TRAP: automated classification, quantification and annotation of tandemly repeated sequences. - Tiago José P. Sobreira; Alan M. Durham; Arthur Gruber (Bioinform., 2006)

Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data. - Tiago José P. Sobreira; Arthur Gruber (Bioinform., 2008)

KVFinder: steered identification of protein cavities as a PyMOL plugin. - Saulo Henrique Pires de Oliveira; Felipe A. N. Ferraz; Rodrigo V. Honorato; José Xavier-Neto; Tiago José P. Sobreira; Paulo S. L. de Oliveira (BMC Bioinform., 2014)