Research Explorer

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Researcher

Stephane Rombauts

Awards & Distinctions

110 Results

2024

Scywalker : scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing

Peter De RijkTijs WatzeelsFahri KüçükaliJasper Van DongenJúlia FauraPatrick WillemsLara De DeynLena DuchateauCarolin GronesThomas Eekhout et al.

A1 Journal Article in BIOINFORMATICS

Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

Xiao MaSteffen VannesteJiyang ChangLuca AmbrosinoKerrie BarryTill BayerAlexander A. BobrovLoriBeth BostonJustin E. CampbellHengchi Chen et al.

A1 Journal Article in NATURE PLANTS

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Jarkko SalojärviAditi RambaniZhe YuRomain GuyotSusan StricklerMaud LepelleyCui WangSitaram RajaramanPasi RastasChunfang Zheng et al.

A1 Journal Article in NATURE GENETICS

The genome‐wide response of Dermatophagoides pteronyssinus to cystatin A, a peptidase inhibitor from human skin, sheds light on its digestive physiology and allergenicity

José Cristian Vidal‐QuistFélix OrtegoStephane RombautsPedro Hernández‐Crespo

U Journal Article in Insect Molecular Biology

2023

Identification and characterization of CYP71 subclade cytochrome P450 enzymes involved in the biosynthesis of bitterness compounds in Cichorium intybus

Charlotte De BruynTom RuttinkElia LacchiniStephane RombautsAnnelies Haegemanellen de keyserChristof Van PouckeSandrien DesmetThomas B. JacobsTom Eeckhaut et al.

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

Industrial chicory genome gives insights into the molecular timetable of anther development and male sterility

Evelien WaegneerStephane RombautsJoost BaertNicolas DauchotAnnick De KeyserTom EeckhautAnnelies HaegemanChang LiuOlivier MaudouxChristine Notté et al.

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

RNA viruses alter house dust mite physiology and allergen production with no detected consequences for allergenicity

José Cristian Vidal‐QuistJozefien DeclercqStijn VanheeBart LambrechtJosé Gómez‐RialCarmen VidalEylem Aydogdu LohausStephane RombautsPedro Hernández‐Crespo

A1 Journal Article in INSECT MOLECULAR BIOLOGY

Suppression of the Arabidopsis cinnamoyl-CoA reductase 1-6 intronic T-DNA mutation by epigenetic modification

Marlies WoutersHéloïse BastiaanseStephane RombautsLisanne de VriesTim De PooterMojca StrazisarGodfrey NeutelingsRuben VanholmeWout Boerjan

A1 Journal Article in PLANT PHYSIOLOGY

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Jarkko SalojärviAditi RambaniZhe YuRomain GuyotSusan StricklerMaud LepelleyCui WangSitaram RajaramanPasi RastasChunfang Zheng et al.

2022

'Nebbiolo' genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.).

Simone MaestriGiorgio GambinoGiulia LopatrielloAndrea MinioIrene PerroneEmanuela CosentinoBarbara GiovannoneLuca MarcolungoMassimiliano AlfanoStephane Rombauts et al.

A1 Journal Article in BMC GENOMICS

Flemish soils contain rhizobia partners for Northwestern Europe‐adapted soybean cultivars

Judith Van DingenenSonia García MéndezStien BeirinckxLena VlaminckAnnick De KeyserNaomi StuerSeverine VerschaeteAlexander ClarysseJoke PannecoucqueStephane Rombauts et al.

A1 Journal Article in ENVIRONMENTAL MICROBIOLOGY

Genomic evidence that a sexually selected trait captures genome-wide variation and facilitates the purging of genetic load

Jonathan M. ParrettSebastian ChmielewskiEylem Aydogdu LohausAleksandra ŁukasiewiczStephane RombautsAgnieszka Szubert-KruszyńskaWiesław BabikMateusz KonczalJacek Radwan

A1 Journal Article in NATURE ECOLOGY & EVOLUTION

The genome of Corydalis reveals the evolution of benzylisoquinoline alkaloid biosynthesis in Ranunculales

Zhichao XuZhen LiFengming RenRanran GaoZhe WangJinlan ZhangTao ZhaoXiao MaXiangdong PuTianyi Xin et al.

