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Filipe Pereira completed the PhD in Genetics in 2009 and BSc in Biologia in 2003 by Faculty of Science, University of Porto (FCUP). He was a researcher at Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP) and Interdisciplinary Centre of Marine and Environmental Research (CIIMAR). Currently is Assistant Professor at University of Trás-os-Montes and Alto Douro (UTAD). MAIN ACHIEVEMENTS: · Publication of 67 papers in international scientific periodicals with referees, 40 as first, senior or corresponding author, h-index of 29, ~3300 citations. Top journals of the research area: Science, PLoS Genetics, Nucleic Acids Research, Molecular Biology and Evolution · Publication of 5 book chapters, 11 papers in conference proceedings · Invention of a method for species identification protected by a patent · Principal investigator of 6 research projects (total budget over 500 000 EUR) · Teaching experience in 4 faculty courses (PhD, MSc, BSc) · Development and curation of 7 public databases (over 10 000 users per year) · Invited for 15 talks in national and international meetings and institutions · 28 oral communications and 37 posters in national and international conferences · Supervisor or co-supervisor of 2 postdocs, 6 PhD and 10 MSc students · Reviewer for > 50 scientific journals and 7 international funding agencies · Organizer of 2 scientific conferences
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Identification

Personal identification

Full name
Filipe Adão Macedo Pereira

Citation names

  • Pereira, Filipe

Author identifiers

Ciência ID
F713-6054-417F
ORCID iD
0000-0001-8950-1036
Google Scholar ID
http://scholar.google.com/citations?user=sUfn29YAAAAJ
Researcher Id
F-6391-2010

Email addresses

  • fpereirapt@gmail.com (Professional)
  • filipep@utad.pt (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences - Genetics and Heredity
  • Natural sciences - Biological Sciences - Molecular Biology
  • Natural sciences - Biological Sciences - Evolutionary Biology

Languages

Language Speaking Reading Writing Listening Peer-review
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Portuguese (Mother tongue)
Education
Degree Classification
2018 - 2019
Concluded
 Master of Business Administration (MBA) (Outros)
Universidade do Porto Porto Business School, Portugal
2009 - 2013
Concluded
 Post-doctoral researcher (Pós-doutoramento)
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2004 - 2009
Concluded
 Genética (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal
"Genetic diversity and structural organization of the mammalian mtDNA: functional and phylogenetic implications" (THESIS/DISSERTATION)
 Aprovado por unanimidade
1999 - 2003
Concluded
 Biologia (Licenciatura)
Universidade do Porto Faculdade de Ciências, Portugal
"n/a" (THESIS/DISSERTATION)
Affiliation

Teaching in Higher Education

Category
Host institution 		Employer
2023/02/20 - Current Assistant Professor (University Teacher) Universidade de Trás-os-Montes e Alto Douro, Portugal
Universidade de Trás-os-Montes e Alto Douro, Portugal

Others

Category
Host institution 		Employer
2013 - Current Topic Editor International Journal of Molecular Science, United Kingdom
2019 - 2023 Visiting Researcher Centro de Ecologia Funcional, Portugal
Centro de Ecologia Funcional, Portugal
2014 - 2023 Visiting Researcher Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2013/07/01 - 2018/06/30 Researcher. Investigator FCT program (1st call, 2012). Portuguese Science and Technology Foundation (FCT) Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2013 - 2018 Invited Assistant Professor Universidade do Porto Faculdade de Ciências, Portugal
2009/01/06 - 2013/06/30 Post doctoral researcher Granted by FCT (SFRH/BPD/44637/2008) Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2004/09/01 - 2008/09/01 PhD student Granted by FCT (SFRH/BD/19585/2004) Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2004/03/01 - 2004/08/31 Research Fellowship Granted by ADI (Agência de Inovação) Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2003/09/01 - 2004/02/29 Research internship Granted by PRODEP III Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
Projects

