJochim Terhaar Sive Droste et al.

A1 Journal Article in ANNALS OF INTERNAL MEDICINE

Prospective validation of a diagnostic urine test for bladder cancer : the HEMAturia study

Kim EM van KesselJoep J de JongAngelique CJ Ziel-van der MadeHossain RoshaniStefan M HaenselJosien H van Montfrans-WolterbeekEgbert R BoeveEric HGM OomensNiels J van CasterenJoost L Boormans et al.

The microbiome in posttraumatic stress disorder and trauma-exposed controls : an exploratory study

Sian MJ HemmingsStefanie Malan-MüllerLeigh L van den HeuvelBrittany A DemmittMaggie A StanislawskiDavid G SmithAdam D BohrChristopher E StamperEmbriette R HydeJames T Morton et al.

A1 Journal Article in PSYCHOSOMATIC MEDICINE

Validation of a DNA methylation-mutation urine assay to select patients with hematuria for cystoscopy

Kim EM van KesselWillemien BeukersIrene LurkinAngelique Ziel-van der MadeKirstin A van der KeurJoost L BoormansLars DyrskjøtMirari MárquezTorben F ØrntoftFrancisco X Real et al.

A1 Journal Article in JOURNAL OF UROLOGY

2016

A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq

Sandra SteyaertJolien DiddensJeroen GalleEllen De MeesterSarah De KeulenaerAntje BakkerNina Sohnius-WilhelmiCarolina Frankl-VilchesAnnemie Van der LindenWim Van Criekinge et al.

A1 Journal Article in SCIENTIFIC REPORTS

Ability of an epigenetic assay to identify anterior prostate tumors based on a negative 12-core biopsy

Todd Matthew MorganSimpa Samuel SalamiJohn Thomas WeiGanesh S PalapattuAmy GurskyWim Van CriekingeLeander Van NesteRohit Mehra

BMP-SMAD signaling regulates lineage priming, but is dispensable for self-renewal in mouse embryonic stem cells

Maria Gomes FernandesRuben DriesMatthias S RoostStefan SemrauAna de Melo BernardoRichard P DavisRamprasad RamakrishnanKaroly SzuhaiElke MaasLieve Umans et al.

A1 Journal Article in STEM CELL REPORTS

Clinical utility of an epigenetic assay to reduce unnecessary repeat prostate biopsies

Jason HafronThanh HuynhAyad S KhourdajiRichard D SanteWim Van CriekingeLeander Van Neste

Combined DNA-methylation intensity and clinical risk score to stratify patients for high-grade disease

Leander Van NesteGrant StewartSandra Marlene GastonWilliam E GrizzleGeorge W AdamsGary P KearneyJonathan I EpsteinDavid James HarrisonAlan W PartinWim Van Criekinge

Detection of high-grade prostate cancer using a urinary molecular biomarker-based risk score

Leander Van NesteRianne J HendriksSiebren DijkstraGeert TrooskensErik B CornelSander A JanninkHans de JongDaphne HesselsFrank P SmitWillem JG Melchers et al.

A1 Journal Article in EUROPEAN UROLOGY

Developing bioinformatics applications for the analysis of epigenetic next-generation sequencing data

Sandra SteyaertTim De MeyerWim Van CriekingeWim Vanden Berghe

Discovery of new methylation markers to improve screening for cervical intraepithelial neoplasia grade 2/3

A BoersR WangRW van LeeuwenHG KlipGH de BockH HollemaWim Van CriekingeTim De MeyerSimon DenilAGJ van der Zee et al.

A1 Journal Article in CLINICAL EPIGENETICS

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

Anneleen DecockMaté OngenaertWim Van CriekingeFranki SpelemanJo Vandesompele

A1 Journal Article in SCIENTIFIC DATA

Dynamic epigenetic changes to VHL occur with sunitinib in metastatic clear cell renal cancer

Grant D StewartThomas PowlesChristophe Van NesteAlison MeynertFiach O'MahonyAlexander LairdDieter DeforceFilip Van NieuwerburghGeert TrooskensWim Van Criekinge et al.

A1 Journal Article in ONCOTARGET

Evaluation of an epigenetic profile for the detection of bladder cancer in patients with hematuria

Kim EM van KesselLeander Van NesteIrene LurkinEllen C ZwarthoffWim Van Criekinge

A1 Journal Article in JOURNAL OF UROLOGY

Forensic Loci Allele Database (FLAD) : automatically generated, permanent identifiers for sequenced forensic alleles

Christophe Van NesteWim Van CriekingeDieter DeforceFilip Van Nieuwerburgh

A1 Journal Article in FORENSIC SCIENCE INTERNATIONAL-GENETICS

Genome-wide methylome analysis using MethylCap-seq uncovers 4 hypermethylated markers with high sensitivity for both adeno- and squamous-cell cervical carcinoma

Rong WangRobert W van LeeuwenAniek BoersHarry G KlipTim De MeyerRenske DM SteenbergenWim Van CriekingeAte GJ van der ZeeEd SchuuringG Bea A Wisman

A1 Journal Article in ONCOTARGET

Identification and validation of WISP1 as an epigenetic regulator of metastasis in oral squamous cell carcinoma

Martijn JAM ClausenLieuwe J MelchersMirjam F MastikLorian Slagter-MenkemaHarry JM GroenBernard FAM van der LaanWim Van CriekingeTim De MeyerSimon DenilG Bea A Wisman et al.

A1 Journal Article in GENES CHROMOSOMES & CANCER

Identification of high-grade prostate cancer using urine-based molecular biomarkers combined with clinical risk factors

Leander Van NesteGeert TrooskensRianne J HendriksJack SchalkenWim Van Criekinge

Molecular and epigenetic features of melanomas and tumor immune microenvironment linked to durable remission to ipilimumab-based immunotherapy in metastatic patients

Teofila SeremetAlexander KochYanina JansenMax SchreuerSofie WilgenhofVéronique Del MarmolDanielle LiènardKris ThielemansKelly SchatsMark Kockx et al.

A1 Journal Article in JOURNAL OF TRANSLATIONAL MEDICINE

RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis

MJAM ClausenLJ MelchersMF MastikL Slagter-MenkemaHJM GroenBFAM van der LaanWim Van CriekingeTim De MeyerSimon DenilB van der Vegt et al.

