Alexander S. Szalay

Interpretable spherical geometry of single-cell state transitions from dominant principal components

The paper introduces SPHERE-PCA, a method to interpret single-cell state transitions using spherical geometry, revealing structured patterns in developmental and disease datasets.

Novel Predictive Spatial Biomarker in Non-Small Cell Lung Carcinoma: The Diversity of Niches Unlocking Treatment Sensitivity (DONUTS)

The paper develops a spatial biomarker, DONUTS, to predict treatment response in lung cancer by analyzing the niche surrounding CD8+FoxP3+ T-cells.

Widespread methylation quantitative trait loci and their role in schizophrenia risk

The paper identifies widespread genetic influences on DNA methylation in the human brain and links schizophrenia GWAS variants to epigenetic changes.

Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex

The paper characterizes dynamic DNA methylation patterns in the prenatal human cortex, identifying loci associated with gene expression, enhancer states, and psychiatric disorder genes.

GPU-accelerated alignment of bisulfite-treated short-read sequences

This paper introduces Arioc, a GPU-accelerated short-read aligner for BS-seq data, showing improved speed and accuracy compared to existing tools.