A1 Journal Article in PLANT JOURNAL

2021

De novo whole-genome assembly and discovery of genes involved in triterpenoid saponin biosynthesis of Vietnamese ginseng (Panax vietnamensis Ha et Grushv.)

Nguyen Quang Duc TienXiao MaLe Quang ManDuong Thi Kim ChiNguyen Xuan HuyDuong-Tan NhutStephane RombautsTran UtNguyen Hoang Loc

A1 Journal Article in PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

RNA viruses in the house dust mite Dermatophagoides pteronyssinus, detection in environmental samples and in commercial allergen extracts used for in vivo diagnosis

Jose Cristian Vidal-QuistCarmen VidalFernando EscolarBart LambrechtStephane RombautsPedro Hernandez-Crespo

A1 Journal Article in ALLERGY

Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

Sarah FarhatPhuong LEEhsan KayalBenjamin NoelEstelle BigeardErwan CorreFlorian MaumusIsabelle FlorentAdriana AlbertiJean-Marc Aury et al.

A1 Journal Article in BMC BIOLOGY

The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago

Nathalie RaharimalalaStephane RombautsAndrew McCarthyAndréa GaravitoSimon Orozco-AriasLaurence BellangerAlexa Yadira Morales-CorreaSolène FrogerStéphane MichauxVictoria Berry et al.

A1 Journal Article in SCIENTIFIC REPORTS

The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments

Stephanie De VosStephane RombautsLouis CoussementWannes DermauwMarnik VuylstekePatrick SorgeloosJames S. CleggZiro NambuFilip Van NieuwerburghParisa Norouzitallab et al.

A1 Journal Article in BMC GENOMICS

Transcriptomic analysis of the poultry red mite, Dermanyssus gallinae, across all stages of the lifecycle

Kathryn BartleyWan ChenRichard I. Lloyd MillsFrancesca NunnDaniel R. G. PriceStephane RombautsYves Van de PeerLise RoyAlasdair J. NisbetStewart T. G. Burgess

A1 Journal Article in BMC GENOMICS

2020

Genome streamlining in a minute herbivore that manipulates its host plant

Robert GreenhalghWannes DermauwJoris J. GlasStephane RombautsNicky WybouwJainy ThomasJuan M. AlbaEllen J. PrithamSaioa LegarreaRené Feyereisen et al.

A1 Journal Article in ELIFE

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 genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression

Stewart TG BurgessEdward J MarrKathryn BartleyFrancesca G NunnRachel E DownRobert J WeaverJessica C PrickettJackie DunnStephane RombautsThomas Van Leeuwen et al.

A1 Journal Article in BMC GENOMICS

A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression

Stewart TG BurgessEdward J MarrKathryn BartleyFrancesca G NunnRachel E DownRobert J WeaverJessica C PrickettJackie DunnStephane RombautsThomas Van Leeuwen et al.

Draft genome assembly of the false spider mite Brevipalpus yothersi

Denise NaviaValdenice M. NovelliStephane RombautsJuliana Freitas-AstuaRenata Santos de MendoncaMaria Andreia NunesMarcos A. MachadoYao-Cheng LinPhuong LEZaichao Zhang et al.

A2 Journal Article in MICROBIOLOGY RESOURCE ANNOUNCEMENTS

Identification of salt stress response genes using the Artemia transcriptome

Stephanie De VosGilbert Van StappenPatrick SorgeloosMarnik VuylstekeStephane RombautsPeter Bossier

A1 Journal Article in AQUACULTURE

Pseudo-chromosome-length genome assembly of a double haploid 'Bartlett' pear (Pyrus communis L.)

Gareth LinsmithStephane RombautsSara MontanariCecilia H DengJean-Marc CeltonPhilippe GuérifChang LiuRolf LohausJason D ZurnAlessandro Cestaro et al.

A1 Journal Article in GIGASCIENCE

2018

Draft genome assembly of the poultry red mite, Dermanyssus gallinae

Stewart TG BurgessKathryn BartleyFrancesca NunnHarry W WrightMargaret HughesMatthew GemmellSam HaldenbySteve PatersonStephane RombautsFiona M Tomley et al.