A1 Journal Article in EPIGENETICS

Risk score predicts high-grade prostate cancer in DNA-methylation positive, histopathologically negative biopsies

Leander Van NesteAlan W PartinGrant D StewartJonathan I EpsteinDavid J HarrisonWim Van Criekinge

A1 Journal Article in PROSTATE

WRN promoter CpG island hypermethylation does not predict more favorable outcomes for patients with metastatic colorectal cancer treated with irinotecan-based therapy

Linda JW BoschYanxin LuoVictoria V LaoPetur SnaebjornssonGeert TrooskensIlse VlassenbroeckSandra MongeraWeiliang TangPiri WelcshJames G Herman et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

2015

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

Alexander KochWim Van CriekingeTim De MeyerGerben Menschaert

Effect of sunitinib treatment on mutations and methylation in metastatic renal cancer

Grant StewartChristophe Van NesteAlison MeynertColin SempleFinch O'MahonyAlexander LairdAlan MackayGeert TrooskensWim Van CriekingeTim De Meyer et al.

Epigenetic assay stratifies prostate cancer patients' risk for aggressiveness

Leander Van NesteWim Van CriekingeJoseph BigleyWilliam E GrizzleGeorge W AdamsGary P KearneySandra M Gaston

Epigenetic profiling of cardiovascular ageing

Simon DenilTim De MeyerWim Van CriekingeSofie Bekaert

Forensic massively parallel sequencing data analysis tool: implementation of MyFLq as a standalone web- and Illumina BaseSpace®-application

Christophe Van NesteYannick GansemansDieter De ConinckDavid Van HoofstatWim Van CriekingeDieter DeforceFilip Van Nieuwerburgh

A1 Journal Article in FORENSIC SCIENCE INTERNATIONAL-GENETICS

Genome-wide DNA methylation detection by MethylCap-seq and Infinium HumanMethylation450 BeadChips: an independent large-scale comparison

Tim De MeyerPierre BadyGeert TrooskensSebastian KurscheidJocelyne BlochJohan M KrosJohannes A HainfellnerRoger StuppMauro DelorenziMonika E Hegi et al.

A1 Journal Article in SCIENTIFIC REPORTS

Global DNA methylation analysis of human atherosclerotic plaques reveals extensive genomic hypomethylation and reactivation at imprinted locus 14q32 involving induction of a miRNA cluster

Einari AavikHenri LumivuoriOlli LeppänenThomas WirthSanna-Kaisa HäkkinenJan-Hinrich BräsenUlrich BeschornerThomas ZellerMaarten BraspenningWim Van Criekinge et al.

A1 Journal Article in EUROPEAN HEART JOURNAL

Identification of a predictive signature based on immunohistochemical (IHC), RNA-seq and epigenetic profiling of melanoma metastases for response to ipilimumab-based immunotherapy

Teofila SeremetAlexander KochSofie WilgenhofMax SchreuerYanina JansenDanielle LienardVeronique Del MarmolKris ThielemansNicolas Van BarenPierre Coulie et al.

MEXPRESS : visualizing expression, DNA methylation and clinical TCGA data

Alexander KochTim De MeyerJana JeschkeWim Van Criekinge

A1 Journal Article in BMC GENOMICS

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

Jeroen CrappéWim Van CriekingeGerben MenschaertGeert Baggerman

Mining for viral fragments in methylation enriched sequencing data

Klaas MensaertWim Van CriekingeOlivier ThasEd SchuuringRenske DM SteenbergenG Bea A WismanTim De Meyer

A1 Journal Article in FRONTIERS IN GENETICS

Porting forensic DNA analysis to deep sequencing

Christophe Van NesteDieter DeforceWim Van CriekingeFilip Van Nieuwerburgh

PROTEOFORMER : deep proteome coverage through ribosome profiling and MS integration

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

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Risk stratification of aggressive prostate cancer based on combined epigenetic and clinical data of men with initial cancer-negative biopsies

Alan W PartinLeander Van NesteGrant D StewartJoseph BigleyDavid J HarrisonWim Van CriekingeJonathan I Epstein

Spectrin Repeat Containing Nuclear Envelope 1 and Forkhead Box Protein E1 are promising markers for the detection of colorectal cancer in blood

Veerle MelotteJoo Mi YiMarjolein HFM LentjesKim M SmitsLeander Van NesteHanneke EC NiessenKim AD WoutersJoost LouwagieKornel E SchuebelJames G Herman et al.

A1 Journal Article in CANCER PREVENTION RESEARCH

We are all individuals...: bioinformatics in the personalized medicine era

Leander Van NesteWim Van Criekinge

A1 Journal Article in CELLULAR ONCOLOGY

WRN Promoter CpG island hypermethylation does not predict a favourable outcome for irinotecan-treated metastatic colorectal cancer patients

LJW BoschY LuoVV LaoP SnaebjornssonGeert TrooskensI VlassenbroeckS MongeraW TangP WelcshJ Herman et al.

2014

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

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

A1 Journal Article in PROTEOMICS

Bacterial diversity assessment in Antarctic terrestrial and aquatic microbial mats : a comparison between bidirectional pyrosequencing and cultivation

Bjorn TytgatElie VerleyenDagmar ObbelsKarolien PeetersAaike De WeverSofie D'hondtTim De MeyerWim Van CriekingeWim VyvermanAnne Willems

A1 Journal Article in PLOS ONE

Clinical validation of an epigenetic assay to predict negative histopathological results in repeat prostate biopsies

Alan W PartinLeander Van NesteEric A KleinLeonard S MarksJason R GeeDean A TroyerKimberly Rieger-ChristJ Stephen JonesCristina Magi-GalluzziLeslie A Mangold et al.

A1 Journal Article in JOURNAL OF UROLOGY

Combination of gene copy gain and epigenetic deregulation are associated with the aberrant expression of a stem cell related HOX-signature in glioblastoma

Sebastian KurscheidPierre BadyDavide SciuscioIvana SamarzijaTal ShayIrene VassalloWim Van CriekingeEytan DomanyRoger StuppMauro Delorenzi et al.

