Research Explorer

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Researcher

Matthijs Vynck

Publications & Research Data

Awards & Distinctions

61 Results

2026

Challenges and good practices in preprocessing and normalization of untargeted DNA adductomics data in exposomics research

Pablo VangeenderhuysenMatthijs VynckLiesa EngelenAdrian CovaciTim NawrotTrancizeo LipengaRoger Peró GascónSarah De SaegerMarthe De BoevreValerie Mccormack et al.

A1 Journal Article in ANALYTICAL CHEMISTRY

Integrated fecal metabolomics and lipidomics : design of experiments-guided development of an automated biphasic extraction and dual UHPLC-HRMS platform

Kimberly De WindtTiffany De TroyerMatthijs VynckBeata PomianEllen De PaepeVera PlekhovaLynn Vanhaecke

Robust metabolomics data normalization across scales and experimental designs

Matthijs VynckPablo VangeenderhuysenEllen De PaepeTim NawrotVera PlekhovaLynn Vanhaecke

A1 Journal Article in ANALYTICAL CHEMISTRY

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

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

A1 Journal Article in ANALYTICA CHIMICA ACTA

Validation and clinical study of single-step vitrification combined with single-step warming of human blastocysts

Jan GunstHubert JorisMatthijs VynckKristof GodderisMartine VercammenSylvie RoggemanArne Van De Vijver

A1 Journal Article in JOURNAL OF ASSISTED REPRODUCTION AND GENETICS

2025

A repository of the salivary metabolome and its key drivers in 1436 European children

Ellen De PaepeEmile CallemeynKimberly De WindtKathleen WijnantVera PlekhovaBeata PomianPablo VangeenderhuysenStefaan De HenauwNathalie MichelsHeli Viljakainen et al.

A1 Journal Article in EBIOMEDICINE

Advances in multiplex digital PCR data analysis : from clustering to uncertainty quantification

Yao ChenOlivier ThasWard De SpiegelaereWim TrypsteenMatthijs Vynck

Automated integration and quality assessment of chromatographic peaks in LC-MS data using TARDIS

Pablo VangeenderhuysenMatthijs VynckBeata PomianKimberly De WindtEmile CallemeynEllen De PaepeLindsey De CommerJeroen RaesTim NawrotJohannes Rainer et al.

Automated integration and quality assessment of chromatographic peaks in LC–MS-based metabolomics and lipidomics using TARDIS

Pablo VangeenderhuysenMatthijs VynckBeata PomianKimberly De WindtEmile CallemeynEllen De PaepeLindsey De CommerJeroen RaesTim NawrotJohannes Rainer et al.

A1 Journal Article in ANALYTICAL CHEMISTRY

Detection of clinically relevant variants in the TP53 gene below 10% allelic frequency : a multicenter study by ERIC, the European Research Initiative on CLL

Sarka PavlovaJitka MalcikovaLenka RadovaSilvia BonfiglioJack B. CowlandChristian BrieghelMette K. AndersenMaria KarypidouBella BidermanMichael Doubek et al.

A1 Journal Article in HEMASPHERE

Development of a fit-for-purpose data preprocessing workflow for untargeted DNA adductomics in exposomics research

Pablo VangeenderhuysenMatthijs VynckLiesa EngelenAdrian CovaciTim NawrotLynn VanhaeckeLieselot Hemeryck

Exploring the salivary metabolome : key drivers and insights from 1,436 European children

Emile CallemeynEllen De PaepeLynn VanhaeckeVera PlekhovaKimberly De WindtMatthijs VynckPablo VangeenderhuysenNathalie MichelsAnja Geerts

Exploring the salivary metabolome : key drivers and insights from European 1,436 children

Ellen De PaepeEmile CallemeynKimberly De WindtVera PlekhovaKathleen WijnantPablo VangeenderhuysenStefaan De HenauwNathalie MichelsBeata PomianHeli Viljakainen et al.

Flexible methods for uncertainty estimation of digital PCR data

Yao ChenWard De SpiegelaereMatthijs VynckWim TrypsteenDavid GleerupJo VandesompeleOlivier Thas

A1 Journal Article in ISCIENCE

LC-MS in the age of omics : development of open-source software and optimized data-analysis strategies

Pablo VangeenderhuysenLynn VanhaeckeLieselot HemeryckMatthijs Vynck

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

Yao ChenWard De SpiegelaereWim TrypsteenJo VandesompeleGertjan WilsDavid GleerupAntoon LievensOlivier ThasMatthijs Vynck

A2 Journal Article in NAR GENOMICS AND BIOINFORMATICS

Robust metabolomics data normalization across scales and experimental designs

Matthijs VynckPablo VangeenderhuysenEllen De PaepeTim NawrotVera PlekhovaLynn Vanhaecke

The pediatric salivary metabolome : non-invasive insights into key drivers across 1,436 children

Emile CallemeynEllen De PaepeKimberly De WindtVera PlekhovaPablo VangeenderhuysenNathalie MichelsAnja GeertsMatthijs VynckLynn Vanhaecke

The poly (ADP-ribose) polymerase-1 enzyme is overexpressed in various solid canine tumours : an immunohistochemical study

Shana De VosSimone JanssenSophie FavrilHilde De CockMatthijs VynckJonas SteenbruggeWard De SpiegelaereHilde De Rooster

A1 Journal Article in VETERINARY AND COMPARATIVE ONCOLOGY

Towards automated integration and quality assessment of chromatographic peaks in targeted LC-MS data with TARDIS

Pablo VangeenderhuysenMatthijs VynckBeata PomianKimberly De WindtEmile CallemeynEllen De PaepeLindsey De CommerJeroen RaesTim MawrotJohannes Rainer et al.

