José M. Fernández

This paper introduces FANTASIA, a tool using protein language models to annotate functions for thousands of animal proteomes, uncovering previously unknown functions across species.

The paper describes the European Reference Genome Atlas (ERGA) pilot project, which tests a decentralized model for producing high-quality reference genomes across 98 European species.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

WOMBAT-P benchmarks label-free proteomics workflows by comparing four analysis pipelines using standardized metrics and datasets.

The paper benchmarks eight tools for identifying and quantifying alternative polyadenylation sites from RNA-seq data using real, synthetic, and 3'-end sequencing data.

The paper integrates multi-omics data from CAKUT patients to identify collagen's role in disease development and provides containerized workflows for analysis.

The paper reports results from the CAFA3 challenge, showing improved computational protein function prediction and new annotations for over 1000 genes through experimental screens in C. albicans, P. aureginosa, and Drosophila.

The paper constructs a disease interaction network from patient molecular profiles to uncover molecular mechanisms of comorbidity and identify associated genes and drugs.

This study compares the epigenomes of neutrophils and monocytes to identify regulatory elements and chromatin states, revealing differences in enhancer activity and DNA methylation.

This paper describes OpenEBench, a continuous automated benchmarking system for bioinformatics methods, tools, and web services to improve reproducibility and interoperability.

The paper measures and compares transcriptional and epigenetic variability across immune cell types and finds neutrophils exhibit higher variability linked to immune pathways and environmental exposure.