Daniel A. Skelly

CellMAGE deconvolves gene expression in multi-parent populations by leveraging known parental genetic contributions, outperforming existing methods in accuracy and efficiency.

The paper identifies that X chromosome dosage influences aneuploidy development in mouse embryonic stem cells, with XO and XY lines showing higher aneuploidy rates than XX lines.

The paper compares mouse and human tumor microenvironments, identifying conserved and species-specific features in immune composition and gene expression programs.

QTLretrievR simplifies molecular QTL identification in genetically diverse populations by integrating existing tools with parallelization, reducing computational time and improving accessibility.

The paper identifies host genetic factors influencing anti-PD-1 response in mice and humans by mapping QTLs and finding a core gene network with prognostic value in human tumors.

The paper models metabolic disease susceptibility and resilience in genetically diverse mice by analyzing diet-induced metabolic responses across three strains.

The paper identifies eQTL in mouse neural progenitor cells and shows their effects on gene regulation across developmental stages.

This study examines retinal aging across nine genetically diverse mouse strains, identifying molecular aging signatures and validating WSB and NZO as models for retinal neurodegenerative diseases.

Enhlink infers enhancer-promoter linkages using scATAC-seq data and outperforms existing methods, revealing a super-enhancer regulating striatal neuron markers.

The paper uses regression modeling to identify genetic-epigenetic interactions in mice, showing they are common and structured by 3D chromatin domains.

This study integrates multi-omics data from mouse embryonic stem cells to identify genetic drivers of proteome variability and uncover regulatory mechanisms in pluripotency.

The paper shows genetic variation in mouse ESCs affects lineage commitment by modulating pluripotency epigenome regulators, with B6 and D2 strains showing distinct differentiation biases.

This study profiles mRNA and protein levels in aging kidneys, finding that protein changes reveal more extensive and functionally significant aging-related alterations than mRNA.

This paper uses Bayesian model selection to show zero inflation in scRNA-Seq data is biological, not technical, and recommends a negative binomial GLM as a reference model.

The paper uses scRNA-seq to show genetic variation in microglia from different mouse strains affects their heterogeneity and response to amyloidosis in Alzheimer's disease models.

The paper introduces a reference trait analysis method to correlate complex traits with molecular features in disjoint samples, showing it outperforms TWAS in identifying associated transcripts.

The paper identifies genetic variants influencing metastability in mouse embryonic stem cells by analyzing gene expression and chromatin accessibility in 185 genetically diverse cells.

The paper introduces a method called private haplotype barcoding to reduce costs of genotyping offspring from multiple crosses by pooling samples and using haplotype information for deconvolution.