BRITO A, RAMOS V, MOTA R, LIMA S, SANTOS A, VIEIRA J, VIEIRA CP, KAŠTOVSKÝ J, VASCONCELOS VM, TAMAGNINI P. 2017. Description of new genera and species of marine cyanobacteria from the Portuguese Atlantic coast.  Molecular Phylogenetics and Evolution, in press.


Reis M, Silva AC, Vieira CP, Vieira J. 2016. The Drosophila melanogaster Muc68E Mucin Gene Influences Adult Size, Starvation Tolerance, and Cold Recovery. G3 (Bethesda). doi: 10.1534/g3.116.029934. [Epub ahead of print]

67) PEREIRA SB, MOTA R, VIEIRA CP, VIEIRA J, TAMAGNINIP. 2015. Phylum-wide analysis of genes/proteins related to the last steps of assembly and export of extracellular polymeric substances (EPS) in cyanobacteria. Scientific Reports 5:14835.
66) REIS M, VALER FB, VIEIRA CP, VIEIRA J. 2015. Drosophila americanaDiapausing Females Show Features Typical of Young Flies. PLoS One. 10(9):e0138758.
65) AGUIAR B, VIEIRA J, CUNHA AE, VIEIRA CP. 2015. No evidence for Fabaceae Gametophytic self-incompatibility being determined by Rosaceae, Solanaceae, and Plantaginaceae S-RNase lineage genes. BMC Plant Biol. 15:129.
64) AGUIAR B, VIEIRA J, CUNHA AE, FONSECA NA, IEZZONI A, VAN NOCKER S, VIEIRA CP. 2015. Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus. PLoS One. 10(5):e0126138.
63) SILLERO N, REIS M, VIEIRA CP, VIEIRA J, MORALES-HOJAS R. 2014. Niche evolution and thermal adaptation in the temperate species Drosophila americana. J Evol Biol. J Evol Biol. 27:1549-1561.
62) REIS M, PÁSCOA I, ROCHA H, AGUIAR B, VIEIRA CP, VIEIRA J. 2014. Genes belonging to the insulin and ecdysone signaling pathways can contribute to developmental time, lifespan and abdominal size variation in Drosophila americana. PLOS One 9:e86690.

61) COSTA M, CRUZ E, BARTON JC, THORSTENSEN K, MORAIS S, SILVA BM, PINTO JP, VIEIRA CP, VIEIRA J, ACTON RT, PORTO G. 2013. Effects of Highly Conserved Major Histocompatibility Complex (MHC) Extended Haplotypes on Iron and Low CD8+ T Lymphocyte Phenotypes in HFE C282Y Homozygous Hemochromatosis Patients from Three Geographically Distant Areas. PLOS ONE, 8(11):e79990.

60) LOUREIRO T, CAMACHO R, VIEIRA J, FONSECA NA. 2013. Improving the performance of Transposable Elements detection tools. Journal of Integrative Bioinformatics, 10(3):231.

59) ARAÚJO AR, REIS M, ROCHA H, AGUIAR B, MORALES-HOJAS R, MACEDO-RIBEIRO S, FONSECA NA, REBOIRO-JATO D, REBOIRO-JATO M, FDEZ-RIVEROLA F, VIEIRA CP, VIEIRA J. 2013. The Drosophila melanogaster methuselah gene: a novel gene with ancient functions. PLOS ONE, 8(5):e63747.

58) FONSECA NA, MORALES-HOJAS, REIS M, ROCHA H, VIEIRA CP, NOLTE V, SCHLÖTTERER C, VIEIRA J. 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.

57) AGUIAR B, VIEIRA J CUNHA AE, FONSECA NA, REBOIRO-JATO D, REBOIRO-JATO M, FDEZ-RIVEROLA F, RASPÉ O, VIEIRA CP. 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.

56) LOUREIRO T, CAMACHO R, FONSECA NA, VIEIRA J. 2013. Boosting the detection of transposable elements using machine learning. 7th International Conference on Practical Applications of Computational Biology & Bioinformatics Advances in Intelligent Systems and Computing Volume 222, 2013, pp 85-91.

