Research Explorer

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Researcher

Yvan Saeys

247 Results

2021

Advances and opportunities in single-cell transcriptomics for plant research

Carolin SeyfferthJim RenemaJos WendrichThomas EekhoutRuth SeurinckNiels VandammeBernhard BlobYvan SaeysYrjo HelariuttaKenneth D. BirnbaumBert De Rybel

A1 Journal Article in ANNUAL REVIEW OF PLANT BIOLOGY

Analyzing high-dimensional cytometry data using FlowSOM

Katrien QuintelierArtuur CouckuytAnnelies EmmaneelJoachim AertsYvan SaeysSofie Van Gassen

A1 Journal Article in NATURE PROTOCOLS

Computational flow cytometry as a diagnostic tool in suspected-myelodysplastic syndromes

Carolien DuetzSofie Van GassenTheresia M. WestersMargot F. van SpronsenCosta BachasYvan SaeysArjan A. van de Loosdrecht

A1 Journal Article in CYTOMETRY PART A

Data processing workflow for large-scale immune monitoring studies by mass cytometry

Paulina RybakowskaSofie Van GassenKatrien QuintelierYvan SaeysMarta E. Alarcón-RiquelmeConcepción Marañón

A1 Journal Article in COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL

Fibrotic enzymes modulate wound-induced skin tumorigenesis

Lisette Van HoveKim LecomteJana RoelsNiels VandammeHanna-Kaisa VikkulaIsabelle HoorensKatia OngenaeTino HochepiedGiacomo DonatiYvan SaeysSven R. QuistFiona M. WattGeert van LooEsther Hoste

A1 Journal Article in EMBO REPORTS

Graph approximations to geodesics on metric graphs

Robin VandaeleYvan SaeysTijl De Bie

ILC3s control splenic cDC homeostasis via lymphotoxin signaling

Matthias VanderkerkenAntonio Pires da Silva BaptistaMarco De GiovanniSatoshi FukuyamaRobin BrowaeysCharlotte ScottPaula S. NorrisGerard EberlJames P. Di SantoEric VivierYvan SaeysHamida HammadJason G. CysterCarl F. WareAlexei V. TumanovCarl De TrezBart Lambrecht

A1 Journal Article in JOURNAL OF EXPERIMENTAL MEDICINE

Immune monitoring in melanoma and urothelial cancer patients treated with anti-PD-1 immunotherapy and SBRT discloses tumor specific immune signatures

Annabel MeiresonSimon TavernierSofie Van GassenNora SundahlAnnelies DemeyerMathieu SpaasVibeke KruseLiesbeth FerdinandeJo Van DorpeBenjamin HennartDelphine AllorgeFilomeen HaerynckKarel DecaesteckerSylvie RotteyYvan SaeysPiet OstLieve Brochez

A1 Journal Article in CANCERS

Maize specialized metabolome networks reveal organ-preferential mixed glycosides

Sandrien DesmetYvan SaeysKevin VerstaenRebecca DauweHoon KimClaudiu NiculaesAtsushi FukushimaGeert GoeminneRuben VanholmeJohn RalphWout BoerjanKris Morreel

A1 Journal Article in COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL

Monocyte-driven atypical cytokine storm and aberrant neutrophil activation as key mediators of COVID-19 disease severity

L. VanderbekeP. Van MolY. Van HerckF. De SmetS. Humblet-BaronK. MartinodA. AntoranzI. ArijsB. BoeckxF. M. BosisioM. CasaerD. DauweW. De WeverC. DoomsE. DreesenAnnelies EmmaneelJ. FiltjensM. GouwyJ. GunstG. HermansS. JansenK. LagrouA. ListonN. LorentP. MeerssemanT. MercierJ. NeytsJ. OdentD. PanovskaP. A. PenttilaE. PolletP. ProostJ. QianKatrien QuintelierJ. RaesS. RexYvan SaeysJ. SprootenS. TejparD. TestelmansK. ThevissenT. Van BuytenJ. VandenhauteSofie Van GassenL. C. Velasquez PereiraR. VosB. WeynandA. WilmerJ. YserbytA. D. GargP. MatthysC. WoutersD. LambrechtsE. WautersJ. Wauters

A1 Journal Article in NATURE COMMUNICATIONS

Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization

Ana Rita Pombo AntunesIsabelle ScheyltjensFrancesca LodiJulie MessiaenAsier AntoranzJohnny DuerinckDaliya KanchevaLiesbet MartensKaren De VlaminckHannah Van HoveSigne Schmidt Kjolner HansenFrancesca Maria BosisioKoen Van der BorghtSteven De VleeschouwerRaf SciotLuc BouwensMichiel VerfaillieNiels VandammeRoosmarijn VandenbrouckeOlivier De WeverYvan SaeysMartin GuilliamsConny GysemansBart NeynsFrederik De SmetDiether LambrechtsJo A. Van GinderachterKiavash Movahedi

A1 Journal Article in NATURE NEUROSCIENCE

Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells

Robrecht CannoodtWouter SaelensLouise DeconinckYvan Saeys

A1 Journal Article in NATURE COMMUNICATIONS

Stabilization of human whole blood samples for multicenter and retrospective immunophenotyping studies

Paulina RybakowskaCatalina BurbanoSofie Van GassenNieves VarelaRocio Aguilar-QuesadaYvan SaeysMarta E. Alarcon-RiquelmeConcepcion Maranon

A1 Journal Article in CYTOMETRY PART A

Stable topological signatures for metric trees through graph approximations

Robin VandaeleBastian RieckYvan SaeysTijl De Bie

A1 Journal Article in PATTERN RECOGNITION LETTERS

The RNA Atlas expands the catalog of human non-coding RNAs

Lucia LorenziHua-Sheng ChiuFrancisco Avila CobosStephen GrossPieter-Jan VoldersRobrecht CannoodtJustine NuytensKatrien VanderheydenJasper AnckaertSteve LefeverAidan TayEric de BonyWim TrypsteenFien GysensMarieke VrommanTine GoovaertsThomas Birkballe HansenScott KuerstenNele NijsTom TaghonKarim VermaelenKen BrackeYvan SaeysTim De MeyerNandan P. DeshpandeGovardhan AnandeTing-Wen ChenMarc R. WilkinsAshwin UnnikrishnanKatleen De PreterJørgen KjemsJan KosterGary P. SchrothJo VandesompelePavel SumazinPieter Mestdagh

A1 Journal Article in NATURE BIOTECHNOLOGY

2020

A cell atlas of human thymic development defines T cell repertoire formation

Jong-Eun ParkRachel A. BottingCecilia Domínguez CondeDorin-Mirel PopescuMarieke LavaertDaniel J. KunzIssac GohEmily StephensonRoberta RagazziniElizabeth TuckAnna Wilbrey-ClarkKenny RobertsVeronika R. KedlianJohn R. FerdinandXiaoling HeSimone WebbDaniel MaunderNiels VandammeKrishnaa T. MahbubaniKrzysztof PolanskiLira MamanovaLiam BoltDavid CrosslandFabrizio de RitaAndrew FullerAndrew FilbyGary ReynoldsDavid DixonKourosh Saeb-ParsySteven LisgoDeborah HendersonRoser Vento-TormoOmer A. BayraktarRoger A. BarkerKerstin B. MeyerYvan SaeysPaola BonfantiSam BehjatiMenna R. ClatworthyTom TaghonMuzlifah HaniffaSarah A. Teichmann

A1 Journal Article in SCIENCE

A scalable SCENIC workflow for single-cell gene regulatory network analysis

Bram van de SandeChristopher FlerinKristofer DavieMaxime De WaegeneerGert HulselmansSara AibarRuth SeurinckWouter SaelensRobrecht CannoodtQuentin RouchonToni VerbeirenDries De MaeyerJoke ReumersYvan SaeysStein Aerts

A1 Journal Article in NATURE PROTOCOLS

An interactive ImageJ plugin for semi-automated image denoising in electron microscopy

Joris RoelsFrank VernaillenAnna KremerAmanda GonçalvesJan AeltermanHiep LuongBart GoossensWilfried PhilipsSaskia LippensYvan Saeys

A1 Journal Article in NATURE COMMUNICATIONS

Asynchronous processing for latent fingerprint identification on heterogeneous CPU-GPU systems

Andres J. Sanchez-FernandezLuis F. RomeroDaniel PeraltaMiguel Angel Medina-PerezYvan SaeysFrancisco HerreraSiham Tabik

A1 Journal Article in IEEE ACCESS

Automated learning of biologically relevant features from primary sequence using convolutional neural networks

Jasper ZuallaertWesley De NeveNico CallewaertYvan Saeys

Calibrated multi-probabilistic prediction as a defense against adversarial attacks

Jonathan PeckBart GoossensYvan Saeys

Classification of human white blood cells using machine learning for stain-free imaging flow cytometry

Maxim LippeveldCarly KnillEmma LadlowAndrew FullerLouise J MichaelisYvan SaeysAndrew FilbyDaniel Peralta

