Research Explorer

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Researcher

Yvan Saeys

Awards & Distinctions

306 Results

2024

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.

U Journal Article in CELL

An introduction to adversarially robust deep learning

Jonathan PeckBart GoossensYvan Saeys

A1 Journal Article in IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Optimizing computational cytometry tools for clinical applications

Artuur CouckuytYvan SaeysTessa Kerre

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

Lauren TheunissenThomas MortierYvan SaeysWillem Waegeman

A1 Journal Article in BIOINFORMATICS

2023

A bispecific Clec9A-PD-L1 targeted type I interferon profoundly reshapes the tumor microenvironment towards an antitumor state

Sandra Van LintAlexander Van ParysBram Van Den EeckhoutNiels VandammeStephane PlaisanceAnnick VerheeDominiek CatteeuwElke RoggeJennifer De GeestNele Vanderroost et al.

A1 Journal Article in MOLECULAR CANCER

A redundant transcription factor network steers spatiotemporal Arabidopsis triterpene synthesis

Trang Hieu NguyenLouis ThiersAlex Van MoerkerckeYuechen BaiPatricia Fernandez CalvoMax MinneThomas DepuydtMaite Colinas MartinezKevin VerstaenGert Van Isterdael et al.

A1 Journal Article in NATURE PLANTS

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

An introduction to information technology for lawyers

Bookchapter in An introduction to law & technology

Cell type-specific attenuation of brassinosteroid signaling precedes stomatal asymmetric cell division

Kim EunjiCheng ZhangBoyu GuoThomas EekhoutAnaxi HoubaertJos WendrichNiels VandammeManish TiwariClaire Simon--VezoIsabelle Vanhoutte et al.

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

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

Ferroptosis and pyroptosis signatures in critical COVID-19 patients

Cédric PelemanSamya Van CoillieSymen LigthartSze Men ChoiJan De WaelePieter DepuydtDominique BenoitHannah SchaubroeckSven M. FrancqueKarolien Dams et al.

A1 Journal Article in CELL DEATH AND DIFFERENTIATION

Functions of the RIP kinase family members in the skin

Corinne UrwylerGiel TangheMichael DevosPaco HulpiauYvan SaeysWim Declercq

A1 Journal Article in CELLULAR AND MOLECULAR LIFE SCIENCES

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

Improving the robustness of deep neural networks to adversarial perturbations

Jonathan PeckYvan SaeysBart Goossens

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

Machine learning pipeline for predicting bone marrow edema along the sacroiliac joints on magnetic resonance imaging

Joris RoelsAnn-Sophie De CraemerThomas RensonManouk de HoogeArne GevaertThomas Van Den BergheLennart JansNele HerregodsPhilippe CarronFilip Van den Bosch et al.

A1 Journal Article in ARTHRITIS & RHEUMATOLOGY

Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability

Anthony SonrelAlmut LuetgeCharlotte SonesonIzaskun MallonaPierre-Luc GermainSergey KnyazevJeroen GilisReto GerberRuth SeurinckDominique Paul et al.

A1 Journal Article in GENOME BIOLOGY

Modeling intercellular communication from transcriptomics data by linking ligands to target genes

Robin BrowaeysYvan Saeys

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

Robin BrowaeysJeroen GilisChananchida Sang-aramPieter De BleserLevi HosteSimon TavernierDiether LambrechtsRuth SeurinckYvan Saeys

QT–GWAS : a novel method for unveiling biosynthetic loci affecting qualitative metabolic traits

Marlies BrouckaertMeng PengRené HöferIlias El HouariChiarina DarrahVeronique StormeYvan SaeysRuben VanholmeGeert GoeminneVitaliy I. Timokhin et al.

A1 Journal Article in MOLECULAR PLANT

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

Sodium perturbs mitochondrial respiration and induces dysfunctional Tregs

Beatriz F. Côrte-RealIbrahim HamadRebeca Arroyo HorneroSabrina GeisbergerJoris RoelsLauren Van ZeebroeckAleksandra DyczkoMarike W. van GisbergenHenry KurniawanAllon Wagner et al.

