Alejandro Reyes

This study investigates the specificity of splicing modulators by analyzing their interactions with RNA structures and demonstrates reprogramming of their specificity through genetic manipulation of the spliceosome.

This paper introduces the Bacteriophage Risk Index (BRI) to predict phage immunogenicity using CpG features, validated through experimental testing and genome-wide analysis.

The paper identifies ZNF469 as a transcription factor regulating collagen production in liver fibrosis through computational analysis and experimental validation.

This study benchmarks nine TF prioritization tools using H3K27ac ChIP-seq data from 84 perturbation experiments, identifying three top-performing tools.

TRAWLING simplifies aberrant splicing detection by providing a splicing-aware transcriptome reference, improving RNAseq analysis across multiple datasets.

The paper introduces regutools, an R package that enables programmatic access to RegulonDB data for analyzing bacterial regulatory networks within the Bioconductor ecosystem.

This paper benchmarks classic and modern false discovery rate methods in computational biology, finding modern methods with informative covariates offer modest power gains without sacrificing FDR control.

The paper investigates transcript isoform diversity across human tissues and finds that alternative transcription start and termination sites drive most tissue-dependent isoform usage, with splicing playing a minor role.