Research Explorer

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Researcher

Frederik Coppens

Awards & Distinctions

53 Results

2023

Galaxy Training : a powerful framework for teaching!

Saskia HiltemannHelena RascheSimon GladmanHans-Rudolf HotzDelphine LarivièreDaniel BlankenbergPratik D. JagtapThomas WollmannAnthony BretaudeauNadia Goué et al.

A1 Journal Article in PLOS COMPUTATIONAL BIOLOGY

2022

Adenosine monophosphate deaminase modulates BIN2 activity through hydrogen peroxide-induced oligomerization

Qing LuAnaxi HoubaertQian MaJingjing HuangLieven SterckCheng ZhangRené BenjaminsFrederik CoppensFrank Van BreusegemEugenia Russinova

A1 Journal Article in PLANT CELL

ELIXIR biovalidator for semantic validation of life science metadata

Isuru LiyanageTony BurdettBert DroesbekeKaroly ErdosRolando FernandezAlasdair GrayMuhammad HaseebSimon JuppFlavia PenimCyril Pommier et al.

A1 Journal Article in BIOINFORMATICS

Expanding the Galaxy’s reference data

Nagampalli VijayKrishnaJayadev JoshiNate CoraorJennifer Hillman-JacksonDave BouvierMarius van den BeekIgnacio EguinoaFrederik CoppensJohn DavisMichał Stolarczyk et al.

A2 Journal Article in BIOINFORMATICS ADVANCES

Galaxy : a decade of realising CWFR concepts

Beatriz Serrano-SolanoAnne FouillouxIgnacio EguinoaMatúš KalašBjörn GrüningFrederik Coppens

A2 Journal Article in DATA INTELLIGENCE

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

Packaging research artefacts with RO-Crate

Stian Soiland-ReyesPeter SeftonMercè CrosasLeyla Jael CastroFrederik CoppensJosé M. FernándezDaniel GarijoBjörn GrüningMarco La RosaSimone Leo et al.

A2 Journal Article in DATA SCIENCE

Plant science data integration, from building community standards to defining a consistent data lifecycle

Cyril PommierFrederik CoppensHanna Ćwiek-KupczyńskaDaniel FariaSebastian BeierCélia MiguelCélia MichoteyFlora D'AnnaStuart OwenKristina Gruden

Bookchapter in Towards responsible plant data linkage : data challenges for agricultural research and development

Self-incompatibility requires GPI anchor remodeling by the poppy PGAP1 ortholog HLD1

Zongcheng LinFei XieMarina Muñoz TriviñoTao ZhaoFrederik CoppensLieven SterckMaurice BoschVernonica E. Franklin-TongMoritz Nowack

A1 Journal Article in CURRENT BIOLOGY

Ten simple rules for making a software tool workflow-ready

Paul BrackPeter CrowtherStian Soiland-ReyesStuart OwenDouglas LoweAlan R. WilliamsQuentin GroomMathias DillenFrederik CoppensBjörn Grüning et al.

Editorial material

2021

A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive

Miguel RoncoroniBert DroesbekeIgnacio EguinoaKim De RuyckFlora D'AnnaDilmurat YusufBjörn GrüningRolf BackofenFrederik Coppens

A1 Journal Article in BIOINFORMATICS

A community roadmap for scientific workflows research and development

Rafael Ferreira da SilvaHenri CasanovaKyle ChardIlkay AltintasRosa M. BadiaBartosz BalisTaina ColemanFrederik CoppensFrank Di NataleBjoern Enders et al.

Ready-to-use public infrastructure for global SARS-CoV-2 monitoring

Wolfgang MaierSimon BrayMarius van den BeekDave BouvierNathan CoraorMilad MiladiBabita SinghJordi Rambla De ArgilaDannon BakerNathan Roach et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

The Arabidopsis condensin CAP‐D subunits arrange interphase chromatin

Celia MunicioWojciech AntoszKlaus D. GrasserEtienne KornobisMichiel Van BelIgnacio EguinoaFrederik CoppensAndrea BräutigamInna LermontovaAstrid Bruckmann et al.

A1 Journal Article in NEW PHYTOLOGIST

2020

Enabling reusability of plant phenomic datasets with MIAPPE 1.1

Evangelia A. PapoutsoglouDaniel FariaDaniel ArendElizabeth ArnaudIoannis N. AthanasiadisInês ChavesFrederik CoppensGuillaume CornutBruno V. CostaHanna Cwiek-Kupczynska et al.

A1 Journal Article in NEW PHYTOLOGIST

No more business as usual : agile and effective responses to emerging pathogen threats require open data and open analytics

Dannon BakerMarius van den BeekDaniel BlankenbergDave BouvierJohn ChiltonNate CoraorFrederik CoppensIgnacio EguinoaSimon GladmanBjörn Grüning et al.

