Research Explorer

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Researcher

Wim Trypsteen

Awards & Distinctions

73 Results

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

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

Willem van SnippenbergPieter MestdaghLinos VandekerckhoveWim Trypsteen

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

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

A1 Journal Article in MOLECULAR ONCOLOGY

2023

Digital PCR partition classification

Matthijs VynckYao ChenDavid GleerupJo VandesompeleWim TrypsteenAntoon LievensOlivier ThasWard De Spiegelaere

A1 Journal Article in CLINICAL CHEMISTRY

Evaluating lncRNA expression patterns during HIV-1 treatment interruption

Tinus SchynkelWillem van SnippenbergClarissa Van HeckeLinos VandekerckhoveWim Trypsteen

A1 Journal Article in INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

Tinus SchynkelLinos VandekerckhoveWim TrypsteenPieter Mestdagh

Targeted plasma proteomics identifies MICA and IL1R1 proteins associated with HIV-1 reservoir size

Marc J. T. BlaauwJessica Cristina dos SantosNadira VadaqWim TrypsteenWouter van der HeijdenAlbert GroenendijkZhenhua ZhangYang LiQuirijn de MastMihai G. Netea et al.

A1 Journal Article in ISCIENCE

The Rainbow 5-plex digital PCR assay improves quantification of the viral reservoir resulting in a better understanding of the HIV-1 proviral landscape

Mareva DelporteLaurens LambrechtsMarion PardonsSofie De BraekeleerEvy BlommeSofie RutsaertWim TrypsteenLinos Vandekerckhove

2022

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

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

A1 Journal Article in BIOTECHNOLOGY JOURNAL

Impact of switch towards 3TC/dolutegravir on the intact and total viral reservoir in the Rumba study

Evy BlommeWim TrypsteenMareva DelporteC. MucciniE. De SmetSophie DegrooteEls TobbackSophie VanherrewegeE. CaluweMarie-Angélique De Scheerder et al.

People with HIV have higher percentages of circulating CCR5+CD8+T cells and lower percentages of CCR5+regulatory T cells

Louise E. van EekerenVasiliki MatzarakiZhenhua ZhangLisa van de WijerMarc J. T. BlaauwMarien I. de JongeLinos VandekerckhoveWim TrypsteenLeo A. B. JoostenMihai G. Netea et al.

A1 Journal Article in SCIENTIFIC REPORTS

Triplex digital PCR assays for the quantification of intact proviral HIV-1 DNA

Willem van SnippenbergDavid GleerupSofie RutsaertLinos VandekerckhoveWard De SpiegelaereWim Trypsteen

A1 Journal Article in METHODS

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

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

2021

Chronic HIV infection induces transcriptional and functional reprogramming of innate immune cells

Wouter A. van der HeijdenLisa Van de WijerFarid KeramatiWim TrypsteenSofie RutsaertRob ter HorstMartin JaegerHans J.P.M. KoenenHendrik G. StunnenbergIrma Joosten et al.

A1 Journal Article in JCI INSIGHT

Digital polymerase chain reaction for assessment of mutant mitochondrial carry-over after nuclear transfer for In Vitro fertilization

Olivier TytgatMX TangWillem van SnippenbergAnnekatrien BoelRR GuggillaYannick GansemansMichiel Van HerpSofie SymoensWim TrypsteenDieter Deforce et al.

A1 Journal Article in CLINICAL CHEMISTRY

Digital polymerase chain reaction for assessment of mutant mitochondrial carry-over after nuclear transfer for in vitro fertilization

Olivier TytgatMaoxing TangWillem van SnippenbergAnnekatrien BoelRamesh GuggillaYannick GansemansMichiel Van HerpSofie SymoensWim TrypsteenDieter Deforce et al.

A1 Journal Article in CLINICAL CHEMISTRY

Organ-specific genome diversity of replication-competent SARS-CoV-2

Jolien Van CleemputWillem van SnippenbergLaurens LambrechtsAmélie DendoovenValentino D'OnofrioLiesbeth CouckWim TrypsteenJan VanrusseltSebastiaan TheunsNick Vereecke et al.

