Research Explorer

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Researcher

Klaas Vandepoele

Publications & Research Data

Awards & Distinctions

208 Results

2026

JASPAR 2026 : expansion of transcription factor binding profiles and integration of deep learning models

Damla Ovek BaydarIeva RauluseviciuteDina R AronsenRomain Blanc-MathieuIne BonthuisHerman De BeukelaerKatalin FerencAlice JegouVipin KumarRoza Berhanu Lemma et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Ready for battle : histone modifications shape rice intergenerational memory to protect against nematode attack

Mohammad Atighi Quchan AtighAniko MeijerTim De MeyerKlaas VandepoeleTina Kyndt

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

2025

A map of integrated cis-regulatory elements enhances gene regulatory analysis in maize

Jasper StautNicolás Manosalva PérezAndres Matres FerrandoIndeewari DissanayakeKlaas Vandepoele

A1 Journal Article in PLANT COMMUNICATIONS

A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators

Yuji KeVincent PujolJasper StautLotte PollarisRuth SeurinckThomas EekhoutCarolin SeyfferthMaite Saura SanchezMichiel Van BelMarnik Vuylsteke et al.

A1 Journal Article in CELL REPORTS

Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean

Gust BilckeLucia CampeseRossella AnnunziataLuz Amadei MartínezCamilla BorgonuovoNadine RijsdijkPeter ChaerleKoen Van den BergeSofie D'hondtDaniele Iudicone et al.

A1 Journal Article in NATURE COMMUNICATIONS

CRISPR/Cas9 editing of p-COUMAROYL-CoA:MONOLIGNOL TRANSFERASE 1 in maize alters phenolic metabolism, lignin structure, and lignin-first biomass processing

Dyoni M. OliveiraMarina de Lyra Soriano SalemeRebecca A. SmithThijs VangeelMarcelo de Freitas LimaAlexandra Alvarenga ChanocaThatiane Rodrigues MotaYasmine VanhevelGriet CoussensKorneel Van Aelst et al.

A1 Journal Article in TRENDS IN BIOTECHNOLOGY

DiatOmicBase : a versatile gene‐centered platform for mining functional omics data in diatom research

Emilie VillarNathanaël ZweigPierre VincensHelena Cruz de CarvalhoCarole DucheneShun LiuRaphael MonteilRichard G. DorrellMichele FabrisKlaas Vandepoele et al.

A1 Journal Article in PLANT JOURNAL

Integrative gene regulatory networks and machine learning unveil the functions of novel maize regulators

Klaas Vandepoele

Editorial material

Modulating the activity of the APC/C regulator SISAMBA improves the sugar and antioxidant content of tomato fruits

Perla Novais de OliveiraLeonardo Perez de SouzaPedro Boscariol FerreiraJean Phillippe MauxionLuis Felipe Correa da SilvaAna Isabela ChangMarina de Lyra Soriano SalemeFeng ZhuSara Selma GarciaHerman De Beukelaer et al.

A1 Journal Article in PLANT BIOTECHNOLOGY JOURNAL

Molecular fingerprints of cell size sensing and mating type differentiation in pennate diatoms

Darja BelišováGust BilckeSien AudoorSofie D'hondtLieven De VeylderKlaas VandepoeleWim Vyverman

A1 Journal Article in NEW PHYTOLOGIST

2024

An improved chromosome‐scale genome assembly and population genetics resource for Populus tremula

Kathryn M. RobinsonBastian SchiffthalerHui LiuSara M. RydmanMartha Rendón‐AnayaTeitur Ahlgren KalmanVikash KumarCamilla CanoviCarolina BernhardssonNicolas Delhomme et al.

A1 Journal Article in PHYSIOLOGIA PLANTARUM

Application of orthology and network biology to infer gene functions in non‐model plants

Klaas VandepoeleSander ThierensMichiel Van Bel

A1 Journal Article in PHYSIOLOGIA PLANTARUM

Arabidopsis transcription factor ANAC102 predominantly expresses a nuclear protein and acts as a negative regulator of methyl viologen-induced oxidative stress responses

Xiaopeng LuoXinqiang JiangVivian SchmittShubhada Rajabhau KulkarniHuy Cuong TranSylwia M KacprzakFrank Van BreusegemOlivier Van AkenKlaas VandepoeleInge De Clercq

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

Exploring the cis-regulatory landscape of plants to unravel gene regulatory networks

Nicolás Manosalva PérezKlaas Vandepoele

Intergenerational acquired resistance against root-knot nematodes in rice : role of DCL3a in spring loading of jasmonate and ethylene responses

Aniko MeijerM. R. AtighiKristof DemeestereTim De MeyerKlaas VandepoeleTina Kyndt

MINI‐AC : inference of plant gene regulatory networks using bulk or single‐cell accessible chromatin profiles

Nicolás Manosalva PérezCamilla FerrariJulia EngelhornThomas DepuydtHilde NelissenThomas HartwigKlaas Vandepoele

A1 Journal Article in PLANT JOURNAL

Molecular fingerprints of cell size sensing and mating type differentiation in pennate diatoms

Darja BelišováGust BilckeSien AudoorSofie D'hondtLieven De VeylderKlaas VandepoeleWim Vyverman

Transcriptional chronology reveals conserved genes involved in pennate diatom sexual reproduction

Sien AudoorGust BilckeKaterina ParganaDarja BelišováSander ThierensMichiel Van BelLieven SterckNadine RijsdijkRossella AnnunziataMaria Immacolata Ferrante et al.

A1 Journal Article in MOLECULAR ECOLOGY

2023

A redundant transcription factor network steers spatiotemporal Arabidopsis triterpene synthesis

Trang Hieu NguyenLouis ThiersAlex Van MoerkerckeYuechen BaiPatricia Fernandez CalvoMax MinneThomas DepuydtMaite Colinas MartinezKevin VerstaenGert Van Isterdael et al.

A1 Journal Article in NATURE PLANTS

Characterization of gene regulatory networks in plants using new methods and data types

Klaas VandepoeleKerstin Kaufmann

Bookchapter in Plant gene regulatory networks : methods and protocols

Charting arabidopsis gene functions from multi-omics and single-cell data

Thomas DepuydtKlaas Vandepoele

Charting plant gene functions in the multi-omics and single-cell era

Thomas DepuydtBert De RybelKlaas Vandepoele

A1 Journal Article in TRENDS IN PLANT SCIENCE

Diatom adhesive trail proteins acquired by horizontal gene transfer from bacteria serve as primers for marine biofilm formation

Jirina Zackova SuchanovaGust BilckeBeata RomanowskaAli FatlawiMartin PippelAlastair SkeffingtonMichael SchroederWim VyvermanKlaas VandepoeleNils Kröger et al.

