The evolutionary origin of protein complexes. - José B. Pereira-Leal (BMC Bioinform., 2005)

3D Complex: A Structural Classification of Protein Complexes. - Emmanuel D. Levy; José B. Pereira-Leal; Cyrus Chothia; Sarah A. Teichmann (PLoS Comput. Biol., 2006)

MAIS-TB: An Integrated Web Tool for Molecular Epidemiology Analysis. - Patricia Soares; Carlos Penha Gonçalves; M. Gabriela Gomes; José B. Pereira-Leal (ITBAM, 2011)

Thousands of Rab GTPases for the Cell Biologist. - Yoan Diekmann; Elsa Seixas; Marc Gouw; Filipe Tavares-Cadete; Miguel C. Seabra; José B. Pereira-Leal (PLoS Comput. Biol., 2011)

Loss of Genetic Redundancy in Reductive Genome Evolution. - André G. Mendonça; Renato J. Alves; José B. Pereira-Leal (PLoS Comput. Biol., 2011)

inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis. - Patricia Soares; Renato J. Alves; Ana B. Abecasis; Carlos Penha Gonçalves; M. Gabriela Gomes; José B. Pereira-Leal (BMC Bioinform., 2013)

Bioinformatics Projects Supporting Life-Sciences Learning in High Schools. - Isabel Marques; Paulo Almeida; Renato J. Alves; Maria João Dias; Ana Godinho; José B. Pereira-Leal (PLoS Comput. Biol., 2014)

Rabifier2: an improved bioinformatic classifier of Rab GTPases. - Jaroslaw Surkont; Yoan Diekmann; José B. Pereira-Leal (Bioinform., 2017)