Publications
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Single cell RNA sequencing analysis did not predict hepatocyte infection by SARS-CoV-2 Vrije Universiteit Brussel
SMARTer single cell total RNA sequencing Ghent University
Lower respiratory tract single-cell RNA sequencing and neutrophil extracellular trap profiling of COVID-19-associated pulmonary aspergillosis: a single centre, retrospective, observational study. KU Leuven Flanders Institute for Biotechnology
BACKGROUND: COVID-19-associated pulmonary aspergillosis (CAPA) is a severe superinfection with the fungus Aspergillus affecting patients who are critically ill with COVID-19. The pathophysiology and the role of neutrophil extracellular traps (NETs) in this infection are largely unknown. We aimed to characterise the immune profile, with a focus on neutrophils and NET concentrations, of critically ill patients with COVID-19, with or without CAPA. ...
Single-Cell RNA Sequencing of the T Helper Cell Response to House Dust Mites Defines a Distinct Gene Expression Signature in Airway Th2 Cells. Flanders Institute for Biotechnology Ghent University
Targeted RNA sequencing for upfront analysis of actionable driver alterations in non-small cell lung cancer KU Leuven
OBJECTIVES: Targeted RNA-based Next-Generation Sequencing (tRNA-seq) is increasingly being used in molecular diagnostics for gene fusion detection in non-small cell lung cancer (NSCLC). However, few data support its clinical application for the detection of single nucleotide variants (SNVs) and small insertions/deletions. In this study, we evaluated the performance of tRNA-seq using Archer FusionPlex for simultaneous detection of actionable gene ...
Inferring developmental chronologies from single cell RNA Ghent University
With the advent of single cell RNA sequencing, it is now possible to analyse the transcriptomes of hundreds of individual cells in an unbiased manner. Reconstructing the developmental chronology of differentiating cells is a challenging task, and doing so in a unsupervised and robust manner is a hitherto untackled problem. We developed a truly unsupervised developmental chronology inference technique, and evaluated its performance and robustness ...
RNA sequencing data : hitchhiker's guide to expression analysis Ghent University
Gene expression is the fundamental level at which the results of various genetic and regulatory programs are observable. The measurement of transcriptome-wide gene expression has convincingly switched from microarrays to sequencing in a matter of years. RNA sequencing (RNA-seq) provides a quantitative and open system for profiling transcriptional outcomes on a large scale and therefore facilitates a large diversity of applications, including ...
Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis. Flanders Institute for Biotechnology KU Leuven University of Antwerp
Recent advances in T-cell receptor repertoire analysis: bridging the gap with multimodal single-cell RNA sequencing Institute of Tropical Medicine University of Antwerp
T cells exercise a multitude of functions such as cytotoxicity, secretion of immunomodulating cytokines or regulation of tolerance, collectively resulting in an effective control of immune-related disease. Through the unique mechanism of V(D)J recombination, T cells express a highly specific receptor complex known as the T-cell receptor (TCR). Single-cell sequencing technologies have paved the road for interrogating the transcriptome and the ...