Christopher S. McGinnis

Systemic iron sequestration restricts the intratumoral CD8+ T cell landscape in pancreas cancer

This study shows that systemic iron sequestration via hepcidin reduces CD8+ T cells in pancreas cancer, linking iron dysregulation to tumoral immunity.

Comparing bulk and single-cell methodologies and models to profile gene expression, chromatin accessibility and regulatory links in endothelial cells treated with TNFα

The paper compares bulk and single-cell RNA-seq/ATAC-seq data and models to assess their impact on predicting causal genes from GWAS variants in TNFα-treated endothelial cells.

Mapping enhancer-gene regulatory interactions from single-cell data

The paper introduces scE2G models to predict enhancer-gene regulatory interactions from single-cell data and demonstrates their performance across multiple cell types and perturbations.

D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response

Tumor Heterogeneity Induces Pro- and Anti-metastatic Myeloid Cell Phenotypes in Breast Cancer Lung Metastasis

The paper profiles myeloid cells in breast cancer primary tumors and metastases to show how tumor heterogeneity drives shifts in myeloid cell phenotypes from anti- to pro-metastatic.

T cell engagers control solid tumors through clonal replacement and IL2-driven effector differentiation of CD8 T-cells

Combining TCE therapy with IL-2 enhances TCE efficacy in aggressive small-cell lung cancer and melanoma models with low target antigen density through T cell clonal replacement and CD8+ effector T cell differentiation.

FAK Inhibition Remodels the Metastatic ECM and Restores CD8+ T Cell Trafficking and Immunosurveillance

This paper shows that FAK inhibition remodels the metastatic ECM, enhancing CD8+ T cell infiltration and immunosurveillance in breast cancer.

Multi-scale gene regulatory networks for resolving transcription factor and autoimmune variant impacts on human B cell fate dynamics

Reducing batch effects in single cell chromatin accessibility measurements by pooled transposition with MULTI-ATAC

The paper introduces MULTI-ATAC, a method to reduce batch effects in scATAC-seq by pooling samples before transposition, enabling scalable and batch-free experiments.

Patterning and folding of intestinal villi by active mesenchymal dewetting

This study identifies an active mechanical mechanism involving PDGFRA+ mesenchymal cells that pattern and fold intestinal villi through myosin II-dependent forces and matrix metalloproteinase-mediated tissue fluidization.

Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains

The paper identifies five discrete metabolic domains in the mouse and human small intestine using transcriptional signatures and machine learning, showing how diet influences domain properties.

Changes in epithelial proportions and transcriptional state underlie major premenopausal breast cancer risks

This study identifies how changes in epithelial proportions and transcriptional states influenced by pregnancy and BMI affect hormone signaling and breast cancer risk in premenopausal women.

A read count-based method to detect multiplets and their cellular origins from snATAC-seq data

This paper introduces ATAC-DoubletDetector, a read count-based method to detect multiplets in snATAC-seq data and annotate their cellular origins, achieving 85% accuracy in annotation.

No detectable alloreactive transcriptional responses during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells

The paper evaluates whether donor-multiplexed scRNA-seq introduces alloreactive gene expression changes and finds no detectable alloreactivity across three workflows.

Single Cell Enhancer Activity Maps Neuronal Lineages in Embryonic Mouse Basal Ganglia

The paper uses scRNA-seq and enhancer-based labeling to map neuronal lineages in embryonic mouse basal ganglia and identifies novel lineage specification paths.

ZipSeq : Barcoding for Real-time Mapping of Single Cell Transcriptomes

ZipSeq maps single-cell transcriptomes in real-time within intact tissues, revealing new gene expression patterns and differentiation trajectories in various biological contexts.

Human microglia upregulate cytokine signatures and accelerate maturation of neural networks

This study maps human microglia development and identifies cytokine-associated subtypes and functional roles in neural network maturation.

MULTI-seq: Scalable sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

The paper introduces MULTI-seq, a method for scalable sample multiplexing in scRNA-seq, enabling analysis of multiple tissues and perturbation experiments while improving data quality.

DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors

DoubletFinder detects doublets in scRNA-seq data by comparing cell expression profiles to artificial doublets generated from real data.