'TransMem': a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins. - Patrick Aloy; Juan Cedano; Baldomero Oliva; Francesc X. Avilés; Enrique Querol (Comput. Appl. Biosci., 1997)

Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: Application to the human procarboxypeptidase A2. - Patrick Aloy; José M. Mas; Marc A. Martí-Renom; Enrique Querol; Francesc X. Avilés; Baldomero Oliva (J. Comput. Aided Mol. Des., 2000)

Classification of protein disulphide-bridge topologies. - José M. Mas; Patrick Aloy; Marc A. Martí-Renom; Baldomero Oliva; R. de Llorens; Francesc X. Avilés; Enrique Querol (J. Comput. Aided Mol. Des., 2001)

TranScout: prediction of gene expression regulatory proteins from their sequences. - Daniel Aguilar; Baldomero Oliva; Francesc X. Avilés; Enrique Querol (Bioinform., 2002)

SNOW: Standard NOmenclature Wizard to help searching for (bio) chemical standardized names. - Daniel Aguilar; Baldomero Oliva; Francesc X. Avilés; Enrique Querol (Bioinform., 2003)

On the Analysis of the Intersection of the Interactome and the Metabolome. - Joan Planas-Iglesias; Daniel Aguilar; Baldomero Oliva (Spanish Bioinformatics Conference, 2004)

ArchDB: automated protein loop classification as a tool for structural genomics. - Jordi Espadaler; Narcis Fernandez-Fuentes; Antonio Hermoso; Enrique Querol; Francesc X. Avilés; Michael J. E. Sternberg; Baldomero Oliva (Nucleic Acids Res., 2004)

Protein Loop Classification Using Artificial Neural Networks. - Armando Vieira; Baldomero Oliva (BSB, 2005)

Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships. - Jordi Espadaler; Oriol Romero-Isart; Richard M. Jackson; Baldo Oliva (Bioinform., 2005)

PIANA: protein interactions and network analysis. - Ramon Aragues; Daniel Jaeggi; Baldo Oliva (Bioinform., 2006)

Identification of function-associated loop motifs and application to protein function prediction. - Jordi Espadaler; Enrique Querol; Francesc X. Avilés; Baldo Oliva (Bioinform., 2006)

Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative Docking. - Simon J. Cockell; Baldo Oliva; Richard M. Jackson (Bioinform., 2007)

Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions. - Ramon Aragues; Andrej Sali; Jaume Bonet; Marc A. Martí-Renom; Baldo Oliva (PLoS Comput. Biol., 2007)

Initial Results on Knowledge Discovery and Decision Support for Intracranial Aneurysms. - Christoph M. Friedrich; Martin Hofmann-Apitius; Robert Dunlop; Ioannis Chronakis; Miriam C. J. M. Sturkenboom; Roelof Risselada; Baldo Oliva; Ferran Sanz (HEALTHINF (1), 2008)

Predicting cancer involvement of genes from heterogeneous data. - Ramon Aragues; Chris Sander; Baldo Oliva (BMC Bioinform., 2008)

Prediction of enzyme function by combining sequence similarity and protein interactions. - Jordi Espadaler; Narayanan Eswar; Enrique Querol; Francesc X. Avilés; Andrej Sali; Marc A. Martí-Renom; Baldomero Oliva (BMC Bioinform., 2008)

Model Formulation: Training Multidisciplinary Biomedical Informatics Students: Three Years of Experience. - Erik M. van Mulligen; Montserrat Cases; Kristina M. Hettne; Eva Molero; Marc Weeber; Kevin A. Robertson; Baldomero Oliva; Guillermo de la Calle; Victor Maojo (J. Am. Medical Informatics Assoc., 2008)

ModLink+: improving fold recognition by using protein-protein interactions. - Oriol Fornes; Ramon Aragues; Jordi Espadaler; Marc A. Martí-Renom; Andrej Sali; Baldo Oliva (Bioinform., 2009)

Biana: a software framework for compiling biological interactions and analyzing networks. - Javier García-García 002; Emre Guney; Ramon Aragues; Joan Planas-Iglesias; Baldo Oliva (BMC Bioinform., 2010)

Toward PWAS: discovering pathways associated with human disorders. - Emre Guney; Baldo Oliva (BMC Bioinform., 2011)

BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference. - Javier García-García 002; Sylvia Schleker; Judith Klein-Seetharaman; Baldo Oliva (Nucleic Acids Res., 2012)

CAPS-DB: a structural classification of helix-capping motifs. - Joan Segura; Baldomero Oliva; Narcis Fernandez-Fuentes (Nucleic Acids Res., 2012)

iLoops: a protein-protein interaction prediction server based on structural features. - Joan Planas-Iglesias; Manuel Alejandro Marín-López; Jaume Bonet; Javier García-García 002; Baldo Oliva (Bioinform., 2013)

Smotifs as structural local descriptors of supersecondary elements: classification, completeness and applications. - Jaume Bonet; András Fiser; Baldo Oliva; Narcis Fernandez-Fuentes (Bio Algorithms Med Syst., 2014)

Frag'r'Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design. - Jaume Bonet; Joan Segura; Joan Planas-Iglesias; Baldomero Oliva; Narcis Fernandez-Fuentes (Bioinform., 2014)

GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms. - Emre Guney; Javier García-García 002; Baldo Oliva (Bioinform., 2014)

ArchDB 2014: structural classification of loops in proteins. - Jaume Bonet; Joan Planas-Iglesias; Javier García-García 002; Manuel Alejandro Marín-López; Narcis Fernandez-Fuentes; Baldo Oliva (Nucleic Acids Res., 2014)

Knowledge-based modeling of peptides at protein interfaces: PiPreD. - Baldo Oliva; Narcis Fernandez-Fuentes (Bioinform., 2015)

On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures. - Manuel Alejandro Marín-López; Joan Planas-Iglesias; Joaquim Aguirre-Plans; Jaume Bonet; Javier García-García 002; Narcis Fernandez-Fuentes; Baldo Oliva (Bioinform., 2018)

Mining drug-target and drug-adverse drug reaction databases to identify target-adverse drug reaction relationships. - Cristiano Galletti; Patricia Mirela Bota; Baldo Oliva; Narcis Fernandez-Fuentes (Database J. Biol. Databases Curation, 2021)

SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions. - Joaquim Aguirre-Plans; Alberto Meseguer; Ruben Molina-Fernandez; Manuel Alejandro Marín-López; Gaurav Jumde; Kevin Casanova; Jaume Bonet; Oriol Fornes; Narcis Fernandez-Fuentes; Baldo Oliva (BMC Bioinform., 2021)

Prediction of Adverse Drug Reaction Linked to Protein Targets Using Network-Based Information and Machine Learning. - Cristiano Galletti; Joaquim Aguirre-Plans; Baldo Oliva; Narcis Fernandez-Fuentes (Frontiers Bioinform., 2022)

SBILib: a handle for protein modeling and engineering. - Patrick Gohl; Jaume Bonet; Oriol Fornes; Joan Planas-Iglesias; Narcis Fernandez-Fuentes; Baldo Oliva (Bioinform., 2023)

How did we get there? AI applications to biological networks and sequences. - Marco Anteghini; Francesco Gualdi; Baldo Oliva (Comput. Biol. Medicine, 2025)

SNPeBoT: a tool for predicting transcription factor allele specific binding. - Patrick Gohl; Baldo Oliva (BMC Bioinform., 2025)