A1 Journal Article in NEW PHYTOLOGIST

Dicer-like 3a mediates intergenerational resistance against root-knot nematodes in rice via hormone responses

Aniko MeijerMohammad Atighi Quchan AtighKristof DemeestereTim De MeyerKlaas VandepoeleTina Kyndt

A1 Journal Article in PLANT PHYSIOLOGY

Distinctive and complementary roles of E2F transcription factors during plant replication stress responses

Maherun NisaThomas EekhoutClara BergisJosé Antonio Pedroza-GarciaXiaoning HeChristelle MazubertIlse VercauterenToon CoolsRim Brik-ChaoucheJeannine Drouin-Wahbi et al.

A1 Journal Article in MOLECULAR PLANT

Evolutionary, regulatory, and functional annotation of long intergenic noncoding RNAs in Arabidopsis thaliana

Li LiuKlaas Vandepoele

Plant gene regulatory networks : methods and protocols

Plant lineage-specific PIKMIN1 drives APC/CCCS52A2 E3-ligase activity-dependent cell division

Alex WillemsYuanke LiangJefri HeymanThomas DepuydtThomas EekhoutBalkan CanherHilde Van Den DaeleIlse VercauterenKlaas VandepoeleLieven De Veylder

A1 Journal Article in PLANT PHYSIOLOGY

Predicting transcriptional responses to heat and drought stress from genomic features using a machine learning approach in rice

Dajo SmetHelder OpdebeeckKlaas Vandepoele

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

Prediction of transcription factor regulators and gene regulatory networks in tomato using binding site information

Nicolás Manosalva PérezKlaas Vandepoele

Bookchapter in Plant gene regulatory networks : methods and protocols

Rhizogenic agrobacterium protein RolB interacts with the TOPLESS repressor proteins to reprogram plant immunity and development

Lore GryffroyEvi CeulemansNicolás Manosalva PérezJhon Jairo Venegas MolinaAna JaramilloSavio D. RodriguesLiesbeth De MildeVeronique JonckheereMarc Van MontaguBarbara De Coninck et al.

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

Single cell RNA-sequencing in Arabidopsis root tissues

Yuji KeMax MinneThomas EekhoutBert De Rybel

Bookchapter in Plant gene regulatory networks : methods and protocols

Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots

Li LiuMichel HeideckerThomas DepuydtNicolás Manosalva PérezMartin CrespiThomas BleinKlaas Vandepoele

A1 Journal Article in PLANT PHYSIOLOGY

2022

Chromosome-scale assembly and annotation of the perennial ryegrass genome

Istvan NagyElisabeth VeeckmanChang LiuMichiel Van BelKlaas VandepoeleChristian Sig JensenTom RuttinkTorben Asp

A1 Journal Article in BMC GENOMICS

Identification of growth regulators using cross-species network analysis in plants

Pasquale Luca CurciJie ZhangNiklas MählerCarolin SeyfferthChanaka MannapperumaTim DielsTom Van HautegemDavid JonsenNathaniel StreetTorgeir R Hvidsten et al.

A1 Journal Article in PLANT PHYSIOLOGY

Inherited memories : the role of epigenetics in intergenerational resistance against nematodes in rice

Aniko MeijerTina KyndtKlaas Vandepoele

Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators

Inge De ClercqJan Van de VeldeXiaopeng LuoLi LiuVeronique StormeMichiel Van BelRobin PottieDries VaneechoutteFrank Van BreusegemKlaas Vandepoele

JASPAR 2022 : the 9th release of the open-access database of transcription factor binding profiles

Jaime A Castro-MondragonRafael Riudavets-PuigIeva RauluseviciuteRoza Berhanu LemmaLaura TurchiRomain Blanc-MathieuJeremy LucasPaul BoddieAziz KhanNicolás Manosalva Pérez et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

MINI-EX : integrative inference of single-cell gene regulatory networks in plants

Camilla FerrariNicolás Manosalva PérezKlaas Vandepoele

A1 Journal Article in MOLECULAR PLANT

PLAZA 5.0 : extending the scope and power of comparative and functional genomics in plants

Michiel Van BelFrancesca SilvestriEric M WeitzLukasz KreftAlexander BotzkiFrederik CoppensKlaas Vandepoele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Spatiotemporal expression profile of novel and known small RNAs throughout rice plant development focussing on seed tissues

Aniko MeijerTim De MeyerKlaas VandepoeleTina Kyndt

A1 Journal Article in BMC GENOMICS

The gene regulation knowledge commons : the action area of GREEKC

Martin KuiperJoseph BonelloJesualdo T. Fernández-BreisPhilipp BucherMatthias E. FutschikPascale GaudetIvan V. KulakovskiyLuana LicataColin LogieRuth C. Lovering et al.

A1 Journal Article in BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS

The quest for orthologs Orthology Benchmark Service in 2022

Laia CodoElspeth A BrufordSalvatore CosentinoIngo EbersbergerKlaas Vandepoele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

The ÓMICAS alliance, an international research program on multi-omics for crop breeding optimization

Andres Jaramillo-BoteroJulian ColoradoMauricio QuimbayaMaria Camila RebolledoMathias LorieuxThaura Ghneim-HerreraCarlos A. ArangoLuis E. TobónJorge FinkeCamilo Rocha et al.

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

2021

A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies

Junha ShinHarald MarxAlicia RichardsDries VaneechoutteDhileepkumar JayaramanJunko MaedaSanhita ChakrabortyMichael SussmanKlaas VandepoeleJean-Michel Ané et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass

José Luis Blanco‐PastorPhilippe BarreThomas KeepThomas LedauphinAbraham Escobar‐GutiérrezAnna Maria RoschanskiEvelyn WillnerKlaus J. DehmerMatthew HegartyHilde Muylle et al.

A1 Journal Article in MOLECULAR ECOLOGY RESOURCES

Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors

Pingtao DingToshiyuki SakaiRam Krishna ShresthaNicolás Manosalva PérezWenbin GuoBruno Pok Man NgouShengbo HeChang LiuXiaoqi FengRunxuan Zhang et al.

