Filipe Pereira

fpereirapt@gmail.com

PUBLICATIONS

New Insights into the Phylogeny and Worldwide Dispersion of Two Closely Related Nematode Species, Bursaphelenchus xylophilus and Bursaphelenchus mucronatus.
Pereira F,Moreira C,Fonseca L,van Asch B,Mota M,Abrantes I,Amorim A
PLoS One.2013;8(2):e56288-.

New method for the simultaneous identification of cow, sheep, goat, and water buffalo in dairy products by analysis of short species-specific mitochondrial DNA targets.
Goncalves J,Pereira F,Amorim A,van Asch B,
J Agric Food Chem.2012;60(42):10480-10485.

SPInDel: a multifunctional workbench for species identification using insertion/deletion variants.
Carneiro J,Pereira F,Amorim A,
Mol Ecol Resour.2012;12(6):1190-1195.

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

Mitochondrial lineages reveal intense gene flow between Iberian wild boars and South Iberian pig breeds.
van Asch B,Pereira F,Santos LS,Carneiro J,Santos N,Amorim A
Anim Genet.2012;43(1):35-41.

Identification of mtDNA lineages of Sus scrofa by multiplex single base extension for the authentication of processed food products.
van Asch B,Silva SL,Carneiro J,Pereira F,Amorim A,
J Agric Food Chem.2011;59(13):6920-6926.

A framework for the development of STR genotyping in domestic animal species: characterization and population study of 12 canine X-chromosome loci.
van Asch B,Pinheiro R,Pereira R,Alves C,Pereira V,Pereira F,Gusmao L,Amorim A,
Electrophoresis.2010;31(2):303-308.

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

Genetic profiles and sex identification of found-dead wolves determined by the use of an 11-loci PCR multiplex.
van Asch B,Alves C,Santos L,Pinheiro R,Pereira F,Gusmao L,Amorim A,
Forensic Sci Int Genet.2010;4(2):68-72.

A new autosomal STR nineplex for canine identification and parentage testing.
van Asch B,Alves C,Gusmao L,Pereira V,Pereira F,Amorim A,
Electrophoresis.2009;30(2):417-423.

Revealing the history of sheep domestication using retrovirus integrations.
Chessa B,Pereira F,Arnaud F,Amorim A,Goyache F,Mainland I,Kao RR,Pemberton JM,Beraldi D,Stear MJ,Alberti A,Pittau M,Iannuzzi L,Banabazi MH,Kazwala RR,Zhang YP,Arranz JJ,Ali BA,Wang Z,Uzun M,Dione MM,Olsaker I,Holm LE,Saarma U,Ahmad S,Marzanov N,Eythorsdottir E,Holland MJ,jmone-Marsan P,Bruford MW,Kantanen J,Spencer TE,Palmarini M,
Science.2009;324(5926):532-536.

Epistatic interactions modulate the evolution of mammalian mitochondrial respiratory complex components.
Azevedo L,Carneiro J,van Asch B,Moleirinho A,Pereira F,Amorim A,
BMC Genomics.2009;10():266-.

Tracing the history of goat pastoralism: new clues from mitochondrial and Y chromosome DNA in North Africa.
Pereira F,Queiros S,Gusmao L,Nijman IJ,Cuppen E,Lenstra JA,Davis SJ,Nejmeddine F,Amorim A,
Mol Biol Evol.2009;26(12):2765-2773.

A multiplex primer extension assay for the rapid identification of paternal lineages in domestic goat (Capra hircus): Laying the foundations for a detailed caprine Y chromosome phylogeny.
Pereira F,Carneiro J,Soares P,Maciel S,Nejmeddine F,Lenstra JA,Gusmao L,Amorim A,
Mol Phylogenet Evol.2008;49(2):663-668.

Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region.
Pereira F,Soares P,Carneiro J,Pereira L,Richards MB,Samuels DC,Amorim A,
Mol Biol Evol.2008;25(12):2759-2770.

