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Brito, Â., Ramos, V., Mota, R., Lima, S., et al. (2017). Description of new genera and species of marine cyanobacteria from the Portuguese Atlantic coast. Molecular Phylogenetics and Evolution, 111, 18 - 34.

Reis, M., Silva, A. C., Vieira, C. P., & Vieira, J. (2016). The Drosophila melanogaster Muc68E mucin gene influences adult size, starvation tolerance, and cold recovery. G3: Genes, Genomes, Genetics, 6(7), 1841 - 1851.

Aguiar, B., Vieira, J., Cunha, A. E., Fonseca, N. A., et al. (2015). Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus. PLoS ONE, 10(5).

Aguiar, B., Vieira, J., Cunha, A. E., & Vieira, C. P. (2015). No evidence for Fabaceae Gametophytic self-incompatibility being determined by Rosaceae, Solanaceae, and Plantaginaceae S-RNase lineage genes. BMC Plant Biology, 15(1).

Aguiar, B., Vieira, J., Cunha, A. E., & Vieira, C. P. (2015). No evidence for Fabaceae Gametophytic self-incompatibility being determined by Rosaceae, Solanaceae, and Plantaginaceae S-RNase lineage genes. BMC Plant Biology.

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.

Loureiro, T., Camacho, R., Vieira, J., & Fonseca, N. A. (2013). Boosting the Detection of Transposable Elements Using Machine Learning. Advances in Intelligent Systems and Computing (Vol. 222, pp. 85 - 91).

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).

Aguiar, B., Vieira, J., Cunha, A. E., Fonseca, N. A., et al. (2013). Patterns of evolution at the gametophytic self-incompatibility Sorbus aucuparia (Pyrinae) S pollen genes support the non-self recognition by multiple factors model. Journal of Experimental Botany, 64(8), 2423 - 2434.

Fonseca, N. A., Vieira, C. P., Schlötterer, C., & Vieira, J. (2012). The DAIBAM MITE element is involved in the origin of one fixed and two polymorphic Drosophila virilis phylad inversions. Fly, 6(2), 71 - 74.

Reboiro-Jato, D., Reboiro-Jato, M., Fdez-Riverola, F., Fonseca, N. A., & Vieira, J. (2012). On the development of a pipeline for the automatic detection of positively selected sites. Advances in Intelligent and Soft Computing (Vol. 154 AISC, pp. 225 - 229).

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).

Reis, M., Sousa-Guimarães, S., Vieira, C. P., Sunkel, C. E., & Vieira, J. (2011). Drosophila genes that affect meiosis duration are among the meiosis related genes that are more often found duplicated. PLoS ONE, 6(3).

Schäfer, M. A., Routtu, J., Vieira, J., Hoikkala, A., et al. (2011). Multiple quantitative trait loci influence intra-specific variation in genital morphology between phylogenetically distinct lines of Drosophila montana. Journal of Evolutionary Biology, 24(9), 1879 - 1886.

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.

Vieira, J., Ferreira, P. G., Aguiar, B., Fonseca, N. A., & Vieira, C. P. (2010). Evolutionary patterns at the RNase based gametophytic self - Incompatibility system in two divergent Rosaceae groups (Maloideae and Prunus). BMC Evolutionary Biology, 10(1).

Vieira, J., & Vieira, C. P. (2010). On the identification of human selected loci in grapevines. Heredity, 104(4), 327 - 328.

Schäfer, M. A., Mazzi, D., Klappert, K., Kauranen, H., et al. (2010). A microsatellite linkage map for Drosophila montana shows large variation in recombination rates, and a courtship song trait maps to an area of low recombination. Journal of Evolutionary Biology, 23(3), 518 - 527.

Santos, J. S., Fonseca, N. A., Vieira, C. P., Vieira, J., & Casares, F. (2010). Phylogeny of the teashirt-related zinc finger (tshz) gene family and analysis of the developmental expression of tshz2 and tshz3b in the zebrafish. Developmental Dynamics, 239(3), 1010 - 1018.

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.

Fonseca, N. A., Vieira, C. P., & Vieira, J. (2009). Gene classification based on amino acid motifs and residues: The DLX (distal-less) test case. PLoS ONE, 4(6).

Vieira, J., Fonseca, N. A., & Vieira, C. P. (2009). RNase-based gametophytic self-incompatibility evolution: Questioning the hypothesis of multiple independent recruitments of the s-pollen gene. Journal of Molecular Evolution, 69(1), 32 - 41.

Tsukamoto, T., Potter, D., Tao, R., Vieira, C. P., et al. (2008). Genetic and molecular characterization of three novel S-haplotypes in sour cherry (Prunus cerasus L.). Journal of Experimental Botany, 59(11), 3169 - 3185.

