Microeconomic Principles Explain an Optimal Genome Size in Bacteria. - Juan Garcia Ranea; Alastair Grant; Janet M. Thornton; Christine A. Orengo (Spanish Bioinformatics Conference, 2004)

A structural perspective on genome evolution. - David A. Lee; Alastair Grant; Ian Sillitoe; Mark Dibley; Juan Garcia Ranea; Christine A. Orengo (RECOMB, 2004)

TSEMA: interactive prediction of protein pairings between interacting families. - José M. G. Izarzugaza; David de Juan; Carles Pons; Juan A. G. Ranea; Alfonso Valencia; Florencio Pazos (Nucleic Acids Res., 2006)

Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic Genomes. - Juan A. G. Ranea; Corin Yeats; Alastair Grant; Christine A. Orengo (PLoS Comput. Biol., 2007)

Novel Angiogenic Functional Targets Predicted through "Dark Matter" Assessment in Protein Networks. - Ian Morilla; Miguel Angel Medina; Juan A. G. Ranea (JBI, 2010)

Finding the "Dark Matter" in Human and Yeast Protein Network Prediction and Modelling. - Juan A. G. Ranea; Ian Morilla; Jonathan G. Lees; Adam James Reid; Corin Yeats; Andrew B. Clegg; Francisca Sánchez-Jiménez; Christine A. Orengo (PLoS Comput. Biol., 2010)

Insights into polypharmacology from drug-domain associations. - Aurelio A. Moya-García; Juan A. G. Ranea (Bioinform., 2013)

A Cloud-based GWAS Analysis Pipeline for Clinical Researchers. - Paul Heinzlreiter; James Richard Perkins; Óscar Torreño Tirado; Tor Johan Mikael Karlsson; Juan Antonio Ranea; Andreas Mitterecker; Miguel Blanca; Oswaldo Trelles (CLOSER, 2014)

FUN-L: gene prioritization for RNAi screens. - Jonathan G. Lees; Jean-Karim Hériché; Ian Morilla; José María Fernández 001; Priit Adler; Martin Krallinger; Jaak Vilo; Alfonso Valencia; Jan Ellenberg; Juan A. G. Ranea; Christine A. Orengo (Bioinform., 2015)

Revealing the Relationship Between Human Genome Regions and Pathological Phenotypes Through Network Analysis. - Elena Rojano; Pedro Seoane; Anibal Bueno-Amoros; James Richard Perkins; Juan Antonio Garcia-Ranea (IWBBIO (1), 2017)

How can functional annotations be derived from profiles of phenotypic annotations? - Beatriz Serrano-Solano; Antonio Díaz Ramos; Jean-Karim Hériché; Juan A. G. Ranea (BMC Bioinform., 2017)

Erratum to: How can functional annotations be derived from profiles of phenotypic annotations? - Beatriz Serrano-Solano; Antonio Díaz Ramos; Jean-Karim Hériché; Juan A. G. Ranea (BMC Bioinform., 2017)

Associating Protein Domains with Biological Functions: A Tripartite Network Approach. - Elena Rojano; James Richard Perkins; Ian Sillitoe; Christine A. Orengo; Juan Antonio Garcia-Ranea; Pedro Seoane (IWBBIO (2), 2019)

Regulatory variants: from detection to predicting impact. - Elena Rojano; Pedro Seoane; Juan A. G. Ranea; James Richard Perkins (Briefings Bioinform., 2019)

Kernel Based Approaches to Identify Hidden Connections in Gene Networks Using NetAnalyzer. - Fernando Moreno Jabato; Elena Rojano; James Richard Perkins; Juan Antonio Garcia-Ranea; Pedro Seoane-Zonjic (IWBBIO, 2020)

Comprehensive Analysis of Patients with Undiagnosed Genetic Diseases Using the Patient Exploration Tools Suite (PETS). - Elena Rojano; Pedro Seoane-Zonjic; Fernando Moreno Jabato; James Richard Perkins; Juan A. G. Ranea (IWBBIO, 2020)

Protein residues determining interaction specificity in paralogous families. - Borja Pitarch; Juan A. G. Ranea; Florencio Pazos (Bioinform., 2021)

Deepening the knowledge of rare diseases dependent on angiogenesis through semantic similarity clustering and network analysis. - Raquel Pagano-Márquez; José Córdoba-Caballero; Beatriz Martínez-Poveda; Ana R. Quesada; Elena Rojano; Pedro Seoane; Juan A. G. Ranea; Miguel Ángel Medina (Briefings Bioinform., 2022)

Assigning protein function from domain-function associations using DomFun. - Elena Rojano; Fernando Moreno Jabato; James Richard Perkins; José Córdoba-Caballero; Federico García-Criado; Ian Sillitoe; Christine A. Orengo; Juan A. G. Ranea; Pedro Seoane-Zonjic (BMC Bioinform., 2022)

Integrating differential expression, co-expression and gene network analysis for the identification of common genes associated with tumor angiogenesis deregulation. - Beatriz Monterde; Elena Rojano; José Córdoba-Caballero; Pedro Seoane; James Richard Perkins; Miguel Ángel Medina; Juan A. G. Ranea (J. Biomed. Informatics, 2023)

Exploring miRNA-target gene pair detection in disease with coRmiT. - José Córdoba-Caballero; James Richard Perkins; Federico García-Criado; Diana Gallego; Alicia Navarro-Sánchez; Mireia Moreno-Estellés; Concepción Garcés; Fernando Bonet; Carlos Romá-Mateo; Rocio Toro; Belén Perez; Pascual Sanz; et al. (Briefings Bioinform., 2024)

CoMentG: comprehensive retrieval of generic relationships between biomedical concepts from the scientific literature. - Jorge Novoa; Javier López-Ibáñez; Monica Chagoyen; Juan Antonio Garcia-Ranea; Florencio Pazos (Database J. Biol. Databases Curation, 2024)

Advancing edge-based clustering and graph embedding for biological network analysis: a case study in RASopathies. - Federico García-Criado; Pedro Seoane; Elena Rojano; Juan Garcia Ranea; James Richard Perkins (Briefings Bioinform., 2025)