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Arenas M, Pereira F, Oliveira M, Pinto N, Lopes AM, Gomes V, Carracedo A, Amorim A 
Forensic genetics and genomics: much more than just a human affair 
PLoS Genetics. 2017. 13(9): e1006960. DOI:

Resende A, Mendes AC, Ramos H, Pereira F 
Detection of Hepatitis B virus (HBV) using multiplex PCR 
Porto Biomedical Journal. In press 

Castro C, Amorim M, Moreira F, Pereira F
A method to assemble DNA fragments mimicking junctions of transgenic elements: application to the AquAdvantage salmon
Food Control. 2017. 82: 179-183. DOI:

Moreira F, Carneiro J, Pereira F
A proposal for standardization of transgenic reference sequences used in food forensics
Forensic Science International: Genetics. 2017. 29: e26-e28. DOI: 10.1016/j.fsigen.2017.04.022

Alves C, Pereira R, Prieto L, Aler M, Amaral C, Arévalo C, Berardi G, Di Rocco F, Caputo M, Carmona CH, Catelli L, Costal HA, Coufalova P, Furfuro S, García O, Gaviria A, Goios A, Gómez JJB, Hernández A, Hernández ECB, Miranda L, Parra D, Pedrosa S, Porto MJA, Rebelo ML, Spirito M, Torres MCV, Amorim A, Pereira F.
Species identification in forensic samples using the SPInDel approach: A GHEP-ISFG inter-laboratory collaborative exercise
Forensic Science International: Genetics. 2017. 28: 219–224. DOI:

Carneiro J, Resende A, Pereira F
The HIV oligonucleotide database (HIVoligoDB)
Database. 2017. 1. DOI:10.1093/database/bax005

Santos C, Pereira F.
Design and evaluation of PCR primers for amplification of four chloroplast DNA regions in plants
Conservation Genetics Resources. 2017. 9(1), 9-12. DOI: 10.1007/s12686-016-0605-0

Carneiro J, Pereira F
EbolaID: An Online Database of Informative Genomic Regions for Ebola Identification and Treatment
PLOS Neglected Tropical Diseases. 2016. 10(7): e0004757. DOI: 10.1371/journal.pntd.0004757

Belmonte FR, Martin JL, Frescura K, Damas J, Pereira F, Tarnopolsky MA, Kaufman BA
Digital PCR methods improve detection sensitivity and measurement precision of low abundance mtDNA deletions
Scientific Reports. 2016. 28(6):25186. DOI: 10.1038/srep25186

Resende A*, Gonçalves J*, Muigai AWT, Pereira F (*joint first authors).
 Mitochondrial DNA variation of domestic sheep (Ovis aries) in Kenya.
Animal Genetics. 2016. 47: 377–381. DOI: 10.1111/age.12412

Gonçalves J, Marks CA, Obendorf D, Amorim A, Pereira F.
A multiplex PCR assay for identification of the red fox (Vulpes vulpes) using the mitochondrial ribosomal RNA genes
Conservation Genetics Resources. 2015. 7(1): 45-48. DOI: 10.1007/s12686-014-0343-0

Gonçalves J, Marks CA, Obendorf D, Amorim A, Pereira F.
The risks of using “species-specific” PCR assays in wildlife research: The case of red fox (Vulpes vulpes) identification in Tasmania.
Forensic Science International: Genetics. 2014. 11:e9-11. doi: 10.1016/j.fsigen.2014.03.009

Moreira C, van Asch B, Fonseca L, Pereira-Castro I, Silva R, Azevedo L, Mota M, Abrantes I, Amorim A, Pereira F.
The mitochondrial genome of the pinewood nematode (Bursaphelenchus xylophilus) lineage introduced in Europe.  
Mitochondrial DNA. 2013. doi: 10.3109/19401736.2013.809438

Pereira F, Moreira C, Fonseca L, van Asch B, Mota M, Abrantes I, Amorim A, 
New insights into the phylogeny and worldwide dispersion of two closely related nematode species, Bursaphelenchus xylophilus and Bursaphelenchus mucronatus. 
PLoS One. 2013. 8(2):e56288.

Gonçalves J, Pereira F, Amorim A, van Asch B.
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.
Journal of Agricultural and Food Chemistry. 2012. 60(42):10480-10485.

Carneiro J, Pereira F, Amorim A.
SPInDel: a multi-functional workbench for species identification using insertion/deletion variants.
Molecular Ecology Resources. 2012. 12(6):1190-5.

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.

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

van Asch B, Silva Santos L, Carneiro J, Pereira F, Amorim A. 
Identification of mtDNA lineages of Sus scrofa by multiplex single base extension for the authentication of processed food products. 
Journal of Agricultural and Food Chemistry. 2011. 59(13): 6920-6926.

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.

van Asch B, Pinheiro R, Pereira R, Alves C, Pereira V, Pereira F, Gusmão L, Amorim, A.
A framework for the development of STR genotyping in domestic animal species: Characterisation and population study of twelve canine X-chromosome loci.
Electrophoresis. 2010. 31(2):303-8.

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

Chessa B, Pereira F, Arnaud F, Amorim A, Goyache F, Mainland I, Kao RR, Pemberton JM, Beraldi D, Stear M, Alberti A, Pittau M, Iannuzzi L, Banabazi MH, Kazwala R, Zhang Y-P, Arranz JJ, Ali BA, Wang Z, Uzun M, Dione M, Olsaker I, Holm L-E, Saarma U, Ahmad S, Marzanov N, Eythorsdottir E, 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.

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

Pereira F, Carneiro J, Soares P, Maciel S, Nejmeddine F, Lenstra JA, Gusmão L, Amorim A.
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.
Molecular Phylogenetics and Evolution. 2008. 49:663-668.

Alonso A, Albarran C, Martín P, García P, Capilla J, García O, de la Rua C, Izaguirre N, Pereira F, Pereira L, Amorim A, Sancho M.
Usefulness of microchip electrophoresis for the analysis of mitochondrial DNA in Forensic and Ancient DNA studies.
Electrophoresis. 2006. 27(24):5101-9.

Frigi S, Pereira F, Pereira L, Yacoubi B, Gusmão L, Alves C, Khil H, Cherni L, Amorim A, El Gaaied A.
Data for Y-chromosome haplotypes defined by 17 STRs (AmpFLSTR® Yfiler™) in two Tunisian Berber communities.
Forensic Science International. 2006. 160(1):80-3.

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.