A1 Journal Article in NATURE COMMUNICATIONS

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

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

A1 Journal Article in GENES CHROMOSOMES & CANCER

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 architecture of circulating immune cells Is dysregulated in people living with HIV on long term antiretroviral treatment and relates with markers of the HIV-1 reservoir, cytomegalovirus, and microbial tanslocation

Lisa Van de WijerWouter A. van der HeijdenRob ter HorstMartin JaegerWim TrypsteenSofie RutsaertBram van CranenbroekEsther van RijssenIrma JoostenLeo Joosten et al.

A1 Journal Article in FRONTIERS IN IMMUNOLOGY

2020

Emerging PCR-based techniques to study HIV-1 reservoir persistence

Laurens LambrechtsBasiel ColeSofie RutsaertWim TrypsteenLinos Vandekerckhove

A1 Journal Article in VIRUSES-BASEL

Evaluating predictive markers for viral rebound and safety assessment in blood and lumbar fluid during HIV-1 treatment interruption

Marie-Angélique De ScheerderClarissa Van HeckeHenrik ZetterbergDietmar FuchsNele De LangheSofie RutsaertBram VranckenWim TrypsteenYtse NoppeBeatrijs Van Der Gucht et al.

A1 Journal Article in JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

Sam KintWim Van CriekingeLinos VandekerckhoveWim Trypsteen

Interferon-mediated long non-coding RNA response in macrophages in the context of HIV

Tinus SchynkelMatthew A. SzaniawskiAdam M. SpivakAlberto BosqueVicente PlanellesLinos VandekerckhoveWim Trypsteen

A1 Journal Article in INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

On the whereabouts of SARS-CoV-2 in the human body : a systematic review

Wim TrypsteenJolien Van CleemputWillem van SnippenbergSarah GerloLinos Vandekerckhove

A1 Journal Article in PLOS PATHOGENS

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

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

Jasper VerwiltWim TrypsteenRuben Van PaemelKatleen De PreterMD GiraldezPieter MestdaghJo Vandesompele

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

2019

Decreased NEAT1 and MALAT1 levels in HIV-1 positive individuals with high viral load

Clarissa Van HeckeSabine Kinloch-de LoesTinus SchynkelEva MalatinkováKaren VervischSofie RutsaertWim TrypsteenLinos Vandekerckhove

Decreased NEAT1 and MALAT1 levels in HIV-1 positive individuals with high viral load

Clarissa Van HeckeSabine Kinloch-de LoesTinus SchynkelEva MalatinkováKaren VervischSofie RutsaertWim Trypsteen

Early treated HIV-1 positive individuals demonstrate similar restriction factor expression profile as long-term non-progressors

Clarissa Van HeckeWim TrypsteenEva MalatinkováWard De SpiegelaereKaren VervischSofie RutsaertSabine Kinloch-de LoesMagdalena SipsLinos Vandekerckhove

A1 Journal Article in EBIOMEDICINE

Interferon-mediated long non-coding RNA response to HIV infection in macrophages

Tinus SchynkelClarissa Van HeckeVicente PlanellesLinos VandekerckhoveWim Trypsteen

Long non-coding RNAs and latent HIV : a search for novel targets for latency reversal

Wim TrypsteenCory H WhiteAmey MukimCelsa A SpinaWard De SpiegelaereSteve LefeverChristopher H WoelkAlberto BosqueLinos VandekerckhoveNadejda Beliakova-Bethell

Long non-coding RNAs and latent HIV : a search for novel targets for latency reversal

Wim TrypsteenCory H WhiteAmey MukimCelsa A SpinaWard De SpiegelaereSteve LefeverVicente PlanellesAlberto BosqueChristopher H WoelkLinos Vandekerckhove et al.