A2 Journal Article in MICROBIOLOGY RESOURCE ANNOUNCEMENTS

Draft genome assembly of the sheep scab mite, Psoroptes ovis

Stewart TG BurgessKathryn BartleyEdward J MarrHarry W WrightRobert J WeaverJessica C PrickettMargaret HughesSam HaldenbyPhuong LEStephane Rombauts et al.

A2 Journal Article in GENOME ANNOUNCEMENTS

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

The 'TranSeq' 3'-end sequencing method for high-throughput transcriptomics and gene space refinement in plant genomes

Oren TzfadiaSamuel BocobzaJonas DefoortEfrat Almekias-SieglSayantan PandaMatan LevyVeronique StormeStephane RombautsDiego Adhemar JaitinHadas Keren-Shaul et al.

A1 Journal Article in PLANT JOURNAL

The Chara genome : secondary complexity and implications for plant terrestrialization

Tomoaki NishiyamaHidetoshi SakayamaJan de VriesHenrik BuschmannDenis Saint-MarcouxKristian K UllrichFabian B HaasLisa VanderstraetenDirk BeckerDaniel Lang et al.

A1 Journal Article in CELL

2017

A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)

A CanaguierJ GrimpletG Di GasperoS ScalabrinE DuchêneN ChoisneN MohellibiC GuichardStephane RombautsI Le Clainche et al.

A2 Journal Article in GENOMICS DATA

Dietary shifts have consequences for the repertoire of allergens produced by the European house dust mite

JC Vidal-QuistF OrtegoStephane RombautsP CastaneraP Hernandez-Crespo

A1 Journal Article in MEDICAL AND VETERINARY ENTOMOLOGY

Draft genome sequences of two unclassified Chitinophagaceae bacteria, IBVUCB1 and IBVUCB2, isolated from environmental samples

Russell JS OrrStephane RombautsYves Van de PeerKamran Shalchian-Tabrizi

A2 Journal Article in GENOME ANNOUNCEMENTS

Draft genome sequences of two unclassified bacteria, Hydrogenophaga sp. strains IBVHS1 and IBVHS2, isolated from environmental samples

Russel J. S. OrrStephane RombautsYves Van de PeerKamran Shalchian-Tabrizi

A2 Journal Article in GENOME ANNOUNCEMENTS

Draft genome sequences of two unclassified bacteria, Sphingomonas sp. strains IBVSS1 and IBVSS2, isolated from environmental samples

Russell J. S. OrrStephane RombautsYves Van de PeerKamran Shalchian-Tabrizi

A2 Journal Article in GENOME ANNOUNCEMENTS

OMSim : a simulator for optical map data

Giles MiclotteStéphane PlaisanceStephane RombautsYves Van de PeerP. AudenaertJan Fostier

A1 Journal Article in BIOINFORMATICS

2016

Complex evolutionary dynamics of massively expanded chemosensory receptor families in an extreme generalist chelicerate herbivore

Thi Ngoc Phuong CaoRobert GreenhalghWannes DermauwStephane RombautsSabina Bajda-WybouwVladimir ZhurovMiodrag GrbićYves Van de PeerThomas Van LeeuwenPierre Rouzé et al.

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

Jabba: hybrid error correction for long sequencing reads

Giles MiclotteMahdi HeydariPiet DemeesterStephane RombautsYves Van de PeerP. AudenaertJan Fostier

A1 Journal Article in ALGORITHMS FOR MOLECULAR BIOLOGY

2015

Identifying prokaryotic consortia that live in close interactions with algae

Assia SaltykovaSergio Pulido-TamayoMarie PazoutovaStefan A RensingTomoaki NishiyamaYves Van de PeerKathleen MarchalStephane Rombauts

2014

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies

Romain Blanc-MathieuBram VerhelstEvelyne DerelleStephane RombautsFrançois-Yves BougetIsabelle CarreAnnie ChateauAdam Eyre-WalkerNigel GrimsleyHervé Moreau et al.

