Research Explorer

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Researcher

Sofie Van Gassen

Publications & Research Data

Awards & Distinctions

56 Results

2026

CARGO: A cytometry analysis framework via Regularized graph optimal-transport

Abida Sanjana ShemontiGrzegorz B. GmyrekKatrien QuintelierSofie Van GassenYvan SaeysMarcella WillemsenJoachim G. J. V. AertsEva V. E. MadsenJ. Paul RobinsonAlex Pothen et al.

U Journal Article in PLOS COMPUTATIONAL BIOLOGY

Cross-species cellular mapping and humanization of Fcγ receptors to advance antibody modeling

Karel Van DammeDorine SichienKatrien Van Der BorghtJustine Van MoorleghemSofie Van GassenJoseph JorssenSeppe De WinterElisabeth De LeeuwCaihong WangQingqing Chai et al.

A1 Journal Article in SCIENCE IMMUNOLOGY

Cyt-Geist : current and future challenges in cytometry : reports of the CYTO 2025 Conference Workshops

Paul K. WallaceEvan R. JellisonSherry ThorntonKathleen KluepfelJessica BackThomas C. BeadnellAttila BebesJochen BehrendsAnna C. BelkinaMichele Black et al.

Editorial material

Effects of testosterone and estrogen on human CD4+ T-cell subsets during gender-affirming hormone therapy

Sebastian RiemannJeroen VervalckeCarolien BonroyYaël SertonsPauline BreugheMalicorne BuysseSofie Van GassenTania MaesGuy T'SjoenGuy Brusselle et al.

PIDgeon : an explainable AI model for improved flow cytometry-based screening of lymphoid primary immunodeficiencies

Annelies EmmaneelJana NeirinckAlba Torres-ValleSofie Van GassenSarah BonteMalicorne BuysseJacques J. M. Van DongenAlberto OrfaoMirjam Van Der BurgTomas Kalina et al.

A1 Journal Article in CLINICAL CHEMISTRY

Scalable analysis of whole slide spatial proteomics with Harpy

Benjamin RombautArne DefauwFrank VernaillenJulien MortierEvelien Van HammeSofie Van GassenRuth SeurinckYvan Saeys

A1 Journal Article in BIOINFORMATICS

Testosterone and estrogen differentially regulate human CD4⁺ T-cell responses during gender-affirming hormone therapy

Sebastian RiemannJeroen VervalckeMattias HofmansYaël SertonsPauline BreugheMalicorne BuysseSofie Van GassenTania MaesGuy T'SjoenGuy Brusselle et al.

2025

Cross-species cellular mapping and humanization of Fc. receptors to advance antibody modeling

Karel Van DammeDorine SichienKatrien Van Der BorghtSofie Van GassenElisabeth De LeeuwVictor BosteelsJoseph JorssenSeppe De WinterAlan KormanFabio Benigni et al.

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

CytoNormPy enables a fast and scalable removal of batch effects in cytometry datasets

Tarik ExnerNicolaj HackertLuca LeomazziSofie Van GassenYvan SaeysHanns-Martin LorenzRicardo Grieshaber-Bouyer

A1 Journal Article in CYTOMETRY PART A

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

2024

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

2023

A robust pipeline for high-content, high-throughput immunophenotyping reveals age- and genetics-dependent changes in blood leukocytes

Thomas LiechtiSofie Van GassenMargaret BeddallReid BallardYaser IftikharRenguang DuThiagarajan VenkataramanDavid NovákMassimo ManginoStephen Perfetto et al.

A2 Journal Article in CELL REPORTS METHODS

Adjuvant dendritic cell-based immunotherapy after cytoreductive surgery and hyperthermic intraperitoneal chemotherapy in patients with malignant peritoneal mesothelioma : a phase II clinical trial

Michelle DietzKatrien QuintelierJob P. van KootenNadine L. de BoerMadelief VinkAlexandra R. M. Brandt-KerkhofCornelis VerhoefYvan SaeysJoachim G. J. V. AertsMarcella Willemsen et al.

