Research Explorer

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Project

Bioinformatics: from nucleotids to networks (N2N)

Outputs and Outcomes

Publications

Network-based modelling for omics data

Mushthofa MushthofaMartine De CockKathleen Marchal

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

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 RombautsThomas Van LeeuwenYves Van de PeerAlasdair J Nisbet et al.

A2 Journal Article in MICROBIOLOGY RESOURCE ANNOUNCEMENTS

MorphDB : prioritizing genes for specialized metabolism pathways and gene ontology categories in plants

Arthur ZwaenepoelTim DielsDavid AmarThomas Van ParysRon ShamirYves Van de PeerOren Tzfadia

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

A genome for gnetophytes and early evolution of seed plants

Tao WanZhi-Ming LiuLing-Fei LiAndrew R LeitchIlia J LeitchRolf LohausZhong-Jian LiuHai-Ping XinYan-Bing GongYang LiuWen-Cai WangLing-Yun ChenYong YangLaura J KellyJi YangJin-Ling HuangZhen LiPing LiuLi ZhangHong-Mei LiuHui WangShu-Han DengMeng LiuJi LiLu MaYan LiuYang LeiWei XuLing-Qing WuFan LiuQian MaXin-Ran YuZhi JiangGuo-Qiang ZhangShao-Hua LiRui-Qiang LiShou-Zhou ZhangQing-Feng WangYves Van de PeerJin-Bo ZhangXiao-Ming Wang et al.

A1 Journal Article in NATURE PLANTS

A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils

Marc W Van GoethemRian PierneefOliver KI BezuidtYves Van de PeerDon A CowanThulani P Makhalanyane

A1 Journal Article in MICROBIOME

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

Daniel LangKristian K UllrichFlorent MuratJoerg FuchsJerry JenkinsFabian B HaasMathieu PiednoelHeidrun GundlachMichiel Van BelRabea MeybergCristina VivesJordi MorataAikaterini SymeonidiManuel HissWellington MucheroYasuko KamisugiOmar SalehGuillaume BlancEva L. DeckerNico van GesselJane GrimwoodRichard D. HayesSean W. GrahamLee E. GunterStuart F. McDanielSebastian N. W. HoernsteinAnders LarssonFay-Wei LiPierre-Francois PerroudJeremy PhillipsPriya RanjanDaniel S. RoksharCarl J. RothfelsLucas SchneiderShengqiang ShuDennis W. StevensonFritz ThummlerMichael TillichJuan C. Villarreal AguilarThomas WidiezGane Ka-Shu WongAnn WymoreYong ZhangAndreas D. ZimmerRalph S. QuatranoKlaus F. X. MayerDavid GoodsteinJosep M. CasacubertaKlaas VandepoeleRalf ReskiAndrew C. CumingGerald A. TuskanFlorian MaumusJerome SalseJeremy SchmutzStefan A. Rensing et al.

A1 Journal Article in PLANT JOURNAL

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 TanDamir BaranasicDavid J ArenillasAlbin SandelinKlaas VandepoeleBoris LenhardBenoit BallesterWyeth W WassermanFrancois ParcyAnthony Mathelier et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

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 EbersbergerJudith BlakeJesualdo Tomas Fernandez BreisBrigitte BoeckmannToni GabaldonErik SonnhammerChristophe DessimozSuzanna Lewis et al.

A1 Journal Article in BIOINFORMATICS

Molecular processes underlying synergistic linuron mineralization in a triple-species bacterial consortium biofilm revealed by differential transcriptomics

Pieter AlbersBram WeytjensRené De MotKathleen MarchalDirk Springael

A1 Journal Article in MICROBIOLOGYOPEN

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

Molecular subtyping of Salmonella Typhimurium with multiplex oligonucleotide ligation-PCR (MOL-PCR)

Véronique WuytsWesley MattheusNancy HC RoosensKathleen MarchalSophie BertrandSigrid CJ De Keersmaecker

Bookchapter in Diagnostic bacteriology : methods and protocols

Network-based identification of adaptive pathways in evolved ethanol-tolerant bacterial populations

Toon SwingsBram WeytjensThomas SchalckCamille BonteNatalie VerstraetenJan MichielsKathleen Marchal

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips

Brenda D WingfieldDave K BergerEmma T SteenkampHye-Jin LimTuan A DuongBurton H BluhmZ Wilhelm De BeerLieschen De VosG FourieKershney NaidooNicky OlivierYao-Cheng LinYves Van de PeerFourie JoubertBridget G CramptonVelushka SwartNicole SoalCatherine TathamMagriet A Van der NestNicolaas A van der MerweStephanie van WykP Markus WilkenMichael J Wingfield et al.

A1 Journal Article in IMA FUNGUS

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

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

Coordinated functional divergence of genes after genome duplication in Arabidopsis thaliana

Riet De SmetEhsan SabaghianZhen LiYvan SaeysYves Van de Peer

A1 Journal Article in PLANT CELL

Reciprocally retained genes in the angiosperm lineage show the hallmarks of dosage balance sensitivity

Setareh TasdighianMichiel Van BelZhen LiYves Van de PeerLorenzo Carretero-PauletSteven Maere

A1 Journal Article in PLANT CELL

Genome of wild olive and the evolution of oil biosynthesis

Turgay UnverZhangyan WuLieven SterckMine TurktasRolf LohausZhen LiMing YangLijuan HeTianquan DengFrancisco Javier EscalanteCarlos LlorensFrancisco J RoigIskender ParmaksizEkrem DundarFuliang XieBaohong ZhangArif lpekSerkan UranbeyMustafa EraymanEmre llhanOussama BadadHassan GhazalDavid A LightfootPavan KasarlaVincent ColantonioHuseyin TombulogluPilar HernandezNurengin MeteOznur CetinMarc Van MontaguHuanming YangQiang GaoGabriel DoradoYves Van de Peer et al.

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

Revisiting ancestral polyploidy in plants

Colin RuprechtRolf LohausKevin VannesteMarek MutwilZoran NikoloskiYves Van de PeerStaffan Persson

A1 Journal Article in SCIENCE ADVANCES

The Apostasia genome and the evolution of orchids

Guo-Qiang ZhangKe-Wei LiuZhen LiRolf LohausYu-Yun HsiaoShan-Ce NiuJie-Yu WangYao-Cheng LinQing XuLi-Jun ChenKouki YoshidaSumire FujiwaraZhi-Wen WangYong-Qiang ZhangNobutaka MitsudaMeina WangGuo-Hui LiuLorenzo PecoraroHui-Xia HuangXin-Ju XiaoMin LinXin-Yi WuWan-Lin WuYou-Yi ChenSong-Bin ChangShingo SakamotoMasaru Ohme-TakagiMasafumi YagiSi-Jin ZengChing-Yu ShenChuan-Ming YehYi-Bo LuoWen-Chieh TsaiYves Van de PeerZhong-Jian Liu et al.

A1 Journal Article in NATURE

Evidence for an ancient whole genome duplication in the cycad lineage

Danielle RoodtRolf LohausLieven SterckRiaan L SwanepoelYves Van de PeerEshchar Mizrachi

A1 Journal Article in PLOS ONE

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

The gene expression landscape of pine seedling tissues

Rafael A CañasZhen LiM Belén PascualVanessa Castro-RodríguezConcepción ÁvilaLieven SterckYves Van de PeerFrancisco M Cánovas

A1 Journal Article in PLANT JOURNAL

OMSim : a simulator for optical map data

Giles MiclotteStéphane PlaisanceStephane RombautsYves Van de PeerP. AudenaertJan Fostier

A1 Journal Article in BIOINFORMATICS

Evaluation of the impact of Illumina error correction tools on de novo genome assembly

Mahdi HeydariGiles MiclottePiet DemeesterYves Van de PeerJan Fostier

A1 Journal Article in BMC BIOINFORMATICS

Single-copy genes as molecular markers for phylogenomic studies in seed plants

Zhen LiAmanda R De La TorreLieven SterckFrancisco M CánovasConcepción AvilaIrene MerinoJose Antonio CabezasMaría Teresa CerveraPar K IngvarssonYves Van de Peer

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

Simulating biological complexity through artificial evolution

Yao YaoYves Van de Peer

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

Panayotis VlastaridisPelagia KyriakidouAnargyros ChaliotisYves Van de PeerStephen G OliverGrigoris D Amoutzias

A1 Journal Article in GIGASCIENCE

The evolutionary significance of polyploidy

Yves Van de PeerEshchar MizrachiKathleen Marchal

A1 Journal Article in NATURE REVIEWS GENETICS

Effect of genomic distance on coexpression of coregulated genes in E. coli

Lucia PannierEnrique MerinoKathleen MarchalJulio Collado-Vides

A1 Journal Article in PLOS ONE

Noncoding after all : biases in proteomics data do not explain observed absence of lncRNA translation products

Kenneth VerheggenPieter-Jan VoldersPieter MestdaghGerben MenschaertPetra Van DammeKris GevaertLennart MartensJo Vandesompele

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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

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

Contrasting rates of molecular evolution and patterns of selection among gymnosperms and flowering plants

Amanda R De La TorreZhen LiYves Van de PeerPär K Ingvarsson

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus

Alexandre CormierKomlan AviaLieven SterckThomas DerrienValentin WucherGwendoline AndresMisharl MonsoorOlivier GodfroyAgnieszka LipinskaMarie-Mathilde PerrineauYves Van de PeerChristophe HitteErwan CorreSusana M CoelhoJ Mark Cock et al.

A1 Journal Article in NEW PHYTOLOGIST

Zipper plot : visualizing transcriptional activity of genomic regions

Francisco Avila CobosJasper AnckaertPieter-Jan VoldersCeline EveraertDries RombautJo VandesompeleKatleen De PreterPieter Mestdagh

A1 Journal Article in BMC BIOINFORMATICS

Principles of systems biology, no. 14 : [...] Network analysis of woody biomass

Eshchar MizrachiLieven VerbekeYves Van de PeerKathleen MarchalAlexander A Myburg

Editorial material

Systems genetics reveals a transcriptional network associated with susceptibility in the maize-grey leaf spot pathosystem

Nanette ChristieAlexander A MyburgFourie JoubertShane L MurrayMaryke CarstensYao-Cheng LinJacqueline MeyerBridget G CramptonShawn A ChristensenJean F NtuliSara S WighardYves Van de PeerDave K Berger et al.

A1 Journal Article in PLANT JOURNAL

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

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

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

A1 Journal Article in ANALYTICAL CHEMISTRY

A Cytoscape app for motif enumeration with ISMAGS

Thomas Van ParysIne MelckenbeeckMaarten HoubrakenP. AudenaertDidier ColleMario PickavetPiet DemeesterYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Stage 4S neuroblastoma tumors show a characteristic DNA methylation portrait

Anneleen DecockMaté OngenaertBram De WildeBénédicte BrichardRosa NogueraFranki SpelemanJo Vandesompele

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

Eshchar MizrachiLieven VerbekeNanette ChristieAna Carolina Elisa Fierro GutierrezShawn D MansfieldMark F DavisErica GjersingGerald A TuskanMarc Van MontaguYves Van de PeerKathleen MarchalAlexander A Myburg et al.

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

Early differences in islets from prediabetic NOD mice : combined microarray and proteomic analysis

Inne CrèvecoeurValborg GudmundsdottirSaurabh VigFernanda Marques Câmara SodréWannes D’HertogAna Carolina Elisa Fierro GutierrezLeentje Van LommelConny GysemansKathleen MarchalEtienne WaelkensFrans SchuitSøren BrunakLut OverberghChantal Mathieu et al.

A1 Journal Article in DIABETOLOGIA

Fermentation assays reveal differences in sugar and (off-) flavor metabolism across different Brettanomyces bruxellensis strains

Sam CrauwelsFilip Van OpstaeleBarbara Jaskula-GoirisJan SteenselsChristel VerrethLien BosmansCaroline PaulussenBeatriz Herrera-MalaverRonnie de JongeJessika De ClippeleerKathleen MarchalGorik De SamblanxKris A WillemsKevin J VerstrepenGuido AertsBart Lievens et al.

A1 Journal Article in FEMS YEAST RESEARCH

A guide to the PLAZA 3.0 plant comparative genomic database

Klaas Vandepoele

Bookchapter in Plant genomics databases : methods and protocols

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 RouzéRichard M Clark et al.

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

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

Elisabeth VeeckmanTom RuttinkKlaas Vandepoele

A1 Journal Article in PLANT CELL

Lack of GLYCOLATE OXIDASE1, but not GLYCOLATE OXIDASE2, attenuates the photorespiratory phenotype of CATALASE2-deficient Arabidopsis

Pavel KerchevCezary WaszczakAleksandra LewandowskaPatrick WillemsAlexey ShapiguzovZhen LiSaleh AlseekhPer MühlenbockFrank HoeberichtsJingjing HuangKatrien Van Der KelenJaakko KangasjarviAlisdair R FernieRiet De SmetYves Van de PeerJoris MessensFrank Van Breusegem et al.

A1 Journal Article in PLANT PHYSIOLOGY

Emergent adaptive behaviour of GRN-controlled simulated robots in a changing environment

Yao YaoVeronique StormeKathleen MarchalYves Van de Peer

A1 Journal Article in PEERJ

The challenges of interpreting phosphoproteomics data : a critical view through the bioinformatics lens

Panayotis VlastaridisStephen G OliverYves Van de PeerGrigoris D Amoutzias

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 BosscheKen HeyndrickxSteffen VannesteAlain GoossensKris GevaertKlaas VandepoeleNathalie Gonzalez SanchezDirk InzéGeert De Jaeger et al.

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

Comparative metagenomic analysis reveals mechanisms for stress response in hypoliths from extreme hyperarid deserts

Phuong LEThulani P MakhalanyaneLeandro D GuerreroSurendra VikramYves Van de PeerDon A Cowan

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

Simultaneous discovery of cancer subtypes and subtype features by molecular data integration

Thanh Le VanMatthijs van LeeuwenAna Carolina Elisa Fierro GutierrezDries De MaeyerJimmy Van den EyndenLieven VerbekeLuc De RaedtKathleen MarchalSiegfries Nijssen

A1 Journal Article in BIOINFORMATICS

SSA-ME Detection of cancer driver genes using mutual exclusivity by small subnetwork analysis

Sergio Pulido TamayoBram WeytjensDries De MaeyerKathleen Marchal

A1 Journal Article in SCIENTIFIC REPORTS

Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

Michele PerazzolliNoemí HerreroLieven SterckLuisa LenziAlberto PellegriniGerardo PuopoloYves Van de PeerIlaria Pertot

A1 Journal Article in BMC GENOMICS

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

Exploiting natural selection to study adaptive behavior

Sergio Pulido TamayoKathleen MarchalJan FostierJos Vanderleyden

Network-based omics data analysis

Dries De MaeyerJos VanderleydenKathleen Marchal

RNA-sequencing of Cercospora beticola DMI-sensitive and -resistant isolates after treatment with tetraconazole identifies common and contrasting pathway induction

Melvin D BoltonMalaika K EbertLuigi FainoVivivana Rivera-VarasRonnie de JongeYves Van de PeerBart PHJ ThommaGary A Secor

A1 Journal Article in FUNGAL GENETICS AND BIOLOGY

Editorial overview: Genome studies and molecular genetics : of plant genes, genomes, and genomics

Yves Van de PeerJ Chris Pires

Editorial material

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

Elisabeth VeeckmanKlaas VandepoeleT AspIsabel Roldán-RuizTom Ruttink

Elucidation of the mode of action of a new antibacterial compound active against Staphylococcus aureus and Pseudomonas aeruginosa

Evelien GeritsEline BlommaertAnna LippellAlex J O'NeillBram WeytjensDries De MaeyerAna Carolina FierroKathleen MarchalArnaud MarchandPatrick ChaltinPieter SpincemailleKatrijn De BruckerKarin ThevissenBruno PA CammueToon SwingsVeerle LiebensMaarten FauvartNatalie VerstraetenJan Michiels et al.

