Research Explorer

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Researcher

Lieven Clement

Awards & Distinctions

92 Results

2024

Methods for differential expression analysis in single-cell transcriptomics at the gene- and subgene level

Jeroen GilisLieven ClementYvan SaeysKoen Van den Berge

Novel statistical strategies for differential PTM abundance analysis in proteomics

Nina DemeulemeesterLennart MartensLieven Clement

msqrob2PTM : differential abundance and differential usage analysis of MS-based proteomics data at the post-translational modification and peptidoform level

Nina DemeulemeesterMarie GébelinLucas Caldi GomesPaul LingorChristine CarapitoLennart MartensLieven Clement

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

2023

Exploring the microbial response as a potential bio-indicator for soil health : insights from a controlled incubator experiment

Lisa JoosCaroline De TenderAstrid HolderbekeLieven ClementBart VandecasteeleJane Debode

A1 Journal Article in AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Juggling offsets unlocks RNA-seq tools for fast scalable differential usage, aberrant splicing and expression analyses

Alexandre SegersJeroen GilisMattias Van HeetveldeElfride De BaereLieven Clement

Jumping over hurdles : deciphering the soil microbiome and its link to soil health

Lisa JoosLieven ClementCaroline De TenderJane DebodeBart Vandecasteele

Quality control for the target decoy approach for peptide identification

Elke DebrieMilan MalfaitRalf GabrielsArthur DeclercqAdriaan StickerLennart MartensLieven Clement

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2022

An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia

Lien ProvezBart Van PuyveldeLaura CorveleynNina DemeulemeesterSigrid VerhelstBeatrice LintermansSimon DaledJuliette RoelsLieven ClementLennart Martens et al.

A1 Journal Article in SCIENTIFIC DATA

2021

Altering the sex pheromone cyclo(L-Pro-L-Pro) of the diatom Seminavis robusta towards a chemical probe

Eli BonneureAmber De BaetsSam De DeckerKoen Van den BergeLieven ClementWim VyvermanSven Mangelinckx

A1 Journal Article in INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Chitin in strawberry cultivation : foliar growth and defense response promotion, but reduced fruit yield and disease resistance by nutrient imbalances

Caroline De TenderBart VandecasteeleBruno VerstraetenSarah OmmeslagTim De MeyerJill De VisscherPeter DawyndtLieven ClementTina KyndtJane Debode

A1 Journal Article in MOLECULAR PLANT-MICROBE INTERACTIONS

Life history regulation of the benthic pennate diatom Seminavis robusta : a transcriptomic, comparative genomic and physiological study

Gust BilckeWim VyvermanLieven De VeylderLieven Clement

Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta

Gust BilckeKoen Van den BergeSam De DeckerEli BonneureNicole PoulsenPetra BulánkováCristina OsunaJack DickensonKoen SabbeGeorg Pohnert et al.

A1 Journal Article in ISME JOURNAL

satuRn : Scalable Analysis of differential Transcript Usage for bulk and single-cell RNA-sequencing applications

Jeroen GilisKristoffer Vitting-SeerupKoen Van den BergeLieven Clement

satuRn: Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications

Jeroen GilisKristoffer Vitting-SeerupKoen Van den BergeLieven Clement

A2 Journal Article in F1000RESEARCH

2020

Daring to be differential : metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units

Lisa JoosStien BeirinckxAnnelies HaegemanJane DebodeBart VandecasteeleSteve BaeyenSofie GoormachtigLieven ClementCaroline De Tender

A1 Journal Article in BMC GENOMICS

MSqRob takes the missing hurdle : uniting intensity- and count-based proteomics

Ludger GoeminneAdriaan StickerLennart MartensKris GevaertLieven Clement

A1 Journal Article in ANALYTICAL CHEMISTRY

Pitfalls in re-analysis of observational omics studies: a post-mortem of the human pathology atlas

Jeroen GilisSteff TaelmanLucas DaveyLennart MartensLieven Clement

Robust summarization and inference in proteome-wide label-free quantification

Adriaan StickerLudger GoeminneLennart MartensLieven Clement

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Trajectory-based differential expression analysis for single-cell sequencing data

Koen Van den BergeHector Roux de BézieuxKelly StreetWouter SaelensRobrecht CannoodtYvan SaeysSandrine DudoitLieven Clement

A1 Journal Article in NATURE COMMUNICATIONS

2019

RNA sequencing data : hitchhiker's guide to expression analysis

Koen Van den BergeKatharina M HembachCharlotte SonesonSimone TiberiLieven ClementMichael I LoveRob PatroMark D Robinson

A2 Journal Article in ANNUAL REVIEW OF BIOMEDICAL DATA SCIENCE

Robust summarisation and inference for Label-Free Quantification

Adriaan StickerLudger GoeminneLennart MartensLieven Clement

Statistical methods for differential expression analysis in bulk and single-cell RNA-sequencing applications