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

Comment on ‘Hayai-annotation plants : an ultrafast and comprehensive functional gene annotation system in plants’ : the importance of taking the GO graph structure into account

Michiel Van BelKlaas Vandepoele

A1 Journal Article in BIOINFORMATICS

Comparative genomics reveals new functional insights in uncultured MAST species

Aurelie LabarreDavid López-EscardóFrancisco LatorreGuy LeonardFrançois BucchiniAleix ObiolCorinne CruaudMichael E. SierackiOlivier JaillonPatrick Wincker et al.

A1 Journal Article in ISME JOURNAL

Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle

Gust BilckeCristina OsunaMarta Santana SilvaNicole PoulsenSofie D'hondtPetra BulánkováWim VyvermanLieven De VeylderKlaas Vandepoele

A1 Journal Article in PLANT JOURNAL

Evolutionary genomics of sex-related chromosomes at the base of the green lineage

Luis Felipe BenitesFrançois BucchiniSophie Sanchez-BrosseauNigel GrimsleyKlaas VandepoeleGwenaël Piganeau

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate

Ramon MassanaAurelie LabarreDavid López-EscardóAleix ObiolFrançois BucchiniThomas HacklMatthias G. FischerKlaas VandepoeleDenis V. TikhonenkovFilip Husnik et al.

A1 Journal Article in ISME JOURNAL

Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators

Inge De ClercqJan Van de VeldeXiaopeng LuoLi LiuVeronique StormeMichiel Van BelRobin PottieDries VaneechoutteFrank Van BreusegemKlaas Vandepoele

A1 Journal Article in NATURE PLANTS

Light intensity and spectral composition drive reproductive success in the marine benthic diatom Seminavis robusta

Gust BilckeLore Van CraenenbroeckAlexandre Castagna Mourão e LimaCristina OsunaKlaas VandepoeleKoen SabbeLieven De VeylderWim Vyverman

A1 Journal Article in SCIENTIFIC REPORTS

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

Mitotic recombination between homologous chromosomes drives genomic diversity in diatoms

Petra BulánkováMirna SekulićDenis JalletCharlotte NefCock van OosterhoutTom O. DelmontIlse VercauterenCristina OsunaEmmelien VancaesterThomas Mock et al.

A1 Journal Article in CURRENT BIOLOGY

Multi‐omics network‐based functional annotation of unknown Arabidopsis genes

Thomas DepuydtKlaas Vandepoele

A1 Journal Article in PLANT JOURNAL

Subfunctionalization of paralog transcription factors contributes to regulation of alkaloid pathway branch choice in Catharanthus roseus

Maite Colinas MartinezJacob PollierDries VaneechoutteDeniz MalatFabian SchweizerLiesbeth De MildeRebecca De ClercqJoana G. GuedesTeresa Martínez-CortésFrancisco Hidalgo et al.

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

TRAPID 2.0 : a web application for taxonomic and functional analysis of de novo transcriptomes

François BucchiniAndrea Del CortonaŁukasz KreftAlexander BotzkiMichiel Van BelKlaas Vandepoele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Understanding benthic diatom biology through comparative genomics and trancriptomic analysis of the model Seminavis robusta

Cristina OsunaKlaas VandepoeleLieven De Veylder

2020

Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth

Jasmien VercruysseMichiel Van BelCristina OsunaShubhada Rajabhau KulkarniVéronique Van den StormeHilde NelissenNathalie Gonzalez SanchezDirk InzéKlaas Vandepoele

A1 Journal Article in PLANT BIOTECHNOLOGY JOURNAL

Comprehensive and functional analysis of horizontal gene transfer events in diatoms

Emmelien VancaesterThomas DepuydtCristina OsunaKlaas Vandepoele

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Distinctive growth and transcriptional changes of the diatom Seminavis robusta in response to quorum sensing related compounds

Frederike Stock genannt SchroerGust BilckeSam De DeckerCristina OsunaKoen Van den BergeEmmelien VancaesterLieven De VeylderKlaas VandepoeleSven MangelinckxWim Vyverman

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Evolution of vascular plants through redeployment of ancient developmental regulators

Kuan-Ju LuNicole van ’t Wout HoflandEliana MorSumanth MuttePaul AbrahamsHirotaka KatoKlaas VandepoeleDolf WeijersBert De Rybel

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

Horizontal gene transfer and gene family evolution in photosynthetic unicellular eukaryotes

Emmelien VancaesterKlaas Vandepoele

Identification and evolution of gene regulatory networks : insights from comparative studies in plants

Marc JonesKlaas Vandepoele

A1 Journal Article in CURRENT OPINION IN PLANT BIOLOGY

Inference of plant gene regulatory networks using data-driven methods : a practical overview

Shubhada Rajabhau KulkarniKlaas Vandepoele

A1 Journal Article in BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS

Light regulation of LHCX genes in the benthic diatom Seminavis robusta

Lander BlommaertEmmelien VancaesterMarie HuysmanCristina OsunaSofie D'hondtJohann LavaudBernard LepetitPer WingeAtle M. BonesKlaas Vandepoele et al.

A1 Journal Article in FRONTIERS IN MARINE SCIENCE

Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds

Andrea Del CortonaChristopher J. JacksonFrançois BucchiniMichiel Van BelSofie D'hondtPavel ŠkaloudCharles F. DelwicheAndrew H. KnollJohn A. RavenHeroen Verbruggen et al.

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

The art in artificial promoters : searching for cis-regulatory elements to design and validate synthetic promoters

Jasmien VercruysseDirk InzéNathalie GonzalezKlaas Vandepoele

The medium-size noncoding RNA transcriptome of Ostreococcus tauri, the smallest living eukaryote, reveals a large family of small nucleolar RNAs displaying multiple genomic expression strategies

Laurie BousquetClaire HemonPaul MalburetFrançois BucchiniKlaas VandepoeleNigel GrimsleyHerve MoreauManuel Echeverria

A2 Journal Article in NAR GENOMICS AND BIOINFORMATICS

The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms

Cristina OsunaGust BilckeEmmelien VancaesterSam De DeckerAtle M. BonesPer WingeNicole PoulsenPetra BulánkováBram VerhelstSien Audoor et al.

A1 Journal Article in NATURE COMMUNICATIONS

The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms (vol 11, 3320, 2020)

Cristina Maria Osuna CruzGust BilckeEmmelien VancaesterSam De DeckerAtle M. BonesPer WingeNicole PoulsenPetra BulánkováBram VerhelstSien Audoor et al.