Towards enhanced reproducibility and performance of quality control sample-based normalization : key issues and new ideas

Matthijs VynckPablo VangeenderhuysenEllen De PaepeLieselot HemeryckVera PlekhovaLynn Vanhaecke

Towards sensitive and cost-effective chimerism assays using FABCASE : a fast approach for estimating assay informativity

A1 Journal Article in INTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY

2024

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

Yao ChenWard De SpiegelaereWim TrypsteenDavid GleerupJo VandesompeleAntoon LievensMatthijs VynckOlivier Thas

A1 Journal Article in BRIEFINGS IN BIOINFORMATICS

Digital PCR threshold robustness analysis and optimization using dipcensR

Matthijs VynckWim TrypsteenOlivier ThasJo VandesompeleWard De Spiegelaere

A1 Journal Article in BRIEFINGS IN BIOINFORMATICS

Treatment randomisation at animal or pen level? Statistical analysis should follow the randomisation pattern!

Luc DuchateauRobrecht DockxKlara GoethalsMatthijs VynckFrédéric VangroenwegheChristian Paul G. Burvenich

A1 Journal Article in LABORATORY ANIMALS

2023

Bias reduction improves accuracy and informativity of high-throughput sequencing chimerism assays

Matthijs VynckFriedel NolletLode SibbensHelena Devos

A1 Journal Article in CLINICA CHIMICA ACTA

Comparative assessment of survival and clinical outcome between two commercial vitrification kits with different warming protocols after blastocyst culture : potential perspectives toward simplified warming procedures

Jan GunstMatthijs VynckKatleen HostensValerie StandaertSylvie RoggemanArne van de Vijver

A1 Journal Article in REPRODUCTIVE SCIENCES

Digital PCR partition classification

Matthijs VynckYao ChenDavid GleerupJo VandesompeleWim TrypsteenAntoon LievensOlivier ThasWard De Spiegelaere

A1 Journal Article in CLINICAL CHEMISTRY

2022

Chimerism monitoring using biallelic single nucleotide or insertion/deletion polymorphisms : how many markers to screen?

Matthijs VynckFriedel NolletLode SibbensHelena Devos

A1 Journal Article in CLINICA CHIMICA ACTA

Some key considerations regarding the design and evaluation of high-throughput sequencing-based biallelic chimerism assays

A1 Journal Article in INTERNATIONAL JOURNAL OF HEMATOLOGY

2021

Dynamics of the cellular and humoral immune response after BNT162b2 mRNA Covid-19 vaccination in Covid-19 naive nursing home residents

Jens Van PraetStefaan VandecasteeleAnneleen De RooMatthijs VynckAn De VrieseMarijke Reynders

A1 Journal Article in JOURNAL OF INFECTIOUS DISEASES

Performance assessment of the Devyser high-throughput sequencing-based assay for chimerism monitoring in patients after allogeneic hematopoietic stem cell transplantation

Matthijs VynckFriedel NolletLode SibbensBernadette LievensAstrid DenysBarbara CauwelierHelena Devos

A1 Journal Article in JOURNAL OF MOLECULAR DIAGNOSTICS

2020

Malignant progression of donor-engrafted clonal hematopoiesis in sibling recipients after stem cell transplantation

Louis NevejanFriedel NolletHelena DevosMatthijs VynckPieter Van VlierbergheMercedeh TajdarTom LodewyckDominik Selleslag

Editorial material

2019

Power Doppler ultrasound and contrast-enhanced ultrasound demonstrate non-invasive tumour vascular response to anti-vascular therapy in canine cancer patients

Eline AbmaEmmelie StockWard De SpiegelaereLeen Van BrantegemKatrien VanderperrenYicheng NiMatthijs VynckSylvie DaminetKaat De ClercqHilde De Rooster

A1 Journal Article in SCIENTIFIC REPORTS

2018

A single dose of intravenous combretastatin A4-phosphate is reasonably well tolerated and significantly reduces tumour vascularization in canine spontaneous cancers

Eline AbmaWard De SpiegelaereKatrien VanderperrenEmmelie StockLeen Van BrantegemIne CornelisSylvie DaminetY NiMatthijs VynckGlenn Verstraete et al.