Contract

Designation Funders
2023/03/01 - 2026/02/28 A variação das ovelhas domésticas Ibéricas: um estudo arqueogenético
2022.04843.PTDC
Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2020/06/01 - 2021/03/30 Development of the CoV2ID platform for sharing data on COVID-19 detection and treatment protocols
60
Principal investigator
Universidade de Coimbra, Portugal
 EOSCsecretariat.eu. European Union's Horizon Programme call H2020-INFRAEOSC-05-2018-2019
Ongoing
2020/05/18 - 2020/08/18 Implementation of rapid endpoint PCR systems for SARS-CoV-2 detection in conventional molecular biology laboratories
029_596289414
Principal investigator
Universidade de Coimbra, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2019 - 2019 Development of a broad-range DNA-based method for the identification of marine species in food products
Idfoodplex
Principal investigator
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
 ASSEMBLE Plus Translational Access
Concluded
2016 - 2019 NOVELMAR - Novel marine products with biotechnological applications
NOVELMAR
Researcher
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
 Norte Portugal Regional Operational Programme (NORTE 2020), European Regional Development Fund (ERDF)
Concluded
2016 - 2018 MarInfo - Integrated Platform for Marine Data Acquisition and Analysis
marinfo
Principal investigator
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
 Norte Portugal Regional Operational Programme (NORTE 2020), European Regional Development Fund (ERDF)
Concluded
2017 - 2017 Development of a genetic assay for detection of transgenic fishes in food and environmental samples
2
Principal investigator
European Marine Biological Research Infrastructure Cluster (EMBRIC) Transnational Access
Concluded
2016 - 2017 Aprender a conhecer o ambiente marinho de Portugal - BioMar PT
PT02_Aviso6_0003
Principal investigator
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
 EEA Grants
Concluded
2014/03 - 2016/02 Structure of the HIV genome: novel frameworks for clinical diagnosis and anti-retroviral therapeutics
123636
Provided by PTCRIS: 123636
Principal investigator
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
 Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2010/05 - 2013/11 The causes and consequences of mitochondrial DNA deletions in animal cells
100881
Provided by PTCRIS: 100881
Principal investigator
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
 Fundação para a Ciência e a Tecnologia, I.P.
2011/01/01 - 2012/12/31 Projecto Estratégico - LA 3 - 2011-2012
PEst-C/SAU/LA0003/2011
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2009 - 2011 Detection, identification and quantification of the pinewood nematode, Bursaphelenchus xylophilus
2
Principal investigator
Portuguese Ministry of Agriculture, Rural Development and Fisheries
Concluded
2007/10/01 - 2010/09/30 ANÁLISE TRANS-ESPECÍFICA DO IMPACTO FISIOLÓGICO DE GENES INACTIVADOS
PTDC/CVT/64154/2006
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2007/10 - 2010/09 A TRANS-SPECIFIC GENOMIC ANALYSIS TO COMPREHEND THE PHYSIOLOGICAL IMPACT OF INACTIVATED GENES
Provided by PTCRIS: 64154
64154
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2006 - 2010 Escola de Ciências da Vida e da Saúde no âmbito da Universidade Júnior da Universidade do Porto
2
Principal investigator
Concluded
2006 - 2007 Concurso Ciência Viva VI - Ensino experimental das ciências na escola
PVI-1450
Principal investigator
Ciência Viva
2004 - 2005 GENCERT: Male and female lineages of domestic animals of economic interest
2
Research Fellow
Portuguese Innovation Agency (ADI)
Outputs