Virus-host coexistence in phytoplankton through the genomic lens

Sheree YauMarc KrasovecL. Felipe BenitesStephane RombautsMathieu GroussinEmmelien VancaesterJean-Marc AuryEvelyne DerelleYves DesdevisesMarie-Line Escande et al.

A1 Journal Article in SCIENCE ADVANCES

2019

A collection of tools and resources to explore gene expression, regulation, and alternative splicing

Dries VaneechoutteKlaas Vandepoele

A new evolutionary model for the vertebrate actin family including two novel groups

Laura WitjesMarleen Van TroysJoël VandekerckhoveKlaas VandepoeleChristophe Ampe

A1 Journal Article in MOLECULAR PHYLOGENETICS AND EVOLUTION

A widespread alternative squalene epoxidase participates in eukaryote steroid biosynthesis

Jacob PollierEmmelien VancaesterUnnikrishnan KuzhiumparambilClaudia E. VickersKlaas VandepoeleAlain GoossensMichele Fabris

A1 Journal Article in NATURE MICROBIOLOGY

Associated bacteria affect sexual reproduction by altering gene expression and metabolic processes in a biofilm inhabiting diatom

Emilio CirriSam De DeckerGust BilckeMarkus WernerCristina OsunaLieven De VeylderKlaas VandepoeleOliver WerzWim VyvermanGeorg Pohnert

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase

Jelle Van LeeneChao HanAstrid GadeyneDominique EeckhoutCaroline MatthijsBernard CannootNancy De WinneGeert PersiauEveline Van De SlijkeBrigitte Van De Cotte et al.

A1 Journal Article in NATURE PLANTS

Curse : building expression atlases and co-expression networks from public RNA-Seq data

Dries VaneechoutteKlaas Vandepoele

A1 Journal Article in BIOINFORMATICS

Delineating gene regulatory networks in Arabidopsis thaliana

Shubhada Rajabhau KulkarniKlaas Vandepoele

Development of genomic resources for perennial ryegrass

Elisabeth VeeckmanKlaas VandepoeleTom RuttinkPeter Dawyndt

Enhanced maps of transcription factor binding sites improve regulatory networks learned from accessible chromatin data

Shubhada Rajabhau KulkarniMarc JonesKlaas Vandepoele

A1 Journal Article in PLANT PHYSIOLOGY

Gene space completeness in complex plant genomes

Michiel Van BelFrançois BucchiniKlaas Vandepoele

A1 Journal Article in CURRENT OPINION IN PLANT BIOLOGY

Neofunctionalization of mitochondrial proteins and incorporation into signaling networks in plants

Sbatie LamaMartyna BrodaZahra AbbasDries VaneechoutteKatharina BeltTorbjörn SällKlaas VandepoeleOlivier Van Aken

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Overcoming challenges in variant calling : exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne)

Elisabeth VeeckmanSabine Van GlabekeAnnelies HaegemanHilde MuylleFrederik RD van ParijsStephen L ByrneTorben AspBruno StuderAntje RohdeIsabel Roldán-Ruiz et al.

A1 Journal Article in DNA RESEARCH

Understanding genetic control of root system architecture in soybean : insights into the genetic basis of lateral root number

Silvas J PrinceBabu ValliyodanHeng YeMing YangShuaishuai TaiWushu HuMackensie MurphyLorellin A DurnellLi SongTrupti Joshi et al.

A1 Journal Article in PLANT CELL AND ENVIRONMENT

2018

Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana

Bjoern Oest HansenEtienne H MeyerCamilla FerrariNeha VaidSara MovahediKlaas VandepoeleZoran NikoloskiMarek Mutwil

A1 Journal Article in NEW PHYTOLOGIST

Gearing up to handle the mosaic nature of life in the quest for orthologs

Kristoffer ForslundCecile PereiraSalvador Capella-GutierrezAlan Sousa da SilvaAdrian AltenhoffJaime Huerta-CepasMatthieu MuffatoMateus PatricioKlaas VandepoeleIngo Ebersberger et al.

A1 Journal Article in BIOINFORMATICS

Genome analyses of the microalga Picochlorum provide insights into the evolution of thermotolerance in the green lineage

Marc KrasovecEmmelien VancaesterStephane RombautsFrançois BucchiniSheree YauClaire HemonHugo LebredonchelNigel GrimsleyHerve MoreauSophie Sanchez-Brosseau et al.

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

GSyellow, a multifaceted tag for functional protein analysis in monocot and dicot plants

Nienke BesbruggeJelle Van LeeneDominique EeckhoutBernard CannootShubhada Rajabhau KulkarniNancy De WinneGeert PersiauEveline Van De SlijkeMichiel BontinckStijn Aesaert et al.

A1 Journal Article in PLANT PHYSIOLOGY

Insights into the evolution of multicellularity from the sea lettuce genome

Olivier De ClerckShu-Min KaoKenny BogaertJonas BlommeFatima FoflonkerMichiel KwantesEmmelien VancaesterLisa VanderstraetenEylem Aydogdu LohausJens Boesger et al.

A1 Journal Article in CURRENT BIOLOGY

JASPAR 2018 : update of the open-access database of transcription factor binding profiles and its web framework

Aziz KhanOriol FornesArnaud StiglianiMarius GheorgheJaime A Castro-MondragonRobin van der LeeAdrien BessyJeanne ChenebyShubhada Rajabhau KulkarniGe Tan et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis

Zhen GaoAnna DanevaYuliya SalanenkaMatthias Van DurmeMarlies HuysmansZongcheng LinFreya De WinterSteffen VannesteMansour KarimiJan Van de Velde et al.

A1 Journal Article in NATURE PLANTS

PLAZA 4.0 : an integrative resource for functional, evolutionary and comparative plant genomics

Michiel Van BelTim DielsEmmelien VancaesterLukasz KreftAlexander BotzkiYves Van de PeerFrederik CoppensKlaas Vandepoele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

TF2Network : predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information

Shubhada Rajabhau KulkarniDries VaneechoutteJan Van de VeldeKlaas Vandepoele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

Daniel LangKristian K UllrichFlorent MuratJoerg FuchsJerry JenkinsFabian B HaasMathieu PiednoelHeidrun GundlachMichiel Van BelRabea Meyberg et al.

