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