Davis James McCarthy

simPIC: flexible simulation of single-cell ATAC-seq paired-insertion counts from individuals to populations

simPIC simulates single-cell ATAC-seq count data across individuals and populations to enable controlled evaluation of chromatin accessibility QTL mapping methods.

Power and linkage disequilibrium differences are major confounders of human eQTL portability across ancestries and cohorts

This paper shows that differences in power and linkage disequilibrium affect eQTL portability across ancestries and introduces a method to correct for these factors.

Frataxin deficiency drives cardiac dysfunction and transcriptional dysregulation in Friedreich ataxia iPSC model

This study uses iPSCs from FRDA patients to model cardiac dysfunction, finding transcriptional dysregulation and phenotypes like increased cell size and mitochondrial stress.

Orchestrating multi-state QTL analysis with Bioconductor

The paper introduces two Bioconductor packages for multi-state QTL analysis, providing tools for data storage, analysis, and simulation.

SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomicsdataset

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

Denoising image-based spatial transcriptomics data with DenoIST

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

A spatial transcriptomic atlas of acute neonatal lung injury across development and disease severity

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.

Flexible and efficient count-distribution and mixed-model methods for eQTL mapping with quasar

The paper introduces quasar, a software for eQTL mapping that offers faster performance and better statistical models compared to existing methods.

Bayesian inference for copy number intra-tumoral heterogeneity from single-cell RNA-sequencing data

This paper introduces a Bayesian model to infer intra-tumoral clonal structure and copy number alterations from scRNA-seq data, achieving high accuracy in clustering and CNA state inference.

Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis

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.

A high-resolution meiotic crossover map from single-nucleus ATAC-seq reveals insights into the recombination landscape in mammalian sperm

This paper uses snATAC-seq to identify meiotic crossovers in sperm, revealing their distribution and molecular features in wildtype and Fancm-deficient mice.

Going beyond cell clustering and feature aggregation: Is there single cell level information in single-cell ATAC-seq data?

This paper reviews challenges in analyzing scATAC-seq data and argues that true single-cell chromatin accessibility profiling has not yet been achieved.

Profiling genetically driven alternative splicing across the Indonesian Archipelago

The paper analyzes alternative splicing variation across 115 Indonesian samples to identify genetic variants influencing splicing, finding over 1,000 differential splicing events and 6,000 sQTLs with some ancestry-specific effects.

De novo transcriptome assembly and genome annotation of the fat-tailed dunnart (Sminthopsis crassicaudata)

The paper presents a de novo transcriptome and improved genome assembly for the fat-tailed dunnart, providing valuable genomic resources for marsupial research.

Demuxafy: Improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

Demuxafy improves droplet assignment and doublet removal in scRNA-seq by combining multiple demultiplexing and doublet detection methods.

MAssively-Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments

MAPFX improves analysis of massively-parallel cytometry data by preprocessing, background correction, and imputing missing markers to enhance biological signal preservation and reduce technical variation.

A comparison of marker gene selection methods for single-cell RNA sequencing data

This study benchmarks 56 marker gene selection methods for scRNA-seq data using real and simulated datasets, finding simple methods like Wilcoxon rank-sum test and t-test to be effective.

Cell type-specific and disease-associated eQTL in the human lung

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.

Trade-off between conservation of biological variation and batch effect removal in deep generative modeling for single-cell transcriptomics

This paper explores the trade-off between preserving biological variation and removing batch effects in scRNA-seq data using Pareto multi-task learning and Mutual Information Neural Estimation.

sgcocaller and comapr: personalised haplotype assembly and comparative crossover map analysis using single-gamete sequencing data

This paper introduces sgcocaller and comapr, tools for haplotype assembly and crossover map analysis from single-gamete sequencing data, showing improved accuracy and efficiency over existing methods.

Fancm regulates meiotic double-strand break repair pathway choice in mammals

This study shows Fancm deficiency increases crossover frequencies and disrupts gametogenesis in mice, with potential implications for human genomic instability disorders.

Proliferation drives quorum sensing of microbial products in human macrophage populations

This study compares proliferation and tolerance in tissue-resident and recruited macrophages using single-cell RNA sequencing, finding that proliferative capacity differs between cell types.

splatPop: simulating population scale single-cell RNA sequencing data

splatPop simulates population-scale scRNA-seq data with eQTL effects and batch effects for method testing.

Optimising expression quantitative trait locus mapping workflows for single-cell studies

This study evaluates normalization, aggregation, and statistical methods for sc-eQTL mapping to improve eQTL discovery in single-cell RNA-seq data.

Genomic properties of structural variants and short tandem repeats that impact gene expression and complex traits in humans

The paper examines how structural variants and short tandem repeats affect gene expression and complex traits, identifying high-impact variants associated with multiple genes and GWAS traits.

Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats

The paper discovers and genotypes a comprehensive set of structural variants and short tandem repeats using multiple algorithms and replicates, creating a well-characterized map of these variants.

Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects

This study benchmarks 13 scRNA-seq protocols to evaluate their effectiveness in characterizing cell types and states for cell atlas projects.

Single-cell RNA-seq of differentiating iPS cells reveals dynamic genetic effects on gene expression

The paper uses single-cell RNA-seq of differentiating iPS cells from 125 donors to identify expression quantitative trait loci influencing gene expression during endoderm differentiation.

Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference

Vireo is a Bayesian model for demultiplexing pooled single-cell RNA-seq data without requiring genotype references, showing robustness in simulations and real data.

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

The paper uses single-cell profiling of expression and DNA methylation to study splicing regulation and heterogeneity in human induced pluripotent stem cells.