A1 Journal Article in PLANT JOURNAL

The rise of Algae: molecular evolution of macroscopic growth in green algae

Andrea Del CortonaOlivier De ClerckKlaas VandepoeleFrédérik Leliaert

2017

A guide to the PLAZA 3.0 plant comparative genomic database

Klaas Vandepoele

Bookchapter in Plant genomics databases : methods and protocols

Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa)

Kristof De SchutterMariya Tsankova TsanevaShubhada Rajabhau KulkarniPierre RougéKlaas VandepoeleEls Van Damme

A1 Journal Article in RICE

Genome-wide characterization of differential transcript usage in Arabidopsis thaliana

Dries VaneechoutteApril R EstradaYing-Chen LinAnn E LoraineKlaas Vandepoele

A1 Journal Article in PLANT JOURNAL

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.

PhyD3 : a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization

Lukasz KreftAlexander BotzkiFrederik CoppensKlaas VandepoeleMichiel Van Bel

A1 Journal Article in BIOINFORMATICS

Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules

Colin RuprechtSebastian ProostMarcela Hernandez-CoronadoCarlos Ortiz-RamirezDaniel LangStefan A RensingJorg D BeckerKlaas VandepoeleMarek Mutwil

A1 Journal Article in PLANT JOURNAL

Studying the regulatory landscape of flowering plants

Jan Van de VeldeKlaas VandepoeleJan Fostier

The mutation nrpb1-A325V in the largest subunit of RNA polymerase II suppresses compromised growth of Arabidopsis plants deficient in a function of the general transcription factor IIF

Elena BabiychukHoang Khai TrinhKlaas VandepoeleEveline Van De SlijkeDanny GeelenGeert De JaegerJunichi ObokataSergei Kushnir

A1 Journal Article in PLANT JOURNAL

The plastid genome in Cladophorales green algae is encoded by hairpin chromosomes

Andrea Del CortonaFrédérik LeliaertKenny BogaertMonique TurmelChristian BoedekerJan JanouškovecJuan M Lopez-BautistaHeroen VerbruggenKlaas VandepoeleOlivier De Clerck

A1 Journal Article in CURRENT BIOLOGY

The transcription factor MYB29 is a regulator of ALTERNATIVE OXIDASE1a

Xinhua ZhangAneta IvanovaKlaas VandepoeleJordan RadomiljacJan Van de VeldeOliver BerkowitzPatrick WillemsYue XuSophia NgOlivier Van Aken et al.

A1 Journal Article in PLANT PHYSIOLOGY

The transcriptional repressor complex FRS7-FRS12 regulates flowering time and growth in Arabidopsis

Andrés Ritter TraubSabrina IñigoPatricia Fernandez CalvoKen HeyndrickxStijn DhondtHua ShiLiesbeth De MildeRobin Vanden BosscheRebecca De ClercqDominique Eeckhout et al.

A1 Journal Article in NATURE COMMUNICATIONS

2016

A collection of conserved noncoding sequences to study gene regulation in flowering plants

Jan Van de VeldeMichiel Van BelDries VaneechoutteKlaas Vandepoele

A1 Journal Article in PLANT PHYSIOLOGY

Are we there yet? : reliably estimating the completeness of plant genome sequences

Elisabeth VeeckmanTom RuttinkKlaas Vandepoele

A1 Journal Article in PLANT CELL

CoExpNetViz: comparative co-expression networks construction and visualization tool

Oren TzfadiaTim DielsSam De MeyerKlaas VandepoeleAsaph AharoniYves Van de Peer

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development

Jelle Van LeeneJonas BlommeShubhada Rajabhau KulkarniBernard CannootNancy De WinneDominique EeckhoutGeert PersiauEveline Van De SlijkeLeen VercruysseRobin Vanden Bossche et al.

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

Genomic variation in the FT gene family of perennial ryegrass (Lolium perenne)

Elisabeth VeeckmanKlaas VandepoeleT AspIsabel Roldán-RuizTom Ruttink

2015

A functional and regulatory perspective on Arabidopsis thaliana

Ken HeyndrickxKlaas Vandepoele

A repressor protein complex regulates leaf growth in Arabidopsis

Nathalie Gonzalez SanchezLaurens PauwelsAlexandra BaekelandtLiesbeth De MildeJelle Van LeeneNienke BesbruggeKen HeyndrickxAmparo Cuéllar PérezAstrid Nagels DurandRebecca De Clercq et al.

A1 Journal Article in PLANT CELL

An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes

Jelle Van LeeneDominique EeckhoutBernard CannootNancy De WinneGeert PersiauEveline Van De SlijkeLeen VercruysseMaarten DedeckerAurine VerkestKlaas Vandepoele et al.

A1 Journal Article in NATURE PROTOCOLS

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

Pieter-Jan VoldersKenneth VerheggenGerben MenschaertKlaas VandepoeleLennart MartensJo VandesompelePieter Mestdagh

A1 Journal Article in NUCLEIC ACIDS RESEARCH

BLSSpeller : exhaustive comparative discovery of conserved cis-regulatory elements

Dieter De WitteJan Van de VeldeDries DecapMichiel Van BelP. AudenaertPiet DemeesterBart DhoedtKlaas VandepoeleJan Fostier

A1 Journal Article in BIOINFORMATICS

Dynamic changes in ANGUSTIFOLIA3 complex composition reveal a growth regulatory mechanism in the maize leaf

Hilde NelissenDominique EeckhoutKirin DemuynckGeert PersiauAlan WaltonMichiel Van BelMarieke VervoortJasper CandaeleJolien De BlockStijn Aesaert et al.

A1 Journal Article in PLANT CELL

Evolutionary trails of plant steroid genes

Cécile VrietKaren LemmensKlaas VandepoeleChristophe ReuzeauEugenia Russinova

A1 Journal Article in TRENDS IN PLANT SCIENCE

Functional analysis of the Arabidopsis TETRASPANIN gene family in plant growth and development

Feng WangAntonella MutoJan Van de VeldePia NeytKristiina HimanenKlaas VandepoeleMaria Van Lijsebettens

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

PLAZA 3.0 : an access point for plant comparative genomics

Sebastian ProostMichiel Van BelDries VaneechoutteYves Van de PeerDirk InzéBernd Mueller-RoeberKlaas Vandepoele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Robust peptide-based models in quantitative proteomics

Ludger GoeminneKlaas VandepoeleKris GevaertLieven Clement

Selection for improved energy use efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes

Aurine VerkestMarina ByzovaCindy MartensPatrick WillemsTom VerwulgenBram SlabbinckDebbie RombautJan Van de VeldeKlaas VandepoeleEvi Standaert et al.