A1 Journal Article in PLOS ONE

hfAIM: a reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms

Qingjun XieOren TzfadiaMatan LevyEfrat WeithornHadas Peled-ZehaviThomas Van ParysYves Van de PeerGad Galili

A1 Journal Article in AUTOPHAGY

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

Of dups and dinos : evolution at the K/Pg boundary

Rolf LohausYves Van de Peer

A1 Journal Article in CURRENT OPINION IN PLANT BIOLOGY

Gene duplicability of core genes is highly consistent across all angiosperms

Zhen LiJonas DefoortSetareh TasdighianSteven MaereYves Van de PeerRiet De Smet

A1 Journal Article in PLANT CELL

Computing attractors of multi-valued gene regulatory networks using fuzzy answer set programming

Mushthofa MushthofaSteven SchockaertMartine De Cock

EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis

Sergio Pulido TamayoJorge DuitamaKathleen Marchal

A1 Journal Article in NUCLEIC ACIDS RESEARCH

FabR regulates Salmonella biofilm formation via its direct target FabB

Kim HermansStefanie RoberfroidInge M ThijsGwendoline KintDavid De CosterKathleen MarchalJos VanderleydenSigrid CJ De KeersmaeckerHans P Steenackers

A1 Journal Article in BMC GENOMICS

Network-based analysis of eQTL data to prioritize driver mutations

Dries De MaeyerBram WeytjensLuc De RaedtKathleen Marchal

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

Jeanine L OlsenPierre RouzéBram VerhelstYao-Cheng LinTill BayerJonas CollenEmanuela DattoloEmanuele De PaoliSimon DittamiFlorian MaumusGurvan MichelAnna KerstingChiara LauritanoRolf LohausMats TöpelThierry TononKevin VannesteMojgan AmirebrahimiJanina BrakelChristoffer BoströmMansi ChovatiaJane GrimwoodJerry W JenkinsAlexander JueterbockAmy MrazWytze T StamHope TiceErich Bornberg-BauerPamela J GreenGareth A PearsonGabriele ProcacciniCarlos M DuarteJeremy SchmutzThorsten BH ReuschYves Van de Peer et al.

A1 Journal Article in NATURE

Complete mitochondrial genome of the Verticillium-wilt causing plant pathogen Verticillium nonalfalfae

Vid JelenRonnie de JongeYves Van de PeerBranka JavornikJernej Jakše

A1 Journal Article in PLOS ONE

The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution

Guo-Qiang ZhangQing XuChao BianWen-Chieh TsaiChuan-Ming YehKe-Wei LiuKouki YoshidaLiang-Sheng ZhangSong-Bin ChangFei ChenYu ShiYong-Yu SuYong-Qiang ZhangLi-Jun ChenYayi YinMin LinHuixia HuangHua DengZhi-Wen WangShi-Lin ZhuXiang ZhaoCao DengShan-Ce NiuJie HuangMeina WangGuo-Hui LiuHai-Jun YangXin-Ju XiaoYu-Yun HsiaoWan-Lin WuYou-Yi ChenNobutaka MitsudaMasaru Ohme-TakagiYi-Bo LuoYves Van de PeerZhong-Jian Liu et al.

A1 Journal Article in SCIENTIFIC REPORTS

Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks

Sofie Van LandeghemThomas Van ParysMarieke DuboisDirk InzéYves Van de Peer

A1 Journal Article in BMC BIOINFORMATICS

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

Cell line name recognition in support of the identification of synthetic lethality in cancer from text

Suwisa KaewphanSofie Van LandeghemTomoko OhtaYves Van de PeerFilip GinterSampo Pyysalo

A1 Journal Article in BIOINFORMATICS

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

Ludger GoeminneKris GevaertLieven Clement

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

High performance computing for large-scale genomic prediction

Arne De ConinckBernard De BaetsJan Fostier

Optimized MOL-PCR for characterization of microbial pathogens

Véronique WuytsNancy HC RoosensSophie BertrandKathleen MarchalSigrid CJ De Keersmaecker

Bookchapter in Current protocols in cytometry

Adaptive self-organizing organisms using a bio-inspired gene regulatory network controller: for the aggregation of evolutionary robots under a changing environment

Yao YaoKathleen MarchalYves Van de Peer

Bookchapter in Handbook of research on design, control and modeling of swarm robotics

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

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

A1 Journal Article in JOURNAL OF CYSTIC FIBROSIS

Studying the relationship between drug resistance and genomic variations in Leishmania donovani using a network-based method

MR Ticlla CcenhuaS Pulido-TamayoH ImamuraLieven VerbekeJ CottonJ-C DujardinKathleen Marchal

Adaptation to high ethanol reveals complex evolutionary pathways

Karin VoordeckersJacek KominekAnupam DasAdriana Espinosa-CantuDries De MaeyerKathleen MarchalAlexander DeLunaRob JelierKevin Verstrepen

Using a novel bio-inspired robotic model to study artificial evolution

Yao YaoYves Van de Peer

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

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

A1 Journal Article in BMC BIOINFORMATICS

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

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

A1 Journal Article in BIOINFORMATICS

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

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

A1 Journal Article in BMC BIOINFORMATICS

Genome-wide DNA methylation detection by MethylCap-seq and Infinium HumanMethylation450 BeadChips: an independent large-scale comparison

Tim De MeyerPierre BadyGeert TrooskensSebastian KurscheidJocelyne BlochJohan M KrosJohannes A HainfellnerRoger StuppMauro DelorenziMonika E HegiWim Van Criekinge et al.

A1 Journal Article in SCIENTIFIC REPORTS

Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda)

Sonali Sachin RanadeYao-Cheng LinYves Van de PeerMaria Rosario García-Gil

A1 Journal Article in BMC GENETICS

User‐friendly WGS analysis of Salmonella Enteritidis PT4 outbreaks

Véronique WuytsSarah DenayerNancy HC RoosensWesley MattheusSophie BertrandKathleen MarchalKatelijne DierickSigrid CJ De Keersmaecker

The usefulness of whole genome sequencing for outbreak investigation of food pathogens, Salmonella Enteritidis as a case study

Véronique WuytsSarah DenayerNancy HC RoosensWesley MattheusSophie BertrandKathleen MarchalKatelijne DierickSigrid CJ De Keersmaecker

Solving disjunctive fuzzy answer set programs

Mushthofa MushthofaSteven SchockaertMartine De Cock

Polyploidy and genome evolution in plants

Pamela S SoltisD Blaine MarchantYves Van de PeerDouglas E Soltis

A1 Journal Article in CURRENT OPINION IN GENETICS & DEVELOPMENT

The plant genome integrative explorer resource : PlantGenIE.org

David SundellChanaka MannapperumaSergiu NetoteaNicolas DelhommeYao-Cheng LinAndreas SjödinYves Van de PeerStefan JanssonTorgeir R HvidstenNathaniel R Street

A1 Journal Article in NEW PHYTOLOGIST

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

PheNetic : network-based interpretation of molecular profiling data

Dries De MaeyerBram WeytjensJoris RenkensLuc De RaedtKathleen Marchal

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Adaptation to high ethanol reveals complex evolutionary pathways

Karin VoordeckersJacek KominekAnupam DasAdriana Espinosa-CantúDries De MaeyerAhmed ArslanMichiel Van PeeElisa van der ZandeWim MeertYudi YangBp ZhuKathleen MarchalAlexander DeLunaVera Van NoortRob JelierKevin J Verstrepen et al.

A1 Journal Article in PLOS GENETICS

Obg and membrane depolarization are part of a microbial bet-hedging strategy that leads to antibiotic tolerance

Natalie VerstraetenWouter Joris KnapenCyrielle Ines KintVeerle LiebensBram Van den BerghLiselot DewachterJoran Elie MichielsQiang FuCharlotte Claudia DavidAna Carolina FierroKathleen MarchalJan BeirlantWim VerséesJohan HofkensMaarten JansenMaarten FauvartJan Michiels et al.

A1 Journal Article in MOLECULAR CELL

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

elPrep: high-performance preparation of sequence alignment/map files for variant calling

Charlotte HerzeelPascal CostanzaDries DecapJan FostierJoke Reumers

A1 Journal Article in PLOS ONE

Pathway relevance ranking for tumor samples through network-based data integration

Lieven VerbekeJimmy Van den EyndenAna Carolina Elisa Fierro GutierrezPiet DemeesterJan FostierKathleen Marchal

A1 Journal Article in PLOS ONE

Halvade: scalable sequence analysis with MapReduce

Dries DecapJoke ReumersCharlotte HerzeelPascal CostanzaJan Fostier

A1 Journal Article in BIOINFORMATICS

Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations

Sergio Pulido TamayoAminael Sanchez RodriguezToon SwingsBram Van den BergheAkanksha DubeyHans SteenackersJan MichielsJan FostierKathleen Marchal

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Jabba: hybrid error correction for long sequencing reads using maximal exact matches

Giles MiclotteMahdi HeydariPiet DemeesterP. AudenaertJan Fostier

Pathway relevance ranking for tumor samples through network-based data integration (award for Outstanding Oral Poster Presentation )

Lieven VerbekeJimmy Van den EyndenPiet DemeesterKathleen MarchalJan Fostier

Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains

S CrauwelsA Van AsscheRonnie de JongeAR BornemanC VerrethP TroelsG De SamblanxKathleen MarchalYves Van de PeerKA WillemsKJ VerstrepenCD CurtinB Lievens et al.

A1 Journal Article in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A long fragment aligner called ALFALFA

Michaël VyvermanBernard De BaetsVeerle FackPeter Dawyndt

A1 Journal Article in BMC BIOINFORMATICS

SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering

Jimmy Van den EyndenAna Carolina Elisa Fierro GutierrezLieven VerbekeKathleen Marchal

A1 Journal Article in BMC BIOINFORMATICS

Serendipitous meta-transcriptomics : the fungal community of Norway spruce (Picea abies)

Nicolas DelhommeGorel SundstromNeda ZamaniHenrik LantzYao-Cheng LinTorgeir R HvidstenMarc P HoppnerPatric JernYves Van de PeerJoakim LundebergManfred G GrabherrNathaniel R Street et al.

A1 Journal Article in PLOS ONE

ddcRquant: threshold determination for single channel droplet digital PCR experiments

Wim TrypsteenMatthijs VynckJan De NevePawel BonczkowskiMaja KiselinovaEva MalatinkováKAREN VERVISCHOlivier ThasLinos VandekerckhoveWard De Spiegelaere

Robust regression methods for real-time PCR

Wim TrypsteenJan De NeveKobus BosmanMonique NijhuisOlivier ThasLinos VandekerckhoveWard De Spiegelaere

Quantifying expression divergence of duplicated genes with microarrays

Koen Van den BergeRiet De SmetYves Van de PeerLieven Clement

Exploration of alternative splicing events in ten different grapevine cultivars

Emilio PotenzaMilvia Luisa RacchiLieven SterckEmanuela CollerElisa AsquiniSilvio CE TosattoRiccardo VelascoYves Van de PeerAlessandro Cestaro

A1 Journal Article in BMC GENOMICS

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 ClercqEveline Van De SlijkeRobin Vanden BosscheDominique EeckhoutKris GevaertKlaas VandepoeleGeert De JaegerAlain GoossensDirk Inzé et al.

A1 Journal Article in PLANT CELL

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 parallel large-scale genomic prediction by coupling sparse and dense matrix algebra

Arne De ConinckDrosos KourounisFabio VerbosioOlaf SchenkBernard De BaetsSteven MaenhoutJan Fostier

Genome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber

Zhonghua ZhangLinyong MaoHuiming ChenFengjiao BuGuangcun LiJinjing SunShuai LiHonghe SunChen JiaoRachel BlakelyJunsong PanRun CaiRuibang LuoYves Van de PeerEvert JacobsenZhangjun FeiSanwen Huang et al.

A1 Journal Article in PLANT CELL

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 StandaertMarrit PeetersMaria Van LijsebettensFrank Van BreusegemMarc De Block et al.

A1 Journal Article in PLANT PHYSIOLOGY

Horsetails are ancient polyploids : evidence from Equisetum giganteum

Kevin VannesteLieven SterckAlexander Andrew MyburgYves Van de PeerEshchar Mizrachi

A1 Journal Article in PLANT CELL

Whole genome sequence analysis of Salmonella Enteritidis PT4 outbreaks from a national reference laboratory’s viewpoint

Véronique WuytsSarah DenayerNancy HC RoosensWesley MattheusSophie BertrandKathleen MarchalKatelijne DierickSigrid CJ De Keersmaecker

A2 Journal Article in PLOS CURRENTS OUTBREAKS

Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays

Sarieh GhorbaniYao-Cheng LinBoris ParizotAna Fernandez SalinaMaria NjoYves Van de PeerTom BeeckmanPierre Hilson

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

Human heart heterogeneity and its role in the onset and perpetuation of cardiac arrhythmias

Arne DefauwAlexander PanfilovPeter Dawyndt

Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

Guillaume MorelLieven SterckDominique SwennenMarina Marcet-HoubenDjamila OnesimeAnthony LevasseurNoémie JacquesSandrine MalletArnaux CoulouxKarine LabadieJoëlle AmselemJean-Marie BeckerichBernard HenrissatYves Van de PeerPatrick WinckerJean-Luc SoucietToni GabaldónColin R TinsleySerge Casaregola et al.

A1 Journal Article in SCIENTIFIC REPORTS

Life's dual nature: a way out of the impasse of the gene-centred 'versus' complex systems controversy on life

Alexis De TiègeKoen TangheJohan BraeckmanYves Van de Peer

Bookchapter in Evolutionary biology : biodiversification from genotype to phenotype

Ultraviolet-B radiation stimulates downward leaf curling in Arabidopsis thaliana

Ana Carolina Elisa Fierro GutierrezOlivier LerouxBarbara De ConinckBruno PA CammueKathleen MarchalEls PrinsenDominique Van Der StraetenFilip Vandenbussche

A1 Journal Article in PLANT PHYSIOLOGY AND BIOCHEMISTRY

MEXPRESS : visualizing expression, DNA methylation and clinical TCGA data

Alexander KochTim De MeyerJana JeschkeWim Van Criekinge

A1 Journal Article in BMC GENOMICS

The MetaProteomeAnalyzer : a powerful open-source software suite for metaproteomics data analysis and interpretation

Thilo MuthAlexander BehneRobert HeyerFabian KohrsDirk BenndorfMarcus HoffmannMiro LehtevaUdo ReichlLennart MartensErdmann Rapp

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Scop3D : three-dimensional visualization of sequence conservation

Tessa VermeireStijn VermaereBert SchepensXavier SaelensSteven Van GuchtLennart MartensElien Vandermarliere

A1 Journal Article in PROTEOMICS

Viewing the proteome : how to visualize proteomics data?

Eystein OvelandThilo MuthErdmann RappLennart MartensFrode S BervenHarald Barsnes

A1 Journal Article in PROTEOMICS

A decoy-free approach to the identification of peptides

Giulia GonnelliMichiel StockJan VerwaerenDavy MaddeleinBernard De BaetsLennart MartensSven Degroeve

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Managing expectations when publishing tools and methods for computational proteomics

Lennart MartensOliver KohlbacherSusan T Weintraub

Editorial material

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 AesaertMaria Van LijsebettensSofie GoormachtigKlaas VandepoeleJelle Van LeeneMichael MuszynskiKris GevaertDirk InzéGeert De Jaeger et al.

