Francisco Avila Cobos

The paper evaluates deconvolution methods for bulk RNA-Seq using scnRNA-Seq data, identifies biases, and introduces SQUID, a method that outperforms others in predicting cell mixtures and identifying cancer subclones.

DECONbench benchmarks deconvolution methods for quantifying tumor cell-type heterogeneity by providing datasets, tools, and performance evaluation.

The paper evaluates RNA purification kits and blood collection tubes for exRNA quality, finding that preservation tubes and purification methods significantly affect RNA stability, sensitivity, and reproducibility.

The paper creates a comprehensive atlas of RNA transcriptomes across 20 human biofluids, revealing significant differences in RNA concentration and composition, and validates potential biomarkers in disease cohorts.

This study benchmarks deconvolution methods for bulk transcriptomics data, showing reference marker selection and normalization impact performance, with single-cell methods performing comparably to bulk methods.

The paper presents a comprehensive human transcriptome atlas with single-nucleotide resolution, identifying thousands of novel RNA species and regulatory interactions.

The paper introduces Zipper plot, a tool to visualize transcriptional activity around TSSs using RNA-seq and other genomic data.