A1 Journal Article in CELL METABOLISM

2022

A cellular hierarchy in melanoma uncouples growth and metastasis

Panagiotis KarrasIgnacio BordeuJoanna PozniakAda NowosadCecilia PazziNina Van RaemdonckEwout LandeloosYannick Van HerckDennis PedriGreet Bervoets et al.

A1 Journal Article in NATURE

A machine learning pipeline for prediction of bone marrow oedema along the sacroiliac joints on magnetic resonance imaging

Joris RoelsAnn-Sophie De CraemerThomas RensonManouk de HoogeArne GevaertLennart JansNele HerregodsThomas Van Den BerghePhilippe CarronFilip Van den Bosch et al.

An introduction to information technology for lawyers

Bookchapter in An introduction to law & technology

Angiogenesis goes computational : the future way forward to discover new angiogenic targets?

Abhishek SubramanianPooya ZakeriMira MousaHalima AlnaqbiFatima Yousif AlshamsiLeo BettoniErnesto DamianiHabiba AlsafarYvan SaeysPeter Carmeliet

A1 Journal Article in COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL

CARD14 signalling ensures cell survival and cancer associated gene expression in prostate cancer cells

Domien VannesteJens StaalMira HaegmanYasmine DriegeMarieke CarelsElien Van NuffelPieter De BleserYvan SaeysRudi BeyaertInna Afonina

A1 Journal Article in BIOMEDICINES

CD8 memory precursor cell generation is a continuous process

Helena TodorovMargaux PrieuxDaphne LaubretonMatteo BouvierShaoying WangSimon de BernardChristophe ArpinRobrecht CannoodtWouter SaelensArnaud Bonnaffoux et al.

A1 Journal Article in ISCIENCE

Cell type-specific attenuation of brassinosteroid signalling drives stomatal asymmetric cell division

Kim EunjiCheng ZhangBoyu GuoThomas EekhoutAnaxi HoubaertJos WendrichNiels VandammeManish TiwariClaire Simon--VezoIsabelle Vanhoutte et al.

Challenges in translational machine learning

Artuur CouckuytRuth SeurinckAnnelies EmmaneelKatrien QuintelierDavid NovákSofie Van GassenYvan Saeys

A1 Journal Article in HUMAN GENETICS

Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

Viacheslav MylkaIrina MatetoviciSuresh PoovathingalJeroen AertsNiels VandammeRuth SeurinckKevin VerstaenGert HulselmansSilvie van den HoeckeIsabelle Scheyltjens et al.

A1 Journal Article in GENOME BIOLOGY

Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition

Johannes BuesMarjan BiocaninJoern PezoldtRiccardo DaineseAntonius ChrisnandySaba RezakhaniWouter SaelensVincent GardeuxRevant GuptaRita Sarkis et al.

A1 Journal Article in NATURE METHODS

Distinct transcriptional programs in ascitic and solid cancer cells induce different responses to chemotherapy in high-grade serous ovarian cancer

Nele LoretNiels VandammeJordy De ConinckJoachim TaminauKato De ClercqGillian BlanckeSven JonckheereSteven GoossensKelly LemeireSofie De Prijck et al.

A1 Journal Article in MOLECULAR CANCER RESEARCH

Evaluating feature attribution methods in the image domain

Arne GevaertAxel-Jan RousseauThijs BeckerDirk ValkenborgTijl De BieYvan Saeys

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

PDD-SHAP: Fast Approximations for Shapley Values using Functional Decomposition

Arne GevaertYvan Saeys

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

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

Single-cell RNA and protein profiling of immune cells from the mouse brain and its border tissues

Isabelle ScheyltjensHannah Van HoveKaren De VlaminckDaliya KanchevaJonathan BastosMonica Vara-PerezAna Rita Pombo AntunesLiesbet MartensCharlotte ScottJo Van Ginderachter et al.