55) MORALES-HOJAS R, VIEIRA J. 2012. Phylogenetic patterns of geographical and ecological diversification in the subgenus Drosophila. PloS ONE 7:e49552. Complete figures doi:10.5061/dryad.v0t0d

54) REBOIRO-JATO D, REBOIRO-JATO M, FDEZ-RIVEROLA F, VIEIRA CP, FONSECA NA, VIEIRA J. 2012. ADOPS - Automatic Detection Of Positively Selected Sites. Journal of Integrative Bioinformatics, 9(3):200.

53) REBOIRO-JATO D, REBOIRO-JATO M, FDEZ-RIVEROLA F, FONSECA NA, VIEIRA J. 2012. On the Development of a Pipeline for the Automatic Detection of Positively Selected Sites. International Conference on Practical Applications of Computational Biology & Bioinformatics (IWPACBB’12) Miguel P. Rocha, Nicholas Luscombe, Florentino Fdez-Riverola and Juan Corchado M. Rodríguez (editors). ISBN Number 978-3-642-28838-8. Volume 154, pp 225-229.

52) FONSECA NA, VIEIRA CP, 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 (Austin) 6(2):71-74.

51) LAGISZ M, WEN SY, ROUTTU J, KLAPPERT K, MAZZI D, MORALES-HOJAS R, SCHÄFER MA, VIEIRA J, HOIKKALA A, RITCHIE MG, BUTLIN RK. 2012. Two distinct genomic regions, harbouring the period and fruitless genes, affect male courtship song in Drosophila montana. Heredity 108(6):602-608.

50) REIS M, VIEIRA CP, MORALES-HOJAS R, AGUIAR B, ROCHA H, SCHLOTTERER C, VIEIRA J. 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): e25520.

 49) SCHÄFER MA, ROUTTU J, VIEIRA J, HOIKKALA A, RITCHIE MG, SCHLÖTTERER C. 2011. Multiple quantitative trait loci influence intra-specific variation in genital morphology between phylogenetically distinct lines of Drosophila montana. Journal of Evolutionary Biology 24: 1879-1886.

48) MORALES-HOJAS R, REIS M, VIEIRA CP, VIEIRA J. 2011. Resolving the phylogenetic relationships and evolutionary history of the Drosophila virilis group using multilocus data. Molecular Phylogenetics and Evolution, 60:249-258.

47) REIS M, SOUSA-GUIMARÃES S, VIEIRA CP, SUNKEL CE, 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): e17512.

46) VIEIRA J, FERREIRA PG, AGUIAR B, FONSECA NA, VIEIRA CP. 2010. Evolutionary patterns at the RNase based gametophytic self - incompatibility system in two divergent Rosaceae groups (Maloideae and Prunus). BMC Evolutionary Biology 10:200.

45) VIEIRA J, VIEIRA CP. 2010. On the identification of human selected loci in grapevines. Heredity 104: 327-328.

44) SANTOS JS, FONSECA NA, VIEIRA CP, 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: 1010-1018.

43) SCHÄFER MA, MAZZI D, KLAPPERT K, KAURANEN H, VIEIRA J, HOIKKALA A, RITCHIE MG, SCHLÖTTERER C. 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: 518-527.

42) FONSECA NA, COSTA VS, CAMACHO R, VIEIRA CP, VIEIRA J. 2009. Partitional Clustering of Protein Sequences – An Inductive Logic Programming Approach. In Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living - Lecture Notes in Computer Science. Springer Berlin,  Heidelberg. ISBN: 978-3-642-02480-1.

41) FONSECA NA, VIEIRA CP, VIEIRA J. 2009. Gene classification based on amino acid motifs and residues: the DLX (distal-less) test case. PLOS ONE, 4(6): e5748.

40) VIEIRA J, FONSECA NA, VIEIRA CP. 2009. RNase based gametophytic self-incompatibility evolution: questioning the hypothesis of multiple independent recruitments of the S-pollen gene. Journal of Molecular Evolution, 69: 32-41.

39) MORALES-HOJAS R., VIEIRA C.P., REIS M., and 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: 573-578.