Emerging evidence for CHFR as a cancer biomarker : from tumor biology to precision medicine

Sarah DerksArjen HG ClevenVeerle MelotteKim M SmitsJohann C BrandesNilofer AzadWim Van CriekingeAdriaan P de BruïneJames G HermanManon van Engeland

A1 Journal Article in CANCER AND METASTASIS REVIEWS

Epigenetic profiling of prostate cancer tissue to identify men with high-risk disease

Leander Van NesteJeffrey FalkMing-Chou LeeJoseph BigleyWim Van CriekingeE David Crawford

Evaluation of different methods to assess homologous recombination status and sensitivity to PARP inhibitors in ovarian cancer

A MukhopadhyayM DixonE MulliganH SchuhwerkJ MurrayJ QuinnLeander Van NesteWim Van CriekingeN CurtinR Edmondson

Food-derived opioid peptides inhibit cysteine uptake with redox and epigenetic consequences

Malav S TrivediJayni S ShahSara Al-MughairyNathaniel W HodgsonBenjamin SimmsGeert TrooskensWim Van CriekingeRichard C Deth

A1 Journal Article in JOURNAL OF NUTRITIONAL BIOCHEMISTRY

Genome-wide methylation profiling reveals Zinc finger protein 516 (ZNF516) and FK-506binding protein 6 (FKBP6) promoters frequently methylated in cervical neoplasia, associated with HPV status and ethnicity in a Chilean population

Priscilla BrebiLeonel MaldonadoMaartje G NoordhuisCarmen IliPamela LealPatricia GarciaMariana BraitJudit RibasChristina MichailidiJimena Perez et al.

A1 Journal Article in EPIGENETICS

Identification by array comparative genomic hybridization of a new amplicon on chromosome 17q highly recurrent in BRCA1 mutated triple negative breast cancer

Sébastien ToffoliIsabelle BarFadi Abdel-SaterPaul DelréePascale HilbertFrédéric CavallinFabrice MoreauWim Van CriekingeMagali Lacroix-TrikiMario Campone et al.

A1 Journal Article in BREAST CANCER RESEARCH

Illumina sequencing of 15 deafness genes using fragmented amplicons

Filip Van NieuwerburghSarah De KeulenaerJoachim De SchrijverJo VandesompeleWim Van CriekingePaul CouckeDieter Deforce

A2 Journal Article in BMC RESEARCH NOTES

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

Jeroen CrappéWim Van CriekingeGerben Menschaert

A2 Journal Article in EUPA OPEN PROTEOMICS

MEN1 Gene mutation and reduced expression are associated with poor prognosis in pulmonary carcinoids

Dorian RA SwartsAldo ScarpaVicenzo CorboWim Van CriekingeManon van EngelandGaia GattiMieke ER HenflingMauro PapottiAurel PerrenFrans CS Ramaekers et al.

A1 Journal Article in JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Methylation-mediated repression of PRDM14 contributes to apoptosis evasion in HPV-positive cancers

Suzanne SnellenbergSaskia AGM CillessenWim Van CriekingeLeontien BoschChris JLM MeijerPeter JF SnijdersRenske DM Steenbergen

A1 Journal Article in CARCINOGENESIS

My-Forensic-Loci-queries (MyFLq) framework for analysis of forensic STR data generated by massive parallel sequencing

Christophe Van NesteMado VandewoestyneWim Van CriekingeDieter DeforceFilip Van Nieuwerburgh

A1 Journal Article in FORENSIC SCIENCE INTERNATIONAL-GENETICS

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

Petra Van DammeDaria FijalkowskaWim Van CriekingeGerben Menschaert

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Next-generation technologies and data analytical approaches for epigenomics

Klaas MensaertSimon DenilGeert TrooskensWim Van CriekingeOlivier ThasTim De Meyer

A1 Journal Article in ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

On cross-sectional associations of leukocyte telomere length with cardiac systolic, diastolic and vascular function: the Asklepios study

Simon DenilErnst RietzschelMarc De BuyzereCaroline Van daelePatrick SegersDirk De BacquerWim Van CriekingeSofie BekaertThierry GillebertTim De Meyer

A1 Journal Article in PLOS ONE

Promoter CpG island hypermethylation of Decoy Receptor 1 (DCR1) is associated with poor response to irinotecan in metastatic colorectal cancer

L BoschG TrooskensP SnaebjornssonJ HaanM KoopmanJ TolT de MeyerJ LouwagieL DehaspeNCT van Grieken et al.

SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data

Sandra SteyaertWim Van CriekingeAyla De PaepeSimon DenilKlaas MensaertKatrien VandepitteWim Vanden BergheGeert TrooskensTim De Meyer

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Strategies for validation and testing of DNA methylation biomarkers

C NoehammerW PulvererMR HasslerM HofnerM WielscherK VierlingerT LiloglouD McCarthyTJ JensenA Nygren et al.

A1 Journal Article in EPIGENOMICS

Systemic suppression of the shoot metabolism upon rice root nematode infection

Tina KyndtSimon DenilLander BautersWim Van CriekingeTim De Meyer

A1 Journal Article in PLOS ONE

2013

Alterations of immune response of non-small lung cancer with azacytidine

John WrangleWei WangAlexander KochHariharan EaswaranHelai P MohammadFrank VendettiWim Van CriekingeTim De MeyerZhengzong DuPrincy Parsana et al.

A1 Journal Article in ONCOTARGET

An epigenomic next-generation sequencing approach to identify predictive markers for PARP inhibitor response in breast cancer cells

Tim De MeyerGeert TrooskensMascha K WibbeSebastian B BartmannManon van EngelandWim Van CriekingeVivianne C Tjan-HeijnenRuth KnüchelJürgen Veeck

An exploration of pathways involved in lung carcinoid progression using gene expression profiling

Dorian RA SwartsLeander Van NesteMieke ER HenflingIvo EijkenboomPaul P EijkMarie-Louise van VelthuysenAryan VinkMarco VolanteBauke YlstraWim Van Criekinge et al.

A1 Journal Article in CARCINOGENESIS

Association of DNA promoter hypermethylation of decoy receptor 1 (DCR1) with poor response to irinotecan in metastatic colorectal cancer

Wim Van CriekingeLinda JW BoschGeert TrooskensPeter SnaebjornssonJosien HaanLorraine Cheryl PelosofMiriam KoopmanJolien TolJoost LouwagieLuc Dehaspe et al.

CD44 and OTP are strong prognostic markers for pulmonary carcinoids

Dorian RA SwartsMieke ER HenflingLeander Van NesteRobert Jan van SuylenAnne-Marie C DingemansWinand NM DinjensAnnick HaesevoetsMartina RudeliusErik ThunnissenMarco Volante et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

CD44 and OTP are strong prognostic markers for pulmonary carcinoids

DRA SwartsM HenflingL van NesteR van SuylenAM DingemansWNM DinjensA HaesevoetsM RudeliusFBJ ThunnissenM Volante et al.

CHFR promoter methylation indicates poor prognosis in stage II microsatellite stable colorectal cancer

Manon van EngelandArjen ClevenSarah DerksMuriel XG DrahtKim M SmitsVeerle MelotteMatty P WeijenbergJames Gordon HermanAdriaan P de BruineWim Van Criekinge

Clinical utility of an epigenetic assay to detect occult prostate cancer in histopathologically negative biopsies: results of the MATLOC study

Grant D StewartLeander Van NestePhilippe DelvennePaul DelréeAgnès DelgaS Alan McNeillMarie O'DonnellJames ClarkWim Van CriekingeJoseph Bigley et al.