A1 Journal Article in BMC GENOMICS

The grapevine gene nomenclature system

Jérôme GrimpletAnne-Françoise Adam-BlondonPierre-François BertOliver BitzDario CantuChristopher DaviesSerge DelrotMario PezzottiStephane RombautsGrant R Cramer

A1 Journal Article in BMC GENOMICS

2013

A link between host plant adaptation and pesticide resistance in the polyphagous spider mite Tetranychus urticae

Wannes DermauwNicky WybouwStephane RombautsBjörn MentenJohn VontasMiodrag GrbićRichard M ClarkRené FeyereisenThomas Van Leeuwen

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

Analysis of RNA-Seq data with TopHat and Cufflinks for genome-wide expression analysis of jasmonate-treated plants and plant cell cultures

Jacob PollierStephane RombautsAlain Goossens

Bookchapter in Jasmonate signaling : methods and protocols

Analysis of the olive fruit fly Bactrocera oleae transcriptome and phylogenetic classification of the major detoxification gene families

Nena PavlidiWannes DermauwStephane RombautsAntonis ChrisargirisThomas Van LeeuwenJohn Vontas

A1 Journal Article in PLOS ONE

CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data

Alex Van MoerkerckeMichele FabrisJacob PollierGino BaartStephane RombautsGhulam HasnainHeiko RischerJohan MemelinkKirsi-Marja Oksman-CaldenteyAlain Goossens

A1 Journal Article in PLANT AND CELL PHYSIOLOGY

Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics

G AndolfoW SanseverinoStephane RombautsYves Van de PeerJM BradeenD CarputoL FruscianteMR Ercolano

A1 Journal Article in NEW PHYTOLOGIST

Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions

Andreas D ZimmerDaniel LangKarol BuchtaStephane RombautsTomoaki NishiyamaMitsuyasu HasebeYves Van de PeerStefan A RensingRalf Reski

A1 Journal Article in BMC GENOMICS

2012

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

In silico cloning of genes encoding neuropeptides, neurohormones and their putative G-protein coupled receptors in a spider mite

Jan A VeenstraStephane RombautsMiodrag Grbić

A1 Journal Article in INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway

Michele FabrisMichiel MatthijsStephane RombautsWim VyvermanAlain GoossensGino Baart

A1 Journal Article in PLANT JOURNAL

The tomato genome sequence provides insights into fleshy fruit evolution

Shusei SatoSatoshi TabataHideki HirakawaErika AsamizuKenta ShirasawaSachiko IsobeTakakazu KanekoYasukazu NakamuraDaisuke ShibataKoh Aoki et al.

A1 Journal Article in NATURE

2011

Search for nodulation-related CLE genes in the genome of Glycine max

Virginie MortierBerhanu Amsalu FentaCindy MartensStephane RombautsMarcella HolstersKarl KunertSofie Goormachtig

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

The Medicago genome provides insight into the evolution of rhizobial symbioses

Nevin D YoungFrédéric DebelléGiles ED OldroydRene GeurtsSteven B CannonMichael K UdvardiVagner A BeneditoKlaus FX MayerJérôme GouzyHeiko Schoof et al.

A1 Journal Article in NATURE

The genome of Tetranychus urticae reveals herbivorous pest adaptations

Miodrag GrbićThomas Van LeeuwenRichard M ClarkStephane RombautsPierre RouzéVojislava GrbićEdward J OsborneWannes DermauwThi Ngoc Phuong CaoFélix Ortego et al.

A1 Journal Article in NATURE

2010

AGRONOMICS1: A New Resource for Arabidopsis Transcriptome Profiling

Hubert RehrauerCatherine AquinoWilhelm GruissemStefan R HenzPierre HilsonSascha LaubingerNaïra NaouarAndrea PatrignaniStephane RombautsHuan Shu et al.

