Incorporating biological knowledge to microarray data classification through genomic data fusion. - Daniel Glez-Peña; Marta Pérez-Fernández; Miguel Reboiro-Jato; Florentino Fdez-Riverola; Marta Pérez; Fernando Díaz 001 (FUSION, 2010)

An Experimental Evaluation of a Novel Stochastic Method for Iterative Class Discovery on Real Microarray Datasets. - Héctor Gómez; Daniel Glez-Peña; Miguel Reboiro-Jato; Reyes Pavón 001; Fernando Díaz 001; Florentino Fdez-Riverola (IWPACBB, 2010)

A Comparative Study of Microarray Data Classification Methods Based on Ensemble Biological Relevant Gene Sets. - Miguel Reboiro-Jato; Daniel Glez-Peña; Juan F. Gálvez; Rosalía Laza; Fernando Díaz 001; Florentino Fdez-Riverola (IWPACBB, 2010)

PathAgent: Multi-agent System for Updated Pathway Information Integration. - Miguel Reboiro-Jato; Daniel Glez-Peña; Rubén Domínguez; Gonzalo Gómez-López; David G. Pisano; Celso Campos; Florentino Fdez-Riverola (PAAMS (Special Sessions and Workshops), 2010)

Multi-agent System for Mass Spectrometry Analysis. - Miguel Reboiro-Jato; Daniel Glez-Peña; Hugo Miguel Santos; Mário S. Diniz; Carlos Lodeiro; José L. Capelo; Florentino Fdez-Riverola (PAAMS (Special Sessions and Workshops), 2010)

A robust algorithm for forming note complexes. - Silvana Gómez-Meire; Miguel Reboiro-Jato; Carlos H. Fajardo Toro; David N. Olivieri; Florentino Fdez-Riverola (Inteligencia Artif., 2010)

AIBench: A rapid application development framework for translational research in biomedicine. - Daniel Glez-Peña; Miguel Reboiro-Jato; Paulo Maia; Miguel Rocha 001; Fernando Díaz 001; Florentino Fdez-Riverola (Comput. Methods Programs Biomed., 2010)

PathJam: a new service for integrating biological pathway information. - Daniel Glez-Peña; Miguel Reboiro-Jato; Rubén Domínguez; Gonzalo Gómez-López; David G. Pisano; Florentino Fdez-Riverola (J. Integr. Bioinform., 2010)

ALTER: program-oriented conversion of DNA and protein alignments. - Daniel Glez-Peña; Daniel Gómez-Blanco; Miguel Reboiro-Jato; Florentino Fdez-Riverola; David Posada (Nucleic Acids Res., 2010)

An Intuitive Workflow to Retrieve Somatic Mutations in Next Generation Sequencing Studies. - Daniel Glez-Peña; Miguel Reboiro-Jato; Florentino Fdez-Riverola; David G. Pisano; Gonzalo Gómez-López (PACBB, 2011)

Assessing the Suitability of MeSH Ontology for Classifying Medline Documents. - Rosalía Laza; Reyes Pavón 001; Miguel Reboiro-Jato; Florentino Fdez-Riverola (PACBB, 2011)

Assessing the Impact of Class-Imbalanced Data for Classifying Relevant/Irrelevant Medline Documents. - Reyes Pavón 001; Rosalía Laza; Miguel Reboiro-Jato; Florentino Fdez-Riverola (PACBB, 2011)

Building Proteomics Applications with the AIBench Application Framework. - Miguel Reboiro-Jato; Daniel Glez-Peña; José Ramón Méndez Reboredo; Hugo Miguel Santos; Ricardo Jorge Carreira; José L. Capelo; Florentino Fdez-Riverola (PACBB, 2011)

PileLine: a toolbox to handle genome position information in next-generation sequencing studies. - Daniel Glez-Peña; Gonzalo Gómez-López; Miguel Reboiro-Jato; Florentino Fdez-Riverola; David G. Pisano (BMC Bioinform., 2011)

Using inductive learning to assess compound feed production in cooperative poultry farms. - Miguel Reboiro-Jato; Julia Glez-Dopazo; D. Glez; Rosalía Laza; Juan F. Gálvez; Reyes Pavón 001; Daniel Glez-Peña; Florentino Fdez-Riverola (Expert Syst. Appl., 2011)

Evaluating the effect of unbalanced data in biomedical document classification. - Rosalía Laza; Reyes Pavón 001; Miguel Reboiro-Jato; Florentino Fdez-Riverola (J. Integr. Bioinform., 2011)

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)

On the Development of a Pipeline for the Automatic Detection of Positively Selected Sites. - David Reboiro-Jato; Miguel Reboiro-Jato; Florentino Fdez-Riverola; Nuno A. Fonseca; Jorge Vieira (PACBB, 2012)

A novel ensemble approach for multicategory classification of DNA microarray data using biological relevant gene sets. - Miguel Reboiro-Jato; Daniel Glez-Peña; Fernando Díaz 001; Florentino Fdez-Riverola (Int. J. Data Min. Bioinform., 2012)

ADOPS - Automatic Detection Of Positively Selected Sites. - David Reboiro-Jato; Miguel Reboiro-Jato; Florentino Fdez-Riverola; Cristina P. Vieira; Nuno A. Fonseca; Jorge Vieira (J. Integr. Bioinform., 2012)

Grindstone4Spam: An optimization toolkit for boosting e-mail classification. - José Ramón Méndez 001; Miguel Reboiro-Jato; Fernando Díaz 001; Eduardo Díaz; Florentino Fdez-Riverola (J. Syst. Softw., 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)

A novel ensemble of classifiers that use biological relevant gene sets for microarray classification. - Miguel Reboiro-Jato; Fernando Díaz 001; Daniel Glez-Peña; Florentino Fdez-Riverola (Appl. Soft Comput., 2014)

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

geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. - Miguel Reboiro-Jato; Joel Arrais; José Luís Oliveira; Florentino Fdez-Riverola (BMC 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)

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)

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)

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)

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)

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)

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)

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)

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)

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)