AutoFlow: an easy way to build workflows. - Pedro Seoane; Rosario Carmona; Rocío Bautista; Darío Guerrero-Fernández; Manuel Gonzalo Claros (IWBBIO, 2014)

Bioinformatics Analyses to Separate Species Specific mRNAs from Unknown Sequences in de novo Assembled Transcriptomes. - David Velasco; Pedro Seoane; M. Gonzalo Claros (IWBBIO (2), 2015)

Automatic Workflow for the Identification of Constitutively-Expressed Genes Based on Mapped NGS Reads. - Rosario Carmona; Pedro Seoane; Adoración Zafra; María José Jiménez-Quesada; Juan de Dios Alché; M. Gonzalo Claros (IWBBIO, 2016)

Obtaining the Most Accurate de novo Transcriptomes for Non-model Organisms: The Case of Castanea sativa. - Marina Espigares; Pedro Seoane; Rocío Bautista; Julia Quintana; Luis Gómez; M. Gonzalo Claros (IWBBIO (2), 2017)

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)

TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms. - Pedro Seoane; Marina Espigares; Rosario Carmona; Álvaro Polonio; Julia Quintana; Enrico Cretazzo; Josefina Bota; Alejandro Pérez-García; Juan de Dios Alché; Luis Gómez; M. Gonzalo Claros (BMC Bioinform., 2018)

De novo Transcriptome Assembly of Solea senegalensis v5.0 Using TransFlow. - José Córdoba-Caballero; Pedro Seoane-Zonjic; Manuel Manchado; M. Gonzalo Claros (IWBBIO (1), 2019)

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)

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)

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)