A1 Journal Article in PLANT PHYSIOLOGY

Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B

Natasha M GloverJosquin DaronLise PingaultKlaas VandepoeleEtienne PauxCatherine FeuilletFrédéric Choulet

A1 Journal Article in GENOME BIOLOGY

Towards an understanding of the cytological diversity of green seaweeds (Ulvophyceae)

Andrea Del CortonaFrédérik LeliaertHeroen VerbruggenJuan M Lopez-BautistaKlaas VandepoeleOlivier De Clerck

2014

A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana

Søren LindemoseMichael K JensenJan Van de VeldeCharlotte O'SheaKen HeyndrickxChristopher T WorkmanKlaas VandepoeleKaren SkriverFederico De Masi

A1 Journal Article in NUCLEIC ACIDS RESEARCH

A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana

Ken HeyndrickxJan Van de VeldeCongmao WangDetlef WeigelKlaas Vandepoele

A1 Journal Article in PLANT CELL

A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification

Aurine VerkestThomas AbeelKen HeyndrickxJelle Van LeeneChrista LanzEveline Van De SlijkeNancy De WinneDominique EeckhoutGeert PersiauFrank Van Breusegem et al.

A1 Journal Article in PLANT PHYSIOLOGY

A parallel, distributed-memory framework for comparative motif discovery

Dieter De WitteMichiel Van BelP. AudenaertPiet DemeesterBart DhoedtKlaas VandepoeleJan Fostier

ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development

Liesbeth VercruyssenAurine VerkestNathalie Gonzalez SanchezKen HeyndrickxDominique EeckhoutSoon-Ki HanTeddy JéguRafal ArchackiJelle Van LeeneMegan Andriankaja et al.

A1 Journal Article in PLANT CELL

Big data and other challenges in the quest for orthologs

Erik LL SonnhammerToni GabaldónAlan W Sousa da SilvaMaria MartinMarc Robinson-RechaviBrigitte BoeckmannPaul D ThomasChristine Dessimozthe Quest Orthologs ConsortiumMichiel Van Bel et al.

Editorial material

Drought tolerance conferred to sugarcane by association with Gluconacetobacter diazotrophicus: a transcriptomic view of hormone pathways

Lívia VargasAilton B Santa BrigidaJosé P Mota FilhoThais G de CarvalhoCristian A RojasDries VaneechoutteMichiel Van BelLaurent FarrinelliPaulo CG FerreiraKlaas Vandepoele et al.

A1 Journal Article in PLOS ONE

Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis

Jan Van de VeldeKen HeyndrickxKlaas Vandepoele

A1 Journal Article in PLANT CELL

MAGIC: access portal to a cross-platform gene expression compendium for maize

Qiang FuAna Carolina Elisa Fierro GutierrezPieter MeysmanAminael Sanchez RodriguezKlaas VandepoeleKathleen MarchalKristof Engelen

A1 Journal Article in BIOINFORMATICS

SHUGOSHINs and PATRONUS protect meiotic centromere cohesion in Arabidopsis thaliana

Linda ZamariolaNico De StormeKatrijn VannerumKlaas VandepoeleSusan J ArmstrongF Christopher H FranklinDanny Geelen

A1 Journal Article in PLANT JOURNAL

Structural and functional partitioning of bread wheat chromosome 3B

Frédéric ChouletAdriana AlbertiSébastien TheilNatasha GloverValérie BarbeJosquin DaronLise PingaultPierre SourdilleArnaud CoulouxEtienne Paux et al.

A1 Journal Article in SCIENCE

2013

Comparative motif discovery in the cloud

Dieter De WitteJan Van de VeldeMichiel Van BelP. AudenaertPiet DemeesterBart DhoedtKlaas VandepoeleJan Fostier

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

Riet De SmetKeith L AdamsKlaas VandepoeleMarc Van MontaguSteven MaereYves Van de Peer

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

ERF115 controls root quiescent center cell division and stem cell replenishment

Jefri HeymanToon CoolsFilip VandenbusscheKen HeyndrickxJelle Van LeeneIlse VercauterenSandy VanderauweraKlaas VandepoeleGeert De JaegerDominique Van Der Straeten et al.

A1 Journal Article in SCIENCE

Molecular and physiological analysis of growth-limiting drought stress in Brachypodium distachyon leaves

Wim VerelstEdoardo BertoliniStefanie De BodtKlaas VandepoeleMarlies DemeulenaereMario Enrico PéDirk Inzé

A1 Journal Article in MOLECULAR PLANT

pico-PLAZA, a genome database of microbial photosynthetic eukaryotes

Klaas VandepoeleMichiel Van BelGuilhem RichardSofie Van LandeghemBram VerhelstHervé MoreauYves Van de PeerNigel GrimsleyGwenael Piganeau

A1 Journal Article in ENVIRONMENTAL MICROBIOLOGY

The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis

Inge De ClercqVanessa VermeirssenOlivier Van AkenKlaas VandepoeleMonika W MurchaSimon R LawAnnelies InzéSophia NgAneta IvanovaDebbie Rombaut et al.

A1 Journal Article in PLANT CELL

TRAPID : an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

Michiel Van BelSebastian ProostChristophe Van NesteDieter DeforceYves Van de PeerKlaas Vandepoele

A1 Journal Article in GENOME BIOLOGY

2012

A high performance computing approach to the dicovery of conserved motifs

Dieter De WitteMichiel Van BelPiet DemeesterBart DhoedtKlaas VandepoeleJan Fostier

Alignment-free genome-wide comparative motif discovery in 4 Monocot species

Dieter De WitteMichiel Van BelPiet DemeesterBart DhoedtKlaas VandepoeleJan Fostier

Comparative analysis of plant genomes through data integration

Michiel Van BelYves Van de PeerKlaas Vandepoele

Comparative co-expression analysis in plant biology

Sara MovahediMichiel Van BelKen HeyndrickxKlaas Vandepoele

A1 Journal Article in PLANT CELL AND ENVIRONMENT

Comparative transcriptomics in plants

Sara MovahediYves Van de PeerKlaas Vandepoele

Dissecting plant genomes with the PLAZA comparative genomics platform

Michiel Van BelSebastian ProostElisabeth WischnitzkiSara MovahediChristopher ScheerlinckYves Van de PeerKlaas Vandepoele

A1 Journal Article in PLANT PHYSIOLOGY

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage

Hervé MoreauBram VerhelstArnaud CoulouxEvelyne DerelleStephane RombautsNigel GrimsleyMichiel Van BelJulie PoulainMichaël KatinkaMartin F Hohmann-Marriott et al.

