Nicholas E. Banovich

This study shows that targeting the TGFβ pathway improves CAR T cell efficacy in glioblastoma by enhancing antitumor activity and modulating the tumor microenvironment.

The paper identifies DNA methylation changes in IPF lung epithelial cells linked to dysregulated transcriptional programs and impaired repair.

This study uses spatial transcriptomics to analyze gene expression in heart transplant recipients during rejection, identifying distinct transcriptomic profiles associated with different rejection types and outcomes.

The paper identifies inflammatory fibroblasts that promote lung repair by enhancing epithelial proliferation through BMP signaling, validated across multiple models and human disease.

The paper combines two spatial transcriptomic chemistries to improve both sensitivity and coverage in a single tissue section, showing high concordance and enabling more comprehensive analysis.

The paper constructs a single-cell eQTL dataset from Asian never-smokers, identifying alveolar cell-specific genes linked to lung cancer susceptibility.

This study identifies eQTLs and environmental influences on immune cell diversity in Indonesian populations, highlighting the role of ancestry and environment in shaping immunity.

The paper introduces SpatialRNA, a Python package enabling the application of Graph Neural Networks to spatial transcriptomics data for domain detection.

The paper identifies T-cell subsets and their interactions with epithelial cells in IPF using multiomic profiling, revealing novel signaling pathways and activation patterns.

DenoIST improves spatial transcriptomics data by removing contaminating transcripts, enhancing gene expression specificity and cell type annotation.

This paper creates a spatial transcriptomic atlas of acute neonatal lung injury across development and disease severity using 1.2 million cells from 17 human infant lungs.

This study identifies SPP1+ macrophages as key drivers of resistance to CAR T therapy in solid tumors and shows that targeting SPP1 can overcome this resistance.

Xenium profiling of 343 genes in 1,126,820 nuclei from 19 human lungs maps fibrosis niches and orders alveolar remodeling from alveolar-capillary disruption to SPP1+ macrophage accumulation.

This study identifies germline and somatic genetic effects on gene expression and patient outcomes in Multiple Myeloma using matched genotype and expression data from 607 patients.

The paper identifies loss of semaphorin signaling and reduced FOXF1 expression in BPD and BPD+PH using single-cell RNA sequencing and validates findings in a murine model.

This study investigates the association between mosaic loss of chromosome Y (mLOY) and pulmonary fibrosis, finding mLOY correlates with age and telomere length but not disease severity, and suggests a potential link between telomere shortening and mLOY.

Head-to-head on serial prostate adenocarcinoma sections: Xenium gave higher sensitivity, wider dynamic range and closer agreement with snRNA-seq; CosMx segmented cells better out of the box.

This study uses scRNA-seq to identify cell types and molecular programs in appendiceal neoplasms, revealing cancer-specific cell states and tumor microenvironment interactions.

The paper identifies cell-type-specific and disease-associated eQTL in the human lung using single-cell RNA-sequencing data from PF and unaffected donors.

The paper identifies four novel genetic variants associated with IPF survival, including a PCSK6 variant, and suggests PCSK6 as a prognostic biomarker and therapeutic target.

The paper identifies dynamic eQTLs in cardiomyocytes under hypoxic stress, showing how genetic variation affects gene expression differently across conditions.

The paper constructs a single-cell RNA sequencing atlas of lung development in mice, revealing cellular dynamics and transcriptional changes during the saccular to alveolar transition.

The paper identifies TMPRSS2 expression patterns in developing lungs and links them to SARS-CoV-2 infection susceptibility in different age groups.

The paper identifies Indonesia-specific eQTLs and methylQTLs linked to local ancestry and archaic introgression, showing their impact on gene regulation and hematological traits.

Single-cell RNA-sequencing identifies distinct epithelial and mesenchymal cell types and their roles in pulmonary fibrosis.

The paper analyzes DNA methylation and gene expression in Indonesian populations to show genetic ancestry, environmental influences, and immune-related differences across regions.

The paper compares gene expression and DNA methylation across tissues and species in primates, finding that only 7-11% of inter-species expression differences are explained by methylation, with higher explanation in tissue-specific genes.

The paper introduces LATE and TRANSLATE autoencoder-based methods for imputing single-cell RNA-seq data, showing improved performance over existing methods.

The paper examines regulatory variation in iPSCs and differentiated cells, finding lower individual variation in iPSCs and identifying shared chromatin regions for some cell type-specific QTLs.