A1 Journal Article in JOURNAL OF UROLOGY

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

Jeroen CrappéWim Van CriekingeGeert TrooskensEisuke HayakawaWalter LuytenGeert BaggermanGerben Menschaert

A1 Journal Article in BMC GENOMICS

Comprehensive analysis of the basal cell carcinoma functional methylome

T BrinkhuizenS DenilGeert TrooskensWim Van CriekingeV WinnepenninckxK MosterdM van EngelandM van Steensel

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

Gerben MenschaertWim Van CriekingeTineke NotelaersAlexander KochJeroen CrappéKris GevaertPetra Van Damme

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Expression of type 2 orexin receptor in human endometrium and its epigenetic silencing in endometrial cancer

P DehanC CanonGeert TrooskensM RehliC MunautWim Van CriekingeP Delvenne

A1 Journal Article in JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

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

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

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

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

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

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

GLUCAN SYNTHASE-LIKE8 and STEROL METHYLTRANSFERASE2 are required for ploidy consistency of the sexual reproduction system in Arabidopsis

Nico De StormeJoachim De SchrijverWim Van CriekingeVera WewerPeter DörmannDanny Geelen

A1 Journal Article in PLANT CELL

Identifying and validating DNA methylation biomarkers: the example of neuroblastoma

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

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

Jeroen CrappéAlexander KochSandra SteyaertWim Van CriekingePetra Van DammeGerben Menschaert

Methylation-specific digital karyotyping of HPV16E6E7 expressing human keratinocytes identifies novel methylation events in cervical carcinogenesis

Renske DM SteenbergenMaté OngenaertSuzanne SnellenbergGeert TrooskensWendy F van der MeideDeeksha PandeyNoga Bloushtain-QimronKornelia PolyakChris JLM MeijerPeter JF Snijders et al.

A1 Journal Article in JOURNAL OF PATHOLOGY

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

Jeroen CrappéGeert TrooskensEisuke HayakawaWalter LuytenGeert BaggermanWim Van CriekingeGerben Menschaert

Prediction of risk for prostate cancer in histopathologically negative biopsies by multigene epigenetic assay

Leander Van NesteWim Van CriekingeOlivier ThasJoseph BigleyGrant Duncan StewartDavid James Harrison

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

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

A1 Journal Article in PLOS ONE

Staphylococcal enterotoxin B influences the DNA methylation pattern in nasal polyp tissue : a preliminary study

Claudina Perez NovoYuan ZhangSimon DenilGeert TrooskensTim De MeyerWim Van CriekingePaul Van CauwenbergeLuo ZhangClaus Bachert

A1 Journal Article in ALLERGY ASTHMA AND CLINICAL IMMUNOLOGY

The CpG island methylator phenotype: what's in a name?

Laura AE HughesVeerle MelotteJoachim De SchrijverMichiel de MaatVincent THBM SmitJudith VMG BovéePim J FrenchPiet A van den BrandtLeo J SchoutenTim De Meyer et al.

A1 Journal Article in CANCER RESEARCH

The effect of VEGF-targeted therapy on biomarker expression in sequential tissue from patients with metastatic clear cell renal cancer

Kevin SharpeGrant D StewartAlan MackayChristophe Van NesteCharlotte RofeDan BerneyIrfan KayaniAxel BexElaine WanFiach C O'Mahony et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

Transcriptional analysis through RNA sequencing of giant cells induced by Meloidogyne graminicola in rice roots

Hongli JiGodelieve GheysenSimon DenilKeith LindseyJennifer F ToppingKamrun NaharAnnelies HaegemanWinnok De VosGeert TrooskensWim Van Criekinge et al.

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

2012

A tissue biopsy-based epigenetic multiplex PCR assay for prostate cancer detection

Leander Van NesteJoseph BigleyAdam TollGaëtan OttoJames ClarkPaul DelréeWim Van CriekingeJonathan I Epstein

A1 Journal Article in BMC UROLOGY

An omnibus consistent adaptive percentile modified Wilcoxon rank sum test with applications in gene expression studies

Olivier ThasLieven ClementJohn RaynerBeatriz CarvalhoWim Van Criekinge

A1 Journal Article in BIOMETRICS

Biomarkers for detection and prognosis of breast cancer identified by a functional hypermethylome screen

Jana JeschkeLeander Van NesteSabine C GlöcknerMashaal DhirMarilia Freitas CalmonValerie DeregowskiWim Van CriekingeIlse VlassenbroeckAlexander KochTimothy A Chan et al.

A1 Journal Article in EPIGENETICS

Colorectal adenoma to carcinoma progression is accompanied by changes in gene expression associated with ageing, chromosomal instability, and fatty acid metabolism.

Beatriz CarvalhoAnke H Sillars-HardebolCindy PostmaSandra MongeraJochim Terhaar Sive DrosteAskar ObulkasimMark van de WielWim Van CriekingeBauke YlstraRemond JA Fijneman et al.

A1 Journal Article in CELLULAR ONCOLOGY

DNA methylation of phosphatase and actin regulator 3 detects colorectal cancer in stool and complements FIT

Linda JW BoschFrank A OortMaarten NeerincxCarolina AJ Khalid-de BakkerJochim S Terhaar sive DrosteVeerle MelotteDaisy MAE JonkersAd AM MascleeSandra MongeraMadeleine Grooteclaes et al.

A1 Journal Article in CANCER PREVENTION RESEARCH

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

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

A1 Journal Article in GENOME BIOLOGY

Genome‐wide RNA‐ and MBD‐sequencing in HCT116 and DKO cells as a global re‐expression model

Joachim De SchrijverGeert TrooskensLinda JW BoschPierre DehanBeatriz CarvalhoLeander Van NesteGerrit MeijerSteve BaylinWim Van Criekinge

Identification of new molecular species using second-generation sequencing

Joachim De SchrijverWim Van CriekingeSofie Bekaert

Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model

Kristof De BeufJoachim De SchrijverOlivier ThasWim Van CriekingeRafael A IrizarryLieven Clement

A1 Journal Article in BMC BIOINFORMATICS

Low dose irradiation of thyroid cells reveals a unique transcriptomic and epigenetic signature in RET/PTC-positive cells

Khalil Abou-El-ArdatPieter MonsieursNataša AnastasovMike AtkinsonHanane DerradjiTim De MeyerSofie BekaertWim Van CriekingeSarah Baatout

A1 Journal Article in MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

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

Jeroen CrappéGeert TrooskensEisuke HayakawaWalter LuytenGeert BaggermanWim Van CriekingeGerben Menschaert

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

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

A1 Journal Article in BMC MEDICAL GENOMICS

Promoter methylation analysis identifies prognostic methylation biomarkers in neuroblastoma

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

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

Gerben MenschaertEisuke HayakawaLiliane SchoofsWim Van CriekingeGeert Baggerman

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

The epigenetic promise for prostate cancer diagnosis.

