NeoScreen: A Software Application for MS/MS Newborn Screening Analysis. - Miguel Pinheiro; José Luís Oliveira; Manuel A. S. Santos; Hugo Rocha; M. Luis Cardoso; Laura Vilarinho (ISBMDA, 2004)

Studying the Evolution of Codon Context in Conserved Gene Sequences. - Miguel Pinheiro; José Luís Oliveira; Gabriela R. Moura; Manuel A. S. Santos (BIOTECHNO, 2008)

Sistema computacional para o estudo da estrutura primária e redesenho de genes - Miguel Pinheiro (2010)

Improving the performance of the iterative signature algorithm for the identification of relevant patterns. - Adelaide Freitas; Vera Afreixo; Miguel Pinheiro; José Luís Oliveira; Gabriela R. Moura; Manuel A. S. Santos (Stat. Anal. Data Min., 2011)

Improvements on bicriteria pairwise sequence alignment: algorithms and applications. - Maryam Abbasi; Luís Paquete; Arnaud Liefooghe; Miguel Pinheiro; Pedro Matias 001 (Bioinform., 2013)

MOSAL: software tools for multiobjective sequence alignment. - Luís Paquete; Pedro Matias 001; Maryam Abbasi; Miguel Pinheiro (Source Code Biol. Medicine, 2014)

Optimizing Variant Calling for Human Genome Analysis: A Comprehensive Pipeline Approach. - Miguel Pinheiro; Jorge Miguel Silva; José Luís Oliveira (IWBBIO (2), 2023)