A1 Journal Article in CYTOMETRY PART A

CytoNorm : a normalization algorithm for cytometry data

Sofie Van GassenBrice GaudilliereMartin S AngstYvan SaeysNima Aghaeepour

A1 Journal Article in CYTOMETRY PART A

Detecting adversarial manipulation using inductive Venn-ABERS predictors

Jonathan PeckBart GoossensYvan Saeys

A1 Journal Article in NEUROCOMPUTING

Inflammatory type 2 cDCs acquire features of cDC1s and macrophages to orchestrate immunity to respiratory virus infection

Cedric BosteelsKatrijn NeytManon VanheerswynghelsMary van HeldenDorine SichienNincy DebeufSofie De PrijckVictor BosteelsNiels VandammeLiesbet MartensYvan SaeysEls LouagieManon LesageDavid L. WilliamsShiau-Choot TangJohannes U. MayerFranca RoncheseCharlotte ScottHamida HammadMartin GuilliamsBart Lambrecht

A1 Journal Article in IMMUNITY

Integrated scRNA-seq identifies human postnatal thymus seeding progenitors and regulatory dynamics of differentiating immature thymocytes

Marieke LavaertKai Ling LiangNiels VandammeJong-Eun ParkJuliette RoelsMonica S. KowalczykBo LiOrr AshenbergMarcin TabakaDanielle DionneTimothy L. TickleMichal SlyperOrit Rozenblatt-RosenBart VandekerckhoveGeorges LeclercqAviv RegevPieter Van VlierbergheMartin GuilliamsSarah A. TeichmannYvan SaeysTom Taghon

A1 Journal Article in IMMUNITY

Mining topological structure in graphs through forest representations

Robin VandaeleYvan SaeysTijl De Bie

A1 Journal Article in JOURNAL OF MACHINE LEARNING RESEARCH

NicheNet : modeling intercellular communication by linking ligands to target genes

Robin BrowaeysWouter SaelensYvan Saeys

A1 Journal Article in NATURE METHODS

OTULIN prevents liver inflammation and hepatocellular carcinoma by inhibiting FADD- and RIPK1 kinase-mediated hepatocyte apoptosis

Lien VerboomArne MartensDario PriemEsther HosteMozes SzeHanna-Kaisa VikkulaLisette Van HoveSofie VoetJana RoelsJonathan MaelfaitLaura BongiovanniAlain de BruinCharlotte ScottYvan SaeysManolis PasparakisMathieu BertrandGeert van Loo

A1 Journal Article in CELL REPORTS

Osteopontin expression identifies a subset of recruited macrophages distinct from Kupffer cells in the fatty liver

Anneleen RemmerieLiesbet MartensTinne ThonéAngela CastoldiRuth SeurinckBenjamin PavieJoris RoelsBavo VannesteSofie De PrijckMathias VanhockerhoutMushida Binte Abdul LatibLindsey DevisscherAnne HoorensJohnny BonnardelNiels VandammeAnna KremerPeter BorghgraefHans Van VlierbergheSaskia LippensEdward PearceYvan SaeysCharlotte Scott

A1 Journal Article in IMMUNITY

Profiling peripheral nerve macrophages reveals two macrophage subsets with distinct localization, transcriptome and response to injury

Elke YdensLukas AmannBob AsselberghCharlotte ScottLiesbet MartensDorine SichienOmar MossadThomas BlankSofie De PrijckDonovan LowTakahiro MasudaYvan SaeysVincent TimmermanRalf StummFlorent GinhouxMarco PrinzSophie JanssensMartin Guilliams

A1 Journal Article in NATURE NEUROSCIENCE

Regional image perturbation reduces Lp norms of adversarial examples while maintaining model-to-model transferability

Utku ÖzbulakJonathan PeckWesley De NeveBart GoossensYvan SaeysArnout Van Messem

Robust unsupervised dimensionality reduction based on feature clustering for single-cell imaging data

Daniel PeraltaYvan Saeys

A1 Journal Article in APPLIED SOFT COMPUTING

Special issue on machine learning for single cell cata

Yvan SaeysGreg Finak

Editorial material

Structure learning to unravel mechanisms of the immune system

Helena TodorovYvan SaeysJacqueline Marvel

TinGa : fast and flexible trajectory inference with Growing Neural Gas

Helena TodorovRobrecht CannoodtWouter SaelensYvan Saeys

A1 Journal Article in BIOINFORMATICS

Topological inference in graphs and images

Robin VandaeleTijl De BieYvan Saeys

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

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

A1 Journal Article in NATURE COMMUNICATIONS

Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions

Jos WendrichBaojun YangNiels VandammeKevin VerstaenWouter SmetCelien Van de VeldeMax MinneBrecht WybouwEliana MorHelena ArentsJonah NolfJulie Van DuyseGert Van IsterdaelSteven MaereYvan SaeysBert De Rybel

A1 Journal Article in SCIENCE

2019

A comparison of single-cell trajectory inference methods

Wouter SaelensRobrecht CannoodtHelena TodorovYvan Saeys

A1 Journal Article in NATURE BIOTECHNOLOGY

A computational pipeline for the diagnosis of CVID patients

Annelies EmmaneelDelfien BogaertSofie Van GassenSimon TavernierMelissa DullaersFilomeen HaerynckYvan Saeys

A1 Journal Article in FRONTIERS IN IMMUNOLOGY

A human immune dysregulation syndrome characterized by severe hyperinflammation with a homozygous nonsense Roquin-1 mutation

Simon TavernierV AthanasopoulosPatrick VerlooG BehrensJens StaalDelfien BogaertLeslie NaesensMarieke De BruyneSofie Van GassenEef ParthoensJ EllyardJ CappelloLX MorrisHanne Van GorpGert Van IsterdaelYvan SaeysMohamed LamkanfiPetra SchelstraeteJo DehoorneMaria Bordon Cueto De BraemRudy Van CosterBart LambrechtBjörn MentenRudi BeyaertCG VinuesaV HeissmeyerMelissa DullaersFilomeen Haerynck

A1 Journal Article in NATURE COMMUNICATIONS

A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment

Hannah Van HoveLiesbet MartensIsabelle ScheyltjensKaren De VlaminckAna Rita Pombo AntunesSofie De PrijckNiels VandammeSebastiaan De SchepperGert Van IsterdaelCharlotte ScottJeroen AertsGeert BerxGuy E. BoeckxstaeneRoosmarijn VandenbrouckeLars VereeckeDiederik MoecharsMartin GuilliamsJo A. Van GinderachterYvan SaeysKiavash Movahedi

A1 Journal Article in NATURE NEUROSCIENCE

Computational approaches for high-throughput single-cell data analysis

Helena TodorovYvan Saeys

A1 Journal Article in FEBS JOURNAL

Detecting adversarial examples with inductive Venn-ABERS predictors

Jonathan PeckBart GoossensYvan Saeys

Developing and benchmarking methods for analysing transcriptomics data

Wouter SaelensYvan SaeysBart Lambrecht

Distillation of Deep Reinforcement Learning Models using Fuzzy Inference Systems

Arne GevaertJonathan PeckYvan Saeys

Distributed, numerically stable distance and covariance computation with MPI for extremely large datasets

Daniel PeraltaYvan Saeys

Domain adaptive segmentation in volume electron microscopy imaging

Joris RoelsJulian HenniesYvan SaeysWilfried PhilipsAnna Kreshuk

Dynbenchmark : accuracy, scalability, robustness and usability of single-cell trajectory inference methods

Robrecht CannoodtWouter SaelensHelena TodorovYvan Saeys

Epithelial HMGB1 delays skin wound healing and drives tumor initiation by priming neutrophils for NET formation

Esther HosteChristian MaueröderLisette Van HoveLeen CatrysseHanna-Kaisa VikkulaMozes SzeBastiaan MaesDyah KarjosukarsoLiesbet MartensAmanda GonçalvesEef ParthoensRia RoelandtWim DeclercqIgnacia FuentesFrancis PalissonSergio GonzalezJulio C Salas-AlanisLouis BoonPeter HuebenerKlaas Willem MulderKodi RavichandranYvan SaeysRobert Felix SchwabeGeert van Loo

A1 Journal Article in CELL REPORTS

Essential guidelines for computational method benchmarking

Lukas M WeberWouter SaelensRobrecht CannoodtCharlotte SonesonAlexander HapfelmeierPaul P GardnerAnne-Laure BoulesteixYvan SaeysMark D Robinson