38) CRUZ E., WHITTINGTON C., KRIKLER S.H., MASCARENHAS C., LACERDA R., VIEIRA J., and PORTO G. 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.

37) REIS M., VIEIRA C.P., MORALES-HOJAS R., and VIEIRA J. 2008. An old bilbo-like non-LTR retroelement insertion provides insight into the relationship of species of the virilis group. Gene, 425: 48-55.

36) VIEIRA J., SANTOS R.A., HABU T., TAO R., and VIEIRA C.P. 2008. The Prunus self-incompatibility locus (S locus) is seldom rearranged. Journal of Heredity, 99: 657-660.

35) VIEIRA J., TELES E., SANTOS R.A.M., and VIEIRA C.P. 2008. Recombination at Prunus S-locus region SLFL1 gene, Genetics, 180: 483-491.

34) VIEIRA J., FONSECA N.A., and VIEIRA C.P. 2008. An S-RNase-Based Gametophytic Self-Incompatibility System Evolved Only Once in Eudicots. Journal of Molecular Evolution, 67: 179-190.

33) FONSECA N.A., VIEIRA C.P., HOLLAND P.W., and VIEIRA J. 2008. Protein evolution of ANTP and PRD homeobox genes. BMC Evolutionary Biology, 8: 200.

32) VIEIRA J., SANTOS R.A.M., FERREIRA S.M., and VIEIRA C.P. 2008. Inferences on the number and frequency of S-pollen gene (SFB) specificities in the polyploid Prunus spinosa. Heredity, 101: 351-358.

31) TSUKAMOTO T., POTTER D., TAO R., VIEIRA C.P., VIEIRA J., and IEZZONI A.F. 2008. Genetic and molecular characterization of three novel S-haplotypes in sour cherry (Prunus cerasus L.). Journal of Experimental Botany, 59: 3169-3185.

30) MORALES-HOJAS R., VIEIRA C.P., and VIEIRA J. 2008. Inferring the evolutionary history of Drosophila americana and D. novamexicana using a multilocus approach and the influence of chromosomal rearrangements in single gene analyses. Molecular Ecology 17: 2910-2926.

29) VIEIRA J., FONSECA N.A., SANTOS R.A.M., HABU T., TAO R., and VIEIRA C.P. 2008. The number, age, sharing and relatedness of S-locus specificities in Prunus. Genetical Research 90: 17-26.

28) VIEIRA J., MORALES-HOJAS R., SANTOS R.A.M., and 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: 175-185.

27) VIEIRA J., CARDOSO C.S., PINTO J., PATIL K., BRAZDIL P., CRUZ E., MASCARENHAS C., LACERDA R., GARTNER A., ALMEIDA S., ALVES H., and PORTO G. 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: 359-367.

26) MORALES-HOJAS R., PÄÄLLYSAHO S., VIEIRA C.P., HOIKKALA A., AND VIEIRA J. 2007. Comparative polytene chromosome maps of D. montana and D. virilis. Chromosoma 116: 21-27.

25) NUNES M.D.S., SANTOS R.A.M., FERREIRA S.M., VIEIRA J., AND 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: 577-587.

24) MORALES-HOJAS R., VIEIRA C.P., AND VIEIRA J. 2006. The evolutionary history of the transposable element Penelope in the Drosophila virilis group of species. Journal of Molecular Evolution 63: 262-273.

23) VIEIRA C.P., ALMEIDA A., DIAS J.D., AND 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: 163-174.

22) CRUZ E., VIEIRA J., ALMEIDA S., LACERDA R., GARTNER A., CARDOSO C.S., ALVES H., AND PORTO G. 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: 16-28.

21) PAALLYSAHO S., VIEIRA C.P, HOIKKALA A., and VIEIRA J. 2005. Evidence for introgression in differentiated North-American and Finnish Drosophila montana populations. Genetica, 123: 285-293.

20) CRUZ E, VIEIRA J, GONÇALVES R, ALVES H, ALMEIDA S, 3, RODRIGUES P, LACERDA R, and PORTO G. 2004. Involvement of the MHC region in the genetic regulation of circulating CD8+ T cell numbers in humans. Tissue Antigens, 64: 25-34.