A1 Journal Article in JOURNAL FOR IMMUNOTHERAPY OF CANCER

Dysregulation of developmental and cell type-specific expression of glycoconjugates on hematopoietic cells : a new characteristic of myelodysplastic neoplasms (MDS)

Margot F. van SpronsenSophie HorrevortsClaudia CaliTheresia M. WestersSofie Van GassenYvan SaeysSandra J. van VlietYvette van KooykArjan A. van de Loosdrecht

A1 Journal Article in LEUKEMIA

Gut inflammation in axial spondyloarthritis patients is characterized by a marked type 17 skewed mucosal innate‐like T cell signature

Céline MortierKatrien QuintelierAnn-Sophie De CraemerThomas RensonLiselotte DerooEmilie DumasEveline VerheugenJulie CoudenysTine DecruyZuzanna Łukasik et al.

A1 Journal Article in ARTHRITIS & RHEUMATOLOGY

LXR signaling controls homeostatic dendritic cell maturation

Victor BosteelsSandra MaréchalClint De NolfSofie RennenJonathan MaelfaitSimon TavernierJessica VettersEvelien Van De VeldeFarzaneh FayazpourKim Deswarte et al.

A1 Journal Article in SCIENCE IMMUNOLOGY

Single-cell molecular profiling using ex vivo functional readouts fuels precision oncology in glioblastoma

Dena PanovskaPouya NazariBasiel ColePieter-Jan CreemersMarleen DerweduweLien SolieSofie Van GassenAnnelies ClaeysTatjana VerbekeElizabeth F. Cohen et al.

A1 Journal Article in CELLULAR AND MOLECULAR LIFE SCIENCES

2022

Challenges in translational machine learning

Artuur CouckuytRuth SeurinckAnnelies EmmaneelKatrien QuintelierDavid NovákSofie Van GassenYvan Saeys

A1 Journal Article in HUMAN GENETICS

Improving diagnosis of primary immunodeficiencies using computional cytometry

Annelies EmmaneelYvan SaeysSofie Van Gassen

Operational tolerance after hematopoietic stem cell transplantation is characterized by distinct transcriptional, phenotypic, and metabolic signatures

Laetitia DubouchetHelena TodorovRuth SeurinckNicolas ValletSofie Van GassenAurelien CorneauCatherine BlancHabib ZoualiAnne BolandJean-Francois Deleuze et al.

A1 Journal Article in SCIENCE TRANSLATIONAL MEDICINE

PeacoQC : peak-based selection of high quality cytometry data

Annelies EmmaneelKatrien QuintelierDorine SichienPaulina RybakowskaConcepcion MaranonMarta E. Alarcon-RiquelmeGert Van IsterdaelSofie Van GassenYvan Saeys

A1 Journal Article in CYTOMETRY PART A

Presence of innate lymphoid cells in allogeneic hematopoietic grafts correlates with reduced graft-versus-host disease

Anna KroezeVera van HoevenMyrddin W. VerheijAnnelies W. TurksmaNaomi WeteringsSofie Van GassenSacha S. ZeerlederBianca BlomCarlijn VoermansMette D. Hazenberg

A1 Journal Article in CYTOTHERAPY

Protocol for large scale whole blood immune monitoring by mass cytometry and Cyto Quality Pipeline

P RybakowskaSofie Van GassenJ Martorell MarugánKatrien QuintelierYvan SaeysME Alarcón-RiquelmeC Marañón

A2 Journal Article in STAR PROTOCOLS

The Euroflow PID Orientation Tube in the diagnostic workup of primary immunodeficiency : daily practice performance in a tertiary university hospital

Jana NeirinckAnnelies EmmaneelMalicorne BuysseJan PhilippéSofie Van GassenYvan SaeysXavier BossuytStefanie De BuyserMirjam van der BurgMartin Perez-Andres et al.

