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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.

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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.

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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).

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.

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).

Fonseca, N. A., Srinivasan, A., Silva, F., & Camacho, R. (2009). Parallel ILP for distributed-memory architectures. Machine Learning, 74(3), 257 - 279.

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Fonseca, N. A., Camacho, R., & Magalhães, A. L. (2008). Amino acid pairing at the N- and C-termini of helical segments in proteins. Proteins: Structure, Function and Genetics, 70(1), 188 - 196.

Fonseca, N. A., Camacho, R., Rocha, R., & Costa, V. S. (2008). Compile the hypothesis space: Do it once, use it often. Fundamenta Informaticae, 89(1), 45 - 67.

Fonseca, N. A., Costa, V. S., Rocha, R., & Camacho, R. (2008). K-RNN: K-relational nearest neighbour algorithm. In Proceedings of the ACM Symposium on Applied Computing (pp. 944 - 948).

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.

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).

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