Publications

Book chapter
  1. Araújo, Ricardo; Pereira, Filipe; Asch, Barbara van. "Applications of DNA-Based Methods in Food Forensics". In Security Science and Technology, 493-517. WORLD SCIENTIFIC (EUROPE), 2016.
    10.1142/9781786340788_0020
  2. Pereira, Filipe; Pereira, F.; Amorim, A.N.; Van Asch, B.. "Genetic and DNA-based techniques". 2013.
    10.1016/B978-0-444-59562-1.00008-6
  3. Pereira, Filipe; Amorim, António. Corresponding author: Pereira, Filipe. "Evolution: Viruses". In Brenner's Encyclopedia of Genetics, 566-568. Elsevier: New York, 2013.
    Published • 10.1128/9781555817626.ch3
  4. Pereira, F.; Amorim, A.. "Origin and Spread of Goat Pastoralism". 2010.
    10.1002/9780470015902.a0022864
  5. van Asch, B.; Luísa pereira; Pereira, Filipe; António Amorim. "Mitochondrial DNA lineages of the Portuguese Podengo autochthonous dog breed". In The Portuguese Podengo, edited by Vítor Veiga, 264-274. 2005.
    Published
Conference paper
  1. Pereira, Filipe; Alves, Cíntia; Couto, Cátia; Díaz, Lourdes López; Parra, David; Furfuro, Sandra; Aler, Mercedes; et al. "Species identification in routine casework samples using the SPInDel kit". 2019.
    10.1016/j.fsigss.2019.09.070
  2. Amaral, C.R.L.; Bitencourt, A.; Teixeira, C.; Pereira, F.; Silva, D.A.; Amorim, A.; Carvalho, E.F.. "Probing the potential of the Shark Panel InDel multiplex v2.0 on the forensic identification of batoid elasmobranchs". 2017.
    10.1016/j.fsigss.2017.09.106
  3. Amaral, C.R.L.; Maciel, V.A.; Pereira, F.; Mazzoni, R.; Silva, D.A.; Amorim, A.; Carvalho, E.F.. "Genetic diversity of freshwater fishes from the South American Atlantic Rainforest: The case study of the genus Phalloceros". 2015.
    10.1016/j.fsigss.2015.09.240
  4. Amaral, C.R.L.; Pereira, F.; Loiola, S.; Silva, D.A.; Amorim, A.; Carvalho, E.F.. "The shark panel: An InDel multiplex for shark species identification". 2015.
    10.1016/j.fsigss.2015.09.171
  5. Alves, Cíntia; Pereira, Rui; Prieto, Lourdes; Amorim, António; Pereira, Filipe. "Results of the GHEP-ISFG collaborative exercise for the taxonomic identification of forensic samples using the SPInDel method". 2015.
    10.1016/j.fsigss.2015.09.074
  6. Pereira, Filipe. "Microevolution in a Natural Population of Daphnia longispina Exposed to Acid Mine Drainage". Paper presented in Interdisciplinary Studies on Environmental Chemistry — Biological Responses to Contaminants, 2010.
  7. Pereira, Filipe. "Mitochondrial DNA haplotyping in Portuguese pig breeds and applications in the traceability of processed products". Paper presented in 6th International Symposium on the Mediterranean Pig, 2007.
  8. Frigi, S.; Yacoubi, B.; Pereira, F.; Pereira, L.; Cherni, L.; Amorim, A.; Elgaaied, A.B.. "mtDNA lineages in two Tunisian Berber communities: Comparing diversities between villages and towns". 2006.
    10.1016/j.ics.2005.09.032
  9. Soares, P.A.; 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". 2006.
    10.1016/j.ics.2005.09.173
Conference poster
  1. Rocha, Miguel; Antas, Paulo; Vasconcelos, Vitor; Cunha, Isabel; Pereira, Filipe; Rocha, M.S.; Vasconcelos, Vitor; Pereira, Filipe; Cunha, Isabel. "Characterization of Pollicipes pollicipes cement protein genes". Paper presented in IJUP 2015 - 8º Encontro de Jovens Investigadores da U.PORTO, 2015.
  2. Moreira, Filipa; Pereira, Filipe. "Development of a multiplex PCR assay for detection of genetically modified plants". Paper presented in III Aeicbas Biomedical Congress, 2015.
Journal article
  1. João Monteiro; Clive A. Marks; Patrícia C. Braga; Raquel L. Bernardino; Marco G. Alves; Alexandre Lobo-da-Cunha; Arnaldo Videira; Filipe Pereira. "The role of ion homeostasis imbalance due to citrate accumulation in fluoroacetic acid (FAA) toxicity in Neurospora crassa". Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology (2023): https://doi.org/10.1016/j.cbpc.2023.109661.