A1 Journal Article in PLANT PHYSIOLOGY

CLE peptides control Medicago truncatula nodulation locally and systemically

Virginie MortierGriet Den HerderRyan WhitfordWillem Van De VeldeStephane RombautsKatrien D'haeseleerMarcella HolstersSofie Goormachtig

A1 Journal Article in PLANT PHYSIOLOGY

Functional modules in the Arabidopsis core cell cycle binary protein-protein interaction network

Joanna BorucHilde Van Den DaeleJens HollunderStephane RombautsEvelien MyllePierre HilsonDirk InzéLieven De VeylderEugenia Russinova

A1 Journal Article in PLANT CELL

Systematic localization of the Arabidopsis core cell cycle proteins reveals novel cell division complexes

Joanna BorucEvelien MylleMaria DudaRebecca De ClercqStephane RombautsDanny GeelenPierre HilsonDirk InzéDaniël Van DammeEugenia Russinova

A1 Journal Article in PLANT PHYSIOLOGY

2009

A snapshot of the emerging tomato genome sequence

Lukas MuellerRené Klein LankhorstSteven D TanksleyJames J GiovannoniRuth WhiteJulia VrebalovZhangjun FeiJoyce van EckRobert BuelsAdri A Mills et al.

A1 Journal Article in PLANT GENOME

Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas

Alexandra Z WordenJea-Hyeok LeeThomas MockPierre RouzéMelinda P SimmonsAndrea L AertsAndrew E AllenMarie L CuvelierEvelyne DerelleMeredith V Everett et al.

A1 Journal Article in SCIENCE

Systematic analysis of cell-cycle gene expression during Arabidopsis development

Janice de Almeida EnglerLieven De VeylderRuth De GroodtStephane RombautsVéronique BoudolfBjörn De MeyerAdriana HemerlyPaulo FerreiraTom BeeckmanMansour Karimi et al.

A1 Journal Article in Plant Journal

2008

Genome annotation in plants and fungi: EuGène as a model platform

Sylvain FoissacJérôme GouzyStephane RombautsCatherine MathéJoëlle AmselemLieven SterckYves Van de PeerPierre RouzéThomas Schiex

A1 Journal Article in CURRENT BIOINFORMATICS

Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5

Moussa BenhamedMarie-Laure Martin-MagnietteLudivine TaconnatFrédérique BittonCaroline ServetRebecca De ClercqBjörn De MeyerCaroline BuysschaertStephane RombautsRaimundo Villarroel-Mandiola et al.

A1 Journal Article in PLANT JOURNAL

Seven in absentia proteins affect plant growth and nodulation in Medicago truncatula

Griet Den HerderAnnick De KeyserRiet De RyckeStephane RombautsWillem Van De VeldeMaría R ClementeChrista VerplanckePeter MergaertEva KondorosiMarcella Holsters et al.

A1 Journal Article in PLANT PHYSIOLOGY

The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants

Stefan A RensingDaniel LangAndreas D ZimmerAstrid TerryAsaf SalamovHarris ShapiroTomoaki NishiyamaPierre-François PerroudErika A LindquistYasuko Kamisugi et al.

A1 Journal Article in SCIENCE

2007

A molecular timetable for apical bud formation and dormancy induction in poplar

Tom RuttinkMatthias ArendKris MorreelVeronique StormeStephane RombautsJörg FrommRishikesh P BhaleraoWout BoerjanAntje Rohde

A1 Journal Article in PLANT CELL

A symbiotic plant peroxidase involved in bacterial invasion of the tropical legume Sesbania rostrata

Jeroen Den HerderSam LievensStephane RombautsMarcella HolstersSofie Goormachtig

A1 Journal Article in PLANT PHYSIOLOGY

Comparative transcriptome analysis reveals common and specific tags for root hair and crack-entry invasion in Sesbania rostrata

Ward CapoenJeroen Den HerderStephane RombautsJeroen De GussemAnnick De KeyserMarcella HolstersSofie Goormachtig

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

The annotation and analysis of the genome of Arabidopsis lyrata

Jeffrey FawcettStephane RombautsPedro PattynLieven SterckYves Van de Peer

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

Brian PalenikJane GrimwoodAndrea AertsPierre RouzéAsaf SalamovNicholas PutnamChris DupontRichard JorgensenEvelyne DerelleStephane Rombauts et al.

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

2006

Aging in legume symbiosis : a molecular view on nodule senescence in Medicago truncatula

Willem Van De VeldeJuan Carlos Pérez GuerraAnnick De KeyserRiet De RyckeStephane RombautsNicolas MaunouryPeter MergaertEva KondorosiMarcella HolstersSofie Goormachtig

A1 Journal Article in PLANT PHYSIOLOGY

Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features

Evelyne DerelleConchita FerrazStephane RombautsPierre RouzéAlexandra Z WordenSteven RobbensFrédéric PartenskySven DegroeveSophie EcheyniéRichard Cooke et al.