A1 Journal Article in NATURE PROTOCOLS

Single-cell transcriptomics sheds light on the identity and metabolism of developing leaf cells

Rubén Tenorio BerrioKevin VerstaenNiels VandammeJulie PevernagieIgnacio AchónJulie Van DuyseGert Van IsterdaelYvan SaeysLieven De VeylderDirk Inzé et al.

A1 Journal Article in PLANT PHYSIOLOGY

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

TIM3+ TRBV11-2 T cells and IFNγ signature in patrolling monocytes and CD16+ NK cells delineate MIS-C

Levi HosteLisa RoelsLeslie NaesensVictor BosteelsStijn VanheeSam DupontCédric BosteelsRobin BrowaeysNiels VandammeKevin Verstaen et al.

A1 Journal Article in JOURNAL OF EXPERIMENTAL MEDICINE

Targeting ferroptosis protects against experimental (multi)organ dysfunction and death

Samya Van CoillieEmily Van SanInes GoetschalckxBartosz WiernickiBanibrata MukhopadhyayWulf TonnusSze Men ChoiRia RoelandtCatalina DumitrascuLudwig Lamberts et al.

A1 Journal Article in NATURE COMMUNICATIONS

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

The curse revisited : when are distances informative for the ground truth in noisy high-dimensional data?

Robin VandaeleBo KangTijl De BieYvan Saeys

Topologically regularized data embeddings

Robin VandaeleBo KangJefrey LijffijtTijl De BieYvan Saeys

2021

A study on the calibration of fingerprint classifiers

Daniel Peralta CámaraLin TangMaxim LippeveldYvan Saeys

A20 deficiency in myeloid cells protects mice from diet-induced obesity and insulin resistance due to increased fatty acid metabolism

Leen CatrysseBastiaan MaesParul MehrotraArne MartensEsther HosteLiesbet MartensChristian MaueröderAnneleen RemmerieAnna BujkoKarolina Slowicka et al.

A1 Journal Article in CELL REPORTS

Advances and opportunities in single-cell transcriptomics for plant research

Carolin SeyfferthJim RenemaJos WendrichThomas EekhoutRuth SeurinckNiels VandammeBernhard BlobYvan SaeysYrjo HelariuttaKenneth D. Birnbaum et al.

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

Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization

Pawel RoszakJung-ok HeoBernhard BlobKoichi ToyokuraYuki SugiyamaMaria Angels de Luis BalaguerWinnie W. Y. LauFiona HameyJacopo CirroneEwelina Madej et al.

A1 Journal Article in SCIENCE

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

DALI (Diversity AnaLysis Interface) : a novel tool for the integrated analysis of multimodal single cell RNAseq data and immune receptor profiling

Kevin VerstaenInés LammensJana RoelsYvan SaeysBart LambrechtNiels VandammeStijn Vanhee

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 Saeys et al.

A1 Journal Article in EMBO REPORTS

Graph approximations to geodesics on metric graphs

Robin VandaeleYvan SaeysTijl De Bie

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

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 Vivier et al.

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 Hennart et al.

A1 Journal Article in CANCERS

Macrophages are metabolically heterogeneous within the tumor microenvironment

Xenia GeeraertsJuan Fernandez-GarciaFelix J. HartmannKyra E. de GoedeLiesbet MartensYvon ElkrimAyla DebraekeleerBenoit StijlemansAnke VandekeereGianmarco Rinaldi et al.

A1 Journal Article in CELL REPORTS

Maize specialized metabolome networks reveal organ-preferential mixed glycosides

Sandrien DesmetYvan SaeysKevin VerstaenRebecca DauweHoon KimClaudiu NiculaesAtsushi FukushimaGeert GoeminneRuben VanholmeJohn Ralph et al.

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. Bosisio et al.

A1 Journal Article in NATURE COMMUNICATIONS

Non-cell autonomous and spatiotemporal signaling from a tissue organizer orchestrates root vascular development

Baojun YangMax MinneFederica BrunoniLenka PlačkováIvan PetříkYanbiao SunJonah NolfWouter SmetKevin VerstaenJos Wendrich et al.