Koen Van den BergeLieven Clement

Statistical methods for differential proteomics at peptide and protein level

Ludger GoeminneLieven ClementKris Gevaert

2018

Effect of management and age of ploughed out grass-clover on forage maize yield and residual soil nitrogen

Mathias CougnonKoen Van den BergeTommy D'HoseLieven ClementDirk Reheul

A1 Journal Article in JOURNAL OF AGRICULTURAL SCIENCE

Experimental design and data-analysis in label-free quantitative LC/MS proteomics : a tutorial with MSqRob

Ludger GoeminneKris GevaertLieven Clement

A1 Journal Article in JOURNAL OF PROTEOMICS

Identification of immune-responsive gene 1 (IRG1) as a target of A20

Emmy Van QuickelbergheArne MartensLudger GoeminneLieven ClementGeert van LooKris Gevaert

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Neurogenomic profiling reveals distinct gene expression profiles between brain parts that are consistent in ophthalmotilapia cichlids

Sofie DeryckeLoic KéverKoen HertenKoen Van den BergeMaarten Van SteenbergeJeroen Van HoudtLieven ClementPascal PoncinEric ParmentierErik Verheyen

A1 Journal Article in FRONTIERS IN NEUROSCIENCE

Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications

Koen Van den BergeFanny PerraudeauCharlotte SonesonMichael I LoveDavide RissoJean-Philippe VertMark D RobinsonSandrine DudoitLieven Clement

A1 Journal Article in GENOME BIOLOGY

2017

A leap over the hurdle in label-free quantitative proteomics

Ludger GoeminneKris GevaertLieven Clement

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

Analyzing repeated measures designs in label-free proteomics with MSqRob (MCP 2016 15(2):657-68.)

Lieven ClementLudger GoeminneEmmy Van QuickelbergheKris Gevaert

BelPHG-21 : a pilot study on genetic variability in the Belgian population

Tine DescampsEls DelporteJoris Robert VermeerschEls GoetghebeurLieven ClementJean TafforeauStefaan DemarestHerman Van OyenMarc Van den BulckeJimmy Van den Eynden

Confronting bias and precision in digital PCR quantification

Bart JacobsEls GoetghebeurLieven Clement

Flow cytometry for immediate follow-up of drinking water networks after maintenance

Sam Van NevelBenjamin BuysschaertKaren De RoyBart De GussemeLieven ClementNico Boon

A1 Journal Article in WATER RESEARCH

Identifying drivers of sympatric speciation in the marine benthic diatom Seminavis robusta using metabolic analysis and whole-genome resequencing

Sam De DeckerPieter VanormelingenJosefin SefbomChristine LembkeKoen Van den BergheKlaas VandepoeleKoen SabbeLieven De VeylderGeorg PohnertLieven Clement et al.

MSqRob : analysis of label-free proteomics data in an R/Shiny environment

Ludger GoeminneKris GevaertLieven Clement

MSqRob: analysis of label-free proteomics data in an R/Shiny environment

Ludger GoeminneEmmy Van QuickelbergheKris GevaertLieven Clement

Mass spectrometrists should search for all peptides, but assess only the ones they care about

Adriaan StickerLennart MartensLieven Clement

A1 Journal Article in NATURE METHODS

Model-based classification for digital PCR : your Umbrella for rain

Bart JacobsEls GoetghebeurJo VandesompeleAriane De GanckNele NijsAnneleen BeckersNina PapazovaNancy H RoosensLieven Clement

A1 Journal Article in ANALYTICAL CHEMISTRY

Using variant databases for variant prioritization and to detect erroneous genotype-phenotype associations

Bart BroeckxLuc PeelmanJimmy SaundersDieter DeforceLieven Clement

A1 Journal Article in BMC BIOINFORMATICS

stageR : a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage

Koen Van den BergeCharlotte SonesonMark D RobinsonLieven Clement

A1 Journal Article in GENOME BIOLOGY

2016

A sex-inducing pheromone triggers cell cycle arrest and mate attraction in the diatom Seminavis robusta

Sara MoeysJohannes FrenkelChristine LembkeJeroen GillardValerie DevosKoen Van den BergeBarbara BouillonMarie HuysmanSam De DeckerJulia Scharf et al.

A1 Journal Article in SCIENTIFIC REPORTS

Dynamics in the strawberry rhizosphere microbiome in response to biochar and Botrytis cinerea leaf infection

Caroline De TenderAnnelies HaegemanBart VandecasteeleLieven ClementPieter CremeliePeter DawyndtMartine MaesJane Debode

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Faecal proteomics : a tool to investigate dysbiosis and inflammation in patients with cystic fibrosis

Griet DebyserBart MesuereLieven ClementJens Van de WeygaertPieter Van HeckeGwen DuytschaeverMaarten AertsPeter DawyndtKris De BoeckPeter Vandamme et al.

