Research Explorer

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Project

Unravelling cellular heterogeneity and dynamics in normal and malignant hematopoiesis using singlecell bioinformatics

Outputs and Outcomes

Publications

Spotless, a reproducible pipeline for benchmarking cell type deconvolution in spatial transcriptomics

Chananchida Sang-aramRobin BrowaeysRuth SeurinckYvan Saeys

A1 Journal Article in ELIFE

Efficient cytometry analysis with FlowSOM in Python boosts interoperability with other single-cell tools

Artuur CouckuytBenjamin RombautYvan SaeysSofie Van Gassen

A1 Journal Article in BIOINFORMATICS

Defining and benchmarking open problems in single-cell analysis

Malte LueckenScott GiganteDaniel BurkhardtRobrecht CannoodtDaniel StroblNikolay MarkovLuke ZappiaGiovanni PallaWesley LewisDaniel DimitrovMichael VinyardDaniel MagruderAlma AnderssonEmma DannQian QinDominik OttoMichal KleinOlga BotvinnikLouise DeconinckKai WaldrantBastian RieckConstantin Ahlmann-EltzeEduardo da Veiga BeltrameAndrew BenzCarmen Bravo González-BlasAnn ChenBenjamin DeMeoCan ErgenSwann Floc'hlayAdam GayosoStephanie Hicksyuge jiVitalii KleshchevnikovGioele La MannoMaximilian LombardoRomain LopezDario RighelliHirak SarkarValentine SvenssonAlexander TongGalen XingChenling XuJonathan BloomAngela PiscoJulio Saez-RodriguezDrausin WulsinLuca PinelloYvan SaeysFabian TheisSmita Krishnaswamy et al.

SpatialData : an open and universal data framework for spatial omics

Luca MarconatoGiovanni PallaKevin A. YamauchiIsaac VirshupElyas HeidariTim TreisWouter-Michiel VierdagMarcella TothSonja StockhausRahul B. ShresthaBenjamin RombautLotte PollarisLaurens LehnerHarald VoehringerIlia KatsYvan SaeysSinem K. SakaWolfgang HuberMoritz GerstungJosh MooreFabian J. TheisOliver Stegle et al.

A1 Journal Article in NATURE METHODS

Myelodysplastic neoplasms dissected into indolent, leukaemic and unfavourable subtypes by computational clustering of haematopoietic stem and progenitor cells

Margot F. van SpronsenSofie Van GassenCarolien DuetzTheresia M. WestersYvan SaeysArjan A. van de Loosdrecht

A1 Journal Article in LEUKEMIA

Uncertainty-aware single-cell annotation with a hierarchical reject option

Lauren TheunissenThomas MortierYvan SaeysWillem Waegeman

A1 Journal Article in BIOINFORMATICS

In vivo macrophage engineering as novel therapeutic strategy against liver metastasis

Marie LavironMartin Guilliams

Editorial material

A TCF4-dependent gene regulatory network confers resistance to immunotherapy in melanoma

Joanna PozniakDennis PedriEwout LandeloosYannick Van HerckAsier AntoranzLukas VanwynsbergheAda NowosadNiccolo RodaSamira MakhzamiGreet BervoetsLucas Ferreira MacielCarlos Ariel Pulido-VicunaLotte PollarisRuth SeurinckFang ZhaoKarine Flem-KarlsenWilliam DamskyLimin ChenDespoina KaragianniSonia CinqueSam KintKaty VandereykenBenjamin RombautThierry VoetFrank VernaillenWim AnnaertDiether LambrechtsVeerle BoecxstaensYvan SaeysJoost van den OordFrancesca BosisioPanagiotis KarrasA. Hunter ShainMarcus BosenbergEleonora LeucciAnnette PaschenFlorian RambowOliver BechterJean-Christophe Marine et al.

A1 Journal Article in CELL

Intrathymic dendritic cell-biased precursors promote human T cell lineage specification through IRF8-driven transmembrane TNF

Kai Ling LiangJuliette RoelsMarieke LavaertTom PuttemanLena BöhmeLaurentijn TillemanImke VelgheValentina PegorettiInge Van de WalleStephanie SontagJolien VandewalleBart VandekerckhoveGeorges LeclercqPieter Van VlierbergheClaude LibertFilip Van NieuwerburghRoman FischerRoland E. KontermannKlaus PfizenmaierGina DoodyMartin ZenkeTom Taghon et al.

A1 Journal Article in NATURE IMMUNOLOGY

BioSegment : active learning segmentation for 3D electron microscopy imaging

Benjamin RombautJoris RoelsYvan Saeys

Loss of GM-CSF-dependent instruction of alveolar macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment

Cedric BosteelsKarel Van DammeElisabeth De LeeuwJozefien DeclercqBastiaan MaesVictor BosteelsLevi HosteLeslie NaesensNincy DebeufJulie DeckersBasiel ColeMarion PardonsDaniela WeiskopfAlessandro SetteYannick Vande WeygaerdeThomas MalfaitStefaan J. VandecasteeleIngel K. DemedtsHans SlabbynckSabine AllardPieter DepuydtEva Van BraeckelJozefien De ClercqLiesbet MartensSam DupontRuth SeurinckNiels VandammeFilomeen HaerynckDebasish F. RoychowdhuryLinos VandekerckhoveMartin GuilliamsSimon TavernierBart Lambrecht et al.

A1 Journal Article in CELL REPORTS MEDICINE

Transcriptional dynamics and epigenetic regulation of E and ID protein encoding genes during human T cell development

Juliette RoelsJolien Van HulleMarieke LavaertAnna KuchmiySteven StrubbeTom PuttemanBart VandekerckhoveGeorges LeclercqFilip Van NieuwerburghLena BöhmeTom Taghon et al.

A1 Journal Article in FRONTIERS IN IMMUNOLOGY

Development of gamma delta T cells in the thymus : a human perspective

Lena BöhmeJuliette RoelsTom Taghon

A1 Journal Article in SEMINARS IN IMMUNOLOGY

Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

Martin GuilliamsJohnny BonnardelBirthe HaestBart VanderborghtCamille WagnerAnneleen RemmerieAnna BujkoLiesbet MartensTinne ThonéRobin BrowaeysFederico Francesco De PontiBavo VannesteChristian ZwickerFreya SvedbergTineke VanhalewynAmanda GonçalvesSaskia LippensBert DevriendtEric CoxGiuliano FerreroValerie WittamerAndy WillaertSuzanne J.F. KapteinJohan NeytsKai DallmeierPeter GeldhofStijn CasaertBart DeplanckePeter ten DijkeAnne HoorensAude VanlanderFrederik BerrevoetYves Van NieuwenhoveYvan SaeysWouter SaelensHans Van VlierbergheLindsey DevisscherCharlotte Scott et al.

A1 Journal Article in CELL