Rapid development of proteomic applications with the AIBench framework. - Hugo López-Fernández; Miguel Reboiro-Jato; Daniel Glez-Peña; José Ramón Méndez Reboredo; Hugo Miguel Santos; Ricardo Jorge Carreira; José Luis Capelo-Martínez; Florentino Fdez-Riverola (J. Integr. Bioinform., 2011)

PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies. - Hugo López-Fernández; Daniel Glez-Peña; Miguel Reboiro-Jato; Gonzalo Gómez-López; David G. Pisano; Florentino Fdez-Riverola (Nucleic Acids Res., 2011)

Applying AIBench Framework to Develop Rich User Interfaces in NGS Studies. - Hugo López-Fernández; Daniel Glez-Peña; Miguel Reboiro-Jato; Gonzalo Gómez-López; David G. Pisano; Florentino Fdez-Riverola (PACBB, 2012)

A JAVA application framework for scientific software development. - Florentino Fdez-Riverola; Daniel Glez-Peña; Hugo López-Fernández; Miguel Reboiro-Jato; José Ramón Méndez 001 (Softw. Pract. Exp., 2012)

A Workflow for the Application of Biclustering to Mass Spectrometry Data. - Hugo López-Fernández; Miguel Reboiro-Jato; Sara C. Madeira; Rubén López-Cortés; J. D. Nunes-Miranda; Hugo Miguel Santos; Florentino Fdez-Riverola; Daniel Glez-Peña (PACBB, 2013)

BioAnnote: A software platform for annotating biomedical documents with application in medical learning environments. - Hugo López-Fernández; Miguel Reboiro-Jato; Daniel Glez-Peña; Fernando Aparicio; Diego Gachet; Manuel Buenaga; Florentino Fdez-Riverola (Comput. Methods Programs Biomed., 2013)

genEnsemble: A new model for the combination of classifiers and integration of biological knowledge applied to genomic data. - Miguel Reboiro-Jato; Rosalía Laza; Hugo López-Fernández; Daniel Glez-Peña; Fernando Díaz 001; Florentino Fdez-Riverola (Expert Syst. Appl., 2013)

Web scraping technologies in an API world. - Daniel Glez-Peña; Anália Lourenço; Hugo López-Fernández; Miguel Reboiro-Jato; Florentino Fdez-Riverola (Briefings Bioinform., 2014)

A comprehensive analysis about the influence of low-level preprocessing techniques on mass spectrometry data for sample classification. - Hugo López-Fernández; Miguel Reboiro-Jato; Daniel Glez-Peña; Florentino Fernández Riverola (Int. J. Data Min. Bioinform., 2014)

Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery. - Hugo López-Fernández; Hugo Miguel Santos; José L. Capelo; Florentino Fdez-Riverola; Daniel Glez-Peña; Miguel Reboiro-Jato (BMC Bioinform., 2015)

RUbioSeq+: An Application that Executes Parallelized Pipelines to Analyse Next-Generation Sequencing Data. - Miriam Rubio-Camarillo; Hugo López-Fernández; Gonzalo Gómez-López; Angel Carro; José María Fernández 001; Florentino Fdez-Riverola; Daniel Glez-Peña; David G. Pisano (PACBB, 2016)

LA-iMageS: a software for elemental distribution bioimaging using LA-ICP-MS data. - Hugo López-Fernández; Gustavo de S. Pessôa; Marco A. Z. Arruda; José Luis Capelo-Martínez; Florentino Fdez-Riverola; Daniel Glez-Peña; Miguel Reboiro-Jato (J. Cheminformatics, 2016)

S2P: A Desktop Application for Fast and Easy Processing of 2D-Gel and MALDI-Based Mass Spectrometry Protein Data. - Hugo López-Fernández; Jose E. Araújo; Daniel Glez-Peña; Miguel Reboiro-Jato; Florentino Fdez-Riverola; José Luis Capelo-Martínez (PACBB, 2017)

Automated Collection and Sharing of Adaptive Amino Acid Changes Data. - Noé Vázquez; Cristina P. Vieira; Bárbara S. R. Amorim; André Torres; Hugo López-Fernández; Florentino Fdez-Riverola; José L. R. Sousa; Miguel Reboiro-Jato; Jorge Vieira (PACBB, 2017)

RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data. - Miriam Rubio-Camarillo; Hugo López-Fernández; Gonzalo Gómez-López; Angel Carro; José María Fernández 001; Coral Fustero Torre; Florentino Fdez-Riverola; Daniel Glez-Peña (Comput. Methods Programs Biomed., 2017)

A Bioinformatics Protocol for Quickly Creating Large-Scale Phylogenetic Trees. - Hugo López-Fernández; Pedro Duque; Sílvia Henriques; Noé Vázquez; Florentino Fdez-Riverola; Cristina P. Vieira; Miguel Reboiro-Jato; Jorge Vieira (PACBB, 2018)

EvoPPI: A Web Application to Compare Protein-Protein Interactions (PPIs) from Different Databases and Species. - Noé Vázquez; Sara Rocha; Hugo López-Fernández; André Torres; Rui Camacho; Florentino Fdez-Riverola; Jorge Vieira; Cristina P. Vieira; Miguel Reboiro-Jato (PACBB, 2018)

Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data. - Osvaldo Graña; Hugo López-Fernández; Florentino Fdez-Riverola; David G. Pisano; Daniel Glez-Peña (Bioinform., 2018)

S2P: A software tool to quickly carry out reproducible biomedical research projects involving 2D-gel and MALDI-TOF MS protein data. - Hugo López-Fernández; Jose E. Araújo; Susana Jorge 001; Daniel Glez-Peña; Miguel Reboiro-Jato; Hugo Miguel Santos; Florentino Fdez-Riverola; José L. Capelo (Comput. Methods Programs Biomed., 2018)

Perceptions of the use of intelligent information access systems in university level active learning activities among teachers of biomedical subjects. - Fernando Aparicio; Maria de la Luz Morales-Botello; Margarita Rubio; Asunción Hernando; Rafael Muñoz 004; Hugo López-Fernández; Daniel Glez-Peña; Florentino Fdez-Riverola; Manuel de la Villa; Manuel J. Maña López; Diego Gachet; Manuel de Buenaga Rodríguez (Int. J. Medical Informatics, 2018)

Deep Learning Techniques for Real Time Computer-Aided Diagnosis in Colorectal Cancer. - Alba Nogueira-Rodríguez; Hugo López-Fernández; Daniel Glez-Peña (DCAI (Special Sessions), 2019)

Proposal of a New Bioinformatics Pipeline for Metataxonomics in Precision Medicine. - Osvaldo Graña-Castro; Hugo López-Fernández; Florentino Fdez-Riverola; Fátima Al-Shahrour; Daniel Glez-Peña (PACBB, 2019)

Inferring Positive Selection in Large Viral Datasets. - Hugo López-Fernández; Pedro Duque; Noé Vázquez; Florentino Fdez-Riverola; Miguel Reboiro-Jato; Cristina P. Vieira; Jorge Vieira (PACBB, 2019)

DEWE: A novel tool for executing differential expression RNA-Seq workflows in biomedical research. - Hugo López-Fernández; Aitor Blanco-Míguez; Florentino Fdez-Riverola; Borja Sánchez; Anália Lourenço (Comput. Biol. Medicine, 2019)

Inferences on Mycobacterium Leprae Host Immune Response Escape and Antibiotic Resistance Using Genomic Data and GenomeFastScreen. - Hugo López-Fernández; Cristina P. Vieira; Florentino Fdez-Riverola; Miguel Reboiro-Jato; Jorge Vieira (PACBB, 2020)

Compi Hub: A Public Repository for Sharing and Discovering Compi Pipelines. - Alba Nogueira-Rodríguez; Hugo López-Fernández; Osvaldo Graña-Castro; Miguel Reboiro-Jato; Daniel Glez-Peña (PACBB, 2020)

The pegi3s Bioinformatics Docker Images Project. - Hugo López-Fernández; Pedro Ferreira 002; Miguel Reboiro-Jato; Cristina P. Vieira; Jorge Vieira (PACBB, 2021)

On the Reproducibility of MiRNA-Seq Differential Expression Analyses in Neuropsychiatric Diseases. - Daniel Pérez-Rodríguez; Hugo López-Fernández; Roberto C. Agís-Balboa (PACBB, 2021)

DREIMT: a drug repositioning database and prioritization tool for immunomodulation. - Kevin Troulé; Hugo López-Fernández; Santiago García-Martín; Miguel Reboiro-Jato; Carlos Carretero-Puche; Jordi Martorell-Marugan; Guillermo Martín-Serrano; Pedro Carmona-Saez; Daniel Glez-Peña; Fátima Al-Shahrour; Gonzalo Gómez-López (Bioinform., 2021)

