Nikhila P. Swarna

clrcycle is a dimensionality reduction method for cyclic data that captures phase and magnitude in biological systems, showing effectiveness in circadian and cell-cycle analysis.

The paper uses hybrid crosses to analyze regulatory variation in mouse tissues, finding cell-type-specific trans-acting effects and highlighting the limitations of bulk tissue analysis.

The paper characterizes transcriptomes across 8 tissues in 8 mouse strains to identify expression variation linked to genetic differences and phenotypic traits.

The paper introduces ember, an entropy-based framework to assess gene specificity in single-cell RNA sequencing data, revealing unexpected patterns in gene expression across tissues and mouse strains.

This paper introduces a method to improve RNA-seq quantification by expanding the transcriptome reference to include both nascent and mature mRNA and using distinguishing flanking k-mers to enhance mapping accuracy.