Leander Van NesteJames G HermanGaëtan OttoJoseph W BigleyJonathan I EpsteinWim Van Criekinge

A1 Journal Article in PROSTATE

Transcriptional reprogramming by root knot and migratory nematode infection in rice

Tina KyndtSimon DenilAnnelies HaegemanGeert TrooskensLander BautersWim Van CriekingeTim De MeyerGodelieve Gheysen

A1 Journal Article in NEW PHYTOLOGIST

Transcriptome analysis of rice mature root tissue and root tips in early development by massive parallel sequencing

Tina KyndtSimon DenilAnnelies HaegemanGeert TrooskensTim De MeyerWim Van CriekingeGodelieve Gheysen

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

2011

A non-parametric method to assess the presence of significant DNA-methylation in enrichment-based NGS data

Klaas MensaertGeert TrooskensWim Van CriekingeOlivier ThasTim De Meyer

Accurate long read mapping using enhanced suffix arrays

Michaël VyvermanJoachim De SchrijverWim Van CriekingePeter DawyndtVeerle Fack

Applying massive parallel sequencing to molecular diagnosis of Marfan and Loeys-Dietz syndromes

Machteld BaetensLut Van LaerKim De LeeneerJan HellemansJoachim De SchrijverHendrik Van de VoordeMarjolijn RenardHal DietzRonald V LacroBjörn Menten et al.

A1 Journal Article in HUMAN MUTATION

Charting the methylome

Geert TrooskensTim De MeyerSimon DenilWim Van Criekinge

Epigenetic, metabolic and signal transduction pathways involved in radiation response of normal and transformed thyrocytes

Khalil AbouelaradatWim Van CriekingeSarah BaatoutTim De MeyerSofie Bekaert

Genome sequence of Helicobacter suis supports its role in gastric pathology

Miet VermooteTom VandekerckhoveBram FlahouFrank PasmansAnnemieke SmetDominic De GrooteWim Van CriekingeRichard DucatelleFreddy Haesebrouck

Genome sequence of Helicobacter suis supports its role in gastric pathology

Miet VermooteTom VandekerckhoveBram FlahouFrank PasmansAnnemieke SmetDominic De GrooteWim Van CriekingeRichard DucatelleFreddy Haesebrouck

A1 Journal Article in VETERINARY RESEARCH

Massive parallel amplicon sequencing of the breast cancer genes BRCA1 and BRCA2: opportunities, challenges, and limitations

Kim De LeeneerJan HellemansJoachim De SchrijverMachteld BaetensBruce PoppeWim Van CriekingeAnne De PaepePaul CouckeKathleen Claes

A1 Journal Article in HUMAN MUTATION

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

Jeroen CrappéGerben MenschaertGeert TrooskensJoachim De SchrijverGeert BaggermanWim Van Criekinge

MutaDATABASE: a centralized and standardized DNA variation database

Sherri BaleMartijn DevisscherWim Van CriekingeHeidi L RehmFrederik DecouttereRobert NussbaumJohan T DunnenPatrick Willems

A1 Journal Article in NATURE BIOTECHNOLOGY

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

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

A1 Journal Article in PLOS ONE

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

Response to low-dose X-irradiation is p53-dependent in a papillary thyroid carcinoma model system

Khalil Abou-El-ArdatHanane DerradjiWinnok De VosTim De MeyerSofie BekaertWim Van CriekingeSarah Baatout

A1 Journal Article in INTERNATIONAL JOURNAL OF ONCOLOGY

Telomere length and cardiovascular aging: the means to the ends?

Tim De MeyerErnst RietzschelMarc De BuyzereWim Van CriekingeSofie Bekaert

A1 Journal Article in AGEING RESEARCH REVIEWS

2010

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

Gerben MenschaertTom VandekerckhoveGeert BaggermanBart LanduytJonathan V SweedlerLiliane SchoofsWalter LuytenWim Van Criekinge

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Accurate long read mapping using enhanced suffix arrays

Michaël VyvermanJoachim De SchrijverWim Van CriekingePeter DawyndtVeerle Fack

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

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

A1 Journal Article in BMC BIOINFORMATICS

Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells

Joyce E OhmPrashant MaliLeander Van NesteDavid M BermanLiang LiangKurinji PandiyanKimberley J BriggsWei ZhangPedram ArganiBrian Simons et al.

A1 Journal Article in CANCER RESEARCH

Evaluation of standard and advanced preprocessing methods for the univariate analysis of blood serum 1H-NMR spectra

Tim De MeyerDavy SinnaeveBjörn Van GasseErnst RietzschelMarc De BuyzereMichel LangloisSofie BekaertJosé MartinsWim Van Criekinge

A1 Journal Article in ANALYTICAL AND BIOANALYTICAL CHEMISTRY

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

Joachim De SchrijverBram De WildeGeert TrooskensJo VandesompeleWim Van Criekinge

Genome sequence of Helicobacter suis supports its role in gastric pathology

Miet VermooteTom VandekerckhoveBram FlahouFrank PasmansAnnemieke SmetDominic De GrooteWim Van CriekingeRichard DucatelleFreddy Haesebrouck

GULP1, a potential tumor suppressor gene in ovarian tumors and its utility as a biomarker

Leonel MaldonadoMariana BraitShahnaz BegumAditi ChatterjeeMyriam LoyoAlvaro BarbosaM Luana PoetaVito M FazioAngioli RobertoElisabetta Tarquini et al.

Identification and validation of the methylated TWIST1 and NID2 genes through real-time methylation-specific polymerase chain reaction assays for the noninvasive detection of primary bladder cancer in urine samples

Isabelle RenardSteven JoniauBen van CleynenbreugelCatherine ColletteChristophe NaôméIlse VlassenbroeckHubert NicolasJean de LevalJosef StraubWim Van Criekinge et al.