A1 Journal Article in PLANT CELL

A multiplex oligonucleotide ligation-PCR as a complementary tool for subtyping of Salmonella Typhimurium

Véronique WuytsWesley MattheusNancy HC RoosensKathleen MarchalSophie BertrandSigrid CJ De Keersmaecker

A1 Journal Article in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Porting forensic DNA analysis to deep sequencing

Christophe Van NesteDieter DeforceWim Van CriekingeFilip Van Nieuwerburgh

Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in Picea gene families

Amanda R De La TorreYao-Cheng LinYves Van de PeerPär K Ingvarsson

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

Using rules of thumb for repairing inconsistent answer set programs

Elie MerhejSteven SchockaertMartine De Cock

Principal bicorrelation analysis: unraveling associations between three data sources

Federico MattielloOlivier ThasBie Verbist

A1 Journal Article in JOURNAL OF BIOPHARMACEUTICAL STATISTICS

Evolutionary trails of plant steroid genes

Cécile VrietKaren LemmensKlaas VandepoeleChristophe ReuzeauEugenia Russinova

A1 Journal Article in TRENDS IN PLANT SCIENCE

PepShell : visualization of conformational proteomics data

Elien VandermarliereDavy MaddeleinNiels HulstaertElisabeth StesMichela Di MicheleKris GevaertEdgar JacobyDirk BrehmerLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Vitamin D3 induces tolerance in human dendritic cells by activation of intracellular metabolic pathways

Gabriela Bomfim FerreiraAn-Sofie VanherwegenGuy EelenAna Carolina Fierro GutíerrezLeentje Van LommelKathleen MarchalLieve VerlindenAnnemieke VerstuyfTatiane NogueiraMaria GeorgiadouFrans SchuitDécio L EizirikConny GysemansPeter CarmelietLut OverberghChantal Mathieu et al.

A1 Journal Article in CELL REPORTS

Guidelines for optimisation of a multiplex oligonucleotide ligation-PCR for characterisation of microbial pathogens in a microsphere suspension array

Véronique WuytsNancy HC RoosensSophie BertrandKathleen MarchalSigrid CJ De Keersmaecker

A1 Journal Article in BIOMED RESEARCH INTERNATIONAL

The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining

Dora SzakonyiSofie Van LandeghemKatja BaerenfallerLieven BaeyensJonas BlommeRubén Casanova-SáezStefanie De BodtDavid Esteve-BrunaFabio FioraniNathalie Gonzalez SanchezJesper GrønlundRichard GH ImminkSara Jover-GilAsuka KuwabaraTamara Muñoz-NortesAalt DJ van DijkDavid Wilson-SánchezVicky Buchanan-WollastonGerco C AngenentYves Van de PeerDirk InzéJosé Luis MicolWilhelm GruissemSean WalshPierre Hilson et al.

A2 Journal Article in CURRENT PLANT BIOLOGY

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

Including explicit marker-by-environment interaction for large-scale genomic prediction

Arne De ConinckDrosos KourounisFabio VerbosioOlaf SchenkBernard De BaetsSteven MaenhoutJan Fostier

PeptideShaker enables reanalysis of MS-derived proteomics data sets

Marc VaudelJulia M BurkhartRené P ZahediEystein OvelandFrode S BervenAlbert SickmannLennart MartensHarald Barsnes

A1 Journal Article in NATURE BIOTECHNOLOGY

An open data ecosystem for cell migration research

Paola MasuzzoLennart Martensthe 2014 Cell Migration workshop participantsChristophe AmpeOlivier De WeverMarleen Van Troys

Editorial material

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

Ludger GoeminneAndrea ArgentiniLennart MartensLieven Clement

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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

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 VandepoeleLennart MartensErwin WittersKris GevaertGeert De Jaeger et al.

A1 Journal Article in NATURE PROTOCOLS

The genome sequence of the orchid Phalaenopsis equestris

Jing CaiXin LiuKevin VannesteSebastian ProostWen-Chieh TsaiKe-Wei LiuLi-Jun ChenYing HeQing XuChao BianZhijun ZhengFengming SunWeiqing LiuYu-Yun HsiaoZhao-Jun PanChia-Chi HsuYa-Ping YangYi-Chin HsuYu-Chen ChuangAnne DievartJean-François DufayardXun XuJun-Yi WangJun WangXin-Ju XiaoXue-Min ZhaoRong DuGuo-Qiang ZhangMeina WangYong-Yu SuGao-Chang XieGuo-Hui LiuLi-Qiang LiLai-Qiang HuangYi-Bo LuoHong-Hwa ChenYves Van de PeerZhong-Jian Liu et al.

A1 Journal Article in NATURE GENETICS

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

Jeroen CrappéElvis NdahAlexander KochSandra SteyaertDaria FijalkowskaSarah De KeulenaerEllen De MeesterTim De MeyerWim Van CriekingePetra Van DammeGerben Menschaert et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Mining for viral fragments in methylation enriched sequencing data

Klaas MensaertWim Van CriekingeOlivier ThasEd SchuuringRenske DM SteenbergenG Bea A WismanTim De Meyer

A1 Journal Article in FRONTIERS IN GENETICS

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

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

A1 Journal Article in DRUG DISCOVERY TODAY

Phospho-iTRAQ : assessing isobaric labels for the large-scale study of phosphopeptide stoichiometry

Pieter GlibertPaulien MeertKatleen Van SteendamFilip Van NieuwerburghDieter De ConinckLennart MartensMaarten DhaenensDieter Deforce

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Genome-scale co-expression network comparison across escherichia coli and salmonella enterica serovar typhimurium reveals significant conservation at the regulon level of local regulators despite their dissimilar lifestyles

P ZarrinehA Sanchez-RodriguezN HosseinkhanZ NarimaniKathleen MarchalA Masoudi-Nejad

A1 Journal Article in PLOS ONE

Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study

Pieter MestdaghNicole HartmannLukas BaeriswyDitte AndreasenNathalie BernardCaifu ChenDavid CheoPetula D'AndradeMike DeMayoLucas DennisStefaan DerveauxYun FengStephanie Fulmer-SmentekBernhard GerstmayerJulia GouffonChris GrimleyEric LaderKathy Y LeeShujun LuoPeter MouritzenAishwarya NarayananSunali PatelSabine PeifferSilvia RubergGary SchrothDave SchusterJonathan M ShafferElliot J SheltonScott SilveriaUmberto UlmanellaVamsi VeeramachaneniFrank StaedtlerThomas PetersToumy GuettoucheLinda WongJo Vandesompele et al.

A1 Journal Article in NATURE METHODS

Early targets of miR-34a in neuroblastoma

Pasqualino De AntonellisMarianeve CarotenutoJonathan VandenbusscheGennaro De VitaVeronica FerrucciChiara MedagliaIolanda BoffaAlessandra GalieroSarah Di SommaDaniela MagliuloNadia AieseAlessandro AlonziDaniela SpanoLucia LiguoriCristina ChiarollaAntonio VerricoJohannes H SchultePieter MestdaghJo VandesompeleKris GevaertMassimo Zollo et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Thanh Le VanMatthijs Van LeeuwenSiegfried NijssenAna Carolina FierroKathleen MarchalLuc De Raedt

A high performance computing approach for genomic prediction

Arne De ConinckJan FostierSteven MaenhoutBernard De Baets

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 MoreauBenoit PieguEric RivalsWendy SchackwitzYves Van de PeerGwenael Piganeau et al.

A1 Journal Article in BMC GENOMICS

SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data

Sandra SteyaertWim Van CriekingeAyla De PaepeSimon DenilKlaas MensaertKatrien VandepitteWim Vanden BergheGeert TrooskensTim De Meyer

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress

Vanessa VermeirssenInge De ClercqThomas Van ParysFrank Van BreusegemYves Van de Peer

A1 Journal Article in PLANT CELL

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 VandepoeleAdriana S Hemerly et al.

A1 Journal Article in PLOS ONE

Expressed repeat elements improve RT-qPCR normalization across a wide range of zebrafish gene expression studies

Suzanne VanhauwaertGert Van PeerAli RihaniEls JanssensPieter RondouSteve LefeverAnne De PaepePaul CouckeFranki SpelemanJo VandesompeleAndy Willaert et al.

A1 Journal Article in PLOS ONE

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary

Kevin VannesteGuy BaeleSteven MaereYves Van de Peer

A1 Journal Article in GENOME RESEARCH

Systemic suppression of the shoot metabolism upon rice root nematode infection

Tina KyndtSimon DenilLander BautersWim Van CriekingeTim De Meyer

A1 Journal Article in PLOS ONE

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

ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation

Tom SanteSarah VergultPieter-Jan VoldersWigard P KloostermanGeert TrooskensKatleen De PreterAnnelies DheedeneFranki SpelemanTim De MeyerBjörn Menten

A1 Journal Article in PLOS ONE

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 BelKlaas Vandepoele et al.

Editorial material

Structural and functional partitioning of bread wheat chromosome 3B

Frédéric ChouletAdriana AlbertiSébastien TheilNatasha GloverValérie BarbeJosquin DaronLise PingaultPierre SourdilleArnaud CoulouxEtienne PauxPhilippe LeroySophie MangenotNicolas GuilhotJacques Le GouisFrançois BalfourierMichael AlauxVéronique JamillouxJulie PoulainCéline DurandArnaud BellecChristine GaspinJan SafarJaroslav DolezelJane RogersKlaas VandepoeleJean-Marc AuryKlaus MayerHélène BergesHadi QuesnevillePatrick WinckerCatherine Feuillet et al.

A1 Journal Article in SCIENCE

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

Inês ChavesYao-Cheng LinC Pinto-RicardoYves Van de PeerCélia Miguel

A1 Journal Article in TREE GENETICS & GENOMES

The (r)evolution of gene regulatory networks controlling Arabidopsis plant reproduction: a two-decade history

Alice PajoroSandra BiewersEvangelia DougaliFelipe Leal ValentimMarta Adelina MendesAimone PorriGeorge CouplandYves Van de PeerAalt DJ van DijkLucia ColomboBrendan DaviesGerco C Angenent et al.

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

Yao-Cheng LinMorgane BooneLeander MeurisIrma LemmensNadine Van RoyArne SoeteJoke ReumersMatthieu MoisseStéphane PlaisanceRadoje DrmanacJason ChenFranki SpelemanDiether LambrechtsYves Van de PeerJan TavernierNico Callewaert et al.

A1 Journal Article in NATURE COMMUNICATIONS

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

Bart JacobsEls GoetghebeurLieven Clement

A1 Journal Article in BMC BIOINFORMATICS

Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis

Jan Van de VeldeKen HeyndrickxKlaas Vandepoele

A1 Journal Article in PLANT CELL

Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera

Sonali Sachin RanadeYao-Cheng LinAndrea ZuccoloYves Van de PeerMaria del Rosario Garcia-Gil

A1 Journal Article in BMC PLANT BIOLOGY

A haploid system of sex determination in the brown alga Ectocarpus sp.

Sophia AhmedJ Mark CockEugenie PessiaRemy LuthringerAlexandre CormierMarine RobuchonLieven SterckAkira F PetersSimon M DittamiErwan CorreMyriam ValeroJean-Marc AuryDenis RozeYves Van de PeerJohn BothwellGabriel AB MaraisSusana M Coelho et al.

A1 Journal Article in CURRENT BIOLOGY

qcML: an exchange format for quality control metrics from mass spectrometry experiments

Mathias WalzerLucia Espona PernasSara NassoWout BittremieuxSven NahnsenPieter KelchtermansPeter PichlerHenk WP van den ToornAn StaesJonathan VandenbusscheMichael MazanekThomas TausRichard A ScheltemaChristian D KelstrupLaurent GattoBas van BreukelenStephan AicheDirk ValkenborgKris LaukensKathryn S LilleyJesper V OlsenAlbert JR HeckKarl MechtlerRuedi AebersoldKris GevaertJuan Antonio VizcaínoHenning HermjakobOliver KohlbacherLennart Martens et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

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

Small size ionic heterogeneities in the human heart can attract rotors

Arne DefauwNele VandersickelPeter DawyndtAlexander Panfilov

A1 Journal Article in AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY

The index-based subgraph matching algorithm with general symmetries (ISMAGS): exploiting symmetry for faster subgraph enumeration

Maarten HoubrakenSofie DemeyerTom MichoelP. AudenaertDidier ColleMario Pickavet

A1 Journal Article in PLOS ONE

A finite-valued solver for disjunctive fuzzy answer set programs

Mushthofa MushthofaSteven SchockaertMartine De Cock

ASP-G: an ASP-based method for finding attractors in genetic regulatory networks

Mushthofa MushthofaGustavo Adolfo Torres TorresYves Van de PeerKathleen MarchalMartine De Cock

A1 Journal Article in BIOINFORMATICS

Assessing genetic diversity among Brettanomyces yeasts by DNA fingerprinting and whole-genome sequencing

Sam CrauwelsBo ZhuJan SteenselsPieter BusschaertGorik De SamblanxKathleen MarchalKris A WillemsKevin J VerstrepenBart Lievens

A1 Journal Article in APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution

Kevin VannesteSteven MaereYves Van de Peer

A1 Journal Article in PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phenotypical and molecular responses of Arabidopsis thaliana roots as a result of inoculation with the auxin-producing bacterium Azospirillum brasilense

Stijn SpaepenStijn BossuytKristof EngelenKathleen MarchalJos Vanderleyden

A1 Journal Article in NEW PHYTOLOGIST

A putative de-N-acetylase of the PIG-L superfamily affects fluoroquinolone tolerance in Pseudomonas aeruginosa

Veerle LiebensValerie DefraineAnnelies Van der LeydenValerie N De GrooteCarolina FierroSerge BeullensNatalie VerstraetenCyrielle KintAnn JansEmanuela FrangipaniPaolo ViscaKathleen MarchalWim VerséesMaarten FauvartJan Michiels et al.

A1 Journal Article in PATHOGENS AND DISEASE

The genome of Eucalyptus grandis

Alexander A MyburgDario GrattapagliaGerald A TuskanUffe HellstenRichard D HayesJane GrimwoodJerry JenkinsErika LindquistHope TiceDiane BauerDavid M GoodsteinInna DubchakAlexandre PoliakovEshchar MizrachiAnand RK KullanSteven G HusseyDesre PinardKaren Van der MerwePooja SinghIda Van JaarsveldOrzenil B SilvaRoberto C TogawaMarilia R PappasDanielle A FariaCarolina P SansaloniCesar D PetroliXiaohan YangPriya RanjanTimothy J TschaplinskiChu-Yu YeTing LiLieven SterckKevin VannesteFlorent MuratMaral SolerHélène San ClementeNaijib SaidiHua Cassan-WangChristophe DunandCharles A HeferErich Bornberg-BauerAnna R KerstingKelly ViningVindhya AmarasingheMartin RanikSushma NaithaniJustin ElserAlexander E BoydAaron ListonJoseph W SpataforaPalitha DharmwardhanaRajani RajaChristopher SullivanElisson RomanelMarcio Alves-FerreiraCarsten KülheimWilliam FoleyVictor CarochaJorge PaivaDavid KudrnaSergio H BrommonschenkelGiancarlo PasqualiMargaret ByrnePhilippe RigaultJosquin TibbitsAntanas SpokeviciusRebecca C JonesDorothy A SteaneRené E VaillancourtBrad M PottsFourie JoubertKerrie BarryGeorgios J Pappas JrSteven H StraussPankaj JaiswalJacqueline Grima-PettenatiJérôme SalseYves Van de PeerDaniel S RokhsarJeremy Schmutz et al.