Vieira, J., Santos, R. A. M., Ferreira, S. M., & Vieira, C. P. (2008). Inferences on the number and frequency of S-pollen gene (SFB) specificities in the polyploid Prunus spinosa. Heredity, 101(4), 351 - 358.

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.

Santos, C. L., Vieira, J., Tavares, F., Benson, D. R., et al. (2008). On the nature of fur evolution: A phylogenetic approach in Actinobacteria. BMC Evolutionary Biology, 8(1).

Cruz, E., Whittington, C., Krikler, S. H., Mascarenhas, C., et al. (2008). A new 500 kb haplotype associated with high CD8+ T-lymphocyte numbers predicts a less severe expression of hereditary hemochromatosis. BMC medical genetics, 9, 97.

Vieira, J., Fonseca, N. A., Santos, R. A. M., Habu, T., et al. (2008). The number, age, sharing and relatedness of S-locus specificities in Prunus. Genetics Research, 90(1), 17 - 26.

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.

Fonseca, N. A., Vieira, C. P., Holland, P. W. H., & Vieira, J. (2008). Protein evolution of ANTP and PRD homeobox genes. BMC Evolutionary Biology, 8(1).

Vieira, J., Santos, R. A. M., Habu, T., Tao, R., & Vieira, C. P. (2008). The Prunus self-incompatibility locus (S locus) is seldom rearranged. Journal of Heredity, 99(6), 657 - 660.

Vieira, J., Teles, E., Santos, R. A. M., & Vieira, C. P. (2008). Recombination at prunus S-locus region SLFL1 gene. Genetics, 180(1), 483 - 491.

Vieira, J., Fonseca, N. A., & Vieira, C. P. (2008). An S-RNase-based gametophytic self-incompatibility system evolved only once in eudicots. Journal of Molecular Evolution, 67(2), 179 - 190.

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.

Santos, C. L., Vieira, J., Sellstedt, A., Normand, P., et al. (2007). Modulation of Frankia alni ACN14a oxidative stress response: Activity, expression and phylogeny of catalases. Physiologia Plantarum, 130(3), 454 - 463.

Vieira, J., Mendes, M. V., Albuquerque, P., Moradas-Ferreira, P., & Tavares, F. (2007). A novel approach for the identification of bacterial taxa-specific molecular markers. Letters in Applied Microbiology, 44(5), 506 - 512.

Vieira, J., Cardoso, C. S., Pinto, J., Patil, K., et al. (2007). A putative gene located at the MHC class I region around the D6S105 marker contributes to the setting of CD8+ T-lymphocyte numbers in humans. International Journal of Immunogenetics, 34(5), 359 - 367.

Temudo, T., Oliveira, P., Santos, M., Dias, K., et al. (2007). Stereotypies in Rett syndrome: Analysis of 83 patients with and without detected MECP2 mutations. Neurology, 68(15), 1183 - 1187.

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.

Vieira, C. P., Almeida, A., Dias, J. D., & Vieira, J. (2006). On the location of the gene(s) harbouring the advantageous variant that maintains the X/4 fusion of Drosophila americana. Genetical Research, 87(3), 163 - 174.

Cruz, E., Vieira, J., Almeida, S., Lacerda, R., et al. (2006). A study of 82 extended HLA haplotypes in HFE-C282Y homozygous hemochromatosis subjects: Relationship to the genetic control of CD8+ T-lymphocyte numbers and severity of iron overload. BMC Medical Genetics, 7.

Nunes, M. D. S., Santos, R. A. M., Ferreira, S. M., Vieira, J., & Vieira, C. P. (2006). Variability patterns and positively selected sites at the gametophytic self-incompatibility pollen SFB gene in a wild self-incompatible Prunus spinosa (Rosaceae) population. New Phytologist, 172(3), 577 - 587.

Päällysaho, S., Vieira, C. P., Hoikkala, A., & Vieira, J. (2005). Evidence for introgression in differentiated North-American and Finnish Drosophila montana populations. Genetica, 123(3), 285 - 293.

Costas, J., Pereira, P. S., Vieira, C. P., Pinho, S., et al. (2004). Dynamics and function of intron sequences of the wingless gene during the evolution of the Drosophila genus. Evolution and Development, 6(5), 325 - 335.

Cruz, E., Vieira, J., Gonçalves, R., Alves, H., et al. (2004). Involvement of the Major Histocompatibility Complex region in the regulation regulation of circulating CD8+ T-cell numbers in humans. Tissue Antigens, 64(1), 25 - 34.