Brian B. Nadel

Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples

This study evaluates ten deconvolution tools on 4,000 clinical and synthetic samples, finding EPIC performs best on Framingham data and HPCA references are generally accurate.

The Gene Expression Deconvolution Interactive Tool (GEDIT): Accurate Cell Type Quantification from Gene Expression Data

GEDIT estimates cell type abundances from gene expression data, outperforming existing tools across multiple platforms and tissue types.

Cell type specific genetic regulation of gene expression across human tissues

The paper uses bulk RNA-seq data to estimate cell type abundances and identifies cell type interaction QTLs that provide finer resolution of tissue specificity than bulk cis-eQTLs.

A Novel Uropathogenic Escherichia Coli Genome (strain D3) and Comparative Analysis with Other Uropathogenic and Nonpathogenic Strains

The paper sequences and analyzes the genome of a uropathogenic E. coli strain, identifying pathogenicity-associated genes and D3-specific transposable elements.