Francisco Avila Cobos

Effective methods for bulk RNA-Seq deconvolution using scnRNA-Seq transcriptomes

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: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification

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

Performance evaluation of RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study

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.

Charting extracellular transcriptomes in The Human Biofluid RNA Atlas

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.

Comprehensive benchmarking of computational deconvolution of transcriptomics data

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 RNA Atlas, a single nucleotide resolution map of the human transcriptome

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

Zipper plot: visualizing transcriptional activity of genomic regions

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