Analyzing high-dimensional cytometry data using FlowSOM

K Quintelier, A Couckuyt, A Emmaneel, J Aerts… - Nature protocols, 2021 - nature.com
The dimensionality of cytometry data has strongly increased in the last decade, and in many
situations the traditional manual downstream analysis becomes insufficient. The field is …

LXR signaling controls homeostatic dendritic cell maturation

V Bosteels, S Maréchal, C De Nolf, S Rennen… - Science …, 2023 - science.org
Dendritic cells (DCs) mature in an immunogenic or tolerogenic manner depending on the
context in which an antigen is perceived, preserving the balance between immunity and …

Challenges in translational machine learning

A Couckuyt, R Seurinck, A Emmaneel, K Quintelier… - Human Genetics, 2022 - Springer
Abstract Machine learning (ML) algorithms are increasingly being used to help implement
clinical decision support systems. In this new field, we define as “translational machine …

Sodium chloride in the tumor microenvironment enhances T cell metabolic fitness and cytotoxicity

D Soll, CF Chu, S Sun, V Lutz, M Arunkumar… - Nature …, 2024 - nature.com
The efficacy of antitumor immunity is associated with the metabolic state of cytotoxic T cells,
which is sensitive to the tumor microenvironment. Whether ionic signals affect adaptive …

[HTML][HTML] Circulating T cells in sarcoidosis have an aberrantly activated phenotype that correlates with disease outcome

JR Miedema, LJ de Jong, D van Uden, IM Bergen… - Journal of …, 2024 - Elsevier
Rationale Disease course in sarcoidosis is highly variable. Bronchoalveolar lavage fluid and
mediastinal lymph nodes show accumulation of activated T cells with a T-helper (Th) 17.1 …

How to prepare spectral flow cytometry datasets for high dimensional data analysis: a practical workflow

H den Braanker, M Bongenaar, E Lubberts - Frontiers in immunology, 2021 - frontiersin.org
Spectral flow cytometry is an upcoming technique that allows for extensive multicolor panels,
enabling simultaneous investigation of a large number of cellular parameters in a single …

flowCut: an R package for automated removal of outlier events and flagging of files based on time versus fluorescence analysis

J Meskas, D Yokosawa, S Wang, GC Segat… - Cytometry Part …, 2023 - Wiley Online Library
Technical artifacts such as clogging that occur during the data acquisition process of flow
cytometry data can cause spurious events and fluorescence intensity shifting that impact the …

Ensuring full spectrum flow cytometry data quality for high‐dimensional data analysis

L Ferrer‐Font, G Kraker, KE Hally, KM Price - Current Protocols, 2023 - Wiley Online Library
Full spectrum flow cytometry (FSFC) allows for the analysis of more than 40 parameters at
the single‐cell level. Compared to the practice of manual gating, high‐dimensional data …

Loss of function of XBP1 splicing activity of IRE1α favors B cell tolerance breakdown

Q Reuschlé, L Van Heddegem, V Bosteels… - Journal of …, 2024 - Elsevier
Anti-nuclear antibodies are the hallmark of autoimmune diseases such as systemic lupus
erythematosus (SLE) and scleroderma. However, the molecular mechanisms of B cell …

Early-life thymectomy leads to an increase of granzyme-producing γδ T cells in children with congenital heart disease

A Cramer, T Yang, L Riemann, V Almeida… - Nature …, 2024 - nature.com
Congenital heart disease (CHD) is the most common birth defect in newborns, often
requiring cardiac surgery with concomitant thymectomy that is known to increase disease …