Publications

Research articles

Carneiro J, Gomes C, Couto C, Pereira F
CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2.
bioRxiv. 2020. DOI: https://doi.org/10.1101/2020.04.19.048991

Campos E, Cuéllar J, Salvador O, García E, Pereira F
The genetic diversity and phylogeography of Mexican domestic sheep.
Small Ruminant Research. 2020. DOI: 10.1016/j.smallrumres.2020.106109

Monteiro J, Videira A., Pereira F
Quantification of Neurospora crassa mitochondrial DNA using quantitative real‐time PCR.
Letters in Applied Microbiology. 2020. DOI: 10.1111/lam.13294

Amaral CR, Chaves AC, Júnior VNB, Pereira F, Silva BM, Silva DA, Amorim A, Elizeu FC, Rocha CF
Amphibians on the hotspot: Molecular biology and conservation in the South American Atlantic Rainforest.
PloS one. 2019. 14(10). DOI: 10.1371/journal.pone.0224320

Pereira F, Alves C, Couto C, Díaz LL, Parra D, Furfuro S, Aler M, Borrego LB, Olekšáková T, Balsa F, Sampaio L, Porto MJA, Costa HA, Voss CA, Caputo M, Corach D, García O, Moro SP, Pereira R, Amorim A
Species identification in routine casework samples using the SPInDel kit.
Forensic Science International: Genetics Supplement Series. 2019. DOI: 10.1016/j.fsigss.2019.09.070

Hjelm BE, Rollins B, Morgan L, Sequeira A, Mamdani F, Pereira F, Damas J, Webb MG, Weber MD, Schatzberg AF, Barchas JD, Lee FS, Akil H, Watson SJ, Myers RM, Chao EC, Kimonis V, Thompson PM, Bunney WE, Vawter MP
Splice-Break: exploiting an RNA-seq splice junction algorithm to discover mitochondrial DNA deletion breakpoints and analyses of psychiatric disorders
Nucleic acids research. 2019. 47.10: e59-e59, DOI: 10.1093/nar/gkz164

Martins MG, Ribeiro I, Ribeiro T, Azevedo I, Pereira F, Urbatzka R, Leão PN, Carvalho MF
Actinobacteria isolated from Laminaria ochroleuca: a source of new bioactive compounds
Frontiers in Microbiology. 2019. 10, 683. DOI: 10.3389/fmicb.2019.00683

Rocha M, Antas P, Castro LF, Campos A, Vasconcelos V, Pereira F, Cunha I
Comparative analysis of the adhesive proteins of the adult stalked goose barnacle Pollicipes pollicipes (Cirripedia: Pedunculata)
Marine Biotechnology. 2019. 21 (1), 38-51. DOI: 10.1007/s10126-018-9856-y

Pratas D, Hosseini M, Grilo G, Pinho AJ, Silva RM, Caetano T, Carneiro J, Pereira F
Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard
Genes. 2018, 9, 445. DOI: https://doi.org/10.3390/genes9090445

Santos C, Pereira F
Identification of plant species using variable length chloroplast DNA sequences
Forensic Science International: Genetics. 2018. 36:1-12. DOI: 10.1016/j.fsigen.2018.05.009

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: https://doi.org/10.1371/journal.pgen.1006960

Amaral CR, Pereira F, Silva DA, Amorim A, de Carvalho EF
The mitogenomic phylogeny of the Elasmobranchii (Chondrichthyes)
Mitochondrial DNA Part A. 2017. 1-12. DOI: 10.1080/24701394.2017.1376052

Alexandrino DA, Ribeiro I, Pinto LM, Cambra R, Oliveira RS, Pereira F, Carvalho, MF
Biodegradation of mono-, di-and trifluoroacetate by microbial cultures with different origins
New Biotechnology. 2017. DOI: https://doi.org/10.1016/j.nbt.2017.08.005

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: https://doi.org/10.1016/j.foodcont.2017.06.037

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

Marks CA, Clark M, Obendorf D, Hall GP, Soares I, Pereira F.
Trends in anecdotal fox sightings in Tasmania accounted for by psychological factors
Conservation Biology. In press. DOI: 10.1111/cobi.12944

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: http://dx.doi.org/10.1016/j.fsigen.2017.03.003

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

Pereira F, Duarte-Pereira S, Silva RM, da Costa LT, Pereira-Castro, I
Evolution of the NET (NocA, Nlz, Elbow, TLP-1) protein family in metazoans: insights from expression data and phylogenetic analysis
Scientific Reports. 2016. 6: 38383. DOI: 10.1038/srep38383

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

Marks CA, Edwards I, Obendorf D, Pereira F, Hall GP.
Did ‘precautionary’ 1080 baiting have a realistic potential to eradicate Red Fox (Vulpes vulpes) in Tasmania without in situ monitoring data?
Ecological Management & Restoration. 2014. 15(3), 196-203. DOI: 10.1111/emr.12121

Dong DW, Pereira F, Barrett SP, Kolesar JE, Cao K, Damas J, Yatsunyk LA, Johnson FB, Kaufman BA.
Association of G-quadruplex forming sequences with human mtDNA deletion breakpoints.
BMC Genomics. 2014. 15(1): 677. DOI:10.1186/1471-2164-15-677

Marks CA, Obendorf D, Pereira F, Edwards I, Hall GP.
Opportunistically acquired evidence is unsuitable data to model fox (Vulpes vulpes) distribution in Tasmania.
Wildlife Society Bulletin. 2014. 38(4), 757-766. DOI: 10.1002/wsb.448

Marks CA, Obendorf D, Pereira F, Edwards I, Graham PH.
The dispersion and detection patterns of mtDNA assigned red fox Vulpes vulpes scats in Tasmania are anomalous.
Journal of Applied Ecology. 2014. 51(4), 1033-1040. DOI: 10.1111/1365-2664.12278

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

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

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.

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.

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

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, 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, 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.

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

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.

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.

van Asch B, Pereira L, Pereira F, Santa-Rita P, Lima M, Amorim A
MtDNA diversity among four Portuguese autochthonous dog breeds: a fine-scale characterisation.
BMC Genetics. 2005 22;6(1):37.

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.

 

 

Letter to the Editor

Gonçalves J, Marks CA, Obendorf D, Amorim A, Pereira F.
Reply to Sarre et al. “Defining specificity in DNA detection of wildlife”.
Forensic science international. Genetics. 2014. DOI:10.1016/j.fsigen.2014.10.024

 

 

Reviews & book chapters

 
Araújo R. Pereira F, van Asch B.
Applications of DNA-based methods in food forensics
In: Amorim A and Budowle B (ed.) Handbook of Forensic Genetics: Biodiversity and Heredity in Civil and Criminal Investigation. Icp Security Science and Technology. Imperial College Press (June 30, 2016). 493-517 p

Pereira F, Amorim A.
Evolution: Viruses.
In: Maloy S and Hughes K (ed.) Brenners Encyclopedia of Genetics, 2013, vol. 2, pp. 566-568. Elsevier: New York

Pereira F, Amorim A, van Asch B.
Genetic and DNA-Based Techniques.
Comprehensive Analytical Chemistry. Food Protected Designation of Origin — Methodologies and Applications. 2013. 60:195-220

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.
WO PCT/IB2007/054509