A1 Journal Article in GENOME BIOLOGY

Geautomatiseerde segmentatie van 3D-elektronenmicroscopiebeelden

Joris RoelsWilfried PhilipsYvan Saeys

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

Andrea CossarizzaHyun-Dong ChangAndreas RadbruchAndreas AcsDieter AdamSabine Adam-KlagesWilliam W AgaceNima AghaeepourMuebeccel AkdisMatthieu AllezLarissa Nogueira AlmeidaGiorgia AlvisiGraham AndersonImmanuel AndraeFrancesco AnnunziatoAchille AnselmoPetra BacherCosima T BaldariSudipto BariVincenzo BarnabaJoana Barros-MartinsLuca BattistiniWolfgang BauerSabine BaumgartNicole BaumgarthDirk BaumjohannBianka BayingMary BebawyBurkhard BecherWolfgang BeiskerVladimir BenesRudi BeyaertAlfonso BlancoDominic A BoardmanChristian BogdanJessica G BorgerGiovanna BorsellinoPhilip E BoulaisJolene A BradfordDirk BrennerRyan R BrinkmanAnna ES BrooksDirk H BuschMartin BuescherTimothy P BushnellFederica CalzettiGarth CameronIlenia CammarataXuetao CaoSusanna L CardellStefano CasolaMarco A CassatellaAndrea CavaniAntonio CeladaLucienne ChatenoudPratip K ChattopadhyaySue ChowEleni ChristakouLuka Cicin-SainMario ClericiFederico S ColomboLaura CookAnne CookeAndrea M CooperAlexandra J CorbettAntonio CosmaLorenzo CosmiPierre G CoulieAna CumanoLjiljana CvetkovicVan Duc DangChantip Dang-HeineMartin S DaveyDerek DaviesSara De BiasiGenny Del ZottoGelo Victoriano Dela CruzMichael DelacherSilvia Della BellaPaolo DellabonaGuennur DenizMark DessingJames P Di SantoAndreas DiefenbachFrancesco DieliAndreas DolfThomas DoernerRegine J DressDiana DudziakMichael DustinCharles-Antoine DutertreFriederike EbnerSidonia BG EckleMatthias EdingerPascale EedeGoetz RA EhrhardtMarcus EichPablo EngelBritta EngelhardtAnna ErdeiCharlotte EsserBart EvertsMaximilien EvrardChristine S FalkTodd A FehnigerMar Felipo-BenaventHelen FerryMarkus FeuererAndrew FilbyKata FilkorSimon FillatreauMarie FolloIrmgard FoersterJohn FosterGemma A FouldsBritta FrehsePaul S FrenetteStefan FrischbutterWolfgang FritzscheDavid W GalbraithAnastasia GangaevNatalio GarbiBrice GaudilliereRicardo T GazzinelliJens GeginatWilhelm GernerNicholas A GherardinKamran GhoreschiLara GibelliniFlorent GinhouxKeisuke GodaDale I GodfreyChristoph GoettlingerJose M Gonzalez-NavajasCarl S GoodyearAndrea GoriJane L GroganDaryl GrummittAndreas GruetzkauClaudia HaftmannJonas HahnHamida HammadGuenter HaemmerlingLeo HansmannGoran HanssonChristopher M HarpurSusanne HartmannAndrea HauserAnja E HauserDavid L HavilandDavid HedleyDaniela C HernandezGuadalupe HerreraMartin HerrmannChristoph HessThomas HoeferPetra HoffmannKristin HogquistTristan HollandThomas HolltRikard HolmdahlPleun HombrinkJessica P HoustonBimba F HoyerBo HuangFang-Ping HuangJohanna E HuberJochen HuehnMichael HundemerChristopher A HunterWilliam YK HwangAnna IannoneFlorian IngelfingerSabine M IvisonHans-Martin JaeckPeter K JaniBeatriz JavegaStipan JonjicToralf KaiserTomas KalinaThomas KamradtStefan HE KaufmannBaerbel KellerSteven LC KetelaarsAhad KhalilnezhadSrijit KhanJan KisielowPaul KlenermanJasmin KnopfHui-Fern KoayKatja KobowJay K KollsWan Ting KongManfred KopfThomas KornKatharina KriegsmannHendy KristyantoThomas KroneisAndreas KruegerJenny KuehneChristian KukatDesiree KunkelHeike Kunze-SchumacherTomohiro KurosakiChristian KurtsPia KvistborgImmanuel KwokJonathan LandryOlivier LantzPaola LanutiFrancesca LaRosaAgnes LehuenSalome LeibundGut-LandmannMichael D LeipoldLeslie YT LeungMegan K LevingsAndreia C LinoFrancesco LiottaVirginia LitwinYanling LiuHans-Gustaf LjunggrenMichael LohoffGiovanna LombardiLilly LopezMiguel Lopez-BotetAmy E Lovett-RackeErik LubbertsHerve LucheBurkhard LudewigEnrico LugliSebastian LunemannHolden T MaeckerLaura MaggiOrla MaguireFlorian MairKerstin H MairAlberto MantovaniRudolf A ManzAaron J MarshallAlicia Martinez-RomeroGloria MartrusIvana MarventanoWlodzimierz MaslinskiGiuseppe MatareseAnna Vittoria MattioliChristian MaueröderAlessio MazzoniJames McCluskeyMairi McGrathHelen M McGuireIain B McInnesHenrik E MeiFritz MelchersSusanne MelzerDirk MielenzStephen D MillerKingston H G. MillsHans MindermanJenny MjosbergJonni MooreBarry MoranLorenzo MorettaTim R MosmannSusann MuellerGabriele MulthoffLuis Enrique MunozChristian MunzToshinori NakayamaMilena NasiKatrin NeumannLai Guan NgAntonia NiedobitekSussan NoursharghGabriel NunezJose-Enrique O'ConnorAaron OchelAnna OjaDiana OrdonezAlberto OrfaoEva Orlowski-OliverWenjun OuyangAnnette OxeniusRaghavendra PalankarIsabel PanseKovit PattanapanyasatMalte PaulsenDinko PavlinicLivius PenterPaert PetersonChristian PethJordi PetrizFederica PianconeWinfried F PicklSilvia PiconeseMarcello PintiA Graham PockleyMalgorzata Justyna PodolskaZhiyong PoonKatharina PrachtImmo PrinzCarlo EM PucilloSally A QuataertLinda QuatriniKylie M QuinnHelena RadbruchTim RDJ RadstakeSusann RahmigHans-Peter RahnBartek RajwaGevitha RavichandranYotam RazJonathan A RebhahnDiether RecktenwaldDorothea ReimerCaetano Reis e SousaEster BM RemmerswaalLisa RichterLaura G RicoAndy RiddellAja M RiegerJ Paul RobinsonChiara RomagnaniAnna RubartelliJuergen RulandArmin SaalmuellerYvan SaeysTakashi SaitoShimon SakaguchiFrancisco Sala-de-OyangurenYvonne SamstagSharon SandersonInga SandrockAngela SantoniRamon Bellmas SanzMarina SaresellaCatherine Sautes-FridmanBirgit SawitzkiLinda SchadtAlexander ScheffoldHans U SchererMatthias SchiemannFrank A SchildbergEsther SchimiskyAndreas SchlitzerJosephine SchlosserStephan SchmidSteffen SchmittKilian SchoberDaniel SchraivogelWolfgang SchuhThomas SchuelerReiner SchulteAxel Ronald SchulzSebastian R. SchulzCristiano ScottaDaniel Scott-AlgaraDavid P SesterT Vincent ShankeyBruno Silva-SantosAnna Katharina SimonKatarzyna M SitnikSilvano SozzaniDaniel E SpeiserJosef SpidlenAnders StahlbergAlan M StallNatalie StanleyRegina StarkChristina StehleTobit SteinmetzHannes StockingerYousuke TakahamaKiyoshi TakedaLeonard TanAttila TarnokGisa TiegsGergely ToldiJulia TornackElisabetta TraggiaiMohamed TrebakTimothy IM TreeJoe TrotterJohn TrowsdaleMaria TsoumakidouHenning UlrichSophia UrbanczykWillem van de VeenMaries van den BroekEdwin van der PolSofie Van GassenGert Van IsterdaelRene AW van LierMarc VeldhoenSalvador Vento-AsturiasPaulo VieiraDavid VoehringerHans-Dieter VolkAnouk von BorstelKonrad von VolkmannAri WaismanRachael V WalkerPaul K WallaceSa A WangXin M WangMichael D WardKirsten A Ward-HartstongeKlaus WarnatzGary WarnesSarah WarthClaudia WaskowJames V WatsonCarsten WatzlLeonie WegenerThomas WeisenburgerAnnika WiedemannJuergen WienandsAnneke WilharmRobert John WilkinsonGerald WillimskyJames B WingRieke WinkelmannThomas H WinklerOliver F WirzAlicia WongPeter WurstJennie HM YangJuhao YangMaria YazdanbakhshLiping YuAlice YueHanlin ZhangYi ZhaoSusanne Maria ZieglerChristina ZielinskiJakob ZimmermannArturo Zychlinsky

A1 Journal Article in EUROPEAN JOURNAL OF IMMUNOLOGY

Investigating the biological relevance in trained embedding representations of protein sequences

Jasper ZuallaertXiaoyong PanYvan SaeysXi WangWesley De Neve

Local topological data analysis to uncover the global structure of data approaching graph-structured topologies

Robin VandaeleTijl De BieYvan Saeys

Mining the enriched subgraphs for specific vertices in a biological graph

Pieter MeysmanYvan SaeysEhsan SabaghianWout BittremieuxYves Van de PeerBart GoethalsKris Laukens

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

Modelling single-cell dynamics with trajectories and gene regulatory networks

Robrecht CannoodtYvan SaeysKatleen De Preter

Network inference from single-cell transcriptomic data

Helena TodorovRobrecht CannoodtWouter SaelensYvan Saeys

Bookchapter in Gene regulatory networks : methods and protocols

Nlrp3 inflammasome activation and Gasdermin D-driven pyroptosis are immunopathogenic upon gastrointestinal norovirus infection

