Salvador Capella-Gutiérrez

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

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.

Rare disease research workflow using multilayer networks elucidates the molecular determinants of severity in Congenital Myasthenic Syndromes

This paper uses multilayer network analysis to identify molecular determinants of severity in Congenital Myasthenic Syndromes by integrating protein-protein interactions, pathways, and metabolomics data.

WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows

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

FAIRsoft - A practical implementation of FAIR principles for research software

The paper proposes FAIRsoft, a framework to assess software quality in Life Sciences research based on FAIR principles, to be implemented in OpenEBench.

SmartRNASeqCaller: improving germline variant calling from RNAseq

SmartRNASeqCaller improves germline variant calling from RNA-Seq by reducing false positives by 50% while maintaining sensitivity, using machine learning trained on diverse datasets.

Unveiling the molecular basis of disease co-occurrence: towards personalized comorbidity profiles

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

Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking

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