Nicholas F. Lahens

MAJIQ-CLIN improves the detection of Mendelian disease-causing variants from RNA-Seq by addressing splicing aberrations, showing better accuracy and efficiency than existing tools.

This study investigates sources of non-uniform coverage in RNA-Seq data and finds that no single factor explains the issue, contradicting prior claims.

This study shows that age-related blood-borne factors alter circadian gene expression in cultured fibroblasts, affecting oxidative phosphorylation and cholesterol biosynthesis pathways.

This study shows that COX-2 deletion or inhibition leads to heart failure with preserved ejection fraction in zebrafish, mice, and humans.

BEERS2 simulates RNA-seq reads with high fidelity, incorporating detailed library preparation and sequencing steps, and evaluates its impact on the Salmon pseudoalignment algorithm.

The paper identifies lipidomic biomarkers and therapeutic targets in sepsis patients, including those with COVID-19, and develops an interactive network analysis tool for multiomic data exploration.

The paper introduces MAJIQ v2, a tool for analyzing RNA splicing in large and heterogeneous RNA-seq datasets, showing improved performance over existing methods and applying it to brain subregion-specific splicing analysis.

MOCCASIN corrects known and unknown confounders in RNA splicing analysis using synthetic and real data from TARGET and ENCODE.

This study evaluates isoform quantification methods using simulated data, finding that no method significantly outperforms a simple approach on realistic data.

The paper introduces a framework to rank genomic features by differential effect size, showing that pseudocounts optimize the balance between fold-change and difference sorting.

This study identifies differences in cyclooxygenase pathway activation and inflammatory biomarker levels as factors associated with variability in ibuprofen analgesic response following third-molar extraction.

The paper profiles transcriptional diversity across skeletal, smooth, and cardiac muscles in mice and rats, revealing extensive gene expression differences and disease associations.

The paper develops a probability model to detect outlier RNA-Seq samples for improved differential splicing analysis, showing it outperforms existing tools in identifying inconsistent replicates.