Ernesto Aparicio‐Puerta

The paper benchmarks normalization and differential expression methods for miRNA-seq using a realistic dataset, finding RPM normalization and edgeR perform best.

PARiS identifies and removes technical isomiR errors in sRNA-seq data, improving miRNA-level differential expression analysis.

The paper identifies that full-length tRNAs with truncated CCA tails are selectively sorted into extracellular vesicles, suggesting a new mechanism for EV cargo selection.

GeneCodis 4 extends functional enrichment analysis to regulatory elements like transcription factors, CpG sites, and miRNAs, with new databases and visualizations.

The paper introduces IsoSeek, a method for unbiased and UMI-informed sequencing of cell-free miRNAs, revealing extensive uridylation of disease-associated miRNAs and improving isomiR detection in extracellular vesicles.

MirGeneDB 2.0 expands curated microRNA gene annotations to 45 metazoan species, revealing many false positives and missing miRNAs in previous annotations.

The paper introduces mirGFF3, a standardized format for miRNA/isomiR analysis, and mirtop, a tool to convert outputs into this format, enabling data sharing and comparative analysis.