Research Explorer

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Researcher

Robrecht Cannoodt

Publications & Research Data

Awards & Distinctions

44 Results

2025

Defining and benchmarking open problems in single-cell analysis

Malte D. LueckenScott GiganteDaniel B. BurkhardtRobrecht CannoodtDaniel C. StroblNikolay S. MarkovLuke ZappiaGiovanni PallaWesley LewisDaniel Dimitrov et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

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

2024

VIB Hackathon on spatial omics tools and methods

Benjamin RombautLotte PollarisChananchida Sang-aramMichiel Ver CruysseRobrecht CannoodtFrank VernaillenArne DefauwJulien MortierMayar AliKresimir Bestak et al.

2023

Dual molecular effects of constitutional SF3B2 variants cause a novel dominant spliceosomopathy displaying retinitis pigmentosa or developmental skeletal anomalies

Stijn Van de SompeleCaroline Van CauwenberghMarjolein CarronAlfredo Dueñas ReyFrauke CoppietersToon RosseelHong TranRobrecht CannoodtThalia Van LaethemBrecht Guillemyn et al.

2022

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

2021

A sandbox for prediction and integration of DNA, RNA, and proteins in single cells

Malte D LueckenDaniel Bernard BurkhardtRobrecht CannoodtChristopher LanceAditi AgrawalHananeh AlieeAnn T ChenLouise DeconinckAngela M DetweilerAlejandro A Granados et al.

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

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

Robrecht CannoodtWouter SaelensLouise DeconinckYvan Saeys

A1 Journal Article in NATURE COMMUNICATIONS

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.

Viash : from scripts to pipelines

Robrecht CannoodtHendrik CannoodtEric Van de KerckhoveAndy BoschmansDries De MaeyerToni Verbeiren

2020

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

The rockerverse : packages and applications for containerisation with R

Daniel NüstDirk EddelbuettelDom BennettRobrecht CannoodtDav ClarkGergely DarócziMark EdmondsonColin FayEllis HughesLars Kjeldgaard et al.

A1 Journal Article in R JOURNAL

TinGa : fast and flexible trajectory inference with Growing Neural Gas

Helena TodorovRobrecht CannoodtWouter SaelensYvan Saeys

A1 Journal Article in BIOINFORMATICS

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

2019

A comparison of single-cell trajectory inference methods

Wouter SaelensRobrecht CannoodtHelena TodorovYvan Saeys

A1 Journal Article in NATURE BIOTECHNOLOGY

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

Robrecht CannoodtWouter SaelensHelena TodorovYvan Saeys

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

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

The RNA Atlas, a single nucleotide resolution map of the human transcriptome

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

2018

A comprehensive evaluation of module detection methods for gene expression data

Wouter SaelensRobrecht CannoodtYvan Saeys

A1 Journal Article in NATURE COMMUNICATIONS

Genomic amplifications and distal 6q loss : novel markers for poor survival in high-risk neuroblastoma patients

Pauline DepuydtValentina BoevaToby D HockingRobrecht CannoodtInge M AmbrosPeter F AmbrosShahab AsgharzadehEdward F AttiyehValérie CombaretRaffaella Defferrari et al.

A1 Journal Article in JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE

IncGraph : incremental graphlet counting for topology optimisation

Robrecht CannoodtJoeri RuyssinckJana RamonKatleen De PreterYvan Saeys

A1 Journal Article in PLOS ONE

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

arrEYE : a customized platform for high-resolution copy number analysis of coding and noncoding regions of known and candidate retinal dystrophy genes and retinal noncoding RNAs

Caroline Van CauwenberghKristof Van SchilRobrecht CannoodtMiriam BauwensThalia Van LaethemSarah De JaegereWouter SteyaertTom SanteBjörn MentenBart Leroy et al.

A1 Journal Article in GENETICS IN MEDICINE

Early and late effects of pharmacological ALK inhibition on the neuroblastoma transcriptome

Shana ClaeysGeertrui DeneckerRobrecht CannoodtCandy KumpsKaat DurinckFranki SpelemanKatleen De Preter

A1 Journal Article in ONCOTARGET

Genomic amplifications and distal 6q loss are novel markers for poor survival in high-risk neuroblastoma patients

Pauline DepuydtValentina BoevaToby D HockingRobrecht CannoodtInge M AmbrosPeter F AmbrosShahab AsgharzadehEdward F AttiyehValérie CombaretRaffaella Defferrari et al.

Identification of novel, rare markers for poor survival in high-risk neuroblastoma patients by merging and reanalysing existing datasets

Pauline DepuydtValentina BoevaToby HockingRobrecht CannoodtInge AmbrosPeter AmbrosShahab AsgharzadehEdward AttiyehValérie CombaretRaffaella Defferrari et al.

2016

Computational methods for trajectory inference from single-cell transcriptomics

Robrecht CannoodtWouter SaelensYvan Saeys

A1 Journal Article in EUROPEAN JOURNAL OF IMMUNOLOGY

Dissecting the NOTCH1 driven transcriptional landscape in T-cell acute lymphoblastic leukemia at single cell level

Karen VerboomKaat DurinckCeline EveraertRobrecht CannoodtPieter Van VlierbergheJo VandesompeleFranki Speleman

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

Robrecht CannoodtWouter SaelensKatleen De PreterYvan Saeys

Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma

Anneleen DecockMaté OngenaertRobrecht CannoodtKimberly VerniersBram De WildeGenevieve LaureysNadine Van RoyAna Pilar BerbegallJulie Bienertova-VaskuNick Bown et al.

A1 Journal Article in ONCOTARGET

Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma

Anneleen DecockMaté OngenaertRobrecht CannoodtKimberly VerniersBram De WildeGenevieve LaureysNadine Van RoyAna Pilar BerbegallJulie Bienertova-VaskuNick Bown et al.

The genomic region encompassing the overlapping SOX11 and Lnc-SOX11-1:1 loci exhibits a complex DNA copy number and mRNA expression pattern

Bieke DecaestekerSara De BrouwerRobrecht CannoodtDries RombautWouter Van LoockeAnnelies FieuwFanny De VloedPieter-Jan VoldersBjörn MentenRogier Versteeg et al.

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

2015

Differential module analysis in neuroblastoma regulatory networks

Robrecht CannoodtAnneleen BeckersCaroline Van CauwenberghFranki SpelemanKatleen De PreterYvan Saeys

Inferring developmental chronologies from single cell RNA

Robrecht CannoodtWouter SaelensKatleen De PreterYvan Saeys

Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma

Anneleen DecockMaté OngenaertRobrecht CannoodtKimberly VerniersBram De WildeGenevieve LaureysNadine Van RoyAna Pilar BerbegallJulie Bienertova-VaskuNick Bown et al.

2014

Differential module analysis in neuroblastoma regulatory networks

Robrecht CannoodtAnneleen BeckersCaroline Van CauwenberghKatleen De PreterYvan Saeys

Identifying novel neuroblastoma oncogenes using semi-supervised learning

Leen De BaetsRobrecht CannoodtJoeri RuyssinckKatleen De PreterTom DhaeneYvan Saeys

2013

Network inference by integrating biclustering and feature selection

Robrecht CannoodtJoeri RuyssinckKatleen De PreterTom DhaeneYvan Saeys