A1 Journal Article in JOURNAL OF CYSTIC FIBROSIS

Measuring the biodiversity of microbial communities by flow cytometry

Ruben PropsPieter MonsieursMohamed MysaraLieven ClementNico Boon

A1 Journal Article in METHODS IN ECOLOGY AND EVOLUTION

Peptide-level robust ridge regression improves estimation, sensitivity, and specificity in data-dependent quantitative label-free shotgun proteomics

Ludger GoeminneKris GevaertLieven Clement

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

moFF : a robust and automated approach to extract peptide ion intensities

Andrea ArgentiniLudger GoeminneKenneth VerheggenNiels HulstaertAn StaesLieven ClementLennart Martens

A1 Journal Article in NATURE METHODS

2015

A cross-sectional and longitudinal metaproteomics approach reveals intestinal dysbiosis, and the presence of markers of chronic inflammation and mucus-related proteins in faecal samples of patients with cystic fibrosis

Griet DebyserBart MesuereJens Van de WeygaertLieven ClementMaarten AertsGwen DuytschaeverPeter DawyndtK De BoeckPeter VandammeBart Devreese

Leaf responses to mild drought stress in natural variants of Arabidopsis

Pieter ClauwFrederik CoppensKristof De BeufStijn DhondtTwiggy Van DaeleKatrien MaleuxVeronique StormeLieven ClementNathalie Gonzalez SanchezDirk Inzé

A1 Journal Article in PLANT PHYSIOLOGY

Peptide-level robust ridge regression modeling improves both sensitivity and specificity in quantitative proteomics

Ludger GoeminneLieven ClementKris GevaertKlaas Vandepoele

QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles

Koen van der BorghtKim ThysYves WetzelsLieven ClementBie VerbistJoke ReumersHerman van VlijmenJeroen Aerssens

A1 Journal Article in BMC BIOINFORMATICS

Quantifying expression divergence of duplicated genes with microarrays

Koen Van den BergeRiet De SmetYves Van de PeerLieven Clement

Robust peptide-based models in quantitative proteomics

Ludger GoeminneKlaas VandepoeleKris GevaertLieven Clement

Summarization vs. peptide-based models in label-free quantitative proteomics : performance, pitfalls, and data analysis guidelines

Ludger GoeminneAndrea ArgentiniLennart MartensLieven Clement

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Using transcriptomics to guide lead optimization in drug discovery projects : lessons learned from the QSTAR project

Bie VerbistGünter KlambauerLiesbet VervoortWillem TalloenZiv ShkedyOlivier ThasAndreas BenderHinrich WH GöhlmannSepp Hochreiterthe QSTAR Consortium et al.

A1 Journal Article in DRUG DISCOVERY TODAY

ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering

Bie VerbistLieven ClementJoke ReumersKim ThysAlexander VapirevWillem TalloenYves WetzelsJoris MeysJeroen AerssensLuc Bijnens et al.

A1 Journal Article in BMC BIOINFORMATICS

VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering

Bie VerbistKim ThysJoke ReumersYves WetzelsKoen Van der BorghtWillem TalloenJeroen AerssensLieven ClementOlivier Thas

A1 Journal Article in BIOINFORMATICS

2014

Impact of variance components on reliability of absolute quantification using digital PCR

Bart JacobsEls GoetghebeurLieven Clement

A1 Journal Article in BMC BIOINFORMATICS

Low-frequency variant detection in viral populations using massively parallel sequencing data

Bie VerbistOlivier ThasLieven Clement

unifiedWMWqPCR: the unified Wilcoxon–Mann–Whitney test for analyzing RT-qPCR data in R

Jan De NeveJoris MeysJean-Pierre OttoyLieven ClementOlivier Thas

A1 Journal Article in BIOINFORMATICS

2013

An extension of the Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data

Jan De NeveOlivier ThasJean-Pierre OttoyLieven Clement

A1 Journal Article in STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY

QTL analysis of high thermotolerance with superior and downgraded parental yeast strains reveals new minor QTLs and converges on novel causative alleles involved in RNA processing

Yudi YangMaria R Foulquié-MorenoLieven ClementÉva ErdeiAn TangheKristien SchaerlaekensFrançoise DumortierJohan M Thevelein

A1 Journal Article in PLOS GENETICS

Simultaneous mapping of multiple gene loci with pooled segregants

Jürgen ClaesenLieven ClementZiv ShkedyMaria R Foulquié-MorenoTomasz Burzykowski

A1 Journal Article in PLOS ONE

Statistical methods for high-throughput genomic data

Kristof De BeufOlivier ThasLieven ClementJean-Pierre Ottoy

beadarrayFilter : an R package to filter beads

Anyiawung Chiara ForchehGeert VerbekeAdetayo KasimDan LinZiv ShkedyWillem TalloenHinrich WH GöhlmannLieven Clement