A1 Journal Article in NATURE

Photoreceptor-mediated bending towards UV-B in Arabidopsis

Filip VandenbusscheKimberley TilbrookAna Carolina FierroKathleen MarchalDirk PoelmanDominique Van Der StraetenRoman Ulm

A1 Journal Article in MOLECULAR PLANT

Next-generation technologies and data analytical approaches for epigenomics

Klaas MensaertSimon DenilGeert TrooskensWim Van CriekingeOlivier ThasTim De Meyer

A1 Journal Article in ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

Rapid genetic adaptation precedes the spread of an exotic plant species

Katrien VandepitteTim De MeyerKenny HelsenKasper Van AckerIsabel Roldán-RuizJoachim MergeayOlivier Honnay

A1 Journal Article in MOLECULAR ECOLOGY

A network-based approach to identify substrate classes of bacterial glycosyltransferases

Aminael Sánchez-RodríguezHanne LP TytgatJoris WinderickxJos VanderleydenSarah LebeerKathleen Marchal

A1 Journal Article in BMC GENOMICS

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

Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks

Kris MorreelYvan SaeysOana DimaFachuang LuYves Van de PeerRuben VanholmeJohn RalphBartel VanholmeWout Boerjan

A1 Journal Article in PLANT CELL

COLOMBOS v2.0 : an ever expanding collection of bacterial expression compendia

Pieter MeysmanPaolo SonegoLuca BiancoQiang FuDaniela Ledezma-TejeidaSocorro Gama-CastroVeerle LiebensJan MichielsKris LaukensKathleen MarchalJulio Collado-VidesKristof Engelen et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia

Ivan IshchukovYan WuSandra Van PuyveldeJos VanderleydenKathleen Marchal

A1 Journal Article in BMC MICROBIOLOGY

Improved linkage analysis of Quantitative Trait Loci using bulk segregants unveils a novel determinant of high ethanol tolerance in yeast

Jorge DuitamaAminael Sánchez-RodriguezAnnelies GoovaertsSergio Pulido TamayoGeorg HubmannMaria R Foulquié-MorenoJohan M TheveleinKelvin J VerstrepenKathleen Marchal

A1 Journal Article in BMC GENOMICS

Shedding light on black boxes in protein identification

Marc VaudelA Saskia VenneFrode S BervenRené P ZahediLennart MartensHarald Barsnes

A1 Journal Article in PROTEOMICS

Airway structural cells regulate TLR5-mediated mucosal adjuvant activity

L Van MaeleD FougeronL JanotA DidierlaurentD CayetJ TabareauM RumboS Corvo-ChamaillardS BoulenouarS JeffsLieselotte Vande WalleMohamed LamkanfiY LemoineF ErardD HotT HussellB RyffelAG BeneckeJ-C Sirard et al.

A1 Journal Article in MUCOSAL IMMUNOLOGY

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 BreusegemDirk InzéKlaas VandepoeleGeert De Jaeger et al.

A1 Journal Article in PLANT PHYSIOLOGY

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 AndriankajaStefanie De BodtThomas AbeelFrederik CoppensStijn DhondtLiesbeth De MildeMattias VermeerschKatrien MaleuxKris GevaertAndrzej JerzmanowskiMoussa BenhamedDoris WagnerKlaas VandepoeleGeert De JaegerDirk Inzé et al.

A1 Journal Article in PLANT CELL

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

Juan A VizcainoEric W DeutschRui WangAttila CsordasFlorian ReisingerDaniel RíosJosé A DianesZhi SunTerry FarrahNuno BandeiraPierre-Alain BinzIoannis XenariosMartin EisenacherGerhard MayerLaurent GattoAlex CamposRobert J ChalkleyHans-Joachim KrausJuan Pablo AlbarSalvador Martinez-BartolomeRolf ApweilerGilbert S OmennLennart MartensAndrew R JonesHenning Hermjakob et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

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

Improving the adaptability of simulated evolutionary swarm robots in dynamically changing environments

Yao YaoKathleen MarchalYves Van de Peer

A1 Journal Article in PLOS ONE

Exoproteome analysis of Starmerella bombicola results in the discovery of an esterase required for lactonization of sophorolipids

Katarzyna CiesielskaInge Van BogaertSamia ChevineauBing LiSara GroeneboerWim SoetaertYves Van de PeerBart Devreese

A1 Journal Article in JOURNAL OF PROTEOMICS

The heterothallic sugarbeet pathogen Cercospora beticola contains exon fragments of both MAT genes that are homogenized by concerted evolution

Melvin D BoltonRonnie de JongePatrik InderbitzinZhaohui LiuKeshav BirlaYves Van de PeerKrishna V SubbaraoBart PHJ ThommaGary A Secor

A1 Journal Article in FUNGAL GENETICS AND BIOLOGY

The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes

Heather Bracken-GrissomAllen G CollinsTimothy CollinsKeith CrandallDaniel DistelCasey DunnGonzalo GiribetSteven HaddockNancy KnowltonMark MartindaleMonica MedinaCharles MessingStephen J O'BrienGustav PaulayNicolas PutnamTimothy RavasiGreg W RouseJoseph F RyanAnja SchulzeGert WorheideMaja AdamskaXavier BaillyJesse BreinholtWilliam E BrowneM Christina DiazNathaniel EvansJean-François FlotNicole FogartyMatthew JohnstonBishoy KamelAkito Y KawaharaTammy LabergeDennis LavrovFrançois MichonneauLeonid L MorozTodd OakleyKaren OsborneShirley A PomponiAdelaide RhodesMauricio Rodriguez-LanettyScott R SantosNori SatohRobert W ThackerYves Van de PeerChristian R VoolstraDavid Mark WelchJudith WinstonXin Zhou et al.

A1 Journal Article in JOURNAL OF HEREDITY

Machine learning applications in proteomics research: how the past can boost the future

Pieter KelchtermansWout BittremieuxKurt De GraveSven DegroeveJan RamonKris LaukensDirk ValkenborgHarald BarsnesLennart Martens

A1 Journal Article in PROTEOMICS

Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways

Florian BeckJörg GeigerStepan GambaryanJohannes VeitMarc VaudelPeter NollauOliver KohlbacherLennart MartensUlrich WalterAlbert SickmannRené P Zahedi et al.

A1 Journal Article in BLOOD

DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra

Thilo MuthLisa WeilnböckErdmann RappChristian G HuberLennart MartensMarc VaudelHarald Barsnes

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics

Marc VaudelAlbert SickmannLennart Martens

A1 Journal Article in BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory

Kenneth VerheggenHarald BarsnesLennart Martens

A1 Journal Article in PROTEOMICS

Reciprocal responses in the interaction between Arabidopsis and the cell-content feeding chelicerate herbivore spider mite

Vladimir ZhurovMarie NavarroKristie A BruinsmaVicent ArbonaM Estrella SantamariaMarc CazauxNicky WybouwEdward J OsborneCherise EnsCristina RiojaVanessa VermeirssenIgnacio Rubio-SomozaPriti KrishnaIsabel DiazMarkus SchmidAurelio Gómez-CadenasYves Van de PeerMiodrag GrbićRichard M ClarkThomas Van LeeuwenVojislava Grbić 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

From DNA- to NA-centrism and the conditions for gene-centrism revisited

Alexis De TiègeKoen TangheJohan BraeckmanYves Van de Peer

A1 Journal Article in BIOLOGY & PHILOSOPHY

Path finding in biological networks

Lore ClootsDries De MaeyerKathleen Marchal

Bookchapter in Springer handbook of bio-/neuroinformatics

Testing for direct genetic effects using a screening step in family-based association studies

Sharon M LutzStijn VansteelandtChristoph Lange

A2 Journal Article in FRONTIERS IN GENETICS

The effect of VEGF-targeted therapy on biomarker expression in sequential tissue from patients with metastatic clear cell renal cancer

Kevin SharpeGrant D StewartAlan MackayChristophe Van NesteCharlotte RofeDan BerneyIrfan KayaniAxel BexElaine WanFiach C O'MahonyMarie O'DonnellSimon ChowdhuryRukma DoshiColan Ho-YenMarco GerlingerDawn BakerNeil SmithBarry DaviesAnju SahdevEkaterini BoletiTim De MeyerWim Van CriekingeLuis BeltranYong-Jie LuDavid J HarrisonAndrew R ReynoldsTom Powles et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

The impact of extensive clonal growth on fine-scale mating patterns: a full paternity analysis of a lily-of-the-valley population (Convallaria majalis)

Katrien VandepitteTim De MeyerHans JacquemynIsabel Roldán-RuizOlivier Honnay

A1 Journal Article in ANNALS OF BOTANY

Dynamics of the Saccharomyces cerevisiae transcriptome during bread dough fermentation

Elham AslankoohiBo ZhuMohammad Naser RezaeiKarin VoordeckersDries De MaeyerKathleen MarchalEmmie DornezChristophe M CourtinKevin J Verstrepen

A1 Journal Article in APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

Pablo MeyerGeoffrey SiwoDanny ZeeviEilon SharonRaquel NorelEran SegalGustavo Stolovitzkythe DREAM6 consortiumYvan SaeysKathleen Marchal

A1 Journal Article in GENOME RESEARCH

Synthetic biology and microdevices : a powerful combination

Lyn VenkenKathleen MarchalJos Vanderleyden

A1 Journal Article in ACM JOURNAL ON EMERGING TECHNOLOGIES IN COMPUTING SYSTEMS

MLVA as a tool for public health surveillance of human Salmonella Typhimurium : prospective study in Belgium and evaluation of MLVA loci stability

Véronique WuytsWesley MattheusGuillaume De Laminne de BexChrista WildemauweNancy HC RoosensKathleen MarchalSigrid CJ De KeersmaeckerSophie Bertrand

A1 Journal Article in PLOS ONE

Identifying relevant pathways for different breast cancer subtypes using network based data integration

Lieven VerbekeAC FierroJimmy Van den EyndenPiet DemeesterJan FostierKathleen Marchal

EPSILON: an eQTL prioritization framework using similarity measures derived from local networks

Lieven VerbekePiet DemeesterJan FostierKathleen Marchal

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

Candida bombicola as a platform organism for the production of tailor-made biomolecules

Sophie RoelantsKaren SaerensThibaut DeryckeBing LiYao-Cheng LinYves Van de PeerSofie De MaeseneireInge Van BogaertWim Soetaert

A1 Journal Article in BIOTECHNOLOGY AND BIOENGINEERING

D-score: a search engine independent MD-score

Marc VaudelDaniela BreiterFlorian BeckJörg RahnenführerLennart MartensRené P Zahedi

A1 Journal Article in PROTEOMICS

Make the most of your samples : Bayes factor estimators for high-dimensional models of sequence evolution

Guy BaelePhilippe LemeyStijn Vansteelandt

A1 Journal Article in BMC BIOINFORMATICS

Staphylococcal enterotoxin B influences the DNA methylation pattern in nasal polyp tissue : a preliminary study

Claudina Perez NovoYuan ZhangSimon DenilGeert TrooskensTim De MeyerWim Van CriekingePaul Van CauwenbergeLuo ZhangClaus Bachert

A1 Journal Article in ALLERGY ASTHMA AND CLINICAL IMMUNOLOGY

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

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

A1 Journal Article in PLOS GENETICS

beadarrayFilter : an R package to filter beads

Anyiawung Chiara ForchehGeert VerbekeAdetayo KasimDan LinZiv ShkedyWillem TalloenHinrich WH GöhlmannLieven Clement

A1 Journal Article in R JOURNAL

Early targets of MIR-34A in neuroblastoma

P De AntonellisM CarotenutoG De VitaJonathan VandenbusscheC MedagliaJ VandesopeleP MestdaghLennart MartensAn StaesKathleen MoensG CinalliKris GevaertM Zollo et al.

Getting intimate with trypsin, the leading protease in proteomics

Elien VandermarliereMichael MuellerLennart Martens

A1 Journal Article in MASS SPECTROMETRY REVIEWS

Asn₃, a reliable, robust, and universal lock mass for improved accuracy in LC-MS and LC-MS/MS

An StaesJonathan VandenbusscheHans DemolMarc GoethalsSule Yilmaz-RumpfNiels HulstaertSven DegroevePieter KelchtermansLennart MartensKris Gevaert

A1 Journal Article in ANALYTICAL CHEMISTRY

MS²PIP: a tool for MS/MS peak intensity prediction

Sven DegroeveLennart Martens

A1 Journal Article in BIOINFORMATICS

CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays

Paola MasuzzoNiels HulstaertLynn HuyckChristophe AmpeMarleen Van TroysLennart Martens

A1 Journal Article in BIOINFORMATICS

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 StraetenLieven De Veylder et al.

A1 Journal Article in SCIENCE

Initiation and dynamics of a spiral wave around an ionic heterogeneity in a model for human cardiac tissue

Arne DefauwPeter DawyndtAlexander Panfilov

A1 Journal Article in PHYSICAL REVIEW E

Action potential duration heterogeneity of cardiac tissue can be evaluated from cell properties using Gaussian Green's function approach

Arne DefauwIvan KazbanovHans DierckxPeter DawyndtAlexander Panfilov

A1 Journal Article in PLOS ONE

Exploration and prediction of interactions between methanotrophs and heterotrophs

Michiel StockSven HoefmanFrederiek-Maarten KerckhofNico BoonPaul De VosBernard De BaetsKim HeylenWillem Waegeman

A1 Journal Article in RESEARCH IN MICROBIOLOGY

Comparative motif discovery in the cloud

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

The complex intron landscape and massive intron invasion in a picoeukaryote provides insights into intron evolution

Bram VerhelstYves Van de PeerPierre Rouzé

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

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 RombautBrigitte Van De CottePinja JaspersYves Van de PeerJaakko KangasjärviJames WhelanFrank Van Breusegem et al.

A1 Journal Article in PLANT CELL

SILAC-based proteome analysis of Starmerella bombicola sophorolipid production

Katarzyna CiesielskaBing LiSara GroeneboerInge Van BogaertYao-Cheng LinWim SoetaertYves Van de PeerBart Devreese

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Identifying common structural DNA properties in transcription factor binding site sets of the LacI-GalR family

Pieter MeysmanKathleen MarchalKristof Engelen

A1 Journal Article in CURRENT BIOINFORMATICS

Omics derived networks in bacteria

Aminael Sánchez-RodríguezLore ClootsKathleen Marchal

A1 Journal Article in CURRENT BIOINFORMATICS

PheNetic: network-based interpretation of unstructured gene lists in E. coli

Dries De MaeyerJoris RenkensLore ClootsLuc De RaedtKathleen Marchal

A1 Journal Article in MOLECULAR BIOSYSTEMS

Alterations of immune response of non-small lung cancer with azacytidine

John WrangleWei WangAlexander KochHariharan EaswaranHelai P MohammadFrank VendettiWim Van CriekingeTim De MeyerZhengzong DuPrincy ParsanaKristen RodgersRay-Whay YenCynthia A ZahnowJanis M TaubeJulie R BrahmerScott S TykodiKeith EastonRichard D CarvajalPeter A JonesPeter W LairdDaniel J WeisenbergerSalina TsaiRosalyn A JuergensSuzanne L TopalianCharles M RudinMalcolm V BrockDrew PardollStephen B Baylin et al.

