Pattern recognition on antigen-antibody interactions from protein microarrays based on data mining and bioinformatics analysis. - Jorge Torres-Almonacid; David Medina-Ortiz; Diego Álvarez-Saravia; Julio Águila-Guerrero; Alvaro Olivera-Nappa; Marcelo A. Navarrete (SCCC, 2019)

Combination of digital signal processing and assembled predictive models facilitates the rational design of proteins. - David Medina-Ortiz; Sebastián Contreras; Juan Amado-Hinojosa; Jorge Torres-Almonacid; Juan A. Asenjo; Marcelo A. Navarrete; Alvaro Olivera-Nappa (CoRR, 2020)

DMAKit: A user-friendly web platform for bringing state-of-the-art data analysis techniques to non-specific users. - David Medina-Ortiz; Sebastián Contreras; Cristofer Quiroz; Juan A. Asenjo; Alvaro Olivera-Nappa (Inf. Syst., 2020)

Peptipedia: a user-friendly web application and a comprehensive database for peptide research supported by Machine Learning approach. - Cristofer Quiroz; Yasna Barrera Saavedra; Benjamín Armijo-Galdames; Juan Amado-Hinojosa; Alvaro Olivera-Nappa; Anamaria Sanchez-Daza; David Medina-Ortiz (Database J. Biol. Databases Curation, 2021)

Peptipedia: a comprehensive database for peptide research supported by Assembled predictive models and Data Mining approaches. - Cristofer Quiroz; Yasna Barrera Saavedra; Benjamín Armijo-Galdames; Juan Amado-Hinojosa; Alvaro Olivera-Nappa; Anamaria Sanchez-Daza; David Medina-Ortiz (CoRR, 2021)

Exploring Machine Learning Algorithms and Numerical Representations Strategies to Develop Sequence-Based Predictive Models for Protein Networks. - David Medina-Ortiz; Pedro Salinas; Gabriel Cabas-Mora; Fabio Durán-Verdugo; Alvaro Olivera-Nappa; Roberto Uribe Paredes (ICCSA (1), 2023)

Exploring Machine Learning Algorithms and Protein Language Models Strategies to Develop Enzyme Classification Systems. - Diego Fernández; Alvaro Olivera-Nappa; Roberto Uribe Paredes; David Medina-Ortiz (IWBBIO (1), 2023)

RUDEUS: A Machine Learning Classification System to Study DNA-Binding Proteins. - David Medina-Ortiz; Gabriel Cabas-Mora; Iván Moya; Nicole Soto-García; Roberto Uribe Paredes (KDIR, 2024)

Peptide-based drug discovery through artificial intelligence: towards an autonomous design of therapeutic peptides. - Montserrat Goles; Anamaria Sanchez-Daza; Gabriel Cabas-Mora; Lindybeth Sarmiento-Varón; Julieta Sepúlveda-Yañez; Hoda Anvari-Kazemabad; Mehdi D. Davari; Roberto Uribe Paredes; Alvaro Olivera-Nappa; Marcelo A. Navarrete; David Medina-Ortiz (Briefings Bioinform., 2024)

Peptipedia v2.0: a peptide sequence database and user-friendly web platform. A major update. - Gabriel Cabas-Mora; Anamaria Sanchez-Daza; Nicole Soto-García; Valentina Garrido; Diego Álvarez-Saravia; Marcelo A. Navarrete; Lindybeth Sarmiento-Varón; Julieta Sepúlveda-Yañez; Mehdi D. Davari; Frédéric Cadet; Alvaro Olivera-Nappa; Roberto Uribe Paredes; et al. (Database J. Biol. Databases Curation, 2024)

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering. - Wen-ran Li; Xavier F. Cadet; David Medina-Ortiz; Mehdi D. Davari; Ramanathan Sowdhamini; Cedric Damour; Yu Li; Alain Miranville; Frédéric Cadet (CoRR, 2025)