Thanasis Margaritis

Lineage tracing in rhabdoid tumor organoids and orthotopic xenografts reveals convergent transcriptional states

The paper uses lineage tracing and single-cell RNA sequencing to show that rhabdoid tumors converge on a limited set of transcriptional states despite clonal diversity.

Spatial multi-omics reveals targetable immunosuppressive macrophage T-cell interactions in human AML bone marrow

This paper uses spatial multi-omics to identify immunosuppressive interactions between AML, macrophages, and T cells in bone marrow, highlighting the Galectin-9 - CD44/TIM-3 axis as a therapeutic target.

Lineage-associated tumor cell states predict outcome and guide immunotherapeutic target selection in pediatric osteosarcoma

This study identifies lineage-associated tumor cell states in pediatric osteosarcoma that correlate with clinical outcomes and guide immunotherapeutic target selection.

Single-cell multiomics of pediatric BM reveals age-dependent differences in lineage differentiation linked to stromal cell heterogeneity

The paper generates a single-cell multi-omics atlas of pediatric bone marrow, revealing age-related shifts in lineage differentiation linked to stromal cell heterogeneity.

Mechanisms of dexamethasone-induced bone toxicity in developing bone: a single-cell perspective

This study investigates dexamethasone-induced bone toxicity in developing bones using single-cell transcriptomics in mice, revealing reduced osteoblast and chondrocyte populations and disrupted B cell development.

Stem cells actively suppress regenerative plasticity in human colon

The paper investigates human colon stem cell function, showing they suppress regenerative plasticity by producing retinoic acid, which inhibits the regenerative response in colonocytes.

Blocking MIF secretion enhances CAR T-cell efficacy against neuroblastoma

This study identifies MIF as a key immunosuppressive factor in neuroblastoma that inhibits CAR T-cell efficacy, showing that blocking MIF enhances T-cell activation and therapeutic potential.

CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing

CHETAH identifies cell types in scRNA-seq data using hierarchical clustering and reference data, offering accuracy and specificity, especially for unknown cell types.

Sharq, a versatile preprocessing and QC pipeline for Single Cell RNA-seq

Sharq preprocesses single cell RNA-seq data from fastq files to gene expression tables, addressing amplification biases and providing quality control diagnostics.