A1 Journal Article in ONCOTARGET

Resilience in the proteomics data ecosystem: how the field cares for its data

Lennart Martens

A1 Journal Article in PROTEOMICS

Bringing proteomics into the clinic: the need for the field to finally take itself seriously

Lennart Martens

A1 Journal Article in PROTEOMICS CLINICAL APPLICATIONS

Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report

Yasset Perez-RiverolHenning HermjakobOliver KohlbacherLennart MartensDavid CreasyJürgen CoxFelipe LeprevostBaozhen Paul ShanVioleta I Pérez-NuenoMichal BlazejczykMarco PuntaKlemens VierlingerPedro A ValientenKalet LeonGlay ChineaOsmany GuirolaRicardo BringasGleysin CabreraGerardo GuillenGabriel PadronLuis Javier GonzalezVladimir Besada et al.

A1 Journal Article in JOURNAL OF PROTEOMICS

ProteoCloud: a full-featured open source proteomics cloud computing pipeline

Thilo MuthJulian PetersJonathan BlackburnErdmann RappLennart Martens

A1 Journal Article in JOURNAL OF PROTEOMICS

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

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

Transcriptional analysis through RNA sequencing of giant cells induced by Meloidogyne graminicola in rice roots

Hongli JiGodelieve GheysenSimon DenilKeith LindseyJennifer F ToppingKamrun NaharAnnelies HaegemanWinnok De VosGeert TrooskensWim Van CriekingeTim De MeyerTina Kyndt et al.

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

The Mycobacterium tuberculosis regulatory network and hypoxia

James E GalaganKyle MinchMatthew PetersonAnna LyubetskayaElham AziziLinsday SweetAntonio GomesTige RustadGregory DolganovIrina GlotovaThomas AbeelChris MahwinneyAdam D KennedyRené AllardWilliam BrabantAndrew KruegerSuma JainiBrent HondaWen-Han YuMark J HickeyJeremy ZuckerChristopher GarayBrian WeinerPeter SiskChristian StolteJessica K WinklerYves Van de PeerPaul IazzettiDiogo CamachoJonathan DreyfussYang LiuAnca DorhoiHans-Joachim MollenkopfPaul DrogarisJulie LamontagneYiyong ZhouJulie PiquenotSang Tae ParkSahadevan RamanStefan HE KaufmannRobert P MohneyDaniel ChelskyD Branch MoodyDavid R ShermanGary K Schoolnik et al.

A1 Journal Article in NATURE

Pan genome of the phytoplankton Emiliania underpins its global distribution

Betsy A ReadJessica KegelMary J KluteAlan KuoStephane C LefebvreFlorian MaumusChristoph MayerJohn MillerAdam MonierAsaf SalamovJeremy YoungMaria AguilarJean-Michel ClaverieStephan FrickenhausKarina GonzalezEmily K HermanYao-Cheng LinJohnathan NapierHiroyuki OgataAnalissa F SarnoJeremy ShmutzDeclan SchroederColomban de VargasFrederic VerretPeter von DassowKlaus ValentinYves Van de PeerGlen WheelerJoel B DacksCharles F DelwicheSonya T DyhrmanGernot GlöcknerUwe JohnThomas RichardsAlexandra Z WordenXiaoyu ZhangIgor V Grigoriev et al.

A1 Journal Article in NATURE

The Norway spruce genome sequence and conifer genome evolution

Björn NystedtNathaniel R StreetAnna WetterbomAndrea ZuccoloYao-Cheng LinDouglas G ScofieldFrancesco VezziNicolas DelhommeStefania GiacomelloAndrey AlexeyenkoRiccardo VicedominiKristoffer SahlinEllen SherwoodMalin ElfstrandLydia GramzowKristina HolmbergJimmie HällmanOlivier KeechLisa KlassonMaxim KoriabineMelis KucukogluMax KällerJohannes LuthmanFredrik LysholmTotte NiittyläÅke OlsonNemanja RilakovicCarol RitlandJosep A RossellóJuliana SenaThomas SvenssonCarlos Talavera-LópezGünter TheißenHannele TuominenKevin VannesteZhi-Qiang WuBo ZhangPhilipp ZerbeLars ArvestadRishikesh BhaleraoJoerg BohlmannJean BousquetRosario Garcia GilTorgeir R HvidstenPieter de JongJohn MacKayMichele MorganteKermit RitlandBjörn SundbergStacey Lee ThompsonYves Van de PeerBjörn AnderssonOve NilssonPär K IngvarssonJoakim LundebergStefan Jansson et al.

A1 Journal Article in NATURE

Orthology Guided Assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity in Lolium perenne

Tom RuttinkLieven SterckAntje RohdeChristian BendixenPierre RouzéTorben AspYves Van de PeerIsabel Roldán-Ruiz

A1 Journal Article in PLANT BIOTECHNOLOGY JOURNAL

Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles

Pieter MeysmanAminael Sánchez-RodríguezQiang FuKathleen MarchalKristof Engelen

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Predicting tryptic cleavage from proteomics data using decision tree ensembles

Thomas FannesElien VandermarliereLeander SchietgatSven DegroeveLennart MartensJan Ramon

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

The index-based subgraph matching algorithm (ISMA): fast subgraph enumeration in large networks using optimized search trees

Sofie DemeyerTom MichoelJan FostierP. AudenaertMario PickavetPiet Demeester

A1 Journal Article in PLOS ONE

Fault tolerant network design inspired by Physarum polycephalum

Maarten HoubrakenSofie DemeyerDimitri StaessensP. AudenaertDidier ColleMario Pickavet

A1 Journal Article in NATURAL COMPUTING

Large-scale event extraction from literature with multi-level gene normalization

Sofie Van LandeghemJari BjorneChih-Hsuan WeiKai HakalaSampo PyysaloSophia AnaniadouHung-Yu KaoZhiyong LuTapio SalakoskiYves Van de PeerFilip Ginter et al.

A1 Journal Article in PLOS ONE

The potential of text mining in data integration and network biology for plant research : a case study on Arabidopsis

Sofie Van LandeghemStefanie De BodtZuzanna DrebertDirk InzéYves Van de Peer

A1 Journal Article in PLANT CELL

The biosynthetic gene cluster for sophorolipids : a biotechnological interesting biosurfactant produced by Starmerella bombicola

Inge Van BogaertKevin HolvoetSophie RoelantsBing LiYao-Cheng LinYves Van de PeerWim Soetaert

A1 Journal Article in MOLECULAR MICROBIOLOGY

Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

Pieter Van den AbbeeleClara BelzerMargot GoossensMichiel KleerebezemWillem M De VosOlivier ThasRosemarie De WeirdtFrederiek-Maarten KerckhofTom Van de Wiele

A1 Journal Article in ISME JOURNAL

Methylation-specific digital karyotyping of HPV16E6E7 expressing human keratinocytes identifies novel methylation events in cervical carcinogenesis

Renske DM SteenbergenMaté OngenaertSuzanne SnellenbergGeert TrooskensWendy F van der MeideDeeksha PandeyNoga Bloushtain-QimronKornelia PolyakChris JLM MeijerPeter JF SnijdersWim Van Criekinge et al.

A1 Journal Article in JOURNAL OF PATHOLOGY

Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing

Tim De MeyerEvi MampaeyMichaël VlemmixSimon DenilGeert TrooskensJean-Pierre RenardSarah De KeulenaerPierre DehanGerben MenschaertWim Van Criekinge

A1 Journal Article in PLOS ONE

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

Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events

Gerben MenschaertWim Van CriekingeTineke NotelaersAlexander KochJeroen CrappéKris GevaertPetra Van Damme

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

EPSILON: an eQTL prioritization framework using similarity measures derived from local networks

Lieven VerbekeLore ClootsPiet DemeesterJan FostierKathleen Marchal

A1 Journal Article in BIOINFORMATICS

essaMEM: finding maximal exact matches using enhanced sparse suffix arrays

Michaël VyvermanBernard De BaetsVeerle FackPeter Dawyndt

A1 Journal Article in BIOINFORMATICS

Simultaneous mapping of multiple gene loci with pooled segregants

Jürgen ClaesenLieven ClementZiv ShkedyMaria R Foulquié-MorenoTomasz Burzykowski

A1 Journal Article in PLOS ONE

Crowdsourcing in proteomics: public resources lead to better experiments

Harald BarsnesLennart Martens

A1 Journal Article in AMINO ACIDS

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

Protein structure as a means to triage proposed PTM sites

Elien VandermarliereLennart Martens

A1 Journal Article in PROTEOMICS

Searching for a needle in a stack of needles: challenges in metaproteomics data analysis

Thilo MuthDirk BenndorfUdo ReichlErdmann RappLennart Martens

A1 Journal Article in MOLECULAR BIOSYSTEMS

Development of an enzyme-linked immunosorbent assay for detection of cellular and in vivo LRRK2 S935 phosphorylation

Lore DelbroekKristof Van KolenLiesbeth SteegmansRaquel da CunhaWim MandemakersGuy DaneelsPieter-Jan De BockJinwei ZhangKris GevaertBart De StrooperDario R AlessiPatrik VerstrekenDiederik W Moechars et al.

A1 Journal Article in JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS

CD44 and OTP are strong prognostic markers for pulmonary carcinoids

Dorian RA SwartsMieke ER HenflingLeander Van NesteRobert Jan van SuylenAnne-Marie C DingemansWinand NM DinjensAnnick HaesevoetsMartina RudeliusErik ThunnissenMarco VolanteWim Van CriekingeManon van EngelandFrans CS RamaekersErnst-Jan M Speel et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

GLUCAN SYNTHASE-LIKE8 and STEROL METHYLTRANSFERASE2 are required for ploidy consistency of the sexual reproduction system in Arabidopsis

Nico De StormeJoachim De SchrijverWim Van CriekingeVera WewerPeter DörmannDanny Geelen

A1 Journal Article in PLANT CELL

Inference of genome duplications from age distributions revisited

Kevin VannesteYves Van de PeerSteven Maere

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Significance and biological consequences of polyploidization in land plant evolution

Jeffrey FawcettYves Van de PeerSteven Maere

Bookchapter in Physical structure, behaviour and evolution of plant genomes

The Online Protein Processing Resource (TOPPR) : a database and analysis platform for protein processing events

Niklaas ColaertDavy MaddeleinFrancis ImpensPetra Van DammeKim PlasmanKenny HelsensNiels HulstaertJoël VandekerckhoveKris GevaertLennart Martens

A1 Journal Article in NUCLEIC ACIDS RESEARCH

LNCipedia : a database for annotated human lncRNA transcript sequences and structures

Pieter-Jan VoldersKenny HelsensXiaowei WangBjörn MentenLennart MartensKris GevaertJo VandesompelePieter Mestdagh

A1 Journal Article in NUCLEIC ACIDS RESEARCH

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

SNP discovery using paired-end RAD-tag sequencing on pooled genomic DNA of Sisymbrium austriacum (Brassicaceae)

K VandepitteO HonnayJ MergeayP BreyneIsabel Roldán-RuizTim De Meyer

A1 Journal Article in MOLECULAR ECOLOGY RESOURCES

The Ectocarpus genome and brown algal genomics : the Ectocarpus Genome Consortium

J Mark CockLieven SterckSophia AhmedAndrew E AllenGrigoris AmoutziasVeronique AnthouardFrançois ArtiguenaveAlok ArunJean-Marc AuryJonathan H BadgerBank BeszteriKenny BilliauEric BonnetJohn H BothwellChris BowlerCatherine BoyenColin BrownleeCarl J CarranoBénédicte CharrierGa Youn ChoSusana M CoelhoJonas CollénGildas Le CorguilléErwan CorreLaurence DartevelleCorinne Da SilvaLudovic DelageNicolas DelaroqueSimon M DittamiSylvie DoulbeauMarek EliasGarry FarnhamClaire MM GachonOlivier GodfroyBernhard GschloesslSvenja HeeschKamel JabbariClaire JubinHiroshi KawaiKei KimuraBernard KloaregFrithjof C KüpperDaniel LangAude Le BailRémy LuthringerCatherine LeblancPatrice LerougeMartin LohrPascal J LopezNicolas MacaisneCindy MartensFlorian MaumusGurvan MichelDiego Miranda-SaavedraJulia MoralesHervé MoreauTaizo MotomuraChikako NagasatoCarolyn A NapoliDavid R NelsonPi Nyvall-CollénAkira F PetersCyril PommierPhilippe PotinJulie PoulainHadi QuesnevilleBetsy ReadStefan A RensingAndrés RitterSylvie RousvoalManoj SamantaGaelle SamsonDeclan C SchroederDelphine ScornetBéatrice SégurensMartina StrittmatterThierry TononJames W TregearKlaus ValentinPeter Von DassowTakahiro YamagishiPierre RouzéYves Van de PeerPatrick Wincker et al.

A1 Journal Article in Advances in Botanical Research

Exploring the complementarity of eQTL mapping methods (poster)

Lieven VerbekeKathleen MarchalJan Fostier

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

Dieter De WitteMichiel Van BelPiet DemeesterBart DhoedtKlaas VandepoeleJan Fostier

A high performance computing approach to the dicovery of conserved motifs

Dieter De WitteMichiel Van BelPiet DemeesterBart DhoedtKlaas VandepoeleJan Fostier

Constrained ordination analysis in the presence of zero inflation

Yingjie ZhangOlivier Thas

A1 Journal Article in STATISTICAL MODELLING

DNA structural properties in the classification of genomic transcription

Pieter MeysmanKathleen MarchalKristof Engelen

A2 Journal Article in BIOINFORMATICS AND BIOLOGY INSIGHTS

Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology

Karin VoordeckersDries De MaeyerElisa van der ZandeMarcelo D VincesWim MeertLore ClootsOwen RyanKathleen MarchalKevin J Verstrepen

A1 Journal Article in MOLECULAR MICROBIOLOGY

Follicle stimulating hormone receptor G-29A, 919A > G, 2039A > G polymorphism and the risk of male infertility: A meta-analysis

Wei WuHongquan CaiHong SunJing LuDan ZhaoYufeng QinXiumei HanXiaobing NiuChuncheng LuYankai XiaShoulin WangBart De MoorKathleen MarchalXinru Wang et al.

A1 Journal Article in GENE

Nucleosomes affect local transformation efficiency

Elham AslankoohiKarin VoordeckersHong SunAminael Sanchez-RodriguezElisa van der ZandeKathleen MarchalKevin J Verstrepen

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Association of the vascular endothelial growth factor gene polymorphisms (-460C/T,+405G/C and+936T/C) with endometriosis: a meta-analysis

Shaohua XuWei WuHong SunJing LuBeilei YuanYankai XiaBart De MoorKathleen MarchalXinru WangPeizhen XuWenjun Cheng et al.

A1 Journal Article in ANNALS OF HUMAN GENETICS

iTRAQ data interpretation

Marc VaudelJulia Maria BurkhartRené Peiman ZahediLennart MartensAlbert Sickmann

Bookchapter in Quantitative methods in proteomics

The PRoteomics IDEntification (PRIDE) converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium

Richard G CôtéJohannes GrissJosé A DianesRui WangJames C WrightHenk WP van den ToornBas van BreukelenAlbert JR HeckNiels HulstaertLennart MartensFlorian ReisingerAttila CsordasDavid OvelleiroYasset Perez-RivevolHarald BarsnesHenning HermjakobJuan Antonio Vizcaíno et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Biomarkers for detection and prognosis of breast cancer identified by a functional hypermethylome screen

Jana JeschkeLeander Van NesteSabine C GlöcknerMashaal DhirMarilia Freitas CalmonValerie DeregowskiWim Van CriekingeIlse VlassenbroeckAlexander KochTimothy A ChanLeslie CopeCraig M HookerKornel E SchuebelEdward GabrielsonAndreas WinterpachtStephen B BaylinJames G HermanNita Ahuja et al.

A1 Journal Article in EPIGENETICS

Colorectal adenoma to carcinoma progression is accompanied by changes in gene expression associated with ageing, chromosomal instability, and fatty acid metabolism.