A paradigm for virus-host coevolution: sequential counter-adaptations between endogenous and exogenous retroviruses.
Arnaud F,Caporale M,Varela M,Biek R,Chessa B,Alberti A,Golder M,Mura M,Zhang YP,Yu L,Pereira F,Demartini JC,Leymaster K,Spencer TE,Palmarini M,
PLoS Pathog.2007;3(11):e170-.

Data for Y-chromosome haplotypes defined by 17 STRs (AmpFLSTR Yfiler) in two Tunisian Berber communities.
Frigi S,Pereira F,Pereira L,Yacoubi B,Gusmao L,Alves C,Khodjet el KH,Cherni L,Amorim A,El GA,
Forensic Sci Int.2006;160(1):80-83.

Usefulness of microchip electrophoresis for the analysis of mitochondrial DNA in forensic and ancient DNA studies.
Alonso A,Albarran C,Martin P,Garcia P,Capilla J,Garcia O,de la RC,Izaguirre N,Pereira F,Pereira L,Amorim A,Sancho M,
Electrophoresis.2006;27(24):5101-5109.

Genetic signatures of a Mediterranean influence in Iberian Peninsula sheep husbandry.
Pereira F,Davis SJ,Pereira L,McEvoy B,Bradley DG,Amorim A,
Mol Biol Evol.2006;23(7):1420-1426.

MtDNA diversity among four Portuguese autochthonous dog breeds: a fine-scale characterisation.
van Asch B,Pereira L,Pereira F,Santa-Rita P,Lima M,Amorim A,
BMC Genet.2005;6():37-.

The mtDNA catalogue of all Portuguese autochthonous goat (Capra hircus) breeds: high diversity of female lineages at the western fringe of European distribution.
Pereira F,Pereira L,van Asch B,Bradley DG,Amorim A,
Mol Ecol.2005;14(8):2313-2318.

CITATIONS

BOOKS/CHAPTERS

Pereira F, Amorim A.
Evolution: Viruses
Encyclopedia of Genetics, 2nd Edition (in press).

Pereira F, Amorim A.
Origin and spread of goat pastoralism
ENCYCLOPEDIA OF LIFE SCIENCES 2010, John Wiley & Sons, Ltd: Chichester (September 2010)

Pereira F, Carneiro J, van Asch B.
A guide for mitochondrial DNA analysis in non-human forensic investigations
The Open Forensic Science Journal. 2009.3:33-44.

van Asch B, Pereira F.
State-of-the-art and future prospects of canine STR-based genotyping
The Open Forensic Science Journal. 2009. 3:45-52.

Pereira F, Carneiro J, Amorim A.
Identification of species with DNA-based technology: current progress and challenges
Recent Patents on DNA & Gene Sequences. 2008. 2:187-200.

van Asch B, Pereira L, Pereira F, Amorim A.
Mitochondrial DNA lineages of the Portuguese Podengo autochthonous dog breed.
The Portuguese Podengo, pp 264-274. Vítor Veiga, Coord.; Alan Hedges, UK Editor.

PATENT

Pereira F, van Asch B, Gusmão L.
Process for animal species identification in samples with genetic material based on mitochondrial DNA size variation.
Portuguese patent application nº 103599. Priority Date: 06 November 2006.

RESEARCH PROJECTS

2012/2014
Structure of the HIV genome: novel frameworks for clinical diagnosis and anti-retroviral therapeutics
PORTUGUESE SCIENCE AND TECHNOLOGY FOUNDATION / National Coordination for HIV/AIDS (VIH/SAU/0011/2011).
Principal Investigator

2010/2013
The causes and consequences of mitochondrial DNA deletions in animal cells.
PORTUGUESE SCIENCE AND TECHNOLOGY FOUNDATION (PTDC/CVT/100881/2008).
Principal Investigator

2009/2011
Detection, identification an quantification of the pinewood nematode, Bursaphelenchus xylophilus
MINISTRY OF AGRICULTURE, RURAL DEVELOPMENT AND FISHERIES
Co-Principal Investigator