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

Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes

Steven B CannonLieven SterckStephane RombautsShusei SatoFoo CheungJérôme GouzyXiaohong WangJoann MudgeJayprakash VasdewaniThomas Schiex et al.

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

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

GA TuskanS DiFazioS JanssonJ BohlmannI GrigorievU HellstenN PutnamS RalphStephane RombautsA Salamov et al.

A1 Journal Article in SCIENCE

2005

EST data suggest that poplar is an ancient polyploid

Lieven SterckStephane RombautsStefan JanssonFredrik SterkyPierre RouzéYves Van de Peer

A1 Journal Article in NEW PHYTOLOGIST

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

Sébastien AubourgVéronique BrunaudClémence BruyèreMark CockRichard CookeAnnick CottetArnaud CoulouxPatrice DéhaisGilbert DeléageAymeric Duclert et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Genome analysis of the world's smallest free-living eukaryote Ostreococcus tauri unveils unique genome heterogeneity

Steven RobbensStephane RombautsPierre RouzéJan WuytsYvan SaeysHervé MoreauYves Van de Peer

Genome-wide analysis of hydrogen peroxide-regulated gene expression in Arabidopsis reveals a high light-induced transcriptional cluster involved in anthocyanin biosynthesis

Sandy VanderauweraPhilip ZimmermannStephane RombautsSteven VandenabeeleChristian LangebartelsWilhelm GruissemDirk InzéFrank Van Breusegem

A1 Journal Article in PLANT PHYSIOLOGY

2004

Annotation of a 95-kb Populus deltoides genomic sequence reveals a disease resistance gene cluster and novel class I and class II transposable elements

Magali LescotStephane RombautsJiong ZhangSébastien AubourgCatherine MathéS JanssonPierre RouzéWout Boerjan

A1 Journal Article in THEORETICAL AND APPLIED GENETICS

Catalase deficiency drastically affects gene expression induced by high light in Arabidopsis thaliana

Steven VandenabeeleSandy VanderauweraMarnik VuylstekeStephane RombautsChristian LangebartelsHarald K SeidlitzMarc ZabeauMarc Van MontaguDirk InzéFrank Van Breusegem

A1 Journal Article in PLANT JOURNAL

Starch division and partitioning: a mechanism for granule propagation and maintenance in the picophytoplanktonic green alga Ostreococcus tauri

Jean-Philippe RalEvelyne DerelleConchita FerrazFabrice WattebledBenoit FarinasFlorence CorellouAlain BuléonMarie-Christine SlomiannyDavid DelvalleChristophe d'Hulst et al.

A1 Journal Article in PLANT PHYSIOLOGY

2003

AFLPinSilico, simulating AFLP fingerprints

Stephane RombautsYves Van de PeerPierre Rouzé

A1 Journal Article in BIOINFORMATICS

Computational approaches to identify promoters and cis-regulatory elements in plant genomes

Stephane RombautsKobe FlorquinMagali LescotKathleen MarchalPierre RouzéYves Van de Peer

A1 Journal Article in PLANT PHYSIOLOGY

Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants

Stefanie De BodtJeroen RaesKobe FlorquinStephane RombautsPierre RouzéGünter TheißenYves Van de Peer

A1 Journal Article in JOURNAL OF MOLECULAR EVOLUTION

Microarray analysis of E2Fa-DPa-overexpressing plants uncovers a cross-talking genetic network between DNA replication and nitrogen assimilation

Kobe VliegheMarnik VuylstekeKobe FlorquinStephane RombautsSara MaesSandra OrmenesePaul Van HummelenYves Van de PeerDirk InzéLieven De Veylder

A1 Journal Article in JOURNAL OF CELL SCIENCE

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

A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes

Gert ThijsKathleen MarchalMagali LescotStephane RombautsBart De MoorPierre RouzéYves Moreau

A1 Journal Article in JOURNAL OF COMPUTATIONAL BIOLOGY

Deciphering cis-acting regulatory elements in plant and drosophila promoter sequences