A1 Journal Article in PLOS PATHOGENS

Plant-RRBS : DNA methylome profiling adjusted to plant genomes, utilizing efficient endonuclease combinations, for multi-sample studies

Martin SchmidtMagdalena WoloszynskaMichiel Van BelFrederik CoppensMaria Van Lijsebettens

Bookchapter in Plant epigenetics and epigenomics : methods and protocols

2019

Multifaceted activity of cytokinin in leaf development shapes its size and structure in Arabidopsis

Jan SkalákLiesbeth VercruyssenHannes ClaeysJana HradilováMartin ČernýOndřej NovákLenka PlačkováIñigo Saiz-FernándezPatricie SkalákováFrederik Coppens et al.

A1 Journal Article in PLANT JOURNAL

2018

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

The TriForC database : a comprehensive up-to-date resource of plant triterpene biosynthesis

Karel MiettinenSabrina IñigoLukasz KreftJacob PollierChristof De BoAlexander BotzkiFrederik CoppensSoren BakAlain Goossens

A1 Journal Article in NUCLEIC ACIDS RESEARCH

The reduction in maize leaf growth under mild drought affects the transition between cell division and cell expansion and cannot be restored by elevated gibberellic acid levels

Hilde NelissenXiaohuan SunBart RymenYusuke JikumaruMikko KojimaYumiko TakebayashiRafael AbbeloosKirin DemuynckVeronique StormeMarnik Vuylsteke et al.

A1 Journal Article in PLANT BIOTECHNOLOGY JOURNAL

2017

Exploring plant co-expression and gene-gene Interactions with CORNET 3.0

Michiel Van BelFrederik Coppens

Bookchapter in Plant genomics databases : methods and protocols

Natural variation of molecular and morphological gibberellin responses

Younjeong NamDorota HermanJonas BlommeEunyoung ChaeMikiko KojimaFrederik CoppensVeronique StormeTwiggy Van DaeleStijn DhondtHitoshi Sakakibara et al.

A1 Journal Article in PLANT PHYSIOLOGY

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

Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions

Martin SchmidtMichiel Van BelMagdalena WoloszynskaBram SlabbinckCindy MartensMarc De BlockFrederik CoppensMaria Van Lijsebettens

A1 Journal Article in BMC PLANT BIOLOGY

Proteome profiling of wheat shoots from different cultivars

Lam Dai VuInge VerstraetenElisabeth StesMichiel Van BelFrederik CoppensKris GevaertIve De Smet

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

Unlocking the potential of plant phenotyping data through integration and data-driven approaches

Frederik CoppensNathalie WuytsDirk InzéStijn Dhondt

A2 Journal Article in CURRENT OPINION IN SYSTEMS BIOLOGY

2016

Combined large-scale phenotyping and transcriptomics in maize reveals a robust growth regulatory network

Joke BauteDorota HermanFrederik CoppensJolien De BlockBram SlabbinckMatteo Dell'AcquaMario Enrico PeSteven MaereHilde NelissenDirk Inzé

A1 Journal Article in PLANT PHYSIOLOGY

It's time for some 'site'-seeing: novel tools to monitor the ubiquitin landscape in Arabidopsis thaliana

Alan WaltonElisabeth StesNicolas CybulskiMichiel Van BelSabrina IñigoAstrid Nagels DurandEvy TimmermanJefri HeymanLaurens PauwelsLieven De Veylder et al.

A1 Journal Article in PLANT CELL

Leaf growth response to mild drought : natural variation in Arabidopsis sheds light on trait architecture

Pieter ClauwFrederik CoppensArthur KorteDorota HermanBram SlabbinckStijn DhondtTwiggy Van DaeleLiesbeth De MildeMattias VermeerschKatrien Maleux et al.

A1 Journal Article in PLANT CELL

Tools and data services registry: a community effort to document bioinformatics resources

Jon IsonKristoffer RapackiHervé MénagerMatúš KalašEmil RydzaPiotr ChmuraChristian AnthonNiall BeardKarel BerkaDan Bolser et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Up-to-date workflow for plant (phospho)proteomics identifies differential drought-responsive phosphorylation events in maize leaves

Lam Dai VuElisabeth StesMichiel Van BelHilde NelissenDavy MaddeleinDirk InzéFrederik CoppensLennart MartensKris GevaertIve De Smet

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2015

A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants

Yadira Olvera CarrilloMichiel Van BelTom Van HautegemMatyas FendrychMarlies HuysmansMária Braun ŠimáškováMatthias Van DurmePierre BuscaillSusana RivasNuria S Coll et al.

A1 Journal Article in PLANT PHYSIOLOGY

Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population

Joke BauteDorota HermanFrederik CoppensJolien De BlockBram SlabbinckMatteo Dell'AcquaMario Enrico PèSteven MaereHilde NelissenDirk Inzé

A1 Journal Article in GENOME BIOLOGY

Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

Matteo Dell'AcquaDaniel M GattiGiorgio PeaFederica CattonaroFrederik CoppensGabriele MagrisAye L HlaingHtay H AungHilde NelissenJoke Baute et al.