Beatriz CarvalhoAnke H Sillars-HardebolCindy PostmaSandra MongeraJochim Terhaar Sive DrosteAskar ObulkasimMark van de WielWim Van CriekingeBauke YlstraRemond JA FijnemanGerrit A Meijer et al.

A1 Journal Article in CELLULAR ONCOLOGY

The epigenetic promise for prostate cancer diagnosis.

Leander Van NesteJames G HermanGaëtan OttoJoseph W BigleyJonathan I EpsteinWim Van Criekinge

A1 Journal Article in PROSTATE

Direct genetic effects and their estimation from matched case-control data

Carlo BerzuiniStijn VansteelandtLuisa FocoRoberta PastorinoLuisa Bernardinelli

A1 Journal Article in GENETIC EPIDEMIOLOGY

Gene-environment interaction testing in family-based association studies with phenotypically ascertained samples: a causal inference approach

David W FardoJinze LiuDawn L DemeoEdwin K SilvermanStijn Vansteelandt

A1 Journal Article in BIOSTATISTICS

Causation and causal inference for genetic effects

Stijn VansteelandtChristoph Lange

A1 Journal Article in HUMAN GENETICS

Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection

Hong SunTias GunsAna Carolina FierroLieven ThorrezSiegfried NijssenKathleen Marchal

A1 Journal Article in NUCLEIC ACIDS RESEARCH

MotifSuite: workflow for probabilistic motif detection and assessment

Marleen ClaeysValerie StormsHong SunTom MichoelKathleen Marchal

A1 Journal Article in BIOINFORMATICS

Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes

Florent MuratYves Van de PeerJérôme Salse

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

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

Kristof De BeufPeter PipelersMegan AndriankajaOlivier ThasDirk InzéCiprian CrainiceanuLieven Clement

A1 Journal Article in BMC BIOINFORMATICS

Current methods for global proteome identification

Marc VaudelAlbert SickmannLennart Martens

A1 Journal Article in EXPERT REVIEW OF PROTEOMICS

Enabling computational proteomics by public and local data management systems

Kenny HelsensLennart Martens

A1 Journal Article in CIRCULATION-CARDIOVASCULAR GENETICS

Transcriptional reprogramming by root knot and migratory nematode infection in rice

Tina KyndtSimon DenilAnnelies HaegemanGeert TrooskensLander BautersWim Van CriekingeTim De MeyerGodelieve Gheysen

A1 Journal Article in NEW PHYTOLOGIST

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers.

Anneleen DecockMaté OngenaertJasmien HoebeeckKatleen De PreterGert Van PeerWim Van CriekingeRuth LadensteinJohannes H SchulteRosa NogueraRaymond L StallingsAn Van DammeGenevieve LaureysJoëlle VermeulenTom Van MaerkenFranki SpelemanJo Vandesompele et al.

A1 Journal Article in GENOME BIOLOGY

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-MarriottGwenael PiganeauPierre RouzéCorinne Da SilvaPatrick WinckerYves Van de PeerKlaas Vandepoele et al.

A1 Journal Article in GENOME BIOLOGY

Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-box gene and species diversification

Dries VekemansSebastian ProostKevin VannesteHeleen CoenenTom ViaenePhilip RuelensSteven MaereYves Van de PeerKoen Geuten

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

ORCAE: online resource for community annotation of eukaryotes

Lieven SterckKenny BilliauThomas AbeelPierre RouzéYves Van de Peer

A1 Journal Article in NATURE METHODS

The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathways

Julia M BurkhartMarc VaudelStepan GambaryanSonja RadauUlrich WalterLennart MartensJörg GeigerAlbert SickmannRené P Zahedi

A1 Journal Article in BLOOD

Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model

Kristof De BeufJoachim De SchrijverOlivier ThasWim Van CriekingeRafael A IrizarryLieven Clement

A1 Journal Article in BMC BIOINFORMATICS

Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform

Sarah De KeulenaerJan HellemansSteve LefeverJean-Pierre RenardJoachim De SchrijverHendrik Van de VoordeMohammad Amin TabatabaiefarFilip Van NieuwerburghDaisy FlamezFilip PattynBieke ScharlakenDieter DeforceSofie BekaertWim Van CriekingeJo VandesompeleGuy Van CampPaul Coucke et al.

A1 Journal Article in BMC MEDICAL GENOMICS

A complex standard for protein identification, designed by evolution

Marc VaudelJulia M BurkhartDaniela BreiterRené P ZahediAlbert SickmannLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation

Agnes KlochendlerNoa Weinberg-CoremMaya MoranAvital SwisaNathalie PochetVirginia SavovaJonas VikesåYves Van de PeerMichael BrandeisAviv RegevFinn Cilius NielsenYuval DorAmir Eden et al.

A1 Journal Article in DEVELOPMENTAL CELL

Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI)

Marc VaudelJulia M BurkhartSonja RadauRené P ZahediLennart MartensAlbert Sickmann

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

No shorter telomeres in subjects with a family history of cardiovascular disease in the Asklepios Study

Tim De MeyerCaroline Van daeleMarc De BuyzereSimon DenilDirk De BacquerPatrick SegersLuc CoomanGui De BackerThierry GillebertSofie BekaertErnst Rietzschel et al.

A1 Journal Article in ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Towards a human proteomics atlas

Giulia GonnelliNiels HulstaertSven DegroeveLennart Martens

A1 Journal Article in ANALYTICAL AND BIOANALYTICAL CHEMISTRY

The effect of peptide identification search algorithms on MS2-based label-free protein quantification

Sven DegroeveAn StaesPieter-Jan De BockLennart Martens

A1 Journal Article in OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

The tomato genome sequence provides insights into fleshy fruit evolution

Shusei SatoSatoshi TabataHideki HirakawaErika AsamizuKenta ShirasawaSachiko IsobeTakakazu KanekoYasukazu NakamuraDaisuke ShibataKoh AokiMichael EgholmJames KnightRobert BogdenChangbao LiYang ShuangXun XuShengkai PanShifeng ChengXin LiuYuanyuan RenJun WangAlessandro AlbieroFrancesca Dal PeroSara TodescoJoyce Van EckRobert M BuelsAureliano BombarelyJoseph R GosselinMinyun HuangJonathan A LetoNaama MendaSusan StricklerLinyong MaoShan GaoIsaak Y TecleThomas YorkYi ZhengJulia T VrebalovJeMin LeeSilin ZhongLukas A MuellerWillem J StiekemaPaolo RibecaTyler AliotoWencai YangSanwen HuangYongchen DuZhonghua ZhangJianchang GaoYanmei GuoXiaoxuan WangYing LiJun HeChuanyou LiZhukuan ChengJianru ZuoJianfeng RenJiuhai ZhaoLiuhua YanHongling JiangBao WangHongshuang LiZhenjun LiFuyou FuBingtang ChenBin HanQi FengDanlin FanYing WangHongqing LingYongbiao XueDoreen WareW Richard McCombieZachary B LippmanJer-Ming ChiaKe JiangShiran PasternakLaura GelleyMelissa KramerLorinda K AndersonSong-Bin ChangSuzanne M RoyerLindsay A ShearerStephen M StackJocelyn KC RoseYimin XuNancy EannettaAntonio J MatasRyan McQuinnSteven D TanksleyFrancisco CamaraRoderic GuigóStephane RombautsJeffrey FawcettYves Van de PeerDani ZamirChunbo LiangManuel SpannaglHeidrun GundlachRemy BruggmannKlaus MayerZhiqi JiaJunhong ZhangZhibiao YeGerard J BishopSarah ButcherRosa Lopez-CobolloDaniel BuchanIoannis FilippisJames AbbottRekha DixitManju SinghArchana SinghJitendra Kumar PalAwadhesh PanditPradeep Kumar SinghAjay Kumar MahatoVivek DograKishor GaikwadTilak Raj SharmaTrilochan MohapatraNagendra Kumar SinghMathilde CausseChristophe RothanThomas SchiexCéline NoirotArnaud BellecChristophe KloppCorinne DelalandeHélène BergesJérôme MariettePierre FrasseSonia VautrinMohamed ZouineAlain LatcheChristine RousseauFarid RegadJean-Claude PechMurielle PhilippotMondher BouzayenPierre PericardSonia OsorioAsunción Fernandez del CarmenAntonio MonforteAntonio GranellRafael Fernandez-MuñozMariana ConteGabriel LichtensteinFernando CarrariGianluca De BellisFabio FuligniClelia PeanoSilvana GrandilloPasquale TermolinoMarco PietrellaElio FantiniGiulia FalconeAlessia FioreGiovanni GiulianoLoredana LopezPaolo FacellaGaetano PerrottaLoretta DaddiegoGlenn BryanModesto OrozcoXavier PastorDavid TorrentsKeygene NV Marco GM van SchriekRichard MC FeronJan van OeverenPeter de HeerLorena daPonteSaskia Jacobs-OomenMike CariasoMarcel PrinsMichiel JT van EijkAntoine JanssenMark JJ van HaarenSung-Hwan JoJungeun KimSuk-Yoon KwonSangmi KimDal-Hoe KooSanghyeob LeeCheol-Goo HurChristopher ClouserAlain RicoAsis HallabChristiane GebhardtKathrin KleeAnika JöckerJens WarfsmannUlrike GöbelShingo KawamuraKentaro YanoJamie D ShermanHiroyuki FukuokaSatomi NegoroSarita BhuttyParul ChowdhuryDebasis ChattopadhyayErwin DatemaSandra SmitEliog WM SchijlenJose van de BeltJan C van HaarstSander A PetersMarjo J van StaverenMarleen HC HenkensPaul JW MooymanThamara HesselinkRoeland CHJ van HamGuoyong JiangMarcus DroegeDoil ChoiByung-Cheol KangByung Dong KimMinkyu ParkSeungill KimSeon-In YeomYong-Hwan LeeYang-Do ChoiGuangcun LiJianwei GaoYongsheng LiuShengxiong HuangVictoria Fernandez-PedrosaCarmen ColladoSheila ZuñigaGuoping WangRebecca CadeRobert A DietrichJane RogersSandra KnappZhangjun FeiRuth A WhiteTheodore W ThannhauserJames J GiovannoniMiguel Angel BotellaLouise GilbertRamon GonzalezJose Luis GoicoecheaYeisoo YuDavid KudrnaKristi ColluraMarina WissotskiRod WingHeiko SchoofBlake C MeyersAishwarya Bala GurazadaPamela J GreenSaloni MathurShailendra VyasAmolkumar U SolankeRahul KumarVikrant GuptaArun K SharmaParamjit KhuranaJitendra P KhuranaAkhilesh K TyagiTamas DalmayIrina MohorianuBrandon WaltsSrikar ChamalaW Brad BarbazukJingping LiHui GuoTae-Ho LeeYupeng WangDong ZhangAndrew H PatersonXiyin WangHaibao TangAmalia BaroneMaria Luisa ChiusanoMaria Raffaella ErcolanoNunzio D'AgostinoMiriam Di FilippoAlessandra TrainiWalter SanseverinoLuigi FruscianteGraham B SeymourMounir ElharamYing FuAxin HuaSteven KentonJennifer LewisShaoping LinFares NajarHongshing LaiBaifang QinChunmei QuRuihua ShiDouglas WhiteJames WhiteYanbo XingKeqin YangJing YiZiyun YaoLiping ZhouBruce A RoeAlessandro VezziMichela D'AngeloRosanna ZimbelloRiccardo SchiavonElisa CaniatoChiara RigobelloDavide CampagnaNicola VituloGiorgio ValleDavid R NelsonEmanuele De PaoliDora SzinayHans H de JongYuling BaiRichard GF VisserRené M Klein LankhorstHelen BeasleyKaren McLarenChristine NicholsonClaire RiddleGiulio Gianese et al.

A1 Journal Article in NATURE

Comparative co-expression analysis in plant biology

Sara MovahediMichiel Van BelKen HeyndrickxKlaas Vandepoele

A1 Journal Article in PLANT CELL AND ENVIRONMENT

Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling

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

A1 Journal Article in PLOS ONE

Integrative genomic analysis implicates gain of PIK3CA at 3q26 and MYC at 8q24 in chronic lymphocytic leukemia

Jennifer R BrownMegan HannaBethany TesarLilian WernerNathalie PochetJohn M AsaraYaoyu E WangPaola dal CinStacey M FernandesChristina ThompsonLaura MacConaillCatherine J WuYves Van de PeerMick CorrellAviv RegevDonna NeubergArnold S Freedman et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

Transcriptional profiling of Plasmodium falciparum parasites from patients with severe malaria identifies distinct low vs. high parasitemic clusters

Danny A, Jr MilnerNathalie PochetMalkie KrupkaChris WilliamsKarl SeydelTerrieE TaylorYves Van de PeerAviv RegevDyann WirthJohanna P DailyJill P Mesirov et al.

A1 Journal Article in PLOS ONE

Prospects and limitations of full-text index structures in genome analysis

Michaël VyvermanBernard De BaetsVeerle FackPeter Dawyndt

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Exploring biomolecular literature with EVEX : connecting genes through events, homology, and indirect associations

Sofie Van LandeghemKai HakalaSamuel RönnqvistTapio SalakoskiYves Van de PeerFilip Ginter

A1 Journal Article in ADVANCES IN BIOINFORMATICS

Semantically linking molecular entities in literature through entity relationships

Sofie Van LandeghemJari BjörneThomas AbeelBernard De BaetsTapio SalakoskiYves Van de Peer

A1 Journal Article in BMC BIOINFORMATICS

Germline copy number variation associated with Mendelian inheritance of CLL in two families

JR BrownM HannaB TesarNathalie PochetA VartanovSM FernandesL WernerM AshCA RodenL MacConaillU HainzJ LongtineYE WangM CorrellYves Van de PeerA RegevC WuD NeubergAS Freedman et al.

A1 Journal Article in LEUKEMIA

Evaluation and properties of the budding yeast phosphoproteome

Grigoris D AmoutziasYing HeKathryn S LilleyYves Van de PeerSthephen G Oliver

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Tetraspanin genes in plants

Feng WangKlaas VandepoeleMaria Van Lijsebettens

A1 Journal Article in PLANT SCIENCE

Getting up to speed

Yves Van de PeerJ ChrisPires

Editorial material

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

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

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

Ken HeyndrickxKlaas Vandepoele

A1 Journal Article in PLANT PHYSIOLOGY

Chromatographic retention time prediction for posttranslationally modified peptides

Luminita MoruzAn StaesJoseph M FosterMaria HatzouEvy TimmermanLennart MartensLukas Käll

A1 Journal Article in PROTEOMICS

Sigpep: calculating unique peptide signature transition sets in a complete proteome background

Kenny HelsensMichael MuellerNiels HulstaertLennart Martens

A1 Journal Article in PROTEOMICS

Redundancy and rewiring of genetic networks following genome-wide duplication events

Riet De SmetYves Van de Peer

A1 Journal Article in CURRENT OPINION IN PLANT BIOLOGY

Semiparametric tests for sufficient cause interaction

Stijn VansteelandtTyler J VanderWeeleJames M Robins

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

Transcriptome analysis of rice mature root tissue and root tips in early development by massive parallel sequencing

Tina KyndtSimon DenilAnnelies HaegemanGeert TrooskensTim De MeyerWim Van CriekingeGodelieve Gheysen

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

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

Low dose irradiation of thyroid cells reveals a unique transcriptomic and epigenetic signature in RET/PTC-positive cells

Khalil Abou-El-ArdatPieter MonsieursNataša AnastasovMike AtkinsonHanane DerradjiTim De MeyerSofie BekaertWim Van CriekingeSarah Baatout

A1 Journal Article in MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses

Ryan WhitfordAna Fernandez SalinaRicardo Tejos UlloaAmparo Cuéllar PérezJürgen Kleine-VehnSteffen VannesteAndrzej DrozdzeckiJohannes LeitnerLindy AbasMaarten AertsKurt HoogewijsPawel Radoslaw BasterRuth De GroodtYao-Cheng LinVeronique StormeYves Van de PeerTom BeeckmanAnnemieke MadderChristian LuschnigBart DevreeseJiri FrimlPierre Hilson et al.