A1 Journal Article in VETERINARY AND COMPARATIVE ONCOLOGY

Data analysis methods for digital PCR quantification

Matthijs VynckOlivier ThasJo Vandesompele

On determining the power of digital PCR experiments

Matthijs VynckJo VandesompeleOlivier Thas

A1 Journal Article in ANALYTICAL AND BIOANALYTICAL CHEMISTRY

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

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

A1 Journal Article in CLINICAL GENITOURINARY CANCER

Reducing bias in digital PCR experiments by appropriate modelling of volume variability

Matthijs VynckOlivier Thas

Reducing bias in digital PCR quantification experiments : the importance of appropriate modelling of volume variability

Matthijs VynckOlivier Thas

A1 Journal Article in ANALYTICAL CHEMISTRY

2017

A digital PCR data analysis workflow : from sample to effective result

Matthijs VynckOlivier Thas

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

Peter PipelersLieven ClementMatthijs VynckJan HellemansJo VandesompeleOlivier Thas

A1 Journal Article in PLOS ONE

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

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

Breath analysis by gas chromatography-mass spectrometry and electronic nose to screen for pleural mesothelioma : a cross-sectional case-control study

Kevin LamotePaul BrinkmanLore VandermeerschMatthijs VynckPeter J SterkHerman Van LangenhoveOlivier ThasJoris Van CleemputKristiaan NackaertsJan Van Meerbeeck

A1 Journal Article in ONCOTARGET

Exhaled breath analysis allows exclusive screening for malignant pleural mesothelioma

Kevin LamoteMatthijs VynckOlivier ThasJoris Van CleemputKristiaan NackaertsJan Van Meerbeeck

Exhaled breath to screen for malignant pleural mesothelioma : a validation study

Kevin LamoteMatthijs VynckOlivier ThasJoris Van CleemputKristiaan NackaertsJan Van Meerbeeck

A1 Journal Article in EUROPEAN RESPIRATORY JOURNAL

Quality control of digital PCR assays and platforms

Matthijs VynckJo VandesompeleOlivier Thas

A1 Journal Article in ANALYTICAL AND BIOANALYTICAL CHEMISTRY

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

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

2016

Detection of malignant pleural mesothelioma in exhaled breath by multicapillary column/ion mobility spectrometry (MCC/IMS)

Kevin LamoteMatthijs VynckJoris Van CleemputOlivier ThasKristiaan NackaertsJan Van Meerbeeck

A1 Journal Article in JOURNAL OF BREATH RESEARCH

Flexible analysis of digital PCR experiments using generalized linear mixed models

Matthijs VynckJo VandesompeleNele NijsBjörn MentenAriane De GanckOlivier Thas

A2 Journal Article in BIOMOLECULAR DETECTION AND QUANTIFICATION

The future of digital polymerase chain reaction in virology

Matthijs VynckWim TrypsteenOlivier ThasLinos VandekerckhoveWard De Spiegelaere

A1 Journal Article in MOLECULAR DIAGNOSIS & THERAPY

Threshold setting in duplex digital PCR experiments

Matthijs VynckOlivier Thas

2015

Breath analysis by ion mobility spectrometry allows discrimination of pleural mesothelioma patients from controls

Kevin LamoteMatthijs VynckJoris Van CleemputOlivier ThasKristiaan NackaertsJan Van Meerbeeck

Data analysis of droplet digital PCR with generalized linear mixed models

Olivier ThasMatthijs VynckJo Vandesompele

ddcRquant: threshold determination for single channel droplet digital PCR experiments

Wim TrypsteenMatthijs VynckJan De NevePawel BonczkowskiMaja KiselinovaEva MalatinkováKAREN VERVISCHOlivier ThasLinos VandekerckhoveWard De Spiegelaere

ddpcRquant: threshold determination for single channel droplet digital PCR experiments

Wim TrypsteenMatthijs VynckJan De NevePawel BonczkowskiMaja KiselinovaEva MalatinkováKAREN VERVISCHOlivier ThasLinos VandekerckhoveWard De Spiegelaere

A1 Journal Article in ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Extreme value theory for threshold determination in droplet digital PCR experiments

Matthijs VynckWim TrypsteenJan De NevePawel BonczkowskiMaja KiselinovaEva MalatinkováKAREN VERVISCHOlivier ThasLinos VandekerckhoveWard De Spiegelaere

GLMMs for nucleic acid concentration estimation in digital droplet PCR

Matthijs VynckJo VandesompeleOlivier Thas

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

Matthijs VynckJo VandesompeleOlivier Thas

Threshold determination in droplet digital PCR experiments using extreme value theory

Matthijs VynckWim TrypsteenJan De NevePawel BonczkowskiMaja KiselinovaEva MalatinkováKAREN VERVISCHOlivier ThasLinos VandekerckhoveWard De Spiegelaere

Volatile organic compounds increase the likelihood of detecting malignant pleural mesothelioma

Kevin LamoteMatthijs VynckJoris Van CleemputOlivier ThasKristiaan NackaertsJan Van Meerbeeck