Organising multi-dimensional biological image information: the BioImage Database. - José María Carazo; Ernst H. K. Stelzer; A. Engel; I. Fita; C. Henn; J. Machtynger; P. McNeil; David M. Shotton; Monica Chagoyen; Pedro A. de Alarcón; R. Fritsch; J. B. Heymann; et al. (Nucleic Acids Res., 1999)

A Semantic Mediation Approach for Problems in Computational Molecular Biology. - Monica Chagoyen; M. Erdem Kurul; Pedro A. de Alarcón; Simone Santini; Bertram Ludäscher; José María Carazo; Amarnath Gupta (CSB, 2003)

Designing and executing scientific workflows with a programmable integrator. - Monica Chagoyen; M. Erdem Kurul; Pedro A. de Alarcón; José María Carazo; Amarnath Gupta (Bioinform., 2004)

Integrated analysis of gene expression by association rules discovery. - Pedro Carmona-Saez; Monica Chagoyen; Andrés Rodríguez Moreno; Oswaldo Trelles; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2006)

A literature-based similarity metric for biological processes. - Monica Chagoyen; Pedro Carmona-Saez; Concha Gil; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2006)

Discovering semantic features in the literature: a foundation for building functional associations. - Monica Chagoyen; Pedro Carmona-Saez; Hagit Shatkay; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2006)

bioNMF: a versatile tool for non-negative matrix factorization in biology. - Alberto D. Pascual-Montano; Pedro Carmona-Saez; Monica Chagoyen; Francisco Tirado; José María Carazo; Roberto D. Pascual-Marqui (BMC Bioinform., 2006)

CBR-Tagger: a case-based reasoning approach to the gene/protein mention problem. - Mariana L. Neves; Monica Chagoyen; José María Carazo; Alberto D. Pascual-Montano (BioNLP, 2008)

Named Entity Recognition and Normalization: A Domain-Specific Language Approach. - Miguel Vázquez; Monica Chagoyen; Alberto D. Pascual-Montano (IWPACBB, 2008)

Assessment of protein set coherence using functional annotations. - Monica Chagoyen; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2008)

SENT: semantic features in text. - Miguel Vázquez; Pedro Carmona-Saez; Rubén Nogales-Cadenas; Monica Chagoyen; Francisco Tirado; José María Carazo; Alberto D. Pascual-Montano (Nucleic Acids Res., 2009)

Quantifying the biological significance of gene ontology biological processes - implications for the analysis of systems-wide data. - Monica Chagoyen; Florencio Pazos (Bioinform., 2010)

MBRole: enrichment analysis of metabolomic data. - Monica Chagoyen; Florencio Pazos (Bioinform., 2011)

Tools for the functional interpretation of metabolomic experiments. - Monica Chagoyen; Florencio Pazos (Briefings Bioinform., 2013)

Practical analysis of specificity-determining residues in protein families. - Monica Chagoyen; Juan A. García-Martín; Florencio Pazos (Briefings Bioinform., 2016)

Characterization of clinical signs in the human interactome. - Monica Chagoyen; Florencio Pazos (Bioinform., 2016)

MBROLE 2.0 - functional enrichment of chemical compounds. - Javier López-Ibáñez; Florencio Pazos; Monica Chagoyen (Nucleic Acids Res., 2016)

Factors affecting interactome-based prediction of human genes associated with clinical signs. - Sara González-Pérez; Florencio Pazos; Monica Chagoyen (BMC Bioinform., 2017)

Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology. - Florencio Pazos; Monica Chagoyen (Briefings Bioinform., 2019)

Bacterial Feature Finder (BaFF) - a system for extracting features overrepresented in sets of prokaryotic organisms. - Javier López-Ibáñez; Laura T. Martín; Monica Chagoyen; Florencio Pazos (Bioinform., 2019)

Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program. - Monica Chagoyen; Juan F. Poyatos (PLoS Comput. Biol., 2019)

Predicting biological pathways of chemical compounds with a profile-inspired approach. - Javier López-Ibáñez; Florencio Pazos; Monica Chagoyen (BMC Bioinform., 2021)

MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis. - Javier López-Ibáñez; Florencio Pazos; Monica Chagoyen (Nucleic Acids Res., 2023)

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)