A1 Journal Article in PLOS ONE

Transcriptomic correlates of HIV reservoir size during antiretroviral therapy

Wim TrypsteenMohamed Abdel-MohsenXutao DengChristopher D PilcherSteven G DeeksLinos VandekerckhoveSatish K Pillai

2018

Beneficial impact of early treatment on restriction factor expression profile

Clarissa Van HeckeMagdalena SipsEva MalatinkováWard De SpiegelaereKaren VervischMargaret JohnsonSabine Kinloch-de LoesWim TrypsteenLinos Vandekerckhove

Beneficial impact of early treatment on restriction factor expression profile

Clarissa Van HeckeWim TrypsteenEva MalatinkováWard De SpiegelaereKaren VervischMargaret JohnsonSabine Kinloch-de LoesMagdalena SipsLinos Vandekerckhove

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

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

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

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

Digital PCR as a tool to measure HIV persistence

Sofie RutsaertKobus BosmanWim TrypsteenMonique NijhuisLinos Vandekerckhove

A1 Journal Article in RETROVIROLOGY

In-depth validation of total HIV-1 DNA assays for quantification of various HIV-1 subtypes

Sofie RutsaertWard De SpiegelaereClarissa Van HeckeMarie-Angélique De ScheerderMaja KiselinovaKaren VervischWim TrypsteenLinos Vandekerckhove

A1 Journal Article in SCIENTIFIC REPORTS

Standardizing digital PCR diagnostics and pioneering long non-coding RNA discovery in the context of HIV cure research

Wim TrypsteenLinos VandekerckhoveWard De Spiegelaere

2017

Beneficial impact of early treatment on restriction factor expression profile

Clarissa Van HeckeMagdalena SipsEva MalatinkováWard De SpiegelaereKaren VervischMargaret JohnsonSabine Kinloch-de LoesWim TrypsteenLinos Vandekerckhove

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

Wim TrypsteenCory WhiteAlberto BosqueCelsa SpinaSteve LefeverPieter MestdaghLinos VandekerckhoveNadejd Beliakova-Bethell

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

Wim TrypsteenCory WhiteAlberto BosqueSteve LefeverPieter MestdaghLinos VandekerckhoveChristopher Woelk

Cross-validation of HIV DNA assays to quantify different HIV-1 subtypes

Sofie RutsaertWard De SpiegelaereClarissa Van HeckeMarie-Angélique De ScheerderMaja KiselinovaKaren VervischWim TrypsteenLinos Vandekerckhove

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

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

Digital PCR in health care and clinical diagnostics : data analysis challenges

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

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

A2 Journal Article in BIOMOLECULAR DETECTION AND QUANTIFICATION

Highlights from the 24th conference on retroviruses and opportunistic infections, 13-16 February 2017, Seattle, Washington, USA

Trevor A CrowellHermione LyallEva MalatinkováSanjay BhaganiDenise HsuDonn J ColbyChristina PolyakChristina PsomasAndrew HillEsther N Gathogo et al.

A1 Journal Article in JOURNAL OF VIRUS ERADICATION

Short-course Toll-like receptor 9 agonist treatment impacts innate immunity and plasma viremia in individuals with human immunodeficiency virus infection

Line VibholmMariane H SchleimannJesper F HøjenThomas BenfieldRasmus OffersenKatrine RasmussenRikke OlesenAnders DigeJørgen AgnholtJudith Grau et al.

A1 Journal Article in CLINICAL INFECTIOUS DISEASES

The expression profile of host restriction factors in different cohorts of HIV-1 infected patients

Clarissa Van HeckeEva MalatinkováMargaret JohnsonSabine Kinloch-de LoesWim TrypsteenLinos Vandekerckhove

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

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

2016

Diagnostic utility of droplet digital PCR for HIV reservoir quantification

Wim TrypsteenMaja KiselinovaLinos VandekerckhoveWard De Spiegelaere

A2 Journal Article in JOURNAL OF VIRUS ERADICATION

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

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

A1 Journal Article in SCIENTIFIC REPORTS

HIV-1 Vpr N-terminal tagging affects alternative splicing of the viral genome

Ann BaeyensEvelien NaessensAnouk Van NuffelKarin WeeningAnne-Marie ReillyEva ClaeysWim TrypsteenLinos VandekerckhoveSven EyckermanKris Gevaert et al.

A1 Journal Article in SCIENTIFIC REPORTS

Modeling HIV-1 latency in primary T cells using a replication-competent virus

Laura MartinsPawel BonczkowskiAdam M SpivakWard De SpiegelaereCamille L NovisAna Beatriz DePaula-SilvaEva MalatinkováWim TrypsteenAlberto BosqueLinos Vandekerckhove et al.