Hanne DuboisFrederic SorgeloosSoroush T. SarvestaniLiesbet MartensYvan SaeysJason M. MackenzieMohamed LamkanfiGeert van LooIan GoodfellowAndy Wullaert

A1 Journal Article in PLOS PATHOGENS

RORγt inhibition selectively targets IL-17 producing iNKT and γδ-T cells enriched in Spondyloarthritis patients

Koen VenkenPeggy JacquesCéline MortierMark E. LabadiaTine DecruyJulie CoudenysKathleen HoytAnita L. WayneRobert HughesMichael TurnerSofie Van GassenLiesbet MartensDustin SmithChristian HarckenJoseph WahleChao-Ting WangEveline VerheugenNadia SchryversGaëlle VarkasHeleen CypersRuth WittoekYves PietteLieve GyselbrechtSerge Van CalenberghFilip Van den BoschYvan SaeysGerald NaboznyDirk Elewaut

A1 Journal Article in NATURE COMMUNICATIONS

Single-cell RNA sequencing of the T helper cell response to house dust mites defines a distinct gene expression signature in airway Th2 cells

Christopher Andrew TibbittJulian Mario StarkLiesbet MartensJunjie MaJeff Eron MoldKim DeswarteGanna OliynykXiaogang FengBart LambrechtPieter De BleserSusanne NylenHamida HammadMarie Arsenian HenrikssonYvan SaeysJonathan Marie Coquet

A1 Journal Article in IMMUNITY

Stellate cells, hepatocytes, and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche

Johnny BonnardelWouter T'JonckDjoere GaublommeRobin BrowaeysCharlotte ScottLiesbet MartensBavo VannesteSofie De PrijckSergei A NedospasovAnna KremerEvelien Van HammePeter BorghgraefWendy ToussaintPieter De BleserInge MannaertsAlain BeschinLeo A van GrunsvenBart LambrechtTom TaghonSaskia LippensDirk ElewautYvan SaeysMartin Guilliams

A1 Journal Article in IMMUNITY

The boundary coefficient : a vertex measure for visualizing and finding structure in weighted graphs

Robin VandaeleYvan SaeysTijl De Bie

Unravelling gene functions in Arabidopsis thaliana by means of network biology and machine learning

Ehsan SabaghianYves Van de PeerYvan Saeys

Weight selection strategies for ordered weighted average based fuzzy rough sets

Sarah VluymansNeil Mac ParthalainChris CornelisYvan Saeys

A1 Journal Article in INFORMATION SCIENCES

2018

A comprehensive evaluation of module detection methods for gene expression data

Wouter SaelensRobrecht CannoodtYvan Saeys

A1 Journal Article in NATURE COMMUNICATIONS

An overview of state-of-the-art image restoration in electron microscopy

Joris RoelsJan AeltermanHiep LuongSaskia LippensAleksandra PizuricaYvan SaeysWilfried Philips

A1 Journal Article in JOURNAL OF MICROSCOPY

Ancient origin of the CARD-coiled coil/Bcl10/MALT1-like paracaspase signaling complex indicates unknown critical functions

Jens StaalYasmine DriegeMira HaegmanAlice BorghiPaco HulpiauLaurens LievensIsmail Sahin GülSrividhya Sundararaman IyerAmanda GonçalvesIneke DhondtJorge H PinzonBart BraeckmanUlrich TechnauYvan SaeysFrans Van RoyRudi Beyaert

A1 Journal Article in FRONTIERS IN IMMUNOLOGY

Dealing with imbalanced and weakly labelled data in machine learning using fuzzy and rough set methods

Sarah VluymansYvan SaeysChris Cornelis

Dynamic affinity-based classification of multi-class imbalanced data with one-versus-one decomposition : a fuzzy rough set approach

Sarah VluymansAlberto FernándezYvan SaeysChris CornelisFrancisco Herrera

A1 Journal Article in KNOWLEDGE AND INFORMATION SYSTEMS

GC content of Early Metazoan genes and its impact on gene expression levels in mammalian cell lines

Ismail Sahin GülJens StaalPaco HulpiauEvi De KeuckelaereKai KammTom DerooEllen SandersKatrien StaesYasmine DriegeYvan SaeysRudi BeyaertUlrich TechnauBernd SchierwaterFrans Van Roy

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

Identifying and classifying protein coding gene polymorphisms between laboratory mouse strains and investigating glucocorticoid actions in sepsis models

Steven TimmermansClaude LibertYvan Saeys

IncGraph : incremental graphlet counting for topology optimisation

Robrecht CannoodtJoeri RuyssinckJana RamonKatleen De PreterYvan Saeys

A1 Journal Article in PLOS ONE

Mechanical strain determines the site-specific localization of inflammation and tissue damage in arthritis

Isabelle CambréDjoere GaublommeArne BurssensPeggy JacquesNadia SchryversAmélie De MuynckLeander MeurisStijn LambrechtShea CarterPieter De BleserYvan SaeysLuc Van HoorebekeGeorge KolliasMatthias MackPaul SimoensRik LoriesNico CallewaertGeorg SchettDirk Elewaut

A1 Journal Article in NATURE COMMUNICATIONS

Multi-label classification using a fuzzy rough neighborhood consensus

Sarah VluymansChris CornelisFrancisco HerreraYvan Saeys

A1 Journal Article in INFORMATION SCIENCES

Myeloid cell heterogeneity in cancer: not a single cell alike

Mate KissSofie Van GassenKiavash MovahediYvan SaeysDamya Laoui

A1 Journal Article in CELLULAR IMMUNOLOGY

Myocarditis elicits dendritic cell and monocyte infiltration in the heart and self-antigen presentation by conventional type 2 dendritic cells

Katrien Van Der BorghtCharlotte ScottLiesbet MartensDorine SichienGert Van IsterdaelVeronika NindlYvan SaeysLouis BoonBurkhard LudewigThierry GillebertBart Lambrecht

A1 Journal Article in FRONTIERS IN IMMUNOLOGY

Nanos genes and their role in development and beyond

Evi De KeuckelaerePaco HulpiauYvan SaeysGeert BerxFrans Van Roy

A1 Journal Article in CELLULAR AND MOLECULAR LIFE SCIENCES

On the use of convolutional neural networks for robust classification of multiple fingerprint captures

Daniel PeraltaIsaac TrigueroSalvador GarcíaYvan SaeysJose M BenitezFrancisco Herrera

A1 Journal Article in INTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS

Response to Orlova et al. 'Science not art: statistically sound methods for identifying subsets in multi-dimensional flow and mass cytometry data sets'

Yvan SaeysSofie Van GassenBart Lambrecht

A1 Journal Article in NATURE REVIEWS IMMUNOLOGY

SpliceRover : interpretable convolutional neural networks for improved splice site prediction

Jasper ZuallaertFréderic GodinMi Jung KimArne SoeteYvan SaeysWesley De Neve

A1 Journal Article in BIOINFORMATICS

Stabilization of cytokine mRNAs in iNKT cells requires the serine-threonine kinase IRE1alpha

Srinath GovindarajanDjoere GaublommeRenée Van der CruyssenEveline VerheugenSofie Van GassenYvan SaeysSimon TavernierTakao IwawakiYehudi BlochSavvas SavvidesBart LambrechtSophie JanssensDirk ElewautMichael Drennan

A1 Journal Article in NATURE COMMUNICATIONS

TISRover : ConvNets learn biologically relevant features for effective translation initiation site prediction

Jasper ZuallaertMijung KimArne SoeteYvan SaeysWesley De Neve

A1 Journal Article in INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS

TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia

Karen VerboomWouter Van LoockeJo VandesompeleNiels VandammeGeert BerxLiesbet MartensYvan SaeysPieter Van VlierbergheFranki SpelemanKaat Durinck

The TLX1 oncogene modules the enhancer RNA landscape in T-ALL

Karen VerboomWouter Van LoockeJo VandesompeleNiels VandammeGeert BerxYvan SaeysLiesbet MartensPieter Van VlierbergheFranki SpelemanKaat Durinck

The transcription factor ZEB2 is required to maintain the tissue-specific identities of macrophages

Charlotte ScottWouter T'JonckLiesbet MartensHelena TodorovDorine SichienBieke SoenJohnny BonnardelSofie De PrijckNiels VandammeRobrecht CannoodtWouter SaelensBavo VannesteWendy ToussaintPieter De BleserNozomi TakahashiPeter VandenabeeleSandrine HenriClare PridansDavid A HumeBart LambrechtPatrick De BaetselierSimon WF MillingJo A Van GinderachterBernard MalissenGeert BerxAlain BeschinYvan SaeysMartin Guilliams

A1 Journal Article in IMMUNITY

2017

A murine intestinal intraepithelial NKp46-negative innate lymphoid cell population characterized by group 1 properties

Aline Van AckerKonrad GronkeAindrila BiswasLiesbet MartensYvan SaeysJessica FiltjensSylvie TaveirneEls Van AmmelTessa KerrePatrick MatthysTom TaghonBart VandekerckhoveJean PlumIldiko Rita DunayAndreas DiefenbachGeorges Leclercq