Magali LescotGert ThijsStephane RombautsPatrice DéhaisDavid MartinDenis ThieffryBernard JacqYves MoreauPierre RouzéJacques van Helden

Genome-wide analysis of core cell cycle genes in Arabidopsis

Klaas VandepoeleJeroen RaesLieven De VeylderPierre RouzéStephane RombautsDirk Inzé

A1 Journal Article in PLANT CELL

INCLUSive: INtegrated Clustering, Upstream of sequence retrieval and motif Sampling

Gert ThijsYves MoreauFrank De SmetJanick MathysMagali LescotStephane RombautsPierre RouzéBart De MoorKathleen Marchal

A1 Journal Article in BIOINFORMATICS

Integrating quality-based clustering of microarray data with Gibbs sampling for the discovery of regulatory motifs

Yves MoreauGert ThijsKathleen MarchalFrank De SmetJanick MathysMagali LescotStephane RombautsPierre RouzéBart De Moor

Moss transcriptome and beyond

Stefan A RensingStephane RombautsYves Van de PeerRalf Reski

Editorial material

PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences

Magali LescotPatrice DéhaisGert ThijsKathleen MarchalYves MoreauYves Van de PeerPierre RouzéStephane Rombauts

A1 Journal Article in NUCLEIC ACIDS RESEARCH

The PlantCARE database and tools for in silico search of plant cis-acting regulatory elements

Stephane RombautsMagali LescotGert ThijsKathleen MarchalYves MoreauPatrice DéhaisYves Van de PeerPierre Rouzé

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

2001

A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling

Gert ThijsMagali LescotKathleen MarchalStephane RombautsBart De MoorPierre RouzéYves Moreau

A1 Journal Article in BIOINFORMATICS

Identification of novel cyclin-dependent kinases interacting with the CKS1 protein of Arabidopsis

Véronique BoudolfStephane RombautsMirande NaudtsDirk InzéLieven De Veylder

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

In silico search of plant cis-acting regulatory elements

Magali LescotStephane RombautsGert ThijsKathleen MarchalBart De MoorYves MoreauPierre Rouzé

2000

Characterization of two distinct DP-related genes from Arabidopsis thaliana

Zoltán MagyarAna AtanassovaLieven De VeylderStephane RombautsDirk Inzé

A1 Journal Article in FEBS LETTERS

Detection of cis-acting regulatory elements in plants : a GIBBS sampling approach

Gert ThijsStephane RombautsMagali LescotKathleen MarchalBart De MoorYves MoreauPierre Rouzé

Gene prediction and gene classes in Arabidopsis thaliana

Catherine MathéPatrice DéhaisNathalie PavyStephane RombautsMarc Van MontaguPierre Rouzé

A1 Journal Article in JOURNAL OF BIOTECHNOLOGY

1999

Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences

Nathalie PavyStephane RombautsPatrice DéhaisCatherine MathéDavuluri VV RamanaPhilippe LeroyPierre Rouzé

A1 Journal Article in BIOINFORMATICS

Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4

Nancy TerrynLeo HeijnenAnnick De KeyserMartien Van AsseldonckRebecca De ClercqHenk VerbakelJan GielenMarc ZabeauRaimundo Villarroel-MandiolaTaco Jesse et al.

A1 Journal Article in FEBS LETTERS

Genome annotation: which tools do we have for it?

Pierre RouzéNathalie PavyStephane Rombauts

A1 Journal Article in CURRENT OPINION IN PLANT BIOLOGY

Génomique et bio-informatique

Nathalie PavyCatherine MathéStephane RombautsPierre Rouzé

A1 Journal Article in OCL-OLEAGINEUX CORPS GRAS LIPIDES

PlantCARE, a plant cis-acting regulatory element database

Stephane RombautsPatrice DéhaisMarc Van MontaguPierre Rouzé

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Recognition of gene regulatory sequences by bagging of neural networks

Gert ThijsYves MoreauStephane RombautsBart De MoorPierre Rouzé

1996

Gene prediction in Arabidopsis thaliana: genomic sequences

Pierre RouzéStephane RombautsG Van LaereLuc Van WiemeerschMarc Van Montagu

A1 Journal Article in ARCHIVES OF PHYSIOLOGY AND BIOCHEMISTRY