A1 Journal Article in AIDS RESEARCH AND HUMAN RETROVIRUSES

The future of digital polymerase chain reaction in virology

Matthijs VynckWim TrypsteenOlivier ThasLinos VandekerckhoveWard De Spiegelaere

A1 Journal Article in MOLECULAR DIAGNOSIS & THERAPY

2015

Accurate quantification of episomal HIV-1 two-long terminal repeat circles by use of optimized DNA isolation and droplet digital PCR

Eva MalatinkováMaja KiselinovaPawel BonczkowskiWim TrypsteenPeter MessiaenJolien VermeireBruno VerhasseltKAREN VERVISCHLinos VandekerckhoveWard De Spiegelaere

A1 Journal Article in JOURNAL OF CLINICAL MICROBIOLOGY

Comparison of methods for in-house screening of HLA*B57:01 to prevent abacavir hypersensitivity in HIV-1 care

Ward De SpiegelaereJan PhilippéKAREN VERVISCHChris VerhofstedeEva MalatinkováMaja KiselinovaWim TrypsteenPawel BonczkowskiDirk VogelaersSteven Callens et al.

A1 Journal Article in PLOS ONE

Extreme value theory for threshold determination in droplet digital PCR experiments

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

HIV-1 RNA and HIV-1 DNA persistence during suppressive ART with PI-based or nevirapine-based regimens

Maja KiselinovaAnna Maria GerettiEva MalatinkováKAREN VERVISCHApostolos BeloukasPeter MessiaenPawel BonczkowskiWim TrypsteenSteven CallensChris Verhofstede et al.

A1 Journal Article in JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Impact of a decade of successful antiretroviral therapy initiated at HIV-1 seroconversion on blood and mucosal reservoirs

Eva MalatinkováWard De SpiegelaerePawel BonczkowskiMaja KiselinovaWim TrypsteenMargaret JohnsonChris VerhofstedeDanny De LoozeCharles MurraySabine Kinloch-de Loes et al.

A1 Journal Article in ELIFE

Impact of a decade of successful antiretroviral therapy started during HIV-1 seroconversion on blood and gut reservoirs

Sabine Kinloch-de LoesEva MalatinkováWard De SpiegelaerePawel BonczkowskiMaja KiselinovaKAREN VERVISCHWim TrypsteenMargaret JohnsonDanny De LoozeLinos Vandekerckhove

Long-term early antiretroviral therapy limits the HIV-1 reservoir size as compared to later treatment initiation but not to levels found in long-term non-progressors

Eva MalatinkováWard De SpiegelaerePawel BonczkowskiMaja KiselinovaKAREN VERVISCHWim TrypsteenMargaret JohnsonChris VerhofstedeDanny De LoozeCharles Murray et al.

Robust regression methods for real-time PCR

Wim TrypsteenJan De NeveKobus BosmanMonique NijhuisOlivier ThasLinos VandekerckhoveWard De Spiegelaere

Robust regression methods for real-time polymerase chain reaction

Wim TrypsteenJan De NeveKobus BosmanMonique NijhuisOlivier ThasLinos VandekerckhoveWard De Spiegelaere

A1 Journal Article in ANALYTICAL BIOCHEMISTRY

Threshold determination in droplet digital PCR experiments using extreme value theory

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

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

2014

Accurate episomal HIV 2-LTR circles quantification using optimized DNA isolation and droplet digital PCR

Eva MalatinkováMaja KiselinovaPawel BonczkowskiWim TrypsteenPeter MessiaenJolien VermeireBruno VerhasseltKaren VervischLinos VandekerckhoveWard De Spiegelaere

Replication competent virus as an important source of bias in HIV latency models utilizing single round viral constructs

Pawel BonczkowskiWard De SpiegelaereAlberto BosqueCory H WhiteAnouk Van NuffelEva MalatinkováMaja KiselinovaWim TrypsteenWojciech WitkowskiJolien Vermeire et al.

A1 Journal Article in RETROVIROLOGY

The impact of nevirapine- versus protease inhibitor-based regimens on virological markers of HIV-1 persistence during seemingly suppressive ART

Maja KiselinovaMaria AnnaEva MalatinkováKAREN VERVISCHApostolos BeloukasPeter MessiaenPawel BonczkowskiWim TrypsteenSteven CallensChris Verhofstede et al.