A2 Journal Article in EUROPEAN UROLOGY

Mining cleavage sites of the mouse peptidome

Kurt De GraveTias GunsTom VandekerckhoveBart LanduytGerben MenschaertWim Van CriekingeLiliane SchoofsWalter Luyten

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

Gerben MenschaertTom VandekerckhoveGeert BaggermanLiliane SchoofsWalter LuytenWim Van Criekinge

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

The N-myc downstream regulated gene (NDRG) family: diverse functions, multiple applications

Veerle MelotteXianghu QuMaté OngenaertWim Van CriekingeAdriaan P de BruineH Scott BaldwinManon van Engeland

A1 Journal Article in FASEB JOURNAL

2009

A plasma-based colorectal cancer (CRC) screening assay using DNA methylation markers: first results of multicenter studies

J LouwagieW PommerienG BrichardG OttoWim Van CriekingeSB BaylinN AhujaHP AdamsD NurnbergK Bierau

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

Gerben MenschaertTom VandekerckhoveGeert BaggermanBart LanduytLiliane SchoofsWalter LuytenWim Van Criekinge

A4 Journal Article in COMMUNICATIONS IN AGRICULTURAL AND APPLIED BIOLOGICAL SCIENCES

Cellular reprogramming

Maté OngenaertWim Van Criekinge

E2Fs mediate a fundamental cell-cycle deregulation in high-grade serous ovarian carcinomas

Tim De MeyerIngrid TGW BijsmansKoen Van de VijverSofie BekaertJan OostingWim Van CriekingeManon van EngelandNathalie LG Sieben

A1 Journal Article in JOURNAL OF PATHOLOGY

External X-irradiation causes a decrease in the proliferation of two papillary thyroid carcinoma cell lines with no significant increase in cell death

Khalil Abou-El-ArdatHanane DerradjiSofie BekaertTim De MeyerWim Van CriekingeSarah Baatout

GATA4 and GATA5 are potential tumor suppressors and biomarkers in colorectal cancer

Debby MEI HellebrekersMarjolein HFM LentjesSandra M van den BoschVeerle MelotteKim AD WoutersKathleen LJ DaenenKim M SmitsYohimitsu AkiyamaYasuhito YuasaSilvia Sanduleanu et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

Pharmacologic unmasking of epigenetically silenced genes in breast cancer

Kimberley Laskie OstrowHannah Lui ParkMohammad Obaidul HoqueMyoung Sook KimJun Wei LiuPedral ArganiWilliam WestraWim Van CriekingeDavid Sidransky

A1 Journal Article in CLINICAL CANCER RESEARCH

Prognostic significance of Gremlin1 (GREM1) promoter CPG island hypermethylation in clear cell renal cell carcinoma

Iris JH van VlodropMarcella BaldewijnsKim SmitsLeo SchoutenLeander Van NesteWim Van CriekingeHein van PoppelEvelyne LerutNita AhujaJames Herman et al.

Promoter DNA methylation of Oncostatin M receptor-β as a novel diagnostic and therapeutic marker in colon cancer

Myoung Sook KimJoost LouwagieBeatriz CarvalhoJochim S Terhaar Sive DrosteHannah Lui ParkYoung Kwang ChaeKeishi YamashitaJun Wei LiuKimberley Laski OstrowShizhang Ling et al.

A1 Journal Article in PLOS ONE

Promoter hypermethylation of Phactr3, a potential new biomarker for colorectal cancer detection

Linda BoschMaarten NeerincxFrank OortSandra MongeraAd MascleeDaisy JonkersCarolina Khalid-de BakkerKatja BierauWim Van CriekingeAdriaan de Bruine et al.

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

Gerben MenschaertTom VandekerckhoveBart LanduytEisuke HayakawaLiliane SchoofsWalter LuytenWim Van Criekinge

A1 Journal Article in PROTEOMICS

Systemic telomere length and preclinical atherosclerosis : the Asklepios study

Tim De MeyerErnst RietzschelMarc De BuyzereMichel LangloisDirk De BacquerPatrick SegersPIET VAN DAMMEGui De BackerPatric Van OostveldtWim Van Criekinge et al.

A1 Journal Article in EUROPEAN HEART JOURNAL

VIP and VIP Validator: a diagnostic amplicon sequencing Variant Interpretation Pipeline and variant detection validator

Joachim De SchrijverWim Van Criekinge

2008

Bioinformatic strategies for more complete and accurate identification of neuropeptides

Timothy A. RichmondGeert BaggermanTom VandekerckhoveGerben MenschaertSteven HussonPeter VerleyenLiliane SchoofsWim Van Criekinge

Defining a chromatin pattern that characterizes DNA-hypermethylated genes in colon cancer cells

KM MCGARVEYLeander Van NesteL COPEJE OHMJG HERMANNWim Van CriekingeKE SCHUEBELSB BAYLIN

A1 Journal Article in CANCER RESEARCH

Discovery of DNA methylation markers in cervical cancer using relaxation ranking

Maté OngenaertG Bea A WismanHaukeline H VoldersAlice J KoningAte GJ van der ZeeWim Van CriekingeEd Schuuring

A1 Journal Article in BMC MEDICAL GENOMICS

GATA4 and GATA5 act as tumor suppressors and are potential biomarkers in colorectal cancer

Debby HellebrekersMarjolein LentjesSandra van den BoschKim WoutersKathleen DaenenVeerle MelotteKim SmitsIris Partouns-HendriksYoshimitsu AkiyamaYasuhito Yuasa et al.

Genome-wide promoter analysis uncovers portions of the cancer methylome

MO HOQUEMS KIMKL OSTROWJ LIUGBA WISMANHL PARKML POETAC JERONIMOR HENRIQUEA LENDVAI et al.

A1 Journal Article in CANCER RESEARCH

Genrisk-T project: response of the TPC-1 papillary thyroid carcinoma cell line to a range of low to high doses of irradiation

K Abou-El-ArdatH DerradjiSofie BekaertTim De MeyerWim Van CriekingeS Baatout

A4 Journal Article in COMMUNICATIONS IN AGRICULTURAL AND APPLIED BIOLOGICAL SCIENCES

Hypermethylation of MCAM gene is associated with advanced tumor stage in prostate cancer

Jun-Wei LiuJatin K NagpalCarmen JeronimoJi Eun LeeRui HenriqueMyoung Sook KimKimberley L OstrowKeishi YamashitaWim Van CriekingeGuojun Wu et al.

A1 Journal Article in PROSTATE

Integration of DNA and expression microarray data unravels seven putative oncogenes on 20Q amplicon involved in colorectal adenoma to carcinoma progression

Beatriz CarvalhoCindy PostmaSandra MongeraErik HopmansSharon DiskinMark van de WielWim Van CriekingeOlivier ThasAnja MathhaiMiguel Cuesta et al.

