GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. - Alberto Risueño; Celia Fontanillo; Marcel E. Dinger; Javier De Las Rivas (BMC Bioinform., 2010)

Protein-Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks. - Javier De Las Rivas; Celia Fontanillo (PLoS Comput. Biol., 2010)

Functional Gene Networks: R/Bioc package to generate and analyse gene networks derived from functional enrichment and clustering. - Sara Aibar; Celia Fontanillo; Conrad Droste; Javier De Las Rivas (Bioinform., 2015)

DECO: decompose heterogeneous population cohorts for patient stratification and discovery of sample biomarkers using omic data profiling. - Francisco J. Campos-Laborie; Alberto Risueño; M. Ortiz-Estévez; B. Rosón-Burgo; Conrad Droste; Celia Fontanillo; Remco Loos; Jose Manuel Sánchez-Santos; Matthew W. B. Trotter; Javier De Las Rivas (Bioinform., 2019)