A1 Journal Article in GENOME BIOLOGY

i-ADHoRe 3.0 : fast and sensitive detection of genomic homology in extremely large data sets

Sebastian ProostJan FostierDieter De WitteBart DhoedtPiet DemeesterYves Van de PeerKlaas Vandepoele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Identification of cis-regulatory elements specific for different types of reactive oxygen species in Arabidopsis thaliana

Veselin PetrovVanessa VermeirssenInge De ClercqFrank Van BreusegemIvan MinkovKlaas VandepoeleTsanko S Gechev

A1 Journal Article in GENE

Identification of putative cancer genes through data integration and comparative genomics between plants and humans

Mauricio Quimbaya GomezKlaas VandepoeleEric RaspéMichiel MatthijsStijn DhondtGerrit BeemsterGeert BerxLieven De Veylder

A1 Journal Article in CELLULAR AND MOLECULAR LIFE SCIENCES

Integration of genomic data to study genome evolution in plants

Sebastian ProostYves Van de PeerKlaas Vandepoele

Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling

Daniel VaulotCécile LepereEve ToulzaRodrigo De la IglesiaJulie PoulainFrédéric GaboyerHervé MoreauKlaas VandepoeleOsvaldo UlloaFrederick Gavory et al.

A1 Journal Article in PLOS ONE

Systematic identification of functional plant modules through the integration of complementary data sources

Ken HeyndrickxKlaas Vandepoele

A1 Journal Article in PLANT PHYSIOLOGY

Tetraspanin genes in plants

Feng WangKlaas VandepoeleMaria Van Lijsebettens

A1 Journal Article in PLANT SCIENCE

Toward community standards in the quest for orthologs

Christophe DessimozToni GabaldónDavid S RoosErik LL SonnhammerJavier Herrerothe Quest Orthologs ConsortiumKlaas VandepoeleMichiel Van Bel

A1 Journal Article in BIOINFORMATICS

2011

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists

Jan FostierSebastian ProostBart DhoedtYvan SaeysPiet DemeesterYves Van de PeerKlaas Vandepoele

A1 Journal Article in BIOINFORMATICS

Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice

Sara MovahediYves Van de PeerKlaas Vandepoele

A1 Journal Article in PLANT PHYSIOLOGY

Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family

Elena BabiychukKlaas VandepoeleJosef WissingMiguel Garcia-DiazRiet De RyckeHana AkbariJérôme JoubèsTom BeeckmanLothar JänschMargrit Frentzen et al.

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

ROS signaling: the new wave?

Ron MittlerSandy VanderauweraNobuhiro SuzukiGad MillerVanesa TognettiKlaas VandepoeleMarty GolleryVladimir ShulaevFrank Van Breusegem

A1 Journal Article in TRENDS IN PLANT SCIENCE

2010

Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling

Marie HuysmanCindy MartensKlaas VandepoeleJeroen GillardEdda RaykoMarc HeijdeChris BowlerDirk InzéYves Van de PeerLieven De Veylder et al.

A1 Journal Article in GENOME BIOLOGY

The MCM-Binding Protein ETG1 Aids Sister Chromatid Cohesion Required for Postreplicative Homologous Recombination Repair

Naoki TakahashiMauricio Quimbaya GomezVeit SchubertTim LammensKlaas VandepoeleIngo SchubertMinami MatsuiDirk InzéGeert BerxLieven De Veylder

A1 Journal Article in PLOS GENETICS

2009

PLAZA : a comparative genomics resource to study gene and genome evolution in plants

Sebastian ProostMichiel Van BelLieven SterckKenny BilliauThomas Van ParysYves Van de PeerKlaas Vandepoele

A1 Journal Article in PLANT CELL

Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

Stefanie De BodtSebastian ProostKlaas VandepoelePierre RouzéYves Van de Peer

A1 Journal Article in BMC Genomics

Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes

Naïra NaouarKlaas VandepoeleTim LammensTineke CasneufGeorg ZellerPaul Van HummelenDetlef WeigelGunnar RätschDirk InzéMartin Kuiper et al.

A1 Journal Article in Plant Journal

The flowering world: a tale of duplications

Yves Van de PeerJeffrey FawcettSebastian ProostLieven SterckKlaas Vandepoele

A1 Journal Article in TRENDS IN PLANT SCIENCE

The Mouse Thymosin Beta15 Gene Family Displays Unique Complexity and Encodes A Functional Thymosin Repeat

Stien DhaeseKlaas VandepoeleDAVY WATERSCHOOTBerlinda VanlooJoël VandekerckhoveChristophe AmpeMarleen Van Troys

A1 Journal Article in JOURNAL OF MOLECULAR BIOLOGY

Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks

Klaas VandepoeleMauricio Quimbaya GomezTine CasneufLieven De VeylderYves Van de Peer

A1 Journal Article in Plant Physiology

Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus

Gwenael PiganeauKlaas VandepoeleSébastien GourbièreYves Van de PeerHervé Moreau

A1 Journal Article in Journal of Molecular Evolution

2008

A constitutional translocation t(1;17)(p36.2;q11.2) in a neuroblastoma patient disrupts the the human NBPF1 and ACCN1 genes

Frans Van RoyKlaas VandepoeleNadine Van RoyVanessa AndriesKatrien StaesJo VandesompeleGenevieve LaureysEls De SmetGeert BerxFranki Speleman

Hydrogen peroxide-induced gene expression across kingdoms: a comparative analysis

Korneel VandenbrouckeSteven RobbensKlaas VandepoeleDirk InzéYves Van de PeerFrank Van Breusegem

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Chris BowlerAndrew E AllenJonathan H BadgerJane GrimwoodKamel JabbariAlan KuoUma MaheswariCindy MartensFlorian MaumusRobert P Otillar et al.

A1 Journal Article in NATURE

The PRA1 gene family in Arabidopsis

Claire Lessa Alvim KameiJoanna BorucKlaas VandepoeleHilde Van Den DaeleSara MaesEugenia RussinovaDirk InzéLieven De Veylder

A1 Journal Article in PLANT PHYSIOLOGY

Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species

Cindy MartensKlaas VandepoeleYves Van de Peer

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

2007

A high quality draft consensus sequence of the genome of a heterozygous grapevine variety

Riccardo VelascoAndrey ZharkikhMichela TroggioDustin A CartwrightAlessandro CestaroDmitry PrussMassimo PindoLisa M FitzGeraldSilvia VezzulliJulia Reid et al.