Lower red blood cell counts in middle-aged subjects with shorter peripheral blood leukocyte telomere length

Tim De MeyerMarc De BuyzereMichel LangloisErnst RietzschelPeter CassimanDirk De BacquerPatric Van OostveldtGui De BackerThierry GillebertWim Van Criekinge et al.

A1 Journal Article in AGING CELL

Multiple putative oncogenes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression

B CarvalhoC PostmaS MongeraE HopmansS DiskinMA van de WielWim Van CriekingeOlivier ThasA MathhaiMA Cuesta et al.

A1 Journal Article in GUT

NMR-based characterization of metabolic alterations in hypertension using an adaptive, intelligent binning algorithm

Tim De MeyerDavy SinnaeveBjörn Van GasseElena TsiporkovaErnst RietzschelMarc De BuyzereThierry GillebertSofie BekaertJosé MartinsWim Van Criekinge

A1 Journal Article in ANALYTICAL CHEMISTRY

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

Maté OngenaertLeander Van NesteTim De MeyerGerben MenschaertSofie BekaertWim Van Criekinge

A1 Journal Article in NUCLEIC ACIDS RESEARCH

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

Maté OngenaertLeander Van NesteTim De MeyerGerben MenschaertSofie BekaertWim Van Criekinge

ssDNA-binding protein 2 is frequently hypermethylated and suppresses cell growth in human prostate cancer

Jun-Wei LiuJatin K NagpalWenyue SunJuna LeeMyoung Sook KimKimberley L OstrowShaoyu ZhouCarmen JeronimoRui HenriqueWim Van Criekinge et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

Studying telomeres in a longitudinal population based study

Tim De MeyerErnst RietzschelMarc De BuyzereWim Van CriekingeSofie Bekaert

A1 Journal Article in Frontiers in Bioscience

The biomarker potential of promoter hypermethylation in HNSCC treated by radiotherapy

Harlinde De SchutterWim Van CriekingeSandra Nuyts

2007

Comparing the DNA hypermethylome with gene mutations in human colorectal cancer

KE SCHUEBELW CHENL COPESC GLOCKNERH SUZUKIJM YITA CHANLeander Van NesteWim Van CriekingeS VAN DEN BOSCH et al.

A1 Journal Article in PLOS GENETICS

Discovery of methylation markers using a relaxation ranking algorithm

Maté OngenaertWim Van CriekingeJ STRAUBA VAN DER ZEEE SCHUURINGH SPOLDERSB WISMAN

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

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

Identification of epigenetically silenced genes in tumor endothelial cells

Debby MEI HellebrekersVeerle MelotteEmmanuelle ViréElise LangenkampGrietje MolemaFrançois FuksJames G HermanWim Van CriekingeArjan W GriffioenManon Van Engeland

A1 Journal Article in CANCER RESEARCH

Paternal age at birth is an important determinant of offspring telomere length

Tim De MeyerErnst RietzschelMarc De BuyzereDirk De BacquerWim Van CriekingeGui De BackerThierry GillebertPatric Van OostveldtSofie Bekaert

A1 Journal Article in HUMAN MOLECULAR GENETICS

Radiosensitization by histone deacetylase inhibitors +/- demethylating agents in head and neck cancer cell lines

Harlinde De SchullerWim Van CriekingeSandra Nuyts

SOS MS : enhancements for Mascot Search engine and other mass spectrometry software

Tom VandekerckhoveGerben MenschaertBart LanduytKurt BoonenWim Van Criekinge

Telomere length and cardiovascular risk factors in a middle-aged population free of overt cardiovascular disease

Sofie BekaertTim De MeyerErnst RietzschelMarc De BuyzereDirk De BacquerMichel LangloisPatrick SegersLuc CoomanPiet Van DammePeter Cassiman et al.

A1 Journal Article in AGING CELL

2006

Detection of putative secreted proteins in the plant-parasitic nematode Heterodera schachtii

Bartel VanholmeM MitrevaWim Van CriekingeMarc LoggheD BirdJP McCarterGodelieve Gheysen

A1 Journal Article in PARASITOLOGY RESEARCH

Informatica in dienst van de biotechnologie

Wim Van Criekinge

A4 Journal Article in HET INGENIEURSBLAD

Quantitation of promoter methylation of multiple genes in urine DNA and bladder cancer detection

MO HOQUES BEGUMO TOPALOGLUA CHATTERJEEE ROSENBAUMWim Van CriekingeWH WESTRAM SCHOENBERGM ZAHURAKSN GOODMAN et al.

A1 Journal Article in JOURNAL OF THE NATIONAL CANCER INSTITUTE

2005

CpG island characterisation

Maté OngenaertWim Van Criekinge

Phylogenetic trees: visualizing, customizing and detecting incongruence

Geert TrooskensDavid De BeuleFrederik DecouttereWim Van Criekinge

A1 Journal Article in BIOINFORMATICS

Quantitative methylation-specific polymerase chain reaction gene patterns in urine sediment distinguish prostate cancer patients from control subjects

MO HOQUEO TOPALOGLUS BEGUMR HENRIQUEE ROSENBAUMWim Van CriekingeWH WESTRAD SIDRANSKY

A1 Journal Article in JOURNAL OF CLINICAL ONCOLOGY

2004

A new class of ubiquitin extension proteins secreted by the dorsal pharyngeal gland in plant parasitic cyst nematodes

Tom TytgatBartel VanholmeJan De MeutterMyriam ClaeysMarjolein CouvreurIsabelle VanhoutteGreetje GheysenWim Van CriekingeGaetan BorgonieAugust Coomans et al.

A1 Journal Article in MOLECULAR PLANT-MICROBE INTERACTIONS

The yeast three-hybrid system as a tool to study caspases

Wim Van CriekingePeter SchotteKaren HeyninckRudi Beyaert

Bookchapter in Apoptosis methods and protocols

2001

Phagocytes: the professional and amateur disposal experts of apoptosis

Elke SmitsWim Van Criekinge

A4 Journal Article in ELSO GAZETTE

2000

Bioinformatics: the goldrush

Wim Van Criekinge

A4 Journal Article in MEDEDELINGEN VAN DE FACULTEIT LANDBOUWKUNDIGE EN TOEGEPASTE BIOLOGISCHE WETENSCHAPPEN, UNIVERSITEIT GENT

Identification and characterization of a dimerization domain in CED-6, an adapter protein involved in engulfment of apoptotic cells

Hua Poo SuEnrico BrugneraWim Van CriekingeElke SmitsMichael HengartnerThierry BogaertKodimangalam S Ravichandran

A1 Journal Article in JOURNAL OF BIOLOGICAL CHEMISTRY

Identification and characterization of a dimerization domain in CED-6, an adapter protein involved in engulfment of apoptotic cells

Hua Poo SuEnrico BrugneraWim Van CriekingeElke SmitsMichael HengartnerThierry BogaertKodimangalam S Ravichandran

1999

Alzheimer's disease associated presenilin 1 interacts with HC5 and ZETA, subunits of the catalytic 20S proteasome.