A1 Journal Article in CELL REPORTS

Computational analysis of multimorbidity between asthma, eczema and rhinitis

Daniel AguilarMariona PinartGerard H KoppelmanYvan SaeysMartijn C NawijnDirkje S PostmaMübeccel AkdisCharles AuffrayStéphane BallereauMarta BenetJudith García-AymerichJuan Ramon GonzálezStefano GuerraThomas KeilManolis KogevinasBart LambrechtNathanael LemonnierErik MelenJordi SunyerRudolf ValentaSergi ValverdeMagnus WickmanJean BousquetBaldo OlivaJosep M Antó

A1 Journal Article in PLOS ONE

ConTra v3 : a tool to identify transcription factor binding sites across species, update 2017

Lukasz KreftArne SoetePaco HulpiauAlexander BotzkiYvan SaeysPieter De Bleser

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Convolutional neural network pruning to accelerate membrane segmentation in electron microscopy

Joris RoelsJonas De VylderJan AeltermanYvan SaeysWilfried Philips

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

Development of machine learning techniques for flow cytometry data

Sofie Van GassenTom DhaeneYvan Saeys

Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay (vol 6, 36111, 2016)

Wim TrypsteenPejman MohammadiClarissa Van HeckePieter MestdaghSteve LefeverYvan SaeysPieter De BleserJo VandesompeleAngela CiuffiLinos VandekerckhoveWard De Spiegelaere

Distributed incremental fingerprint identification with reduced database penetration rate using a hierarchical classification based on feature fusion and selection

Daniel PeraltaIsaac TrigueroSalvador GarcíaYvan SaeysJose M BenitezFrancisco Herrera

A1 Journal Article in KNOWLEDGE-BASED SYSTEMS

Evolution and diversity of cadherins and catenins

Ismail Sahin GülPaco HulpiauYvan SaeysFrans Van Roy

A1 Journal Article in EXPERIMENTAL CELL RESEARCH

Interpretable convolutional neural networks for effective translation initiation site prediction

Jasper ZuallaertMi Jung KimYvan SaeysWesley De Neve

Lower bounds on the robustness to adversarial perturbations

Jonathan PeckJoris RoelsBart GoossensYvan Saeys

Machine learning for biological network inference

Joeri RuyssinckTom DhaeneYvan Saeys

Mechanisms of the Development of Allergy (MeDALL) : introducing novel concepts in allergy phenotypes

Josep M AntoJean BousquetMubeccel AkdisCharles AuffrayThomas KeilIsabelle MomasDirkje S PostmaRudolf ValentaMagnus WickmanAnne Cambon-ThomsenTari HaahtelaBart LambrechtKarin C Lodrup CarlsenGerard H KoppelmanJordi SunyerTorsten ZuberbierIsabelle Annesi-MaesanoAlbert ArnoCarsten Bindslev-JensenGiuseppe De CarloFrancesco ForastiereJoachim HeinrichMarek L KowalskiDieter MaierErik MelénHenriette A SmitMarie StandlJohn WrightAnna AsarnojMarta BenetNatalia BallardiniJudith Garcia-AymerichUlrike GehringStefano GuerraCynthia HohmannInger KullChristian LupinekMariona PinartIngebjorg SkrindoMarit WestmanDelphine SmaggheCezmi AkdisNiklas AnderssonClaus BachertStephane BallereauFerran BallesterXavier BasaganaAnna BedbrookAnna BergstromAndrea von BergBert BrunekreefEmilie BurteKai-Hakon CarlsenLeda ChatziJonathan M CoquetMirela CurinPascal DemolyEsben EllerMaria Pia FantiniLeena von HertzenVergard HovlandBenedicte JacqueminJocelyne JustTheresa KellerRenata KissManolis KogevinasSibylle KoletzkoSusanne LauIrina LehmannNicolas LemonnierMika MäkeläJordi MestresPeter MowinckelRachel NadifMartijn C NawijnJohan PelletIsabelle PinDaniela PortaFanny RancièreEmmanuelle Rial-SebbagYvan SaeysMartijn J SchuijsValerie SirouxChristina G TischerMathies TorrentRaphaelle VarrasoKalus WenzelCheng-Jian Xu

A1 Journal Article in JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Metazoan evolution of the armadillo repeat superfamily

Ismail Sahin GülPaco HulpiauYvan SaeysFrans Van Roy

A1 Journal Article in CELLULAR AND MOLECULAR LIFE SCIENCES

Myocardial infarction primes autoreactive T cells through activation of dendritic cells

Katrien Van Der BorghtCharlotte ScottVeronika NindlAnn BouchéLiesbet MartensDorine SichienJustine Van MoorleghemManon VanheerswynghelsSofie De PrijckYvan SaeysBurkhard LudewigThierry GillebertMartin GuilliamsPeter CarmelietBart Lambrecht

A1 Journal Article in CELL REPORTS

Nlrp6-and ASC-dependent inflammasomes do not shape the commensal gut microbiota composition

Michail MamantopoulosFrancesca RonchiFilip Van HauwermeirenSara Vieira-SilvaBahtiyar YilmazLiesbet MartensYvan SaeysStefan K DrexlerAmir S YazdiJeroen RaesMohamed LamkanfiKathy D McCoyAndy Wullaert

A1 Journal Article in IMMUNITY

TGFβR signalling controls CD103⁺CD11b⁺ dendritic cell development in the intestine

CC BainJ MontgomeryCharlotte ScottJM KelMJH Girard-MadouxLiesbet MartensTFP Zangerle-MurrayJ Ober-BlobaumD Lindenbergh-KortleveJN SamsomS HenriT LawrenceYvan SaeysB MalissenM DalodBE ClausenA Mcl Mowat

A1 Journal Article in NATURE COMMUNICATIONS

The checkpoint for agonist selection precedes conventional selection in human thymus

Greet VerstichelDavid VermijlenLiesbet MartensGlenn GoetgelukMargreet BrouwerNicolas ThiaultYasmine Van CaeneghemStijn De MunterKarin WeeningSarah BonteGeorges LeclercqTom TaghonTessa KerreYvan SaeysJo Van DorpeHilde CheroutreBart Vandekerckhove

A1 Journal Article in SCIENCE IMMUNOLOGY

The checkpoint for agonist selection precedes conventional selection in human thymus

Greet VerstichelDavid VermijlenLiesbet MartensGlenn GoetgelukMargreet BrouwerNicolas ThiaultYasmine Van CaeneghemStijn De MunterKarin WeeningSarah BonteGeorges LeclercqTom TaghonTessa KerreYvan SaeysJo Van DorpeHilde CheroutreBart Vandekerckhove

U Journal Article in science immunology

2016

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes

N AghaeepourP ChattopadhyayM ChikinaTom DhaeneSofie Van GassenM KursaBart LambrechtM MalekGJ McLachlanY QianP QiuYvan SaeysR StantonD TongCeline VensS WalkowiakK WangG FinakR GottardoT MosmannGP NolanRH ScheuermannRR Brinkman

A1 Journal Article in CYTOMETRY PART A

An evolutionary perspective on the necroptotic pathway

Yves DondelingerPaco HulpiauYvan SaeysMathieu BertrandPeter Vandenabeele

A1 Journal Article in TRENDS IN CELL BIOLOGY

Automated Membrane Detection in Electron Microscopy using Convolutional Neural Networks

Joris RoelsJonas De VylderJan AeltermanYvan SaeysWilfried Philips

Bayesian deconvolution of scanning electron microscopy images using point-spread function estimation and non-local regularization

Joris RoelsJan AeltermanJonas De VylderHiep LuongYvan SaeysWilfried Philips

Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells

Charlotte ScottFang ZhengPatrick De BaetselierLiesbet MartensYvan SaeysSofie De PrijckSaskia LippensChloé AbelsSteve SchoonoogheGeert RaesNick DevoogdtBart LambrechtAlain BeschinMartin Guilliams

A1 Journal Article in NATURE COMMUNICATIONS

Computational flow cytometry: helping to make sense of high-dimensional immunology data

Yvan SaeysSofie Van GassenBart Lambrecht

A1 Journal Article in NATURE REVIEWS IMMUNOLOGY

Computational methods for trajectory inference from single-cell transcriptomics

Robrecht CannoodtWouter SaelensYvan Saeys

A1 Journal Article in EUROPEAN JOURNAL OF IMMUNOLOGY

Decreasing time consumption of microscopy image segmentation through parallel processing on the GPU

Joris RoelsJonas De VylderYvan SaeysBart GoossensWilfried Philips

Development and validation of a small single-domain antibody that effectively inhibits matrix metalloproteinase 8

Delphine DemeestereEline DejonckheereSophie SteelandPaco HulpiauJurgen HaustraeteNick DevoogdtRielana WichertChristoph Becker-PaulyElien Van WonterghemSylviane DewaeleGriet Van ImschootJeroen AertsLutgarde ArckensYvan SaeysClaude LibertRoosmarijn Vandenbroucke

A1 Journal Article in MOLECULAR THERAPY

Differential expression of lncRNAs during the HIV replication cycle : an underestimated layer in the HIV-host interplay

