VIB Single Cell Core

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Title DOI
https://doi.org/10.1126/sciimmunol.add3955 LXR signaling controls homeostatic dendritic cell maturation
https://doi.org/10.1093/plcell/koae003 Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics
https://doi.org/10.1016/j.xcrm.2024.101516 Neoantigen-targeted dendritic cell vaccination in lung cancer patients induces long-lived T cells exhibiting the full differentiation spectrum
https://doi.org/10.1073/pnas.2303758120 Cell type–specific attenuation of brassinosteroid signaling precedes stomatal asymmetric cell division
https://doi.org/10.1038/s41477-023-01419-8 A redundant transcription factor network steers spatiotemporal Arabidopsis triterpene synthesis
https://doi.org/10.1038/s41467-024-46076-3 Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF
https://doi.org/10.1016/j.celrep.2025.115240 A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators
https://doi.org/10.1158/2326-6066.cir-23-0677 Knocking Out CD70 Rescues CD70-Specific NanoCAR T Cells from Antigen-Induced Exhaustion
https://doi.org/10.1111/acel.14120 S100A8 ‐enriched microglia populate the brain of tau‐seeded and accelerated aging mice
https://doi.org/10.1016/j.celrep.2024.114020 An autophagy program that promotes T cell egress from the lymph node controls responses to immune checkpoint blockade
https://doi.org/10.1084/jem.20220942 Single-cell profiling identifies a novel human polyclonal unconventional T cell lineage
https://doi.org/10.1016/j.jhep.2024.07.007 Infection history imprints prolonged changes to the epigenome, transcriptome and function of Kupffer cells
https://doi.org/10.1080/15548627.2023.2247742 Autophagy critically controls skin inflammation and apoptosis-induced stem cell activation
https://doi.org/10.2337/db22-0852 A Plasma miR-193b-365 Signature Combined With Age and Glycemic Status Predicts Response to Lactococcus lactis–Based Antigen-Specific Immunotherapy in New-Onset Type 1 Diabetes
https://doi.org/10.1038/s41477-025-01938-6 The dynamic and diverse nature of parenchyma cells in the Arabidopsis root during secondary growth
https://doi.org/10.1186/s12943-023-01908-6 A bispecific Clec9A-PD-L1 targeted type I interferon profoundly reshapes the tumor microenvironment towards an antitumor state
https://doi.org/10.1007/978-1-0716-3354-0_4 Single Cell RNA-Sequencing in Arabidopsis Root Tissues
https://doi.org/10.1186/s13045-024-01629-3 A single-cell transcriptomic map of the murine and human multiple myeloma immune microenvironment across disease stages
https://doi.org/10.1093/bioinformatics/btae549 Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing
https://doi.org/10.1002/eji.202451265 ThymoSpheres culture: A model to study human polyclonal unconventional T cells
https://doi.org/10.1016/j.isci.2024.111169 ZEB2 drives intra-tumor heterogeneity and skin squamous cell carcinoma formation with distinct EMP transition states
https://doi.org/10.1172/jci176403 Neutrophil-enriched gene signature correlates with teplizumab therapy resistance in different stages of type 1 diabetes
https://doi.org/10.1101/2021.12.07.471549 DALI (Diversity AnaLysis Interface): a novel tool for the integrated analysis of multimodal single cell RNAseq data and immune receptor profiling
https://doi.org/10.1101/2023.01.22.523482 Knocking out CD70 rescues CD70-specific nanoCAR T cells from antigen induced exhaustion
https://doi.org/10.1101/2022.05.24.492634 Single-cell profiling identifies a spectrum of human unconventional intraepithelial T lineage cells
https://doi.org/10.1101/2023.11.10.566543 S100A8-enriched microglia populate the brain of tau-seeded and accelerated aging mice
https://doi.org/10.1101/2024.02.22.581508 Scywalker: scalable end-to-end data analysis workflow for nanopore single-cell transcriptome sequencing
https://doi.org/10.1101/2024.07.18.604073 The dynamic and diverse nature of parenchyma cells in the Arabidopsis root during secondary growth
https://doi.org/10.1101/2025.06.22.659756 Gene regulatory network analysis of somatic embryogenesis identifies morphogenic genes that increase maize transformation frequency
https://doi.org/10.1101/2023.07.17.549282 An autophagy program that promotes T cell egress from the lymph node controls responses to immune checkpoint blockade
https://doi.org/10.7554/elife.98344 TCR transgenic clone selection guided by immune receptor analysis and single-cell RNA expression of polyclonal responders
https://doi.org/10.7554/elife.98344.1 TCR transgenic clone selection guided by immune receptor analysis and single cell RNA expression of polyclonal responders
https://doi.org/10.1101/2024.08.30.610433 Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics
https://doi.org/10.7554/elife.98344.2.sa0 Author response: TCR transgenic clone selection guided by immune receptor analysis and single cell RNA expression of polyclonal responders
https://doi.org/10.7554/elife.98344.2 TCR transgenic clone selection guided by immune receptor analysis and single cell RNA expression of polyclonal responders
https://doi.org/10.7554/elife.98344.3 TCR transgenic clone selection guided by immune receptor analysis and single-cell RNA expression of polyclonal responders
https://doi.org/10.1101/2025.09.05.674408 Conserved transcriptional reprogramming in nematode infected root cells
https://doi.org/10.64898/2026.01.22.701092 Decoding stage-specific symbiotic programs in the Rhizophagus irregularis –tomato interaction using single-nucleus transcriptomics
https://doi.org/10.64898/2026.03.25.714157 A Myb-dominated gene regulatory network universally controls sexual cell fate transitions in diatoms
https://doi.org/10.64898/2026.03.25.714282 Beyond a binary view of cystic fibrosis: systemic immunity and inflammation across the spectrum of CFTR dysfunction