Zev J. Gartner

The paper shows that mechanical sorting, driven by adhesion and contractility differences, maintains basal-luminal compartmentalization and influences lineage outcomes in glandular epithelia.

This study identifies CD38 as a regulator of interferon responses in juvenile dermatomyositis and suggests its inhibition as a potential therapeutic strategy.

The paper uses spatial transcriptomics to identify and characterize two distinct macrophage populations in the normal human breast at microanatomical resolution.

This study uses single-cell RNA-sequencing to track how Pik3caH1047R mutation drives mammary tumor progression by altering epithelial and fibroblast transcriptional states.

This study maps the extracellular matrix gene expression landscape in human pancreas using spatial transcriptomics, revealing pericytes as the main source of vascular basement membrane components and identifying disease-related changes in type 2 diabetes.

This paper introduces a tunable granular biomaterial, MAGIC matrix, that enables precise control of initial conditions for tissue growth, leading to improved organoid reproducibility and complexity.

The paper shows the enteric nervous system (ENS) lacks intrinsic regionalization but is shaped by PTPRZ1 signaling from the gut microenvironment during development.

CONCORD is a self-supervised framework that integrates single-cell datasets across batches, technologies, and species, producing high-resolution cell atlases with improved biological resolution and reduced noise.

This study uses single-cell RNA sequencing to show that testosterone treatment reduces estrogen signaling in mammary gland cells of transgender men compared to cisgender women.

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.

This study shows that swirling motion of breast cancer cells aligns collagen fibers radially, enabling collective invasion by generating contractile stresses.

The paper identifies age-dependent selection forces that drive mtDNA mutation accumulation in liver cells, leading to functional decline.

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.

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.

deMULTIplex2 improves sample demultiplexing in scRNA-seq by accurately associating cell tags with sample tags, outperforming existing methods on large, noisy, and imbalanced datasets.

The paper introduces PIP-seq, a microfluidics-free method for single-cell RNA sequencing that enables high-throughput, scalable, and flexible processing of samples.

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.

The paper quantifies morphological features of organoids under perturbations to identify constraints on their phenotypes, finding scaling relationships and parameter caps that vary with age and culture conditions.

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.

The paper uses single-cell RNA-sequencing to study environmental enteropathy, identifying epithelial and immune correlates of disease severity and suggesting new therapeutic targets.

This paper engineers T cells with a two-step positive feedback circuit to kill target cells based on an ultrasensitive antigen density threshold.

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

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

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

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

Quantius provides a crowd-based image annotation platform that achieves high-fidelity human annotation at 105 clicks per hour, matching deep learning performance while reducing time and cost.