A1 Journal Article in NATURE PLANTS

OTULIN maintains skin homeostasis by controlling keratinocyte death and stem cell identity

Esther HosteKim LecomteKarl AnnusverNiels VandammeJana RoelsSophia MaschalidiLien VerboomHanna-Kaisa VikkulaMozes SzeLisette Van Hove et al.

A1 Journal Article in NATURE COMMUNICATIONS

Recent advances in trajectory inference from single-cell omics data

Louise DeconinckRobrecht CannoodtWouter SaelensBart DeplanckeYvan Saeys

A2 Journal Article in CURRENT OPINION IN SYSTEMS BIOLOGY

SCMFTS : scalable and distributed complexity measures and features for univariate and multivariate time series in Big Data environments

Francisco J. BaldanDaniel Peralta CámaraYvan SaeysJose M. Benitez

A1 Journal Article in INTERNATIONAL JOURNAL OF COMPUTATIONAL INTELLIGENCE SYSTEMS

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 Hove et al.

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

Targeting ferroptosis protects against multiorgan dysfunction and death

Tom Vanden BergheSamya Van CoillieInes GoetschalckxBartosz WiernickiBanibrata MukhopadhyayWulf TonnusEmily Van SanSze Men ChoiRia RoelandtCatalina Dumitrascu et al.

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

Lucia LorenziHua-Sheng ChiuFrancisco Avila CobosStephen GrossPieter-Jan VoldersRobrecht CannoodtJustine NuytensKatrien VanderheydenJasper AnckaertSteve Lefever et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

The RNA Atlas expands the catalog of human non-coding RNAs (June, 10.1038/s41587-021-00936-1, 2021)

Lucia LorenziHua-Sheng ChiuFrancisco Avila CobosStephen GrossPieter-Jan VoldersRobrecht CannoodtJustine NuytensKatrien VanderheydenJasper AnckaertSteve Lefever et al.

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 Tuck et al.

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 Rouchon et al.

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 Peralta CámaraMiguel 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 Cámara

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

Cédric BosteelsKatrijn NeytManon VanheerswynghelsMary van HeldenDorine SichienNincy DebeufSofie De PrijckVictor BosteelsNiels VandammeLiesbet Martens et al.

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 Dionne et al.

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 Maelfait et al.

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 Vanhockerhout et al.

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 Low et al.

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 Peralta CámaraYvan 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 Arents et al.

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 Parthoens et al.

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 Scott et al.

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 Peralta CámaraYvan 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 Gonçalves et al.

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 Allez et al.

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 Turner et al.

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 Bleser et al.

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 Kremer et al.

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 Dhondt et al.

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 Saeys et al.

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 Bleser et al.

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 Gillebert et al.

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 Peralta CámaraIsaac 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 Savvides et al.

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 Cannoodt et al.

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 Matthys et al.

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 Benet et al.

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 Vandekerckhove et al.

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

Daniel Peralta CámaraIsaac 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-Thomsen et al.

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 Saeys et al.

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 Raes et al.

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 Samsom et al.

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 Bonte et al.

A1 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 Qian et al.

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 Raes et al.

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 Dewaele et al.

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 Vandekerckhove et al.

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 Salerno et al.

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 Vanheerswynghels et al.

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-Thomsen et al.

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 Haigh et al.

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 Prijck et al.

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 Lambrecht et al.

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 Bachert et al.

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 Rancière et al.

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 Pouliot et al.

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 Stolovitzky et al.

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 Bielza et al.

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 JoshiYvan SaeysTim Van den BulckeKoenraad Van LeemputPiet Van RemortelMartin KuiperKathleen Marchal et al.

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 Cooke et al.

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 DegroeveYves 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

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

Building genomic profiles for uncovering segmental homology in the twilight zone

Cedric SimillionKlaas VandepoeleYvan SaeysYves Van de Peer

A1 Journal Article in GENOME RESEARCH

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