A1 Journal Article in DEVELOPMENTAL CELL

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

Deconstruction of the (paleo)polyploid grapevine genome based on the analysis of transposition events involving NBS resistance genes

Giulia MalacarneMichele PerazzolliAlessandro CestaroLieven SterckPaolo FontanaYves Van de PeerRoberto ViolaRiccardo VelascoFrancesco Salamini

A1 Journal Article in PLOS ONE

A comprehensive analysis of genes encoding small secreted proteins identifies candidate effectors in Melampsora larici-populina (poplar leaf rust)

Stéphane HacquardDavid L JolyYao-Cheng LinEmilie TisserantNicolas FeauChristine DelaruelleValérie LeguéAnnegret KohlerPhilippe TanguayBenjamin PetrePascal FreyYves Van de PeerPierre RouzéFrancis MartinRichard C HamelinSébastien Duplessis et al.

A1 Journal Article in MOLECULAR PLANT-MICROBE INTERACTIONS

Flow cytometry for fast microbial community fingerprinting

Karen De RoyLieven ClementOlivier ThasYingying WangNico Boon

A1 Journal Article in WATER RESEARCH

The HUPO initiative on Model Organism Proteomes, iMOP

Alexandre ME JonesRuedi AebersoldChristian H AhrensRolf ApweilerKatja BaerenfallerMark BakerEmøke BendixenSteve BriggsPhilip BrownridgeErich BrunnerMichael DaubeEric W DeutschUeli GrossniklausJoshua HeazlewoodMichael O HengartnerHenning HermjakobMarko JovanovicCraig LawlessGünter LochnitLennart MartensChristian RavnsborgSabine P SchrimpfYhong-Hee ShimDeni SubasicAndreas TholeyKlaas van WijkChristian von MeringManuel WeissXue Zheng et al.

A1 Journal Article in PROTEOMICS

An omnibus consistent adaptive percentile modified Wilcoxon rank sum test with applications in gene expression studies

Olivier ThasLieven ClementJohn RaynerBeatriz CarvalhoWim Van Criekinge

A1 Journal Article in BIOMETRICS

Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome

Jeffrey FawcettPierre RouzéYves Van de Peer

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

GenomeView : a next-generation genome browser

Thomas AbeelThomas Van ParysYvan SaeysJames GalaganYves Van de Peer

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Fast wavelet based functional models for transcriptome analysis with tiling arrays

Lieven ClementKristof De BeufOlivier ThasMarnik VuylstekeRafael IrizarryCiprian M Crainiceanu

A1 Journal Article in STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY

TraML: a standard format for exchange of selected reaction monitoring transition lists

Eric W DeutschMatthew ChambersSteffen NeumannFredrik LevanderPierre-Alain BinzJim ShofstahlDavid S CampbellLuis MendozaDavid OvelleiroKenny HelsensLennart MartensRuedi AebersoldRobert L MoritzMi-Youn Brusniak et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

PRIDE Inspector: a tool to visualize and validate MS proteomics data

Rui WangAntonio FabregatDaniel RíosDavid OvelleiroJoseph M FosterRichard G CôtéJohannes GrissAttila CsordasYasset Perez-RiverolFlorian ReisingerHenning HermjakobLennart MartensJuan Antonio Vizca et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

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

A bio-inspired agent-based system for controlling robot behaviour

Yao YaoGuy BaeleYves Van de Peer

Aggregated fuzzy answer set programming

Jeroen JanssenSteven SchockaertDirk VermeirMartine De Cock

A1 Journal Article in ANNALS OF MATHEMATICS AND ARTIFICIAL INTELLIGENCE

Flexibility and utility of the Cell Cycle Ontology

Vladimir MironovErick AntezanaMikel EgañaWard BlondéBernard De BaetsMartin KuiperRobert Stevens

A1 Journal Article in APPLIED ONTOLOGY

Reasoning with bio-ontologies: using relational closure rules to enable practical querying

Ward BlondéVladimir MironovAravind VenkatesanErick AntezanaBernard De BaetsMartin Kuiper

A1 Journal Article in BIOINFORMATICS

miRNA Expression profiling enables risk stratification in archived and fresh neuroblastoma tumor samples

Katleen De PreterPieter MestdaghJoëlle VermeulenFjoralba ZekaAlene NaranjoIsabella BrayVictoria CastelCaifu ChenElzbieta DrozynskaAngelika EggertMichael D HogartyEwa Iżycka-SwieszewskaWendy B LondonRosa NogueraMarta PiquerasKenneth BryanBenjamin SchowePeter van SluisJan J MolenaarAlexander SchrammJohannes H SchulteRaymond L StallingsRogier VersteegGenevieve LaureysNadine Van RoyFranki SpelemanJo Vandesompele et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

Hsa-mir-145 is the top EWS-FLI1-repressed microRNA involved in a positive feedback loop in Ewing's sarcoma

J BanG JugPieter MestdaghR SchwentnerM KauerDNT AryeeK-L SchaeferF NakataniK ScotlandiM ReiterD StrunkFranki SpelemanJo VandesompeleH Kovar et al.

A1 Journal Article in ONCOGENE

Combining disease models to test for gene-environment interaction in nuclear families

Thomas J HoffmannStijn VansteelandtChristoph LangeEdwin K SilvermanDawn L DeMeoNan M Laird

A1 Journal Article in BIOMETRICS

Probabilistic index models

Jan De NeveOlivier ThasLieven ClementJean-Pierre Ottoy

Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control

Robert S CoyneLinda HannickDhanasekaran ShanmugamJessica B HostetlerDaniel BramiVinita S JoardarJustin JohnsonDiana RaduneIrtisha SinghJonathan H BadgerUjjwal KumarMilton SaierYuFeng WangHong CaiJianYing GuMichael W MatherAkhil B VaidyaDavid E WilkesVidyalakshmi RajagopalanDavid J AsaiChad G PearsonRobert C FindlyHarry W DickersonMartin WuCindy MartensYves Van de PeerDavid S RoosDonna M Cassidy-HanleyTheodore G Clark et al.

A1 Journal Article in GENOME BIOLOGY

Development of a multicomponent prediction model for acute esophagitis in lung cancer patients receiving chemoradiotherapy

Kim De RuyckNick SabbeCary OberijeKatrien VandecasteeleOlivier ThasDirk De RuysscherPhillipe LambinJan Van MeerbeeckWilfried De NeveHubert Thierens

A1 Journal Article in INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS

Practical tools to implement massive parallel pyrosequencing of PCR products in next generation molecular diagnostics

Kim De LeeneerJoachim De SchrijverLieven ClementMachteld BaetensSteve LefeverSarah De KeulenaerWim Van CriekingeDieter DeforceFilip Van NieuwerburghSofie BekaertFilip PattynBram De WildePaul CouckeJo VandesompeleKathleen ClaesJan Hellemans et al.

A1 Journal Article in PLOS ONE

Smooth tests of goodness of fit

JCW RaynerOlivier ThasDJ Best

A2 Journal Article in WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL STATISTICS

A discussion on the accuracy-complexity relationship in modelling fish habitat preference using genetic Takagi-Sugeno fuzzy systems

Shinji FukudaJun NakajimaBernard De BaetsWillem WaegemanTakahiko MukaiAns MoutonNorio Orikura

ERA ranking representability: the missing link between ordinal regression and multi-class classification

Willem WaegemanBernard De Baets

'4D Biology for health and disease' workshop report

Jan-Pieter AbrahamsRolf ApweilerRudi BallingMichela G BerteroJanusz M BujnickiNaomi E ChayenPatrick ChèneGary L CorthalsTomasz DylągFriedrich FörsterAlbert JR HeckPeter JF HendersonRalf HerwigPhilippe JehensonSasa Jenko KokaljErnest LauePierre LegrainLennart MartensCristiano MiglioriniAndrea MusacchioMarjetka PodobnikGebhard FX SchertlerGideon SchreiberTitia K SixmaAugust B SmitDavid StuartDmitri I SvergunMichael J Taussig et al.

A1 Journal Article in NEW BIOTECHNOLOGY

EVEX: a PubMed-scale resource for homology-based generalization of text mining predictions

Sofie Van LandeghemFilip GinterYves Van de PeerTapio Salakoski

U-Compare bio-event meta-service : compatible BioNLP event extraction services

Yoshinobu KanoJari BjorneFilip GinterTapio SalakoskiEkaterina BuykoUdo HahnKevin CohenKarin VerspoorChristophe RoederLawrence HunterHalil KilicogluSabine BerglerSofie Van LandeghemThomas Van ParysYves Van de PeerMakoto MiwaSophia AnaniadouMariana NevesAlberto Pascual-MontanoArzucan OzgurDragomir RadevSebastian RiedelRune SaetreHong-Woo ChunJin-Dong KimSampo PyysaloTomoko OhtaJun'ichi Tsujii et al.

A1 Journal Article in BMC BIOINFORMATICS

EVI1-mediated down regulation of MIR449A is essential for the survival of EVI1 positive leukaemic cells

An De WeerJoni Van der MeulenPieter RondouTom TaghonTorsten A KonradKatleen De PreterPieter MestdaghTom Van MaerkenNadine Van RoyMarta JeisonIsaac YanivBarbara CauwelierLucien NoensHélène-Antoine PoirelPeter VandenbergheFrédéric LambertAnne De PaepeMaria García SánchezMaria OderoBruno VerhasseltJan PhilippéJo VandesompeleRotraud WieserNicole DastuguePieter Van VlierbergheBruce PoppeFranki Speleman et al.

A1 Journal Article in BRITISH JOURNAL OF HAEMATOLOGY

The microRNA body map : dissecting microRNA function through integrative genomics

Pieter MestdaghSteve LefeverFilip PattynDana RidzonErik FredlundAnnelies FieuwMaté OngenaertJoëlle VermeulenAnne De PaepeLinda WongFranki SpelemanCaiFu ChenJo Vandesompele et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Pharmacological activation of p53 and gene therapy as emerging treatment options for neuroblastoma

Tom Van MaerkenAli RihaniAnne De PaepeJo VandesompeleFranki Speleman

A2 Journal Article in BELGIAN JOURNAL OF MEDICAL ONCOLOGY

Experiment-model interaction for analysis of epicardial activation during human ventricular fibrillation with global myocardial ischaemia

RH ClaytonMP NashCP BradleyAlexander PanfilovDJ PatersonP Taggart

A1 Journal Article in PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Minimum information about a cardiac electrophysiology experiment (MICEE): standardised reporting for model reproducibility, interoperability, and data sharing

TA QuinnS GraniteMA AllessieC AntzelevitchC BollensdorffG BubRAB BurtonE CerbaiPS ChenM DelmarD DiFrancescoYE EarmIR EfimovM EggerE EntchevaM FinkR FischmeisterMR FranzA GarnyWR GilesT HannesSE HardingPJ HunterG IribeJ JalifeCR JohnsonRS KassI KodamaG KorenP LordVS MarkhasinS MatsuokaAD McCullochGR MiramsGE MorleyS NattelD NobleSP OlesenAlexander PanfilovNA TrayanovaU RavensS RichardDS RosenbaumY RudyF SachsFB SachseDA SaintU SchottenO SolovyovaP TaggartL TungA VarroPG VoldersK WangJN WeissE WettwerE WhiteR WildersRL WinslowP Kohl et al.

A1 Journal Article in PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Classification and identification of the Burkholderia cepacia complex: past, present and future

Peter VandammePeter Dawyndt

A1 Journal Article in SYSTEMATIC AND APPLIED MICROBIOLOGY

Using parallel corpora for word sense disambiguation

Els LefeverVeronique HosteMartine De Cock

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 SchoofYves Van de PeerSebastian ProostDouglas R CookBlake C MeyersManuel SpannaglFoo CheungStéphane De MitaVivek KrishnakumarHeidrun GundlachShiguo ZhouJoann MudgeArvind K BhartiJeremy D MurrayMarina A NaoumkinaBenjamin RosenKevin AT SilversteinHaibao TangStephane RombautsPatrick X ZhaoPeng ZhouValérie BarbePhilippe BardouMichael BechnerArnaud BellecAnne BergerHélène BergèsShelby BidwellTon BisselingNathalie ChoisneArnaud CoulouxRoxanne DennyShweta DeshpandeXinbin DaiJeff J DoyleAnne-Marie DudezAndrew D FarmerStéphanie FouteauCarolien FrankenChrystel GibelinJohn GishSteven GoldsteinAlvaro J GonzálezPamela J GreenAsis HallabMarijke HartogAxin HuaSean J HumphrayDong-Hoon JeongYi JingAnika JöckerSteve M KentonDong-Jin KimKathrin KleeHongshing LaiChunting LangShaoping LinSimone L MacmilGhislaine MagdelenatLucy MatthewsJamison McCorrisonErin L MonaghanJeong-Hwan MunFares Z NajarChristine NicholsonCélilne NoirotMajesta O'BlenessCharles R PauleJulie PoulainFlorent PrionBaifang QinChunmei QuErnest F RetzelClaire RiddleErika SalletSylvie SamainNicolas SamsonIryna SandersOlivier SauratClaude ScarpelliThomas SchiexBéatrice SegurensAndrew J SeverinD. Janine SherrierRuihua ShiSarah SimsSusan R SingerSenjuti SinharoyLieven SterckAgnès ViolletBing-Bing WangKeqin WangMingyi WangXiaohong WangJens WarfsmannJean WeissenbachDoug D WhiteJim D WhiteGraham B WileyPatrick WinckerYanbo XingLimei YangZiyun YaoFu YingJixian ZhaiLiping ZhouAntoine ZuberJean DénariéRichard A DixonGregory D MayDavid C SchwartzJane RogersFrancis QuétierChristopher D TownBruce A Roe et al.

