Ariel Madrigal
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View article: IL-4 induces CD22 expression to restrain the effector program of virtual memory T cells
IL-4 induces CD22 expression to restrain the effector program of virtual memory T cells Open
Parasitic helminths induce the production of interleukin-4 (IL-4), which causes the expansion of virtual memory CD8 + T cells (T VM cells), a cell subset that contributes to the control of coinfection with intracellular pathogens. However,…
View article: A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data
A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data Open
Single-cell analysis across multiple samples and conditions requires quantitative modeling of the interplay between the continuum of cell states and the technical and biological sources of sample-to-sample variability. We introduce GEDI, a…
View article: Source data for GEDI - part 2
Source data for GEDI - part 2 Open
Source data and models used in the manuscript that describes Gene Expression Decomposition and Integration (GEDI). This is part 2 of the dataset; part 1 can be found here: https://zenodo.org/deposit/8222040.
View article: Source data for GEDI - part 1
Source data for GEDI - part 1 Open
Source data and models used in the manuscript that describes Gene Expression Decomposition and Integration (GEDI). This is part 1 of the dataset; part 2 can be found here: https://zenodo.org/deposit/8222698.
View article: PHF6-mediated transcriptional control of NSC via Ephrin receptors is impaired in the intellectual disability syndrome BFLS
PHF6-mediated transcriptional control of NSC via Ephrin receptors is impaired in the intellectual disability syndrome BFLS Open
The plant homeodomain zinc-finger protein, PHF6, is a transcriptional regulator, and PHF6 germline mutations cause the X-linked intellectual disability (XLID) Börjeson-Forssman-Lehmann syndrome (BFLS). The mechanisms by which PHF6 regulate…
View article: A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data
A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data Open
Analysis of single cells across multiple samples and/or conditions encompasses a series of interrelated tasks, which range from normalization and inter-sample harmonization to identification of cell state shifts associated with experimenta…
View article: Source data for GEDI - part 1
Source data for GEDI - part 1 Open
Source data and models used in the manuscript that describes Gene Expression Decomposition and Integration (GEDI). This is part 1 of the dataset; part 2 can be found here: https://zenodo.org/deposit/8222698.
View article: Source data for GEDI - part 2
Source data for GEDI - part 2 Open
Source data and models used in the manuscript that describes Gene Expression Decomposition and Integration (GEDI). This is part 2 of the dataset; part 1 can be found here: https://zenodo.org/deposit/8222040.
View article: A4 HELMINTH-DERIVED METABOLITES INDUCE A TOLEROGENIC PROFILE IN DENDRITIC CELLS AND ALLEVIATE EXPERIMENTAL COLITIS
A4 HELMINTH-DERIVED METABOLITES INDUCE A TOLEROGENIC PROFILE IN DENDRITIC CELLS AND ALLEVIATE EXPERIMENTAL COLITIS Open
Background Inflammatory bowel diseases (IBD) are chronic inflammatory diseases characterized by abdominal pain, bloody diarrhea, fatigue, weight loss, and diminished quality of life. The morbidity associated with IBD is a result of loss of…
View article: Single-cell eQTL analysis of activated T cell subsets reveals activation and cell type–dependent effects of disease-risk variants
Single-cell eQTL analysis of activated T cell subsets reveals activation and cell type–dependent effects of disease-risk variants Open
The impact of genetic variants on cells challenged in biologically relevant contexts has not been fully explored. Here, we activated CD4 + T cells from 89 healthy donors and performed a single-cell RNA sequencing assay with >1 million cell…
View article: Transcriptional control of brain tumor stem cells by a carbohydrate binding protein
Transcriptional control of brain tumor stem cells by a carbohydrate binding protein Open
Brain tumor stem cells (BTSCs) and intratumoral heterogeneity represent major challenges in glioblastoma therapy. Here, we report that the LGALS1 gene, encoding the carbohydrate binding protein, galectin1, is a key regulator of BTSCs and g…
View article: Transcriptional Control of Brain Tumour Stem Cells by a Carbohydrate Binding Protein
Transcriptional Control of Brain Tumour Stem Cells by a Carbohydrate Binding Protein Open
Summary Brain tumour stem cells (BTSCs) and intratumoural heterogeneity represent major challenges in glioblastoma therapy. Here, we report that the LGALS1 gene, encoding the carbohydrate binding protein, galectin1, is a key regulator of B…
View article: COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types
COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types Open
Common genetic polymorphisms associated with severity of COVID-19 illness can be utilized for discovering molecular pathways and cell types driving disease pathogenesis. Here, we assessed the effects of 679 COVID-19-risk variants on gene e…
View article: CD4<sup>+</sup>follicular helper-like T cells are key players in anti-tumor immunity
CD4<sup>+</sup>follicular helper-like T cells are key players in anti-tumor immunity Open
To determine the nature of CD4 + T cells that provide ‘help’ for generating robust anti-tumor CD8 + cytotoxic T cell (CTL) responses, we profiled the transcriptomes of patient-matched CD4 + and CD8 + T cells present in the tumor micro-envi…
View article: Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer
Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer Open
High numbers of tissue-resident memory T (TRM) cells are associated with better clinical outcomes in cancer patients. However, the molecular characteristics that drive their efficient immune response to tumors are poorly understood. Here, …
View article: Precursors of human CD4 <sup>+</sup> cytotoxic T lymphocytes identified by single-cell transcriptome analysis
Precursors of human CD4 <sup>+</sup> cytotoxic T lymphocytes identified by single-cell transcriptome analysis Open
Human CD4 + cytotoxic T lymphocytes that play a vital role in antiviral immunity are highly heterogeneous.