Tamim Abdelaal
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View article: IL-21-dependent Ly6C+Ly6G+CD4+ T cells found in lung enhance macrophages function against Actinobacillus pleuropneumoniae infection in mice
IL-21-dependent Ly6C+Ly6G+CD4+ T cells found in lung enhance macrophages function against Actinobacillus pleuropneumoniae infection in mice Open
IL-21/IL-21R signaling is crucial in various immune diseases and cellular development, however, its role in bacterial pneumonia remains unclear. Here, IL-21R knockout (IL-21R − /− ) mice were more susceptible to Actinobacillus pleuropneumo…
View article: A single-cell atlas of mouse central nervous system immune cells reveals unique infection-stage immune signatures during the progression of meningitis caused by Streptococcus suis
A single-cell atlas of mouse central nervous system immune cells reveals unique infection-stage immune signatures during the progression of meningitis caused by Streptococcus suis Open
Meningitis caused by Streptococcus suis serotype 2 (SS2) in humans and pigs is an acute nervous disorder associated with serious sequelae. Bacterial meningitis is tightly associated with immune cell responses and the local immune microenvi…
View article: Mass cytometry analysis reveals a cross-tissue immune landscape in <i>Actinobacillus pleuropneumoniae</i> -induced pneumonia
Mass cytometry analysis reveals a cross-tissue immune landscape in <i>Actinobacillus pleuropneumoniae</i> -induced pneumonia Open
Porcine contagious pleuropneumonia caused by Actinobacillus pleuropneumoniae (APP) is a fatal respiratory disease that threatens the worldwide farming industry’s health. The immune responses of extrapulmonary tissues play an important role…
View article: Benchmarking of automated cancer cell annotation methods for scRNA-seq data reveals Consensus annotation as the preferred method
Benchmarking of automated cancer cell annotation methods for scRNA-seq data reveals Consensus annotation as the preferred method Open
Targeted cancer therapies have shown therapeutic advantages due to tumor-specific drug activity. Single-cell RNA-sequencing has been widely used in cancer studies to define different cellular identities. However, accurate identification of…
View article: Integration of mass cytometry and mass spectrometry imaging for spatially resolved single-cell metabolic profiling
Integration of mass cytometry and mass spectrometry imaging for spatially resolved single-cell metabolic profiling Open
View article: SIRV: spatial inference of RNA velocity at the single-cell resolution
SIRV: spatial inference of RNA velocity at the single-cell resolution Open
RNA Velocity allows the inference of cellular differentiation trajectories from single-cell RNA sequencing (scRNA-seq) data. It would be highly interesting to study these differentiation dynamics in the spatial context of tissues. Estimati…
View article: Activated HLA-DR+CD38+ Effector Th1/17 Cells Distinguish Crohn’s Disease-associated Perianal Fistulas from Cryptoglandular Fistulas
Activated HLA-DR+CD38+ Effector Th1/17 Cells Distinguish Crohn’s Disease-associated Perianal Fistulas from Cryptoglandular Fistulas Open
Background Perianal fistulas are a debilitating complication of Crohn’s disease (CD). Due to unknown reasons, CD-associated fistulas are in general more difficult to treat than cryptoglandular fistulas (non-CD-associated). Understanding th…
View article: SpaceWalker enables interactive gradient exploration for spatial transcriptomics data
SpaceWalker enables interactive gradient exploration for spatial transcriptomics data Open
View article: An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics
An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics Open
Multi-omic analyses are necessary to understand the complex biological processes taking place at the tissue and cell level, but also to make reliable predictions about, for example, disease outcome. Several linear methods exist that create…
View article: Combining Mass Cytometry Data by CyTOFmerge Reveals Additional Cell Phenotypes in the Heterogeneous Ovarian Cancer Tumor Microenvironment: A Pilot Study
Combining Mass Cytometry Data by CyTOFmerge Reveals Additional Cell Phenotypes in the Heterogeneous Ovarian Cancer Tumor Microenvironment: A Pilot Study Open
The prognosis of high-grade serous ovarian carcinoma (HGSOC) is poor, and treatment selection is challenging. A heterogeneous tumor microenvironment (TME) characterizes HGSOC and influences tumor growth, progression, and therapy response. …
View article: Benchmarking variational AutoEncoders on cancer transcriptomics data
Benchmarking variational AutoEncoders on cancer transcriptomics data Open
Deep generative models, such as variational autoencoders (VAE), have gained increasing attention in computational biology due to their ability to capture complex data manifolds which subsequently can be used to achieve better performance i…
View article: High-dimensional analysis reveals an immune atlas and novel neutrophil clusters in the lungs of model animals with Actinobacillus pleuropneumoniae-induced pneumonia
High-dimensional analysis reveals an immune atlas and novel neutrophil clusters in the lungs of model animals with Actinobacillus pleuropneumoniae-induced pneumonia Open
View article: Integration of Mass Cytometry and Mass Spectrometry Imaging for Spatially Resolved Single Cell Metabolic Profiling
Integration of Mass Cytometry and Mass Spectrometry Imaging for Spatially Resolved Single Cell Metabolic Profiling Open
Integration of spatial omics technologies can provide important insights into the biology of tissues. We combined mass spectrometry imaging-based metabolomics and imaging mass cytometry-based immunophenotyping on the same single tissue sec…
View article: Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models
Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models Open
View article: Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain
Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain Open
View article: Spondyloarthritis mass cytometry immuno-monitoring: a proof of concept study in the tight-control and treat-to target TiCoSpA trial
Spondyloarthritis mass cytometry immuno-monitoring: a proof of concept study in the tight-control and treat-to target TiCoSpA trial Open
Objective Mass cytometry (MC) immunoprofiling allows high-parameter phenotyping of immune cells. We set to investigate the potential of MC immuno-monitoring of axial spondyloarthritis (axSpA) patients enrolled in the Tight Control Spondylo…
View article: An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics
An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics Open
Multi-omic analyses contribute to understanding complex biological processes, but also to making reliable predictions about, for example, disease outcomes. Several linear joint dimensionality reduction methods exist, but recently neural ne…
View article: SpaceWalker: Interactive Gradient Exploration for Spatial Transcriptomics Data
SpaceWalker: Interactive Gradient Exploration for Spatial Transcriptomics Data Open
Summary Spatial transcriptomics (ST) enables profiling the expression of hundreds of genes in tissue sections, down to the level of single cells in their tissue environment. The gradient structure of ST data is particularly interesting for…
View article: OX40 agonism enhances PD-L1 checkpoint blockade by shifting the cytotoxic T cell differentiation spectrum
OX40 agonism enhances PD-L1 checkpoint blockade by shifting the cytotoxic T cell differentiation spectrum Open
View article: Benchmarking Variational AutoEncoders on cancer transcriptomics data
Benchmarking Variational AutoEncoders on cancer transcriptomics data Open
Deep generative models, such as variational autoencoders (VAE), have gained increasing attention in computational biology due to their ability to capture complex data manifolds which subsequently can be used to achieve better performance i…
View article: scTopoGAN: unsupervised manifold alignment of single-cell data
scTopoGAN: unsupervised manifold alignment of single-cell data Open
Motivation Single-cell technologies allow deep characterization of different molecular aspects of cells. Integrating these modalities provides a comprehensive view of cellular identity. Current integration methods rely on overlapping featu…
View article: Processed data used for spatial analysis of DMD mouse models
Processed data used for spatial analysis of DMD mouse models Open
This repository contains seurat objects and .H5AD files that were used in the analysis described in the paper titled "Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models"<…
View article: Processed data used for spatial analysis of DMD mouse models
Processed data used for spatial analysis of DMD mouse models Open
This repository contains seurat objects and .H5AD files that were used in the analysis described in the paper titled "Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models"<…
View article: A third vaccination with a single T cell epitope confers protection in a murine model of SARS-CoV-2 infection
A third vaccination with a single T cell epitope confers protection in a murine model of SARS-CoV-2 infection Open
Understanding the mechanisms and impact of booster vaccinations are essential in the design and delivery of vaccination programs. Here we show that a three dose regimen of a synthetic peptide vaccine elicits an accruing CD8 + T cell respon…
View article: SIRV: Spatial inference of RNA velocity at the single-cell resolution
SIRV: Spatial inference of RNA velocity at the single-cell resolution Open
Spatial transcriptomics and scRNA-seq datasets used for integration and prediction of un/spliced expression for spatially measured genes using SIRV, used to infer the RNA velocity in the spatial context
View article: SIRV: Spatial inference of RNA velocity at the single-cell resolution
SIRV: Spatial inference of RNA velocity at the single-cell resolution Open
Spatial transcriptomics and scRNA-seq datasets used for integration and prediction of un/spliced expression for spatially measured genes using SIRV, used to infer the RNA velocity in the spatial context
View article: Local and systemic immune profiles of human pancreatic ductal adenocarcinoma revealed by single-cell mass cytometry
Local and systemic immune profiles of human pancreatic ductal adenocarcinoma revealed by single-cell mass cytometry Open
Background Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy in need of effective (immuno)therapeutic treatment strategies. For the optimal application and development of cancer immunotherapies, a comprehensive understa…
View article: Identification of a Disease-Associated Network of Intestinal Immune Cells in Treatment-Naive Inflammatory Bowel Disease
Identification of a Disease-Associated Network of Intestinal Immune Cells in Treatment-Naive Inflammatory Bowel Disease Open
Chronic intestinal inflammation underlies inflammatory bowel disease (IBD). Previous studies indicated alterations in the cellular immune system; however, it has been challenging to interrogate the role of all immune cell subsets simultane…
View article: scTopoGAN: unsupervised manifold alignment of single-cell data
scTopoGAN: unsupervised manifold alignment of single-cell data Open
Motivation Single-cell technologies allow deep characterization of different molecular aspects of cells. Integrating these modalities provides a comprehensive view of cellular identity. Current integration methods rely on overlapping featu…
View article: Reference-based cell type matching of spatial transcriptomics data
Reference-based cell type matching of spatial transcriptomics data Open
With the advent of multiplex fluorescence in situ hybridization (FISH) and in situ RNA sequencing technologies, spatial transcriptomics analysis is advancing rapidly. Spatial transcriptomics provides spatial location and pattern informatio…