Wim TrypsteenPejman MohammadiClarissa Van HeckePieter MestdaghSteve LefeverYvan SaeysPieter De BleserJo VandesompeleAngela CiuffiLinos VandekerckhoveWard De Spiegelaere

A1 Journal Article in SCIENTIFIC REPORTS

EPRENNID : an evolutionary prototype reduction based ensemble for nearest neighbor classification of imbalanced data

Sarah VluymansIsaac TrigueroChris CornelisYvan Saeys

A1 Journal Article in NEUROCOMPUTING

Early TCRA rearrangements favor development of agonist selected CD8ααhi T cells in human

Greet VerstichelGlenn GoetgelukLiesbet MartensYvan SaeysTessa KerreHilde CheroutreDavid VermijlenBart Vandekerckhove

Efficient analysis of mouse genome sequences reveal many nonsense variants

Sophie SteelandSteven TimmermansSara Van RyckeghemPaco HulpiauYvan SaeysMarc Van MontaguRoosmarijn VandenbrouckeClaude Libert

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

FloReMi : flow density survival regression using minimal feature redundancy

Sofie Van GassenCeline VensTom DhaeneBart LambrechtYvan Saeys

A1 Journal Article in CYTOMETRY PART A

From a biological sample to high-quality digital image representation : avoiding and restoring image artifacts through proper acquisition and image restoration

Joris RoelsJan AeltermanJonas De VylderHiep LuongSaskia LippensChris GuerinYvan SaeysWilfried Philips

Fuzzy multi-instance classifiers

Sarah VluymansDánel Sánchez TarragóYvan SaeysChris CornelisFrancisco Herrera

A1 Journal Article in IEEE TRANSACTIONS ON FUZZY SYSTEMS

Fuzzy rough classifiers for class imbalanced multi-instance data

Sarah VluymansDánel Sánchez TarragóYvan SaeysChris CornelisFrancisco Herrera

A1 Journal Article in PATTERN RECOGNITION

Fuzzy rough sets for self-labelling : an exploratory analysis

Sarah VluymansNeil Mac ParthaláinChris CornelisYvan Saeys

GATA1-deficient dendritic cells display impaired CCL21-dependent migration toward lymph nodes due to reduced levels of polysialic acid

Maaike R ScheenstraIris M De CuyperFilipe Branco MadeiraPieter De BleserMirjam KoolMarjolein MeindersMark HoogenboezemErik MuMonika C WolkersFiamma SalernoBenjamin NotaYvan SaeysSjoerd KlarenbeekWilfred FJ van IJckenHamida HammadSjaak PhilipsenTimo K van den BergTaco W KuijpersBart LambrechtLaura Gutierrez

A1 Journal Article in JOURNAL OF IMMUNOLOGY

IRF8 transcription factor controls survival and function of terminally differentiated conventional and plasmacytoid dendritic cells, respectively

Dorine SichienCharlotte ScottLiesbet MartensMatthias VanderkerkenSofie Van GassenMaud PlantingaThorsten JoerisSofie De PrijckLeen VanhoutteManon VanheerswynghelsGert Van IsterdaelWendy ToussaintFilipe Branco MadeiraKarl VergoteWilliam W AgaceBjörn E ClausenHamida HammadMarc DalodYvan SaeysBart LambrechtMartin Guilliams

A1 Journal Article in IMMUNITY

Improving marker gene discovery from high-dimensional single-cell snapshot data

Robrecht CannoodtWouter SaelensKatleen De PreterYvan Saeys

Improving nearest neighbor classification using Ensembles of Evolutionary Generated Prototype Subsets

Nele VerbiestSarah VluymansChris CornelisNicolás García-PedrajasYvan Saeys

A1 Journal Article in APPLIED SOFT COMPUTING

Machine learning challenges for single cell data

Sofie Van GassenTom DhaeneYvan Saeys

Netter: re-ranking gene network inference predictions using structural network properties

Joeri RuyssinckPiet DemeesterTom DhaeneYvan Saeys

A1 Journal Article in BMC BIOINFORMATICS

Paving the way of systems biology and precision medicine in allergic diseases: the MeDALL success story Mechanisms of the Development of ALLergy; EUFP7-CP-IP; project no: 261357; 2010-2015

J BousquetJM AntoM AkdisC AuffrayT KeilI MomasDS PostmaR ValentaM WickmanA Cambon-ThomsenT HaahtelaBart LambrechtKCL CarlsenGH KoppelmanJ SunyerT ZuberbierI Annesi-MaesanoA ArnoC Bindslev-JensenG De CarloF ForastiereJ HeinrichML KowalskiD MaierE MelenS PalkonenHA SmitM StandlJ WrightA AsarnojM BenetN BallardiniJ Garcia-AymerichU GehringS GuerraC HohmanI KullC LupinekM PinartI SkrindoM WestmanD SmaggheC AkdisR AlbangV AnastasovaN AndersonClaus BachertS BallereauF BallesterX BasaganaA BedbrookA BergstromA von BergB BrunekreefE BurteKH CarlsenL ChatziJonathan CoquetM CurinP DemolyE EllerMP FantiniB GerhardHamida HammadL von HertzenV HovlandB JacqueminJ JustT KellerM KerkhofR KissM KogevinasS KoletzkoS LauI LehmannN LemonnierR McEachanM MakelaJ MestresE MininaP MowinckelR NadifM NawijnS OddieJ PelletI PinD PortaF RanciereA Rial-SebbagYvan SaeysMartijn SchuijsV SirouxCG TischerM TorrentR VarrasoJ De VochtK WengerS WieserC Xu

A1 Journal Article in ALLERGY

Radiation-induced alternative transcription and splicing events and their applicability to practical biodosimetry

Ellina MacaevaYvan SaeysKevin TaburyAnn JanssenArlette MichauxMohammed A BenotmaneWinnok De VosSarah BaatoutRoel Quintens

A1 Journal Article in SCIENTIFIC REPORTS

Semi-automated segmentation in 3D electron microscopy imaging

Joris RoelsJan AeltermanJonas De VylderHiep LuongSaskia LippensYvan SaeysWilfried Philips

Superpixel quality in microscopy images: the impact of noise & denoising

Joris RoelsJonas De VylderJan AeltermanSaskia LippensYvan SaeysWilfried Philips

The checkpoint for agonist selection precedes conventional selection in human thymus

Greet VerstichelDavid VermijlenLiesbet MartensGlenn GoetgelukYvan SaeysHilde CheroutreBart Vandekerckhove

The transcription factor Zeb2 regulates development of conventional and plasmacytoid DCs by repressing Id2

Charlotte ScottBieke SoenLiesbet MartensNicolas SkrypekWouter SaelensJoachim TaminauGillian BlanckeGert Van IsterdaelDanny HuylebroeckJody HaighYvan SaeysMartin GuilliamsBart LambrechtGeert Berx

A1 Journal Article in JOURNAL OF EXPERIMENTAL MEDICINE

Unbiased modelling of dynamic processes with single-cell RNA-sequencing

Robrecht CannoodtWouter SaelensKatleen De PreterYvan Saeys

Unbiased modelling of dynamic processes with single-cell RNA-sequencing

Robrecht CannoodtWouter SaelensKatleen De PreterYvan Saeys

Unbiased modelling of dynamic processes with single-cell RNA-sequencing

Robrecht CannoodtWouter SaelensKatleen De PreterYvan Saeys

Unsupervised high-dimensional analysis aligns dendritic cells across tissues and species

Martin GuilliamsCharles-Antoine DutertreCharlotte ScottNaomi McGovernDorine SichienSvetoslav ChakarovSofie Van GassenJinmiao ChenMichael PoidingerSofie De PrijckSimon TavernierIvy LowSergio Erdal IracCitra Nurfarah MattarHermi Rizal SumatohGillian Hui Ling LowTam John Kit ChungDedrick Kok Hong ChanKer Kan TanTony Lim Kiat HonEven FossumBjarne BogenMahesh ChoolaniJerry Kok Yen ChanAnis LarbiHervé LucheSandrine HenriYvan SaeysEvan William NewellBart LambrechtBernard MalissenFlorent Ginhoux

A1 Journal Article in IMMUNITY

Yolk sac macrophages, fetal liver, and adult monocytes can colonize an empty niche and develop into functional tissue-resident macrophages

Lianne van de LaarWouter SaelensSofie De PrijckLiesbet MartensCharlotte ScottGert Van IsterdaelEik HoffmannRudi BeyaertYvan SaeysBart LambrechtMartin Guilliams

A1 Journal Article in IMMUNITY

2015

An integrated network of Arabidopsis growth regulators and its use for gene prioritization

Ehsan SabaghianZuzanna DrebertDirk InzéYvan Saeys

A1 Journal Article in SCIENTIFIC REPORTS

Applications of fuzzy rough set theory in machine learning: a survey

Sarah VluymansLynn D'eerYvan SaeysChris Cornelis

A1 Journal Article in FUNDAMENTA INFORMATICAE

Are allergic multimorbidities and IgE polysensitization associated with the persistence or re-occurrence of foetal type 2 signalling? : the MeDALL hypothesis

