Comparative Analysis of Different Methods for the Detection of Specificity Regions in Protein Families. - Florencio Pazos; Luis Sánchez-Pulido; Juan Antonio Garcia-Ranca; Miguel A. Andrade; Silvia Atrian; Alfonso Valencia (BCEC, 1997)

A graphical interface for correlated mutations and other protein structure prediction methods. - Florencio Pazos; O. Olmea; Alfonso Valencia (Comput. Appl. Biosci., 1997)

A platform for integrating threading results with protein family analyses. - Florencio Pazos; Burkhard Rost; Alfonso Valencia (Bioinform., 1999)

EVA: continuous automatic evaluation of protein structure prediction servers. - Volker A. Eyrich; Marc A. Martí-Renom; Dariusz Przybylski; Mallur S. Madhusudhan; András Fiser; Florencio Pazos; Alfonso Valencia; Andrej Sali; Burkhard Rost (Bioinform., 2001)

EVA: evaluation of protein structure prediction servers. - Ingrid Y. Y. Koh; Volker A. Eyrich; Marc A. Martí-Renom; Dariusz Przybylski; Mallur S. Madhusudhan; Narayanan Eswar; Osvaldo Graña; Florencio Pazos; Alfonso Valencia; Andrej Sali; Burkhard Rost (Nucleic Acids Res., 2003)

The Biodegradation Network, a New Scenario for Computational Systems Biology Research. - Florencio Pazos; David Guijas; Manuel J. Gómez; Almudena Trigo; Victor de Lorenzo; Alfonso Valencia (CMSB, 2004)

Modelling Inhibition in Metabolic Pathways Through Abduction and Induction. - Alireza Tamaddoni-Nezhad; Antonis C. Kakas; Stephen H. Muggleton; Florencio Pazos (ILP, 2004)

EVAcon: a protein contact prediction evaluation service. - Osvaldo Graña; Volker A. Eyrich; Florencio Pazos; Burkhard Rost; Alfonso Valencia (Nucleic Acids Res., 2005)

MetaRouter: bioinformatics for bioremediation. - Florencio Pazos; David Guijas; Alfonso Valencia; Victor de Lorenzo (Nucleic Acids Res., 2005)

Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories. - Manuel J. Gómez; Ramón Alonso-Allende; Florencio Pazos; Osvaldo Graña; David de Juan; Alfonso Valencia (Trans. Comp. Sys. Biology, 2005)

Phylogeny-independent detection of functional residues. - Florencio Pazos; Antonio Rausell; Alfonso Valencia (Bioinform., 2006)

TreeDet: a web server to explore sequence space. - Angel Carro; Michael L. Tress; David de Juan; Florencio Pazos; Pedro Lopez-Romero; Antonio del Sol; Alfonso Valencia; Ana María Rojas (Nucleic Acids Res., 2006)

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)

Computational Methods to Predict Protein Interaction Partners. - Alfonso Valencia; Florencio Pazos (Protein-protein Interactions and Networks, 2008)

Enhancing the prediction of protein pairings between interacting families using orthology information. - José M. G. Izarzugaza; David de Juan; Carles Pons; Florencio Pazos; Alfonso Valencia (BMC Bioinform., 2008)

Defining functional distances over Gene Ontology. - Angela del Pozo; Florencio Pazos; Alfonso Valencia (BMC Bioinform., 2008)

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

Studying the co-evolution of protein families with the Mirrortree web server. - David Ochoa; Florencio Pazos (Bioinform., 2010)

Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds. - Juan C. Triviño; Florencio Pazos (BMC Syst. Biol., 2010)

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

Selection of organisms for the co-evolution-based study of protein interactions. - Dorota Herman; David Ochoa; David de Juan; Daniel Lopez; Alfonso Valencia; Florencio Pazos (BMC Bioinform., 2011)

JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. - Thilo Muth; Juan A. García-Martín; Antonio Rausell; David de Juan; Alfonso Valencia; Florencio Pazos (Bioinform., 2012)

Computational Prediction of Important Regions in Protein Sequences [Life Sciences]. - Natalia Pietrosemoli; Daniel Lopez; Aldo Segura-Cabrera; Florencio Pazos (IEEE Signal Process. Mag., 2012)

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

COPRED: prediction of fold, GO molecular function and functional residues at the domain level. - Daniel Lopez; Florencio Pazos (Bioinform., 2013)

Concomitant prediction of function and fold at the domain level with GO-based profiles. - Daniel Lopez; Florencio Pazos (BMC Bioinform., 2013)

Detection of significant protein coevolution. - David Ochoa; David de Juan; Alfonso Valencia; Florencio Pazos (Bioinform., 2015)

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)

Breaking-Cas - interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes. - Juan C. Oliveros; Mònica Franch; Daniel Tabas-Madrid; David San-León; Lluis Montoliu; Pilar Cubas; Florencio Pazos (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)

Effect of the sequence data deluge on the performance of methods for detecting protein functional residues. - Diego Garrido-Martín; Florencio Pazos (BMC Bioinform., 2018)

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)

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

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)