A1 Journal Article in PLOS ONE

Cold nights impair leaf growth and cell cycle progression in maize through transcriptional changes of cell cycle genes

Bart RymenFabio FioraniFatma KartalKlaas VandepoeleDirk InzéGerrit Beemster

A1 Journal Article in PLANT PHYSIOLOGY

How many genes are there in plants (... and why are they there)?

Lieven SterckStephane RombautsKlaas VandepoelePierre RouzéYves Van de Peer

A1 Journal Article in CURRENT OPINION IN PLANT BIOLOGY

Novel plant-specific cyclin-dependent kinase inhibitors induced by biotic and abiotic stresses

Adrian PeresMichelle L ChurchmanSrivaidehirani HariharanKristiina HimanenAurine VerkestKlaas VandepoeleZoltán MagyarYves HatzfeldEls Van Der SchuerenGerrit Beemster et al.

A1 Journal Article in JOURNAL OF BIOLOGICAL CHEMISTRY

On the origin and evolution of vertebrate and viral profilins

Debby PoletAnja LambrechtsKlaas VandepoeleJoël VandekerckhoveChristophe Ampe

A1 Journal Article in FEBS LETTERS

2006

Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics

Klaas VandepoeleTineke CasneufYves Van de Peer

A1 Journal Article in GENOME BIOLOGY

The gain and loss of genes during 600 million years of vertebrate evolution

Tine BlommeKlaas VandepoeleStefanie De BodtCedric SimillionSteven MaereYves Van de Peer

A1 Journal Article in GENOME BIOLOGY

2005

Ancient duplication of cereal genomes

Andrew H PatersonJoch E BowersYves Van de PeerKlaas Vandepoele

Editorial material

Exploring the plant transcriptome through phylogenetic profiling

Klaas VandepoeleYves Van de Peer

A1 Journal Article in PLANT PHYSIOLOGY

Genome-wide identification of potential plant E2F target genes

Klaas VandepoeleKobe VliegheKobe FlorquinLars HennigGerrit BeemsterWilhelm GruissemYves Van de PeerDirk InzéLieven De Veylder

A1 Journal Article in PLANT PHYSIOLOGY

Mode and tempo of gene and genome evolution in plants

Klaas VandepoeleYves Van de Peer

2004

A small CDC25 dual-specificity tyrosine-phosphatase isoform in Arabidopsis thaliana

Isabelle LandrieuMarco da CostaLieven De VeylderFrédérique DewitteKlaas VandepoeleSahar HassanJean-Michel WieruszeskiFlorence CorellouJean-Denis FaureMarc Van Montagu et al.

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

Building genomic profiles for uncovering segmental homology in the twilight zone

Cedric SimillionKlaas VandepoeleYvan SaeysYves Van de Peer

Building genomic profiles for uncovering segmental homology in the twilight zone

Cedric SimillionKlaas VandepoeleYvan SaeysYves Van de Peer

A1 Journal Article in GENOME RESEARCH

Gene duplication and biased functional retention of paralogs in bacterial genomes

Dirk GeversKlaas VandepoeleCedric SimillionYves Van de Peer

A1 Journal Article in TRENDS IN MICROBIOLOGY

Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates

Klaas VandepoeleWouter De VosJohn S TaylorAxel MeyerYves Van de Peer

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

Recent developments in computational approaches for uncovering genomic homology

Cedric SimillionKlaas VandepoeleYves Van de Peer

A1 Journal Article in BIOESSAYS

The quest for genomic homology

Klaas VandepoeleCedric SimillionYves Van de Peer

A2 Journal Article in CURRENT GENOMICS

Type II metacaspases Atmc4 and Atmc9 of Arabidopsis thaliana cleave substrates after arginine and lysine

Dominique VercammenBrigitte Van De CotteGeert De JaegerDominique EeckhoutPeter CasteelsKlaas VandepoeleIsabel VandenbergheJozef Van BeeumenDirk InzéFrank Van Breusegem

A1 Journal Article in JOURNAL OF BIOLOGICAL CHEMISTRY

2003

Evidence that rice and other cereals are ancient aneuploids

Klaas VandepoeleCedric SimillionYves Van de Peer

A1 Journal Article in PLANT CELL

Investigating ancient duplication events in the Arabidopsis genome

Jeroen RaesKlaas VandepoeleCedric SimillionYvan SaeysYves Van de Peer

Bookchapter in Genome evolution : gene and genome duplications and the origin of novel gene functions

Investigating ancient duplication events in the Arabidopsis genome

Jeroen RaesKlaas VandepoeleCedric SimillionYvan SaeysYves Van de Peer

A2 Journal Article in JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS

Quantitative cDNA-AFLP analysis for genome-wide expression studies

Peter BreyneRozemarijn DreesenBernard CannootDebbie RombautKlaas VandepoeleStephane RombautsRudy VanderhaeghenDirk InzéMarc Zabeau

A1 Journal Article in MOLECULAR GENETICS AND GENOMICS

2002

Detecting microcolinearity between Arabidopsis and Rice

Klaas VandepoeleYvan SaeysCedric SimillionJ RAESYves Van de Peer

Detecting the undetectable : uncovering duplicated segments in Arabidopsis by comparison with rice.

Klaas VandepoeleCedric SimillionYves Van de Peer

A1 Journal Article in TRENDS IN GENETICS

Genome-wide analysis of core cell cycle genes in Arabidopsis

Klaas VandepoeleJeroen RaesLieven De VeylderPierre RouzéStephane RombautsDirk Inzé

A1 Journal Article in PLANT CELL

The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice

Klaas VandepoeleYvan SaeysCedric SimillionJeroen RaesYves Van de Peer

A1 Journal Article in GENOME RESEARCH

The hidden duplication past of Arabidopsis thaliana

Cedric SimillionKlaas VandepoeleMarc Van MontaguMarc ZabeauYves Van de Peer

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

Transcriptome analysis during cell division in plants

Peter BreyneRozemarijn DreesenKlaas VandepoeleLieven De VeylderFrank Van BreusegemLindy CallewaertStephane RombautsJeroen RaesBernard CannootGilbert Engler et al.

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