J BousquetJM AntoM WickmanT KeilR ValentaT HaahtelaK Lodrup CarlsenM van HageC AkdisClaus BachertM AkdisC AuffrayI Annesi-MaesanoC Bindslev-JensenA Cambon-ThomsenKH CarlsenL ChatziF ForastiereJ Garcia-AymerichU GehrigS GuerraJ HeinrichGH KoppelmanML KowalskiBart LambrechtC LupinekD MaierE MelénI MomasS PalkonenM PinartD PostmaV SirouxHA SmitJ SunyerJ WrightT ZuberbierSH ArshadR NadifC ThijsN AnderssonA AsarnojN BallardiniS BallereauA BedbrookM BenetA BergstromB BrunekreefE BurteM CalderonG De CarloP DemolyE EllerMP FantiniHamida HammadC HohmanJ JustM KerkhofM KogevinasI KullS LauN LemonnierM MommersM NawijnA NeubauerS OddieJ PelletI PinD PortaYvan SaeysI SkrindoCG TischerM TorrentL von Hertzen

A1 Journal Article in ALLERGY

CATCh, an ensemble classifier for chimera detection in 16S rRNA sequencing studies

Mohamed MysaraYvan SaeysNatalie LeysJeroen RaesPieter Monsieurs

A1 Journal Article in APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization of genome-wide ordered sequence-tagged Mycobacterium mutant libraries by Cartesian Pooling-Coordinate Sequencing

Kristof VandewalleNele FestjensEvelyn PletsMarnik VuylstekeYvan SaeysNico Callewaert

A1 Journal Article in NATURE COMMUNICATIONS

Complex aggregates over clusters of elements

Celine VensSofie Van GassenTom DhaeneYvan Saeys

Computational inference of developmental chronology using flow cytometry data

Leen De BaetsTom DhaeneYvan Saeys

Differential module analysis in neuroblastoma regulatory networks

Robrecht CannoodtAnneleen BeckersCaroline Van CauwenberghFranki SpelemanKatleen De PreterYvan Saeys

Distributed fuzzy rough prototype selection for big data regression

Sarah VluymansHasan AsfoorYvan SaeysChris CornelisMatthew TolentinoAnkur TeredesaiMartine De Cock

Evolutionary undersampling for imbalanced big data classification

Isaac TrigueroMikel GalarSarah VluymansChris CornelisHumberto BustinceFrancisco HerreraYvan Saeys

FlowSOM: using self-organizing maps for visualization and interpretation of cytometry data

Sofie Van GassenBritt CallebautMary van HeldenBart LambrechtPiet DemeesterTom DhaeneYvan Saeys

A1 Journal Article in CYTOMETRY PART A

Fuzzy rough set prototype selection for regression

Sarah VluymansYvan SaeysChris CornelisAnkur TeredesaiMartine De Cock

Inferring developmental chronologies from single cell RNA

Robrecht CannoodtWouter SaelensKatleen De PreterYvan Saeys

Noise analysis in 3D electron microscopy

Joris RoelsJan AeltermanJonas De VylderHiep LuongSaskia LippensYvan SaeysWilfried Philips

Phenotyping asthma, rhinitis and eczema in MeDALL population-based birth cohorts: an allergic comorbidity cluster

J Garcia-AymerichM BenetYvan SaeysM PinartX BasagañaHA SmitV SirouxJ JustI MomasF RancièreT KeilC HohmannS LauU WahnJ HeinrichCG TischerMP FantiniJ LenziD PortaGH KoppelmanDS PostmaD BerdelS KoletzkoM KerkhofU GehringM WickmanE MelénJ HallbergC Bindslev-JensenE EllerI KullKC Lødrup CarlsenK-H CarlsenBart LambrechtM KogevinasJ SunyerF KauffmannJ BousquetJM Antó

A1 Journal Article in ALLERGY

Semi-supervised fuzzy-rough feature selection

Richard JensenSarah VluymansNeil Mac ParthaláinChris CornelisYvan Saeys

Unsupervised trajectory inference using graph mining

Leen De BaetsSofie Van GassenTom DhaeneYvan Saeys

2014

Differential module analysis in neuroblastoma regulatory networks

Robrecht CannoodtAnneleen BeckersCaroline Van CauwenberghKatleen De PreterYvan Saeys

Fuzzy rough and evolutionary approaches to instance selection

Nele VerbiestChris CornelisYvan Saeys

Identifying novel neuroblastoma oncogenes using semi-supervised learning

Leen De BaetsRobrecht CannoodtJoeri RuyssinckKatleen De PreterTom DhaeneYvan Saeys

Image optimization for 3D electron microscopy images

Joris RoelsJan AeltermanHiep LuongJonas De VylderWilfried PhilipsSaskia LippensYvan Saeys

Instance selection for imbalanced data

Sarah VluymansNele VerbiestChris CornelisYvan Saeys

NIMEFI: gene regulatory network inference using multiple ensemble feature importance algorithms

Joeri RuyssinckAnh Huynh-Thu VanPierre GeurtsTom DhaenePiet DemeesterYvan Saeys

A1 Journal Article in PLOS ONE

Noise analysis and removal in 3D electron microscopy

Joris RoelsJan AeltermanJonas De VylderHiep LuongYvan SaeysSaskia LippensWilfried Philips

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

The function of Fcγ receptors in dendritic cells and macrophages

Martin GuilliamsPierre BruhnsYvan SaeysHamida HammadBart Lambrecht

A1 Journal Article in NATURE REVIEWS IMMUNOLOGY

The image processing revolution: the next step in electron microscopy

Jan AeltermanJonas De VylderHiep LuongSaskia LippensYvan SaeysBart GoossensWilfried Philips

The unfolded-protein-response sensor IRE-1α regulates the function of CD8α⁺ dendritic cells

Fabiola OsorioSimon TavernierEik HoffmannYvan SaeysLiesbet MartensJessica VettersIris DelrueRiet De RyckeEef ParthoensPhilippe PouliotTakao IwawakiSophie JanssensBart Lambrecht

A1 Journal Article in NATURE IMMUNOLOGY

2013

A re-ranking algorithm for gene regulatory network predictions using graphlets and graph-invariant properties

Joeri RuyssinckTom DhaeneYvan Saeys

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

Network inference by integrating biclustering and feature selection

Robrecht CannoodtJoeri RuyssinckKatleen De PreterTom DhaeneYvan Saeys

Stable feature selection techniques for microarray data

Sofie Van GassenJoeri RuyssinckYvan SaeysTom Dhaene

2012

Flexible motif discovery using feature selection trees: a high performance computing approach

Dries DecapBart DhoedtJan FostierYvan Saeys

Flexible motif discovery using feature selection trees: a high performance computing approach (poster)

Dries DecapBart DhoedtJan FostierYvan Saeys

GenomeView : a next-generation genome browser

Thomas AbeelThomas Van ParysYvan SaeysJames GalaganYves Van de Peer

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Inferring gene regulatory network topologies using ensembles of feature selection techniques

Joeri RuyssinckTom DhaeneYvan Saeys

Inferring gene regulatory networks using ensembles of feature selection techniques

Joeri RuyssinckVân anh Huynh-thuPierre GeurtsTom DhaenePiet DemeesterYvan Saeys

Playing hide and seek on the genomic playground: unveiling biological function from literature

Sofie Van LandeghemYves Van de PeerBernard De BaetsYvan Saeys

SBFC: an efficient feature frequency-based approach to tackle cross-lingual word sense disambiguation

Dieter MourisseEls LefeverNele VerbiestYvan SaeysMartine De CockChris Cornelis

Statistical interpretation of machine learning-based feature importance scores for biomarker discovery

Anh Huynh-Thu VanYvan SaeysLouis WehenkelPierre Geurts

A1 Journal Article in BIOINFORMATICS

Wisdom of crowds for robust gene network inference

Daniel MarbachJames C CostelloRobert KüffnerNicole M VegaRobert J PrillDiogo M CamachoKyle R AllisonManolis KellisJames J CollinsGustavo Stolovitzkythe DREAM5 ConsortiumYvan Saeys

A1 Journal Article in NATURE METHODS

2011

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

Jan FostierSebastian ProostBart DhoedtYvan SaeysPiet DemeesterYves Van de PeerKlaas Vandepoele

A1 Journal Article in BIOINFORMATICS

An alternative approach to avoid overfitting for surrogate models

Huu Minh NguyenIvo CouckuytLuc KnockaertTom DhaeneDirk GorissenYvan Saeys

Avoiding overfitting in surrogate modeling: an alternative approach

Huu Minh NguyenIvo CouckuytYvan SaeysLuc KnockaertTom DhaeneDirk Gorissen

Exploring signature multiplicity in microarray data using ensembles of randomized trees

Pierre GeurtsYvan Saeys

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

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

2010

Discriminative and informative features for biomolecular text mining with ensemble feature selection

Sofie Van LandeghemThomas AbeelYvan SaeysYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Event based text mining for integrated network construction

Yvan SaeysSofie Van LandeghemYves Van de Peer

Highlights of the BioTM 2010 workshop on advances in bio text mining

Thomas AbeelSofie Van LandeghemRoser MoranteVincent Van AschYves Van de PeerWalter DaelemansYvan Saeys

