Filipe Pereira

CIIMAR - University of Porto, Portugal




Software & databases

MitoBreak


EbolaID


HIVoligoDB


PlantAligDB


GMOrefseq


SPInDel




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Overview

We study the DNA molecule using computational and biochemical methods. Our research activity spans from the computational prediction of alternative DNA structures to the history of animal populations. We also develop molecular diagnostic systems and databases for biological identifications at different levels. See more information on current projects here.


Research topics

Non-B DNA conformations, genomic rearrangements and disease

Genetic analysis of animal domestication

Molecular diagnostics and species identification


  • The mtDNA catalogue of all Portuguese autochthonous goat (Capra hircus) breeds... Mol Eco. 2005.
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Selected Publications


 Damas J, Carneiro J, Amorim A, Pereira F. MitoBreak: The mitochondrial DNA breakpoints database. Nucleic Acids Research. 2014. 42 (D1): D1261-D1268 doi:10.1093/nar/gkt982

 Damas J, Samuels DC, Carneiro J, Amorim A, Pereira F. Mitochondrial DNA rearrangements in health and disease - a comprehensive study. Human mutation. 2014. 35(1):1-14. doi: 10.1002/humu.22452

 Damas J, Carneiro J, Gonçalves J, Stewart JB, Samuels DC, Amorim A, Pereira F Mitochondrial DNA deletions are associated with non-B DNA conformations. Nucleic Acids Research. 2012. 40 (16): 7606-7621.

 Pereira F, Carneiro J, Matthiesen R, van Asch B, Pinto N, Gusmão L, Amorim A. Identification of species by multiplex analysis of variable-length sequences. Nucleic Acids Research. 2010. 38 (22): e203.

 Pereira F, Queirós S, Gusmão L, Nijman IJ, Cuppen E, Lenstra JA, the Econogene Consortium, Davis SJM, Nejmeddine F, Amorim A. Tracing the history of goat pastoralism: new clues from mitochondrial and Y chromosome DNA in North Africa. Molecular Biology and Evolution. 2009. 26:2765-73.

 Chessa B, Pereira F, Arnaud F, Amorim A, Goyache F, (...) Holland MJ, Ajmone-Marsan P, Bruford MW, Kantanen J, Spencer TE and Palmarini M. Revealing the history of sheep domestication using retrovirus integrations. Science. 2009. 324:532-536.

 Pereira F, Soares P, Carneiro J, Pereira L, Richards M, Samuels DC, Amorim A. Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region. Molecular Biology and Evolution. 2008. 25:2759–2770.

 Pereira F, Davis S, Pereira L, McEvoy B, Bradley DG, Amorim A Genetic signatures of a Mediterranean influence in Iberian peninsula sheep husbandry. Molecular Biology and Evolution. 2006. 23(7):1420–6.

 Pereira F, Pereira L, Van Asch B, Bradley DG, Amorim A. The mtDNA catalogue of all Portuguese autochthonous goat (Capra hircus) breeds: high diversity of female lineages at the western fringe of European distribution. Molecular Ecology. 2005 14:2313-2318.


Join us
We welcome interested students with any educational background to work with us.
If you find our work interesting and you wish to spend some time working in our group, please contact us.