AlterORF: a database of alternate open reading frames. - Inti Pedroso; Gustavo Rivera; Felipe Lazo; Max Chacón; Francisco Ossandón; Felipe A. Veloso; David S. Holmes (Nucleic Acids Res., 2008)

AFAL: a web service for profiling amino acids surrounding ligands in proteins. - Mauricio Arenas-Salinas; Samuel Ortega-Salazar; Fernando Gonzales-Nilo; Ehmke Pohl; David S. Holmes; Raquel Quatrini (J. Comput. Aided Mol. Des., 2014)

SinEx DB: a database for single exon coding sequences in mammalian genomes. - Roddy Jorquera; Rodrigo Ortiz; Francisco Ossandón; Juan Pablo Cárdenas; Rene Sepúlveda; Carolina González; David S. Holmes (Database J. Biol. Databases Curation, 2016)

Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins. - Braulio Valdebenito-Maturana; José Antonio Reyes-Suárez; Jaime Henriquez; David S. Holmes; Raquel Quatrini; Ehmke Pohl; Mauricio Arenas-Salinas (J. Comput. Chem., 2017)

Improved ontology for eukaryotic single-exon coding sequences in biological databases. - Roddy Jorquera; Carolina González; Philip T. L. C. Clausen; Bent Petersen; David S. Holmes (Database J. Biol. Databases Curation, 2018)

AciDB 1.0: a database of acidophilic organisms, their genomic information and associated metadata. - Gonzalo Neira; Diego Cortez; Joaquin Jil; David S. Holmes (Bioinform., 2020)

SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences. - Roddy Jorquera; Carolina González; Philip T. L. C. Clausen; Bent Petersen; David S. Holmes (Database J. Biol. Databases Curation, 2021)