Application of miRNA-seq in neuropsychiatry: A methodological perspective. - Daniel Pérez-Rodríguez; Hugo López-Fernández; Roberto C. Agís-Balboa (Comput. Biol. Medicine, 2021)

Deep Neural Networks approaches for detecting and classifying colorectal polyps. - Alba Nogueira-Rodríguez; Rubén Domínguez-Carbajales; Hugo López-Fernández; Águeda Iglesias; Joaquín Cubiella; Florentino Fdez-Riverola; Miguel Reboiro-Jato; Daniel Glez-Peña (Neurocomputing, 2021)

Compi: a framework for portable and reproducible pipelines. - Hugo López-Fernández; Osvaldo Graña-Castro; Alba Nogueira-Rodríguez; Miguel Reboiro-Jato; Daniel Glez-Peña (PeerJ Comput. Sci., 2021)

Towards a Flexible and Portable Workflow for Analyzing miRNA-Seq Neuropsychiatric Data: An Initial Replicability Assessment. - Daniel Pérez-Rodríguez; Mateo Pérez-Rodríguez; Roberto C. Agís-Balboa; Hugo López-Fernández (PACBB, 2022)

EvoPPI 2: A Web and Local Platform for the Comparison of Protein-Protein Interaction Data from Multiple Sources from the Same and Distinct Species. - Miguel Reboiro-Jato; Jorge Vieira; Sara Rocha; André D. Sousa; Hugo López-Fernández; Cristina P. Vieira (PACBB, 2022)

Real-time polyp detection model using convolutional neural networks. - Alba Nogueira-Rodríguez; Rubén Domínguez-Carbajales; Fernando Campos-Tato; Jesús Herrero; Manuel Puga; David Remedios; Laura Rivas; Eloy Sánchez; Águeda Iglesias; Joaquín Cubiella; Florentino Fdez-Riverola; Hugo López-Fernández; et al. (Neural Comput. Appl., 2022)

SEDA: A Desktop Tool Suite for FASTA Files Processing. - Hugo López-Fernández; Pedro Duque; Noé Vázquez; Florentino Fdez-Riverola; Miguel Reboiro-Jato; Cristina P. Vieira; Jorge Vieira (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Auto-phylo: A Pipeline Maker for Phylogenetic Studies. - Hugo López-Fernández; Miguel Pinto; Cristina P. Vieira; Pedro Duque; Miguel Reboiro-Jato; Jorge Vieira (PACBB, 2023)

On the identification of potential novel therapeutic targets for spinocerebellar ataxia type 1 (SCA1) neurodegenerative disease using EvoPPI3. - André D. Sousa; Sara Rocha; Jorge Vieira; Miguel Reboiro-Jato; Hugo López-Fernández; Cristina P. Vieira (J. Integr. Bioinform., 2023)

PanDrugs2: prioritizing cancer therapies using integrated individual multi-omics data. - María José Jiménez-Santos; Alba Nogueira-Rodríguez; Elena Piñeiro-Yáñez; Hugo López-Fernández; Santiago García-Martín; Paula Gómez-Plana; Miguel Reboiro-Jato; Gonzalo Gómez-López; Daniel Glez-Peña; Fátima Al-Shahrour (Nucleic Acids Res., 2023)

Inferences on the evolution of the ascorbic acid synthesis pathway in insects using Phylogenetic Tree Collapser (PTC), a tool for the automated collapsing of phylogenetic trees using taxonomic information. - Daniel Glez-Peña; Hugo López-Fernández; Pedro Duque; Cristina P. Vieira; Jorge Vieira (J. Integr. Bioinform., 2024)

Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels and identification of positively selected amino acid sites. - Hugo López-Fernández; Miguel Pinto; Cristina P. Vieira; Pedro Duque; Miguel Reboiro-Jato; Jorge Vieira (J. Integr. Bioinform., 2024)

SEDA 2024 update: enhancing the SEquence DAtaset builder for seamless integration into automated data analysis pipelines. - Miguel Reboiro-Jato; Daniel Pérez-Rodríguez; Miguel José Da Silva; David Vila-Fernández; Cristina P. Vieira; Jorge Vieira; Hugo López-Fernández (BMC Bioinform., 2024)