1. 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, Ajmone-Marsan P, Bruford MW, Kantanen J, Spencer TE, Palmarini M

Revealing the history of sheep domestication using retrovirus integrations. Science (New York, N.Y.) 324: 532-6, 2009.  [Article] 

 doi: 10.1126/science.1170587 PMID: 19390051.

 

2. Pereira F, Queirós S, Gusmão L, Nijman IJ, Cuppen E, Lenstra JA, Consortium E, Davis SJ, 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 26: 2765-73, 2009.  [Article] 

 doi: 10.1093/molbev/msp200 PMID: 19729424.

 

3. 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

A paradigm for virus-host coevolution: sequential counter-adaptations between endogenous and exogenous retroviruses. PLoS pathogens 3: e170, 2007.  [Article] 

 doi: 10.1371/journal.ppat.0030170 PMID: 17997604.

 

4. Damas J, Carneiro J, Amorim A, Pereira F

MitoBreak: the mitochondrial DNA breakpoints database. Nucleic acids research 42: D1261-8, 2014.  [Article] 

 doi: 10.1093/nar/gkt982 PMID: 24170808.

 

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 40: 7606-21, 2012.  [Article] 

 doi: 10.1093/nar/gks500 PMID: 22661583.

 

6. 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 38: e203, 2010.  [Article] 

 doi: 10.1093/nar/gkq865 PMID: 20923781.

 

7. Carneiro J, Pereira F, Amorim A

SPInDel: a multifunctional workbench for species identification using insertion/deletion variants. Molecular ecology resources 12: 1190-5, 2012.  [Article] 

 doi: 10.1111/1755-0998.12011 PMID: 22978681.

 

8. Pereira F, Soares P, Carneiro J, Pereira L, Richards MB, 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 25: 2759-70, 2008.  [Article] 

 doi: 10.1093/molbev/msn225 PMID: 18845547.

 

9. Pereira F, Davis SJ, Pereira L, McEvoy B, Bradley DG, Amorim A

Genetic signatures of a Mediterranean influence in Iberian Peninsula sheep husbandry. Molecular biology and evolution 23: 1420-6, 2006.  [Article] 

 doi: 10.1093/molbev/msl007 PMID: 16672283.

 

10. Damas J, Samuels DC, Carneiro J, Amorim A, Pereira F

Mitochondrial DNA rearrangements in health and disease-a comprehensive study. Human mutation 35: 1-14, 2014.  [Review] 

 doi: 10.1002/humu.22452 PMID: 24115352.

 

11. 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 16: e1-2, 2015.  [Letter] 

 doi: 10.1016/j.fsigen.2014.10.024 PMID: 25466969.

 

12. 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 11C: e9-e11, 2014.  [Letter] 

 doi: 10.1016/j.fsigen.2014.03.009 PMID: 24742708.

 

13. 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 14: 2313-8, 2005.  [Article] 

 doi: 10.1111/j.1365-294X.2005.02594.x PMID: 15969716.

 

14. 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 6: 38383, 2016.  [Article] 

 doi: 10.1038/srep38383 PMID: 27929068.

 

15. 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 27: 5101-9, 2006.  [Article] 

 doi: 10.1002/elps.200600331 PMID: 17120261.

 

16. 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 49: 663-8, 2008.  [Article] 

 doi: 10.1016/j.ympev.2008.08.026 PMID: 18809503.

 

17. 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 10: 266, 2009.  [Article] 

 doi: 10.1186/1471-2164-10-266 PMID: 19523237.

 

18. 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: characterization and population study of 12 canine X-chromosome loci. Electrophoresis 31: 303-8, 2010.  [Article] 

 doi: 10.1002/elps.200900389 PMID: 20024924.

 

19. 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 8: e56288, 2013.  [Article] 

 doi: 10.1371/journal.pone.0056288 PMID: 23409167.

 

20. 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 30: 417-23, 2009.  [Article] 

 doi: 10.1002/elps.200800307 PMID: 19204943.

 

21. 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 60: 10480-5, 2012.  [Article] 

 doi: 10.1021/jf3029896 PMID: 23025240.

 

22. 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 4: 68-72, 2010.  [Article] 

 doi: 10.1016/j.fsigen.2009.05.003 PMID: 20129463.

 

23. 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 59: 6920-6926, 2011.  [Article] 

 doi: 10.1021/jf201283r PMID: 21688854.

 

24. van Asch B, Pereira F, Santos LS, Carneiro J, Santos N, Amorim A

Mitochondrial lineages reveal intense gene flow between Iberian wild boars and South Iberian pig breeds. Animal genetics 43: 35-41, 2012.  [Article] 

 doi: 10.1111/j.1365-2052.2011.02222.x PMID: 22221023.

 

25. 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 6: 37, 2005.  [Article] 

 doi: 10.1186/1471-2156-6-37 PMID: 15972107.

 

26. Frigi S, Pereira F, Pereira L, Yacoubi B, Gusmão L, Alves C, Khodjet el 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 160: 80-3, 2006.  [Editorial Material] 

 doi: 10.1016/j.forsciint.2005.05.007 PMID: 16005592.

 

27. 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 25: 420-1, 2014.  [Article] 

 doi: 10.3109/19401736.2013.809438 PMID: 23841612.

 

28. 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  1, 2015.  [Article] 

 doi: 10.1007/s12686-014-0343-0.

 

29. Araujo R, Pereira F, Van Asch B

Applications of DNA-based methods in food forensics
 Handbook of Forensic Genetics  1, 2016.  [] 

 doi: 10.1142/9781786340788_0020.

 

30. 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 apllication I: 1, 2006.  [] 

.

 

31. Silva RM, Pereira F, Carneiro J, Amorim A

Microevolution in a Natural Population of Daphnia longispina Exposed to Acid Mine Drainage Interdisciplinary Studies on Environmental Chemestry  213-218, 2010.  [] 

.

 

32. Pereira F, Carneiro J, Amorim A

Identification of species with DNA-based technology: current progress and challenges. Recent patents on DNA & gene sequences 2: 187-99, 2008.  [] 

 PMID: 19075956.

 

33. Pereira F, Carneiro J, van Asch B

A guide for mitochondrial DNA analysis in non-human forensic investigations The Open Forensic Science Jounal 3: 33-44, 2010.  [] 

 doi: 10.2174/1874402801003010033.

 

34. Soares PA, Pereira F, Brion M, Alves C, Richards M, Carracedo A, Amorim A, Gusmão L

Relative Y-STR mutation rates estimated from the variance inside SNP defined lineages International Congress Series 1288: 82-84, 2006.  [] 

 doi: 10.1016/j.ics.2005.09.173.

 

35. van Asch B, Pereira F

State-of-the-art and future prospects of canine STR-based genotyping The Open Forensic Science Jounal 3: 45-52, 2010.  [] 

 doi: 10.2174/1874402801003010045.

 

36. Pereira F

Origin and spread of goat pastoralism Encyclopedia of Life Sciences  1, 2010.  [] 

 doi: 10.1002/9780470015902.a0022864/abastract.

 

37. Pereira F, Amorim A

Evolution: Viruses Brenner's Encyclopedia of Genetics  407-411, 2013.  [] 

 doi: 4.

 

38. Pereira F, Amorim A, van Asch B

Genetic and DNA-Based Techniques Elsevier Science  195-220, 2013.  [] 

 doi: 10.1016/B978-0-444-59562-1.00008-6.