G VAN GASSENC DE JONGHES PYPEWim Van CriekingeA JULLIAMSI VANDERHOEVENS WOODROWRudi BeyaertD HUYLEBROECKC VAN BROECKHOVEN

A1 Journal Article in NEUROBIOLOGY OF DISEASE

GAL4 is a substrate for caspases : implications for two-hybrid screening and other GAL4-based assays

Wim Van CriekingeSigrid CornelisMarc Van De CraenPeter VandenabeeleWalter FiersRudi Beyaert

A2 Journal Article in MOLECULAR CELL BIOLOGY RESEARCH COMMUNICATIONS

Identification of caspases that cleave presenilin-1 and presenilin-2 - Five presenilin-1 (PS1) mutations do not alter the sensitivity of PS1 to caspases.

Marc Van De CraenC DE JONGHEI VAN DEN BRANDEWim DeclercqG VAN GASSENWim Van CriekingeI VANDERHOEVENWalter FiersC VAN BROECKHOVENL HENDRIKS et al.

A1 Journal Article in FEBS LETTERS

The human homologue of Caenorhabditis elegans CED-6 specifically promotes phagocytosis of apoptotic cells

Elke SmitsWim Van CriekingeGeert PlaetinckThierry Bogaert

A1 Journal Article in CURRENT BIOLOGY

The zinc finger protein A20 inhibits TNF-induced NF-kappa B-dependent gene expression by interfering with an RIP- or TRAF2-mediated transactivation signal and directly binds to a novel NF-kappa B-inhibiting protein ABIN.

Karen HeyninckDirk De ValckWim Vanden BergheWim Van CriekingeRoland ContrerasWalter FiersGuy HaegemanRudi Beyaert

A1 Journal Article in JOURNAL OF CELL BIOLOGY

Yeast two-hybrid : state of the art

Wim Van CriekingeRudi Beyaert

A2 Journal Article in BIOLOGICAL PROCEDURES ONLINE

1998

Cathepsin B-mediated activation of the proinflammatory caspase-11

Peter SchotteWim Van CriekingeMarc Van De CraenGeert van LooMarjory DesmedtJohan GrootenMaria CornelissenLeo De RidderJoël VandekerckhoveWalter Fiers et al.

A1 Journal Article in BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Identification of a new caspase homologue: caspase-14.

Marc Van De CraenGeert van LooS PYPEWim Van CriekingeI VAN DEN BRANDEFrancis MolemansWalter FiersWim DeclercqPeter Vandenabeele

A1 Journal Article in CELL DEATH AND DIFFERENTIATION

Is er leven na de (cel)dood?

Wim Van CriekingeElke SmitsChristian Paul G. BurvenichRudi Beyaert

A2 Journal Article in VLAAMS DIERGENEESKUNDIG TIJDSCHRIFT

Karakterisering van caspasen in een '2 en 3-hybrid'-systeem

Wim Van CriekingeRudi BeyaertWalter FiersRoland Contreras

Use of the yeast three-hybrid system as a tool to study caspases.

Wim Van CriekingeMaria (Marjan) van GurpEls DecosterPeter SchotteMarc Van De CraenWalter FiersPeter VandenabeeleRudi Beyaert

A1 Journal Article in ANALYTICAL BIOCHEMISTRY

1997

A20 inhibits NF-kappa B activation independently of binding to 14-3-3 proteins.

Dirk De ValckKaren HeyninckWim Van CriekingePeter VandenabeeleWalter FiersRudi Beyaert

A1 Journal Article in BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Characterization of seven murine caspase family members

Marc Van de CraenPeter VandenabeeleWim DeclercqIlse Van den BrandeGeert van LooFrancis MolemansPeter SchotteWim Van CriekingeRudi BeyaertWalter Fiers

A1 Journal Article in FEBS LETTERS

Presenilins and Alzheimer's disease: identification of proteins that interact with presenilin I using the yeast two-hybrid system

Geert Van GassenWim Van CriekingeRudi BeyaertJurgen Del-FaveroChristine Van BroeckhovenM Cruts

A2 Journal Article in ARCHIVES OF PHYSIOLOGY AND BIOCHEMISTRY

1996

A20, an inhibitor of cell death, self-associates by its zinc finger domain.

Dirk De ValckKaren HeyninckWim Van CriekingeRoland ContrerasRudi BeyaertWalter Fiers

A1 Journal Article in FEBS LETTERS

Functional characterization of the prodomain of interleukin-1 beta-converting enzyme.

Wim Van CriekingeRudi BeyaertM VANDECRAENPeter VandenabeelePeter SchotteD DEVALCKWalter Fiers

A1 Journal Article in JOURNAL OF BIOLOGICAL CHEMISTRY

TNF-induced intracellular signaling leading to gene induction or to cytotoxicity by necrosis or by apoptosis.

Walter FiersRudi BeyaertElke BooneSigrid CornelisWim DeclercqEls DecosterGeertrui DeneckerBart DepuydtDirk De ValckG DEWILDE et al.

A1 Journal Article in JOURNAL OF INFLAMMATION

1995

Intraliposomale precipitatie: de natuur als leermeester

Wim Van CriekingePaul Van der Meeren

A4 Journal Article in HET INGENIEURSBLAD

On-line simulation as a methodology to recover size distributions from dynamic light scattering experiments.

Wim Van CriekingeP VANDERMEERENJean VanderdeelenLeon Baert

A1 Journal Article in PARTICLE & PARTICLE SYSTEMS CHARACTERIZATION

1994

Phospholipid-omposition of r-DNA hepatitis-B surface-antigens.

P VANDERMEERENWim Van CriekingeJean VanderdeelenLeon Baert

A1 Journal Article in INTERNATIONAL JOURNAL OF PHARMACEUTICS

Physicochemical characterization of liposomes for use as a biomimeting precipitation reactor

Wim Van CriekingeMP De PoorterPaul Van der Meeren

A4 Journal Article in MEDEDELINGEN VAN DE FACULTEIT LANDBOUWKUNDIGE EN TOEGEPASTE BIOLOGISCHE WETENSCHAPPEN, UNIVERSITEIT GENT