Santiago J. Carmona

IL-23 licenses the transition from preclinical autoimmunity to inflammatory arthritis through IL-17A-dependent mechanisms

This study shows IL-23 promotes the transition from preclinical autoimmunity to arthritis by enhancing IL-17A and IFN-gamma production, and identifies IL-23 pathway changes in at-risk individuals.

Evaluating cell type annotations in single-cell omics in the absence of ground truth

This paper introduces ISC, a framework to evaluate cell type annotations in single-cell RNA-seq without ground truth, revealing reproducibility gaps and enabling tool benchmarking.

KLRG1 identifies circulating cytotoxic CD4 T cells with selective anti-tumor function in human cancer

This study identifies KLRG1 as a marker for cytotoxic CD4 T cells in cancer patients and shows their anti-tumor function and regulation by IL-6.

Cell type composition drives patient stratification in single-cell RNA-seq cohorts

The paper evaluates methods for patient stratification in scRNA-seq cohorts and finds that cell-type composition-based approaches outperform complex methods in stratification performance and computational efficiency.

Metabolic reinvigoration of NK cells by IL-21 enhances immunotherapy against MHC-I deficient solid tumors

This paper shows that IL-21-Fc reprograms NK cell metabolism to enhance their function against MHC-I deficient tumors, leading to tumor eradication in preclinical models.

ECM Signatures Reveal Quiescent Stem Cell Diversity in the Colonic Niche

The paper identifies quiescent stem cell subtypes in the colon using ECM gene signatures and shows their presence in colorectal cancer and pancreas.

Semi-supervised integration of single-cell transcriptomics data

This study introduces STACAS v2, a semi-supervised method for integrating scRNA-seq data that outperforms existing methods by preserving biological variability using cell type annotations.

Metacells untangle large and complex single-cell transcriptome networks

The paper introduces metacells to address scalability issues in scRNA-seq data by merging similar cells, improving downstream analyses and accelerating atlas construction.

scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets

scGate automates marker-based purification of cell populations from single-cell RNA-seq data, outperforming existing methods in benchmark tests.

Projecting single-cell transcriptomics data onto a reference T cell atlas to interpret immune responses

The paper introduces ProjecTILs, a method to project scRNA-seq data onto T cell reference atlases to interpret immune responses and perturbations.

UCell: robust and scalable single-cell gene signature scoring

UCell provides a fast and robust method for scoring gene signatures in single-cell data using the Mann-Whitney U statistic.

STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data

STACAS improves integration of single-cell RNA-seq datasets with partial cell type overlap by correcting batch effects and filtering anchors.