Andrea M Baran

An assessment of normalization and differential expression methods for miRNA-seq analysis using a realistic benchmark dataset

The paper benchmarks normalization and differential expression methods for miRNA-seq using a realistic dataset, finding RPM normalization and edgeR perform best.

PARiS: Probabilistic Assignment and Repartitioning of isomiR Sequences: A data-driven method for denoising isomiR read count data

PARiS identifies and removes technical isomiR errors in sRNA-seq data, improving miRNA-level differential expression analysis.

miRglmm: a generalized linear mixed model of isomiR-level counts improves estimation of miRNA-level differential expression and uncovers variable differential expression between isomiRs

A curated human cellular microRNAome based on 196 primary cell types

The paper curates a comprehensive reference of miRNA expression across 196 human primary cell types using public datasets and provides access through a UCSC Genome Browser track and R/Bioconductor package.

Gene Expression Risk Scores for COVID-19 Illness Severity

The paper develops a gene expression risk score to predict severe COVID-19 illness using peripheral blood samples and validates it in independent cohorts.

Lymphocyte-Specific Biomarkers Associated with Preterm Birth and Bronchopulmonary Dysplasia

The paper identifies gene expression patterns in CD8+ T cells associated with BPD and PRD in preterm infants using transcriptomic data from the PROP cohort.