Editorial material

In-silico prediction methods for genome annotation: promoter prediction, biomarker discovery and next-generation sequencing analysis

Thomas AbeelYves Van de PeerYvan Saeys

Influence of feature selection on ensemble diversity

Huu Minh NguyenLuc KnockaertTom DhaenePiet DemeesterYvan Saeys

Robust biomarker identification for cancer diagnosis with ensemble feature selection methods

Thomas AbeelThibault HelleputteYves Van de PeerPierre DupontYvan Saeys

A1 Journal Article in BIOINFORMATICS

Towards an ASR-free objective analysis of pathological speech

Catherine MiddagYvan SaeysJean-Pierre Martens

2009

Analyzing text in search of bio-molecular events: a high-precision machine learning framework

Sofie Van LandeghemYvan SaeysBernard De BaetsYves Van de Peer

Comparison of embedded feature selection algorithms for splice site detection

Huu Minh NguyenYvan SaeysLuc KnockaertTom Dhaene

Java-ML: a machine learning library

Thomas AbeelYves Van de PeerYvan Saeys

A1 Journal Article in JOURNAL OF MACHINE LEARNING RESEARCH

Toward a gold standard for promoter prediction evaluation

Thomas AbeelYves Van de PeerYvan Saeys

A1 Journal Article in BIOINFORMATICS

Valued constraint satisfaction problems applied to functional harmony

Nele VerbiestChris CornelisYvan Saeys

2008

A review of estimation of distribution algorithms in bioinformatics

Rubén ArmañanzasIñaki InzaRoberto SantanaYvan SaeysJose Luis FloresJose Antonio LozanoYves Van de PeerRosa BlancoVictor RoblesConcha BielzaPedro Larrañaga

A1 Journal Article in BIODATA MINING

Benchmarking machine learning techniques for the extraction of protein-protein interactions from text

Sofie Van LandeghemYvan SaeysYves Van de PeerBernard De Baets

Comparing distance measures with visual methods

Isis BonetAbdel RodríguezRicardo GrauMaria M GarcíaYvan SaeysAnn Nowé

Extracting protein-protein interactions from text using rich feature vectors and feature selection

Sofie Van LandeghemYvan SaeysYves Van de PeerBernard De Baets

FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA

Michiel Van BelYvan SaeysYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Generic eukaryotic core promoter prediction using structural features of DNA

Thomas AbeelYvan SaeysEric BonnetPierre RouzéYves Van de Peer

A1 Journal Article in GENOME RESEARCH

ProSOM: core promoter identification in the human genome

Thomas AbeelYvan SaeysYves Van de Peer

ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles

Thomas AbeelYvan SaeysPierre RouzéYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Robust feature selection using ensemble feature selection techniques

Yvan SaeysThomas AbeelYves Van de Peer

Towards robust feature selection techniques

Yvan SaeysThomas AbeelYves Van de Peer

2007

A review of feature selection techniques in bioinformatics

Yvan SaeysIñaki InzaPedro Larrañaga

A1 Journal Article in BIOINFORMATICS

Enhancing coding potential prediction for short sequences using complementary sequence features and feature selection

Yvan SaeysYves Van de Peer

In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists

Yvan SaeysPierre RouzéYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Predicting human immunodeficiency virus (HIV) drug resistance using recurrent neural networks

Isis BonetMaria M GarcíaYvan SaeysYves Van de PeerRicardo Grau

Translation initiation site prediction on a genomic scale : beauty in simplicity

Yvan SaeysThomas AbeelSven DegroeveYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Validating module network learning algorithms using simulated data

Tom MichoelSteven MaereEric BonnetAnagha Madhusudan JoshiYvan SaeysTim Van den BulckeKoenraad Van LeemputPiet Van RemortelMartin KuiperKathleen MarchalYves Van de Peer

A1 Journal Article in BMC BIOINFORMATICS

2006

A Scalable Hardware Accelerator for Comparing Protein Sequences

Philippe FaesBram MinnaertM CHRISTIAENSEric BonnetYvan SaeysDirk StroobandtYves Van de Peer

Annual Machine Learning Conference of Belgium and The Netherlands

Combining signal processing and machine learning techniques for coding potential prediction

Yvan SaeysYves Van de Peer

Enhancing coding potential prediction for short sequences using complementary sequence features and feature selection

Yvan SaeysYves Van de Peer

Feature extraction using clustering of protein

Iris BonetYvan SaeysRicardo Grau ÁbaloMaria M GarcíaRobersy SanchezYves Van de Peer

A1 Journal Article in Lecture Notes in Computer Science

Feature ranking using an EDA-based wrapper approach

Yvan SaeysSven DegroeveYves Van de Peer

Bookchapter in Towards a new evolutionary computation : advances in estimation of distribution algorithms

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

Evelyne DerelleConchita FerrazStephane RombautsPierre RouzéAlexandra Z WordenSteven RobbensFrédéric PartenskySven DegroeveSophie EcheyniéRichard CookeYvan SaeysJan WuytsKamel JabbariChris BowlerOlivier PanaudBenoît PiéguSteven G BallJean-Philippe RalFrançois-Yves BougetGwenael PiganeauBernard De BaetsAndré PicardMichel DelsenyJacques DemailleYves Van de PeerHervé Moreau

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

Improved core promoter prediction using ensembles of Support Vector Machines

Thomas AbeelYvan SaeysYves Van de Peer

Predicting human immunodeficiency virus (HIV) drug resistance using recurrent neural networks

Isis BonetMaria M GarcíaSain SalazarRobersy SanchezYvan SaeysYves Van de PeerRicardo Grau

2005

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

Steven RobbensStephane RombautsPierre RouzéJan WuytsYvan SaeysHervé MoreauYves Van de Peer

Large-scale structural analysis of the core promoter in mammalian and plant genomes

Kobe FlorquinYvan SaeysSven DegroevePierre RouzéYves Van de Peer

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Large-scale structural analysis of the core promoter in mammalian and plant genomes

Kobe FlorquinYvan SaeysSven DegroeveYves Van de Peer

SpliceMachine: predicting splice sites from high-dimensional local context representations

Sven DegroeveYvan SaeysBernard De BaetsPierre RouzéYves Van de Peer

A1 Journal Article in BIOINFORMATICS

2004

Building genomic profiles for uncovering segmental homology in the twilight zone

Cedric SimillionKlaas VandepoeleYvan SaeysYves Van de Peer

A1 Journal Article in GENOME RESEARCH

Building genomic profiles for uncovering segmental homology in the twilight zone

Cedric SimillionKlaas VandepoeleYvan SaeysYves Van de Peer

Digging into acceptor splice site prediction : an iterative feature selection approach

Yvan SaeysSven DegroeveYves Van de Peer

A1 Journal Article in LECTURE NOTES IN ARTIFICIAL INTELLIGENCE

Feature selection for classification of nucleic acid sequences

Yvan SaeysYves Van de PeerDirk Aeyels

Feature selection for splice site prediction: A new method using EDA-based feature ranking

Yvan SaeysSven DegroeveDirk AeyelsPierre RouzéYves Van de Peer

A1 Journal Article in BMC BIOINFORMATICS

Selecting relevant features for gene structure prediction

Yvan SaeysSven DegroeveDirk AeyelsPierre RouzéYves Van de Peer

Splice site prediction in eukaryote genome sequences : the algorithmic issues

Sven DegroeveYvan SaeysBernard De BaetsYves Van de PeerPierre Rouzé

Bookchapter in The new avenues in bioinformatics

The role of non-linear DNA structures in transcription

Kobe FlorquinSven DegroeveYvan SaeysYves Van de Peer

2003

Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction

Yvan SaeysSven DegroeveDirk AeyelsYves Van de PeerPierre Rouzé

A1 Journal Article in BIOINFORMATICS

Feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction

Yvan SaeysSven DegroeveDirk AeyelsYves Van de PeerPierre Rouzé

Investigating ancient duplication events in the Arabidopsis genome

Jeroen RaesKlaas VandepoeleCedric SimillionYvan SaeysYves Van de Peer

A2 Journal Article in JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS

Investigating ancient duplication events in the Arabidopsis genome

Jeroen RaesKlaas VandepoeleCedric SimillionYvan SaeysYves Van de Peer

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

2002

Detecting microcolinearity between Arabidopsis and Rice

Klaas VandepoeleYvan SaeysCedric SimillionJ RAESYves Van de Peer

Feature subset selection for splice site prediction by estimation of distribution algorithms

Yvan SaeysSven DegroeveDirk AeyelsYves Van de PeerPierre Rouzé

Retrieving DNA sequence information from mass spectra of nucleic acids: application to the detection and identification of SNPs

Yvan SaeysDirk AeyelsPatrick StanssensYves Van de PeerMarc Zabeau

Selecting Relevant Features for Splice Site Prediction by Estimation of Distribution Algorithms.

Yvan SaeysSven DegroeveDirk AeyelsYves Van de PeerPierre Rouzé

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

Klaas VandepoeleYvan SaeysCedric SimillionJeroen RaesYves Van de Peer

A1 Journal Article in GENOME RESEARCH

2000

A Study and Improvement of the Genetic Algorithm in the CAM-Brain Machine

Yvan SaeysH VAN MARCK