Muredach P. Reilly

Associations Between Plasma Lipoprotein(a) Levels and Circulating Monocyte Subsets Differ across Populations

This study examines how plasma Lp(a) levels and monocyte subsets differ between Black and White individuals using scRNA-seq, finding race modifies associations between Lp(a) and monocyte proportions.

IgG Propels Atherosclerosis by Noncanonically Activating Macrophages

This study identifies IgG's pro-atherogenic role through noncanonical activation of macrophages, independent of its classical function, by acting as a TLR4 ligand and promoting inflammation.

Toward Computationally Complete Spatial Omics

COSIE is a computational framework that integrates multiple spatial omics modalities to generate high-resolution molecular landscapes, outperforming existing methods across diverse datasets.

Decoding the MYC locus reveals a druggable ultraconserved RNA element

The paper maps the functional fitness landscape of the MYC locus, identifies an ultraconserved RNA element critical for MYC function, and shows it can be targeted to kill MYC-addicted cancer cells.

Polygenic Risk and Rare Variants in Endotypes of Idiopathic Pulmonary Fibrosis

This study identifies independent associations between IPF risk and rare variants, the MUC5B SNP, and polygenic scores, showing that telomere-associated common variants improve disease prediction and explain genetic heterogeneity in IPF.

Pathogenetic mechanisms of muscle-specific ribosomes in dilated cardiomyopathy

The paper identifies a pathogenetic mechanism for RPL3L-linked dilated cardiomyopathy, showing that gain-of-toxicity variants in muscle-specific ribosomes cause severe neonatal heart failure.

Single cell spatial transcriptomics integration deciphers the morphological heterogeneity of atherosclerotic carotid arteries

This study integrates single-cell spatial transcriptomics with bulk and single-cell RNA sequencing to reveal the molecular heterogeneity and mechanisms of atherosclerotic carotid artery plaques.

PRDM16 controls smooth muscle cell fate in atherosclerosis

This study shows PRDM16 maintains SMC identity and regulates atherosclerotic plaque composition by inhibiting synthetic gene programs during SMC fate switching.

Single-Cell Multimodal Profiling Reveals a Novel CD26+ Fibroblast Subpopulation in Atherosclerosis

The paper identifies a novel CD26+ fibroblast subpopulation in atherosclerosis using CITE-seq and shows its expansion into fibrous caps during disease progression.

Comprehensive Multimodal Profiling of Atherosclerosis Reveals Bhlhe40 as a Potential Regulator of Vascular Smooth Muscle Cell Phenotypic Modulation

Single-cell multimodal profiling of atherosclerosis identifies CD200 as a lineage marker of vascular smooth muscle cells and their derived cells

The paper identifies CD200 as a specific marker for vascular smooth muscle cells and their derived cells in atherosclerosis using CITE-seq and validates it across multiple techniques.

Single-cell multimodal profiling of monocytes reveals diverse phenotypes and alterations linked to cardiovascular disease risks

The paper uses multimodal single-cell profiling to identify diverse monocyte subtypes and links them to cardiovascular disease risk factors.

Genome-Wide DNA Methylation Profiling of the Failing Human Heart with Mechanical Unloading Identifies LINC00881 as an Essential Regulator of Calcium Handling in the Cardiomyocyte

This study identifies LINC00881 as a key regulator of calcium handling in failing human hearts through DNA methylation analysis and functional studies in iPSC-derived cardiomyocytes.

A Joint Deep Learning Model for Simultaneous Batch Effect Correction, Denoising and Clustering in Single-Cell Transcriptomics

This paper introduces CarDEC, a deep learning model that simultaneously corrects batch effects, denoises, and clusters scRNA-seq data, outperforming existing methods in multiple evaluations.

Deep learning enables accurate clustering and batch effect removal in single-cell RNA-seq analysis

This paper introduces DESC, a deep learning method for single-cell clustering that improves accuracy and removes batch effects.

ASEP: gene-based detection of allele-specific expression in a population by RNA-seq

ASEP detects gene-level allele-specific expression in populations using RNA-seq, identifying differential ASE between conditions and extending findings to cardiometabolic traits.