19) COSTAS J, PEREIRA P. S., VIEIRA C. P., PINHO S., VIEIRA J., and CASARES F. 2004. Dynamics and function of intron sequences of the wingless gene during the evolution of the Drosophila genus. Evolution and Development, 6: 325-335.

18) COSTAS J, VIEIRA CP, CASARES F, VIEIRA J. 2003. Genomic characterization of a repetitive motif strongly associated with developmental genes in Drosophila. BMC Genomics 4: 52-64.

17) VIEIRA C.P, COELHO P.A, and VIEIRA J. 2003. Inferences on the evolutionary history of the Drosophila americana polymorphic X/4 fusion from patterns of polymorphism at the X-linked paralytic and elav genes. Genetics, 164: 1459-1469.

16) COSTAS J., CASARES F., and VIEIRA J. 2003. Turnover of binding sites for transcription factors involved in early Drosophila development. Gene 310: 215-220.

15) VIEIRA C.P., CHARLESWORTH D., and VIEIRA J. 2003. Evidence for rare recombination at the gametophytic self-incompatibility locus. Heredity, 91: 261-267.

14) HUTTUNEN S., VIEIRA J., and HOIKKALA A. 2002. Nucleotide and repeat length variation at the nonA gene of the Drosophila virilis group species and its effects on male courtship song. Genetica 115: 159-167.

13) VIEIRA J. 2001. Two divergent species of the virilis group, Drosophila littoralis and Drosophila virilis, share a replacement polymorphism at the fused locus. Molecular Biology and Evolution 19: 579-581.

12) VIEIRA J., McALLISTER B. F., and CHARLESWORTH B. 2001. Evidence for selection at the fused1 locus of Drosophila americana. Genetics 158: 279-290.

11) VIEIRA J., and HOIKKALA A. 2001. Variability levels, population size and structure of American and European Drosophila montana populations. Heredity 86: 506-511.

10) McVEAN G. A. T., and J. VIEIRA. 2001. Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila. Genetics 157: 245-257.

9) VIEIRA J., and B. CHARLESWORTH. 2000. Evidence for selection at the fused locus of Drosophila virilis. Genetics 155: 1701-1709.

8) VIEIRA J., and B. CHARLESWORTH. 1999. X-chromosome DNA variation in Drosophila virilis. Proceedings of the Royal Society of London B 266: 1905-1912.

7) VIEIRA C. P., J. VIEIRA, and D. CHARLESWORTH. 1999. Evolution of the cycloidea gene family in the genera Antirrhinum and Misopates. Molecular Biology and Evolution 16: 1474-1483.

6) McVEAN G. A. T., and J. VIEIRA. 1999. The evolution of codon preferences in Drosophila: a maximum-likelihood approach to parameter estimation and hypothesis testing. Journal of Molecular Evolution 49: 63-75.

5) VIEIRA J., C. P. VIEIRA, D. L. HARTL, and E. R. LOZOVSKAYA. 1998. Factors contributing to the hybrid dysgenesis syndrome in Drosophila virilis. Genetical Research 71: 109-118.

4) VIEIRA C. P., J. VIEIRA, and D. L. HARTL. 1997. The evolution of small gene clusters: evidence for an independent origin of the maltase gene cluster in D. virilis and D. melanogaster. Molecular Biology and Evolution 14: 985-993.

3) VIEIRA J., C. P. VIEIRA, D. L. HARTL, and E. R. LOZOVSKAYA. 1997. Discordant rates of chromosome evolution in Drosophila virilis species group. Genetics 147: 223-230.

2) VIEIRA J., C. P. VIEIRA, D. L. HARTL, and E. R. LOZOVSKAYA. 1997. A framework physical map of Drosophila virilis based on P1 clones: applications in genome evolution. Chromosoma 106: 99-107.

1) VIEIRA J., and N. FERRAND. 1995. Four new alleles at the mannose-6- phosphate isomerase locus. Animal Genetics 26: 37-38.