A1 Journal Article in GENOME BIOLOGY

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

2014

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

Combining growth-promoting genes leads to positive epistasis in Arabidopsis thaliana

Hannes VanhaerenNathalie Gonzalez SanchezFrederik CoppensLiesbeth De MildeTwiggy Van DaeleMattias VermeerschNubia Barbosa EloyVeronique StormeDirk Inzé

A1 Journal Article in eLIFE

High-resolution time-resolved imaging of in vitro Arabidopsis rosette growth

Stijn DhondtNathalie Gonzalez SanchezJonas BlommeLiesbeth De MildeTwiggy Van DaeleDirk Van AkoleyenVeronique StormeFrederik CoppensGerrit BeemsterDirk Inzé

A1 Journal Article in PLANT JOURNAL

2013

Brassinosteroid production and signaling differentially control cell division and expansion in the leaf

Miroslava ZhiponovaIsabelle VanhoutteVéronique BoudolfCamilla BettiStijn DhondtFrederik CoppensEvelien MylleSara MaesMary-Paz González-GarcíaAna I Caño-Delgado et al.

A1 Journal Article in NEW PHYTOLOGIST

Kinematic analysis of cell division in leaves of mono- and dicotyledonous species: a basis for understanding growth and developing refined molecular sampling strategies

Hilde NelissenBart RymenFrederik CoppensStijn DhondtFabio FioraniGerrit Beemster

Bookchapter in Plant organogenesis : methods and protocols

2012

Exit from proliferation during leaf development in Arabidopsis thaliana: a not-so-gradual process

Megan AndriankajaStijn DhondtStefanie De BodtHannes VanhaerenFrederik CoppensLiesbeth De MildePer MühlenbockAleksandra SkiryczNathalie Gonzalez SanchezGerrit Beemster et al.

A1 Journal Article in DEVELOPMENTAL CELL

2011

Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis

Steffen VannesteFrederik CoppensEunKyoung LeeTyler J. DonnerZidian XieGert Van IsterdaelStijn DhondtFreya De WinterBert De RybelMarnik Vuylsteke et al.

A1 Journal Article in EMBO JOURNAL

Low magnesium status in plants enhances tolerance to cadmium exposure

Christian HermansJiugeng ChenFrederik CoppensDirk InzéNathalie Verbruggen

A1 Journal Article in NEW PHYTOLOGIST

Pause-and-stop: the effects of osmotic stress on cell proliferation during early leaf development in Arabidopsis and a role for ethylene signaling in cell cycle arrest

Aleksandra SkiryczHannes ClaeysStefanie De BodtAkira OikawaShoko ShinodaMegan AndriankajaKatrien MaleuxNubia Barbosa EloyFrederik CoppensSang-Dong Yoo et al.

A1 Journal Article in PLANT CELL

The plant-specific family of DNA-binding proteins containing three HMG-box domains interacts with mitotic and meiotic chromosomes

Dorthe S. PedersenFrederik CoppensLu MaMartin AntoschBarbara MarktlThomas MerkleGerrit BeemsterAndreas HoubenKlaus D. Grasser

A1 Journal Article in NEW PHYTOLOGIST

Transcriptional and post-transcriptional regulation of leaf development in Arabidopsis thaliana

Frederik CoppensDirk Inzé

2010

Early transcriptomic changes induced by magnesium deficiency in Arabidopsis thaliana reveal the alteration of circadian clock gene expression in roots and the triggering of abscisic acid-responsive genes

Christian HermansMarnik VuylstekeFrederik CoppensAdrain CraciunDirk InzéNathalie Verbruggen

A1 Journal Article in NEW PHYTOLOGIST

Kinematic analysis of cell division and expansion

Bart RymenFrederik CoppensStijn DhondtFabio FioraniGerrit Beemster

Bookchapter in Plant developmental biology : methods and protocols

SHORT-ROOT and SCARECROW regulate leaf growth in Arabidopsis by stimulating S-phase progression of the cell cycle

Stijn DhondtFrederik CoppensFreya De WinterKamal SwarupRoeland MerksDirk InzéMalcolm J BennettGerrit Beemster

A1 Journal Article in PLANT PHYSIOLOGY

Systems analysis of the responses to long-term magnesium deficiency and restoration in Arabidopsis thaliana

Christian HermansMarnik VuylstekeFrederik CoppensSimona M CristescuFrans JM HarrenDirk InzéNathalie Verbruggen

A1 Journal Article in NEW PHYTOLOGIST

2009

Gibberellin signaling controls cell proliferation rate in Arabidopsis

Patrick AchardAndi GustiSolzic CheminantMalek AliouaStijn DhondtFrederik CoppensGerrit BeemsterPascal Genschik

A1 Journal Article in Current Biology

2006

The Arabidopsis anaphase promoting complex (APC): regulation through subunit availability in plant tissues

Nubia Barbosa EloyFrederik CoppensGerrit BeemsterAdriana HemerlyPaulo Cavalcanti Gomes Ferreira

A1 Journal Article in CELL CYCLE