Filipe Pereira

CIIMAR - University of Porto, Portugal




Software & databases

MitoBreak


EbolaID


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.



Latest News


 26 May 2014: The MitoBreak data can be found on the “Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium.
 1 March 2014: Collaborative exercise GHEP-ISFG “SPInDel - Taxonomic identification of forensic samples”now open.
 30 December 2013: MitoBreak paper in NAR 2014 Database issue.
 14 October 2013: Reference to our work on mtDNA in the Fight Aging! website.
 15 July 2013: Cientistas da U.Porto abrem caminho no tratamento de doença dos pinheiros (source: UPorto Notícias).



  • 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.