A1 Journal Article in FRONTIERS IN IMMUNOLOGY

2021

An updated guide for the perplexed : cytometry in the high-dimensional era

Thomas LiechtiLukas M. WeberThomas M. AshhurstNatalie StanleyMartin PrlicSofie Van GassenFlorian Mair

A1 Journal Article in NATURE IMMUNOLOGY

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

High dimensional profiling identifies specific immune types along the recovery trajectories of critically ill COVID19 patients

P. A. PenttilaSofie Van GassenD. PanovskaL. VanderbekeY. Van HerckKatrien QuintelierAnnelies EmmaneelJ. FiltjensB. Malengier-DevliesK. Ahmadzadeh et al.

A1 Journal Article in CELLULAR AND MOLECULAR LIFE SCIENCES

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 Hennart et al.

A1 Journal Article in CANCERS

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. Bosisio et al.

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

2020

CytoNorm : a normalization algorithm for cytometry data

Sofie Van GassenBrice GaudilliereMartin S AngstYvan SaeysNima Aghaeepour

A1 Journal Article in CYTOMETRY PART A

TAO-kinase 3 governs the terminal differentiation of conventional dendritic cells

Matthias VanderkerkenBastiaan MaesLana VandersarrenWendy ToussaintKim DeswarteManon VanheerswynghelsPhilippe PouliotLiesbet MartensSofie Van GassenConnie M. Arthur et al.

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

2019

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 Parthoens et al.

A1 Journal Article in NATURE COMMUNICATIONS

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 Allez et al.

A1 Journal Article in EUROPEAN JOURNAL OF IMMUNOLOGY

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 Turner et al.

A1 Journal Article in NATURE COMMUNICATIONS

The ORMDL3 asthma susceptibility gene regulates systemic ceramide levels without altering key asthma features in mice

Nincy DebeufAssem ZhakupovaRegula SteinerSofie Van GassenKim DeswarteFarzaneh FayazpourJustine Van MoorleghemKarl VergoteBenjamin PavieKelly Lemeire et al.

A1 Journal Article in JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

2018

Myeloid cell heterogeneity in cancer: not a single cell alike

Mate KissSofie Van GassenKiavash MovahediYvan SaeysDamya Laoui

A1 Journal Article in CELLULAR IMMUNOLOGY

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

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 Savvides et al.

A1 Journal Article in NATURE COMMUNICATIONS

2017

An immune clock of human pregnancy

Nima AghaeepourEdward A GanioDavid McilwainAmy S TsaiMartha TingleSofie Van GassenDyani K GaudilliereQuentin BacaLeslie McNeilRobin Okada et al.

A1 Journal Article in SCIENCE IMMUNOLOGY

Development of machine learning techniques for flow cytometry data

Sofie Van GassenTom DhaeneYvan Saeys

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 Qian et al.

A1 Journal Article in CYTOMETRY PART A

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

Yvan SaeysSofie Van GassenBart Lambrecht

A1 Journal Article in NATURE REVIEWS IMMUNOLOGY

FloReMi : flow density survival regression using minimal feature redundancy

Sofie Van GassenCeline VensTom DhaeneBart LambrechtYvan Saeys

A1 Journal Article in CYTOMETRY PART A

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 Vanheerswynghels et al.

A1 Journal Article in IMMUNITY

Machine learning challenges for single cell data

Sofie Van GassenTom DhaeneYvan 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 Prijck et al.

A1 Journal Article in IMMUNITY

2015

Complex aggregates over clusters of elements

Celine VensSofie Van GassenTom DhaeneYvan 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

Unsupervised trajectory inference using graph mining

Leen De BaetsSofie Van GassenTom DhaeneYvan Saeys

2013

Stable feature selection techniques for microarray data

Sofie Van GassenJoeri RuyssinckYvan SaeysTom Dhaene