A1 Journal Article in NATURE

High-precision bio-molecular event extraction from text using parallel binary classifiers

Sofie Van LandeghemBernard De BaetsYves Van de PeerYvan Saeys

A1 Journal Article in COMPUTATIONAL INTELLIGENCE

Practical aggregation operators for gradual trust and distrust

Patricia VictorChris CornelisMartine De CockEnrique Herrera-Viedma

A1 Journal Article in FUZZY SETS AND SYSTEMS

Estimation of direct effects for survival data by using the Aalen additive hazards model

Torben MartinussenStijn VansteelandtMette GersterJacob von Bornemann Hjelmborg

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

A weighting approach to causal effects and additive interaction in case-control studies: marginal structural linear odds models

Tyler J VanderWeeleStijn Vansteelandt

A1 Journal Article in AMERICAN JOURNAL OF EPIDEMIOLOGY

Bacterial species identification from MALDI-TOF mass spectra through data analysis and machine learning

Katrien De BruyneBram SlabbinckWillem WaegemanPaul VauterinBernard De BaetsPeter Vandamme

A1 Journal Article in SYSTEMATIC AND APPLIED MICROBIOLOGY

Complexity of fuzzy answer set programming under Łukasiewicz semantics: first results

Marjon BlondeelSteven SchockaertMartine De CockDirk Vermeir

Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast

Anagha JoshiYves Van de PeerTom Michoel

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Weak and strong disjunction in possibilistic ASP

Kim BautersSteven SchockaertMartine De CockDirk Vermeir

Analysis of the resolution limitations of peptide identification algorithms

Niklaas ColaertSven DegroeveKenny HelsensLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Protein alpha-N-acetylation studied by N-terminomics

Petra Van DammeThomas ArnesenKris Gevaert

A1 Journal Article in FEBS JOURNAL

State sequence prediction in imprecise hidden Markov models

Jasper De BockGert de Cooman

The genome of Tetranychus urticae reveals herbivorous pest adaptations

Miodrag GrbićThomas Van LeeuwenRichard M ClarkStephane RombautsPierre RouzéVojislava GrbićEdward J OsborneWannes DermauwThi Ngoc Phuong CaoFélix OrtegoPedro Hernández-CrespoIsabel DiazManuel MartinezMaria NavajasElio SucenaSara MagalhãesLisa NagyRyan M PaceSergej DjuranovićGuy SmaggheMasatoshi IgaOlivier ChristiaensJan A VeenstraJohn EwerRodrigo Mancilla VillalobosJeffrey L HutterStephen D HudsonMarisela VelezSoojin V YiJia ZengAndre Pires-daSilvaFernando RochMarc CazauxMarie NavarroVladimir ZhurovGustavo AcevedoAnica BjelicaJeffrey FawcettEric BonnetCindy MartensGuy BaeleLothar WisslerAminael Sanchez-RodriguezLuc TirryCatherine BlaisKristof DemeestereStefan R HenzT Ryan GregoryJohannes MathieuLou VerdonLaurent FarinelliJeremy SchmutzErika LindquistRené FeyereisenYves Van de Peer et al.

A1 Journal Article in NATURE

Response to low-dose X-irradiation is p53-dependent in a papillary thyroid carcinoma model system

Khalil Abou-El-ArdatHanane DerradjiWinnok De VosTim De MeyerSofie BekaertWim Van CriekingeSarah Baatout

A1 Journal Article in INTERNATIONAL JOURNAL OF ONCOLOGY

jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions

Kenny HelsensMi-Youn BrusniakEric DeutschRobert L MoritzLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

The human N-alpha-acetyltransferase 40 (hNaa40p/hNatD) is conserved from yeast and N-terminally acetylates histones H2A and H4

Kristine HolePetra Van DammeMonica DalvaHenriette AksnesNina GlomnesJan Erik VarhaugJohan R LillehaugKris GevaertThomas Arnesen

A1 Journal Article in PLOS ONE

Integrating coarse-scale uncertain soil moisture data into a fine-scale hydrological modelling scenario

Hilde VernieuweBernard De BaetsJ MinetValentijn PauwelsS LambotM VancloosterNiko Verhoest

A1 Journal Article in HYDROLOGY AND EARTH SYSTEM SCIENCES

A novel strategy for the comprehensive analysis of the biomolecular composition of isolated plasma membranes

Deepak B Thimiri Govinda RajBart GhesquièreArun Kumar Tharkeshwar RaghunathKatrijn CoenRita DeruaDieter VanderschaegheEvelien RysmanMurali BagadiPieter BaatsenBart De StrooperEtienne WaelkensGustaaf BorghsNico CallewaertJohan SwinnenKris GevaertWim Annaert et al.

A1 Journal Article in MOLECULAR SYSTEMS BIOLOGY

Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks

Tom MichoelAnagha JoshiBruno NachtergaeleYves Van de Peer

A1 Journal Article in MOLECULAR BIOSYSTEMS

ParaSense or how to use parallel corpora for word sense disambiguation

Els LefeverVeronique HosteMartine De Cock

On instrumental variables estimation of causal odds ratios

Stijn VansteelandtJack BowdenManoochehr BabanezhadEls Goetghebeur

A1 Journal Article in STATISTICAL SCIENCE

Applying massive parallel sequencing to molecular diagnosis of Marfan and Loeys-Dietz syndromes

Machteld BaetensLut Van LaerKim De LeeneerJan HellemansJoachim De SchrijverHendrik Van de VoordeMarjolijn RenardHal DietzRonald V LacroBjörn MentenWim Van CriekingeJulie De BackerAnne De PaepeBart LoeysPaul Coucke et al.

A1 Journal Article in HUMAN MUTATION

Selecting protein N-terminal peptides by combined fractional diagonal chromatography

An StaesFrancis ImpensPetra Van DammeBart RuttensMarc GoethalsHans DemolEvy TimmermanJoël VandekerckhoveKris Gevaert

A1 Journal Article in NATURE PROTOCOLS

thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files

Niklaas ColaertHarald BarsnesMarc VaudelKenny HelsensEvy TimmermanAlbert SickmannKris GevaertLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Neuroblastoma epigenetics : from candidate gene approaches to genome-wide screenings

Anneleen DecockMaté OngenaertJo VandesompeleFranki Speleman

A1 Journal Article in EPIGENETICS

Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation

Kenny HelsensPetra Van DammeSven DegroeveLennart MartensThomas ArnesenJoël VandekerckhoveKris Gevaert

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes

Guy BaeleYves Van de PeerStijn Vansteelandt

A1 Journal Article in BMC EVOLUTIONARY BIOLOGY

NatF contributes to an evolutionary shift in protein N-terminal acetylation and is important for normal chromosome segregation

Petra Van DammeKristine HoleAna Pimenta-MarquesKenny HelsensJoël VandekerckhoveRui G MartinhoKris GevaertThomas Arnesen

A1 Journal Article in PLOS GENETICS

Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

Emilie ChancerelCamille LepoittevinGregoire Le ProvostYao-Cheng LinJuan Pablo Jaramillo-CorreaAndrew J EckertJill L WegrzynDiana ZelenikaAnne BolandJean-Marc FrigerioPhilippe ChaumeilPauline Garnier-GereChristophe BouryDelphine GrivetSantiago C Gonzalez-MartinezPierre RouzéYves Van de PeerDavid B NealeMaria T CerveraAntoine KremerChristophe Plomion et al.

A1 Journal Article in BMC GENOMICS

A posteriori quality control for the curation and reuse of public proteomics data

Joseph M FosterSven DegroeveLaurent GattoMatthieu VisserRui WangJohannes GrissRolf ApweilerLennart Martens

A1 Journal Article in PROTEOMICS

Combining quantitative proteomics data processing workflows for greater sensitivity

Niklaas ColaertChristophe Van HueleSven DegroeveAn StaesJoël VandekerckhoveKris GevaertLennart Martens

A1 Journal Article in NATURE METHODS

Proteome-derived peptide libraries allow detailed analysis of the substrate specificities of Nα-acetyltransferases and point to hNaa10p as the post-translational actin Nα-acetyltransferase

Petra Van DammeRune EvjenthHavard FoynKimberly DemeyerPieter-Jan De BockJohan R LillehaugJoël VandekerckhoveThomas ArnesenKris Gevaert

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

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

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

Tina T HuPedro PattynErica G BakkerJun CaoJan-Fang ChengRichard M ClarkNoah FahlgrenJeffrey FawcettJane GrimwoodHeidrun GundlachGeorg HabererJesse D HollisterStephan OssowskiRobert P OttilarAsaf A SalamovKorbinian SchneebergerManuel SpannaglXi WangLiang YangMikhail E NasrallahJoy BergelsonJames C CarringtonBrandon S GautJeremy SchmutzKlaus FX MayerYves Van de PeerIgor V GrigorievMagnus NordborgDetlef WeigelYa-Long Guo et al.

A1 Journal Article in NATURE GENETICS

Peptide identification quality control

Marc VaudelJulia M BurkhartAlbert SickmannLennart MartensRene P Zahedi

A1 Journal Article in PROTEOMICS

RIBAR and xRIBAR: methods for reproducible relative MS/MS-based label-free protein quantification

Niklaas ColaertKris GevaertLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Functional analysis of the p53 pathway in neuroblastoma cells using the small-molecule MDM2 antagonist Nutlin-3

Tom Van MaerkenAli RihaniDaniel DreidaxSarah De ClercqNurten YigitJean-Christophe MarineFrank WestermannAnne De PaepeJo VandesompeleFranki Speleman

A1 Journal Article in MOLECULAR CANCER THERAPEUTICS

Fuzzy autoepistemic logic: reflecting about knowledge of truth degrees

Marjon BlondeelSteven SchockaertMartine De CockDirk Vermeir

Models of cardiac tissue electrophysiology: progress, challenges and open questions

RH ClaytonOlivier BernusEM CherryHans DierckxFH FentonL MirabellaAlexander PanfilovFB SachseG SeemannH Zhang

A1 Journal Article in PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Diversification of search results as a fuzzy satisfiability problem

Steven SchockaertMartine De Cock

Communicating ASP and the polynomial hierarchy

Kim BautersSteven SchockaertDirk VermeirMartine De Cock

CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks

P. AudenaertThomas Van ParysFlorian BrondelMario PickavetPiet DemeesterYves Van de PeerTom Michoel

A1 Journal Article in BIOINFORMATICS

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

Sébastien DuplessisChristina A CuomoYao-Cheng LinAndrea AertsEmilie TisserantClaire Veneault-FourreyDavid L JolyStéphane HacquardJoëlle AmselemBrandi L CantarelReadman ChiuPedro M CoutinhoNicolas FeauMatthew FieldPascal FreyEric GelhayeJonathan GoldbergMandred G GrabherrChinnappa D KodiraAnnegret KohlerUrsula KüesErika A LindquistSusan M LucasRohit MagoEvan MauceliEmmanuelle MorinClaude MuratJasmyn L PangilinanRobert ParkMatthew PearsonHadi QuesnevilleNicolas RouhierSharadha SakthikumarAsaf A SalamovJeremy SchmutzBenjamin SellesHarris ShapiroPhilippe TanguayGerald A TuskanBernard HenrissatYves Van de PeerPierre RouzéJeffrey G EllisPeter N DoddsJacqueline E ScheinShaobin ZhongRichard C HamelinIgor V GrigorievLes J SzaboFrancis Martin et al.

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

MicroRNA expression in induced sputum of smokers and patients with chronic obstructive pulmonary disease

Geert Van PottelbergePieter MestdaghKen BrackeOlivier ThasYANNICK VAN DURMEGuy JoosJo VandesompeleGuy Brusselle

A1 Journal Article in AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Accurate long read mapping using enhanced suffix arrays

Michaël VyvermanJoachim De SchrijverWim Van CriekingePeter DawyndtVeerle Fack

Fuzzy methods on the web: a critical discussion

Steven SchockaertNataliya MakarytskaMartine De Cock

Bookchapter in 35 Years of fuzzy set theory : celebratory volume dedicated to the retirement of Etienne E. Kerre

Trust networks for recommender systems

Patricia VictorChris CornelisMartine De Cock

Trust and distrust-based recommendations for controversial reviews

Patricia VictorChris CornelisMartine De CockAnkur Teredesai

A1 Journal Article in IEEE INTELLIGENT SYSTEMS

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 FrentzenMarc Van MontaguSergei Kushnir et al.

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

Mendelian randomization analysis of case-control data using structural mean models

Jack BowdenStijn Vansteelandt

A1 Journal Article in STATISTICS IN MEDICINE

Modification of citrulline residues with 2,3-butanedione facilitates their detection by liquid chromatography/mass spectrometry

Marlies De CeuleneerVanessa De WitKatleen Van SteendamFilip Van NieuwerburghKelly TillemanDieter Deforce

A1 Journal Article in RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Make Histri: reconstructing the exchange history of bacterial and archaeal type strains

Bert VerslyppeWim De SmetBernard De BaetsPaul De VosPeter Dawyndt

A1 Journal Article in SYSTEMATIC AND APPLIED MICROBIOLOGY

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

Peakbin selection in mass spectrometry data using a consensus approach with estimation of distribution algorithms

Rubén ArmananzasYvan SaeysIñaki InzaMiguel Garcia-TorresConcha BielzaYves Van de PeerPedro Larranaga

A1 Journal Article in IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

Journey through the past: 150 million years of plant genome evolution

Sebastian ProostPedro PattynTom GeratsYves Van de Peer

A1 Journal Article in PLANT JOURNAL

compomics-utilities: an open-source Java library for computational proteomics

Harald BarsnesMarc VaudelNiklaas ColaertKenny HelsensAlbert SickmannFrode S BervenLennart Martens

A1 Journal Article in BMC BIOINFORMATICS

SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches

Marc VaudelHarald BarsnesFrode S BervenAlbert SickmannLennart Martens

A1 Journal Article in PROTEOMICS

mzML: a community standard for mass spectrometry data

Lennart MartensMatthew ChambersMarc SturmDarren KessnerFredrik LevanderJim ShofstahlWilfred H TangAndreas RoppSteffen NeumannAngel D PizarroLuisa Montecchi-PalazziNatalie TasmanMike ColemanFlorian ReisingerPuneet SoudaHenning HermjakobPierre-Alain BinzEric W Deutsch et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Massive parallel amplicon sequencing of the breast cancer genes BRCA1 and BRCA2: opportunities, challenges, and limitations

Kim De LeeneerJan HellemansJoachim De SchrijverMachteld BaetensBruce PoppeWim Van CriekingeAnne De PaepePaul CouckeKathleen Claes

A1 Journal Article in HUMAN MUTATION

A global analysis of peptide fragmentation variability

Harald BarsnesIngvar EidhammerLennart Martens

A1 Journal Article in PROTEOMICS

iTRAQ protein quantification: a quality-controlled workflow

Julia M BurkhartMarc VaudelReneP ZahediLennart MartensAlbert Sickmann

A1 Journal Article in PROTEOMICS

A stringent approach to improve the quality of nitrotyrosine peptide identifications

Bart GhesquièreKenny HelsensJoël VandekerckhoveKris Gevaert

A1 Journal Article in PROTEOMICS

A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision

Niklaas ColaertJoël VandekerckhoveKris GevaertLennart Martens

A1 Journal Article in PROTEOMICS

A reproducibility-based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methods

Sven DegroeveNiklaas ColaertJoël VandekerckhoveKris GevaertLennart Martens

A1 Journal Article in PROTEOMICS

Genome sequence of Helicobacter suis supports its role in gastric pathology

Miet VermooteTom VandekerckhoveBram FlahouFrank PasmansAnnemieke SmetDominic De GrooteWim Van CriekingeRichard DucatelleFreddy Haesebrouck

A1 Journal Article in VETERINARY RESEARCH

MicroRNA miR-885-5p targets CDK2 and MCM5, activates p53 and inhibits proliferation and survival

EA AfanasyevaPieter MestdaghCandy KumpsJo VandesompeleV EhemannJ TheissenMark ZapatkaBenedikt BrorsL SavelyevaV SagulenkoManfred SchwabFranki SpelemanFrank Westermann et al.

A1 Journal Article in CELL DEATH AND DIFFERENTIATION

Laser microdissection for the assessment of the clonal relationship between chronic lymphocytic leukemia/small lymphocytic lymphoma and proliferating B cells within lymph node pseudofollicles

Mado VandewoestyneValerie PedeKathleen LambeinMaarten DhaenensFritz OffnerMarleen PraetJan PhilippéThomas J KippsDieter Deforce

A1 Journal Article in LEUKEMIA

Optimal restoration of stochastic monotonicity with respect to cumulative label frequency loss functions

Michaël RademakerBernard De Baets

A1 Journal Article in INFORMATION SCIENCES

Modelling gene and protein regulatory networks with answer set pogramming

Timur FayruzovJeroen JanssenDirk VermeirChris CornelisMartine De Cock

A1 Journal Article in INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS

Trust and recommendations

Patricia VictorChris CornelisMartine De Cock

Bookchapter in Recommender systems handbook