Research Explorer

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Project

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

Outputs & Impact

Publications & research data ( 18 )

funkyheatmap : visualising data frames with mixed data types

Robrecht CannoodtLouise DeconinckArtuur CouckuytNikolay S. Markov*Luke ZappiaMalte D. LueckenMarta InterlandiYvan SaeysWouter Saelens

A2 Journal Article in JOURNAL OF OPEN SOURCE SOFTWARE

Unraveling cell-cell communication with NicheNet by inferring active ligands from transcriptomics data

Chananchida Sang-aramRobin BROWAEYSRuth SeurinckYvan Saeys

A1 Journal Article in NATURE PROTOCOLS

Unraveling genotype–phenotype associations and predictive modeling of outcome in acute myeloid leukemia

Artuur CouckuytSofie Van GassenAnnelies EmmaneelVince JandaMalicorne BuysseIne MoorsJan PhilippéMattias HofmansTessa KerreYvan Saeys et al.

A1 Journal Article in CYTOMETRY PART B-CLINICAL CYTOMETRY

CytoNorm 2.0 : a flexible normalization framework for cytometry data without requiring dedicated controls

Katrien QuintelierMarcella WillemsenVictor BosteelsJoachim G. J. V. AertsYvan SaeysSofie Van Gassen

A1 Journal Article in CYTOMETRY PART A

SpatialData : an open and universal data framework for spatial omics

Luca MarconatoGiovanni PallaKevin A. YamauchiIsaac VirshupElyas HeidariTim TreisWouter-Michiel VierdagMarcella TothSonja StockhausRahul B. Shrestha et al.

A1 Journal Article in NATURE METHODS

A spatial human thymus cell atlas mapped to a continuous tissue axis

Nadav YayonVeronika R. KedlianLena BoehmeChenqu SuoBrianna T. WachterRebecca T. BeuschelOren AmsalemKrzysztof PolanskiSimon KoplevElizabeth Tuck et al.

A1 Journal Article in NATURE

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

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 Bervoets 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 BoehmeLaurentijn TillemanImke VelgheValentina PegorettiInge Van de WalleStephanie Sontag 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 Deckers 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 Boehme 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 Browaeys et al.

A1 Journal Article in CELL

Activities ( 0 )

Results

Impact narratives ( 1 )

Area(s): Health

Patents ( 0 )