A1 Journal Article in R JOURNAL

2012

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

Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling)

Kristof De BeufPeter PipelersMegan AndriankajaOlivier ThasDirk InzéCiprian CrainiceanuLieven Clement

A1 Journal Article in BMC BIOINFORMATICS

Fast wavelet based functional models for transcriptome analysis with tiling arrays

Lieven ClementKristof De BeufOlivier ThasMarnik VuylstekeRafael IrizarryCiprian M Crainiceanu

A1 Journal Article in STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY

Flow cytometry for fast microbial community fingerprinting

Karen De RoyLieven ClementOlivier ThasYingying WangNico Boon

Flow cytometry for fast microbial community fingerprinting

Karen De RoyLieven ClementOlivier ThasYingying WangNico Boon

A1 Journal Article in WATER RESEARCH

Gene filtering in the analysis of illumina microarray experiments

Anyiawung Chiara ForchehGeert VerbekeAdetayo KasimDan LinZiv ShkedyWillem TalloenHinrich WH GoehlmannLieven Clement

A1 Journal Article in STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY

Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis

Steve SwinnenKristien SchaerlaekensThiago PaisJürgen ClaesenGeorg HubmannYudi YangMekonnen DemekeMaria R Foulquié-MorenoAnnelies GoovaertsKris Souvereyns et al.

A1 Journal Article in GENOME RESEARCH

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

Probabilistic index models

Olivier ThasJan De NeveLieven ClementJean-Pierre Ottoy

A1 Journal Article in JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

2011

Flow cytometry community fingerprinting to detect quickly stress in drinking water systems

Karen De RoyYingying WangLieven ClementOlivier ThasNico Boon

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

Probabilistic index models

Jan De NeveOlivier ThasLieven ClementJean-Pierre Ottoy

The use of semiparametric mixed models to analyze PamChip® peptide array data: an application to an oncology experiment

Pushpike J ThilakarathneLieven ClementDan LinZiv ShkedyAdetayo KasimWillem TalloenMatthias VerseleGeert Verbeke

A1 Journal Article in BIOINFORMATICS

2009

A semiparametric unified approach for the detection of differential gene expression in microarrays

Jan De NeveOlivier ThasLieven ClementJean-Pierre Ottoy

Initial community evenness favours functionality under selective stress

Lieven WittebolleMassimo MarzoratiLieven ClementAnnalisa BalloiDaniele DaffonchioKim HeylenPaul De VosWilly VerstraeteNico Boon

A1 Journal Article in NATURE

Monte Carlo simulation of false change in the overlay of misregistered forest vector maps

Eva M De ClercqLieven ClementRobert De Wulf

A1 Journal Article in LANDSCAPE AND URBAN PLANNING

Nonparametric trend detection in river monitoring network data: a spatio-temporal approach

Lieven ClementOlivier Thas

A1 Journal Article in ENVIRONMETRICS

Testing for trends in the violation frequency of an environmental threshold in rivers

Lieven ClementOlivier Thas

A1 Journal Article in ENVIRONMETRICS

2007

Data management of river water quality data: a semi-automatic procedure for data validation

Lieven ClementOlivier ThasJean-Pierre OttoyPeter A Vanrolleghem

A1 Journal Article in WATER RESOURCES RESEARCH

Estimating and modeling spatio-temporal correlation structures for river monitoring networks

Lieven ClementOlivier Thas

A1 Journal Article in JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS

Statistical validation and spatio-temporal modelling of river monitoring networks

Lieven ClementO ThasP Vanrolleghem

2006

Nonparametric trend detection in spatio-temporal river monitoring networks

Lieven ClementOlivier Thas

Spatio-temporal statistical models for river monitoring networks

Lieven ClementOlivier ThasPeter VanrolleghemJean-Pierre Ottoy

A1 Journal Article in WATER SCIENCE AND TECHNOLOGY

2005

Spatio-temporal river monitoring network modelling

Lieven ClementOlivier Thas

2004

Spatio-Temporal Statistical Models for River Monitoring Networks

Lieven ClementOlivier ThasPeter VanrolleghemJean-Pierre Ottoy

2003

Statistical validation of water quality data

Lieven ClementOlivier ThasPeter VanrolleghemJean-Pierre Ottoy

2001

An overview of the posters presented at Watermatex 2000. II. Sensor/monitoring, control and decision support systems

Eveline VolckeLieven ClementM VAN DE STEENEPA VANROLLEGHEM

A1 Journal Article in WATER SCIENCE AND TECHNOLOGY