J. Christian J. Ray

Comparing local point neighborhoods before and after dimensionality reduction reveals that standard scRNA-seq pipelines, t-SNE, and UMAP often distort local neighborhoods by more than 95%, altering downstream clustering.

This study compares EV transcriptomics, proteomics, and cfDNA methylation for detecting colorectal neoplasia, finding EV transcriptomics most sensitive for advanced adenomas and CRC.

This study identifies RNA biomarkers in salivary extracellular vesicles for diagnosing Sjogrens subtypes with high sensitivity and specificity.

The paper develops a targeted RNA capture method to enhance detection of long RNAs in EVs from human biofluids, revealing biofluid-specific transcriptomes and splicing patterns.

The paper shows that E. coli exhibits overlapping stress responses to starvation and lactose toxicity, with distinct gene expression shifts and functional signatures in each condition.

The paper introduces a framework for evaluating edited cell libraries generated by genome engineering, defining metrics and connecting analysis to phenotyping approaches.

The paper uses simulations and experimental data to show that lineage dependence influences growth arrest in bacterial populations, with diversity peaking near a critical regime.

The paper shows that metabolic flickering predicts phenotypic switches in bacteria near enzyme saturation thresholds.