Sillero, N., Reis, M., Vieira, C. P., Vieira, J., & Morales-Hojas, R. (2014). Niche evolution and thermal adaptation in the temperate species Drosophila americana. Journal of Evolutionary Biology.

Fonseca, N. A., Morales-Hojas, R., Reis, M., Rocha, H., et al. (2013). Drosophila americana as a model species for comparative studies on the molecular basis of phenotypic variation. Genome Biology and Evolution, 5(4), 661 - 679.

Araújo, A. R., Reis, M., Rocha, H., Aguiar, B., et al. (2013). The Drosophila melanogaster methuselah Gene: A Novel Gene with Ancient Functions. PLoS ONE, 8(5).

Morales-Hojas, R., & Vieira, J. (2012). Phylogenetic Patterns of Geographical and Ecological Diversification in the Subgenus Drosophila. PLoS ONE, 7(11).

Lagisz, M., Wen, S. - Y., Routtu, J., Klappert, K., et al. (2012). Two distinct genomic regions, harbouring the period and fruitless genes, affect male courtship song in Drosophila montana. Heredity, 108(6), 602 - 608.

Reis, M., Vieira, C. P., Morales-Hojas, R., Aguiar, B., et al. (2011). A comparative study of the short term cold resistance response in distantly related Drosophila species: The role of regucalcin and Frost. PLoS ONE, 6(10).

Morales-Hojas, R., Reis, M., Vieira, C. P., & Vieira, J. (2011). Resolving the phylogenetic relationships and evolutionary history of the Drosophila virilis group using multilocus data. Molecular Phylogenetics and Evolution, 60(2), 249 - 258.

Faísca, P., Morales-Hojas, R., Alves, M., Gomes, J., et al. (2010). A case of canine ocular onchocercosis in Portugal. Veterinary Ophthalmology, 13(2), 117 - 121.

Johanet, A., Picard, D., Garner, T. W. J., Dawson, D. A., et al. (2009). Characterization of microsatellite loci in two closely related Lissotriton newt species. Conservation Genetics, 10(6), 1903 - 1906.

Morales-Hojas, R., Vieira, C. P., Reis, M., & Vieira, J. (2009). Comparative analysis of five immunity-related genes reveals different levels of adaptive evolution in the virilis and melanogaster groups of Drosophila. Heredity, 102(6), 573 - 578.

Morales-Hojas, R. (2009). Molecular systematics of filarial parasites, with an emphasis on groups of medical and veterinary importance, and its relevance for epidemiology. Infection, Genetics and Evolution, 9(5), 748 - 759.

Morales-Hojas, R., & Krueger, A. (2009). The species delimitation problem in the Simulium damnosum complex, blackfly vectors of onchocerciasis. Medical and Veterinary Entomology, 23(3), 257 - 268.

Morales-Hojas, R., Vieira, C. P., & Vieira, J. (2008). Inferring the evolutionary history of Drosophila americana and Drosophila novamexicana using a multilocus approach and the influence of chromosomal rearrangements in single gene analyses. Molecular Ecology, 17(12), 2910 - 2926.

Reis, M., Vieira, C. P., Morales-Hojas, R., & Vieira, J. (2008). An old bilbo-like non-LTR retroelement insertion provides insight into the relationship of species of the virilis group. Gene, 425(1-2), 48 - 55.

Morales-Hojas, R., Päällysaho, S., Vieira, C. P., Hoikkala, A., & Vieira, J. (2007). Comparative polytene chromosome maps of D. montana and D. virilis. Chromosoma, 116(1), 21 - 27.

Vieira, J., Morales-Hojas, R., Santos, R. A. M., & Vieira, C. P. (2007). Different positively selected sites at the gametophytic self-incompatibility pistil S-RNase gene in the Solanaceae and Rosaceae (Prunus, Pyrus, and Malus). Journal of Molecular Evolution, 65(2), 175 - 185.

Krueger, A., Fischer, P., & Morales-Hojas, R. (2007). Molecular phylogeny of the filaria genus Onchocerca with special emphasis on Afrotropical human and bovine parasites. Acta Tropica, 101(1), 1 - 14.

Morales-Hojas, R., Cheke, R. A., & Post, R. J. (2007). A preliminary analysis of the population genetics and molecular phylogenetics of Onchocerca volvulus (Nematoda: Filarioidea) using nuclear ribosomal second internal transcribed spacer sequences. Memorias do Instituto Oswaldo Cruz, 102(7), 879 - 882.

Morales-Hojas, R., Vieira, C. P., & Vieira, J. (2006). The evolutionary history of the transposable element Penelope in the Drosophila virilis group of species. Journal of Molecular Evolution, 63(2), 262 - 273.