    10.1016/j.cbpc.2023.109661
  2. Filipa Moreira; Miguel Arenas; Arnaldo Videira; Filipe Pereira. "Evolution of TOP1 and TOP1MT Topoisomerases in Chordata". Journal of Molecular Evolution (2023): https://doi.org/10.1007/s00239-022-10091-z.
    10.1007/s00239-022-10091-z
  3. Filipe Pereira. "Molecular dynamics and intrinsic disorder analysis of the SARS-CoV-2 Nsp1 structural changes caused by substitution and deletion mutations". Molecular Simulation 48 13 (2022): 1192-1201. http://dx.doi.org/10.1080/08927022.2022.2075546.
    10.1080/08927022.2022.2075546
  4. Filipe Pereira. "Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions". Molecular Ecology 31 16 (2022): 4364-4380. http://dx.doi.org/10.1111/mec.16579.
    10.1111/mec.16579
  5. Filipa Moreira; Miguel Arenas; Arnaldo Videira; Filipe Pereira. Corresponding author: Filipe Pereira. "Evolutionary History of TOPIIA Topoisomerases in Animals". Journal of Molecular Evolution (2022): https://doi.org/10.1007/s00239-022-10048-2.
    10.1007/s00239-022-10048-2
  6. J. Monteiro; D. Pratas; A. Videira; F. Pereira. Corresponding author: F. Pereira. "Revisiting the Neurospora crassa mitochondrial genome". Letters in Applied Microbiology (2021): https://doi.org/10.1111/lam.13538.
    10.1111/lam.13538
  7. Filipa Moreira; Miguel Arenas; Arnaldo Videira; Filipe Pereira. Corresponding author: Filipe Pereira. "Molecular Evolution of DNA Topoisomerase III Beta (TOP3B) in Metazoa". Journal of Molecular Evolution 89 6 (2021): 384-395. https://doi.org/10.1007/s00239-021-10011-7.
    10.1007/s00239-021-10011-7
  8. Filipe Pereira. Corresponding author: Filipe Pereira. "SARS-CoV-2 variants lacking ORF8 occurred in farmed mink and pangolin". Gene 784 (2021): 145596-145596. https://doi.org/10.1016/j.gene.2021.145596.
    10.1016/j.gene.2021.145596
  9. Pereira, Filipe. Corresponding author: Pereira, Filipe. "SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring". Biochemical and Biophysical Research Communications (2021): https://doi.org/10.1016/j.bbrc.2021.02.080.
    In press • 10.1016/j.bbrc.2021.02.080
  10. Filipe Pereira. Corresponding author: Filipe Pereira. "Evolutionary dynamics of the SARS-CoV-2 ORF8 accessory gene". Infection, Genetics and Evolution 85 (2020): 104525-104525. https://doi.org/10.1016/j.meegid.2020.104525.
    10.1016/j.meegid.2020.104525
  11. Inês Ribeiro; Mariana Girão; Diogo A. M. Alexandrino; Tiago Ribeiro; Chiara Santos; Filipe Pereira; Ana P. Mucha; et al. "Diversity and Bioactive Potential of Actinobacteria Isolated from a Coastal Marine Sediment in Northern Portugal". Microorganisms 8 11 (2020): 1691-1691. https://doi.org/10.3390/microorganisms8111691.
    10.3390/microorganisms8111691
  12. Pereira F. Corresponding author: Pereira F. "SARS-CoV-2 variants lacking a functional ORF8 may reduce accuracy of serological testing.". Journal of immunological methods (2020): http://europepmc.org/abstract/med/33137303.
    10.1016/j.jim.2020.112906
  13. Amorim A; Pereira F; Alves C; García O. "Species assignment in forensics and the challenge of hybrids.". Forensic science international. Genetics (2020): http://europepmc.org/abstract/med/32615399.
    10.1016/j.fsigen.2020.102333
  14. Campos, Edwina; Cuéllar, Jorge; Salvador, Omar; García-Trejo, Erick A.; Pereira, Filipe. Corresponding author: Pereira, Filipe. "The genetic diversity and phylogeography of Mexican domestic sheep". Small Ruminant Research 187 (2020): 106109. http://dx.doi.org/10.1016/j.smallrumres.2020.106109.
    10.1016/j.smallrumres.2020.106109
  15. João Monteiro; Arnaldo Videira; Filipe Pereira. Corresponding author: Filipe Pereira. "Quantification of Neurospora crassa mitochondrial DNA using quantitative real-time PCR". Letters in Applied Microbiology (2020): https://doi.org/10.1111/lam.13294.
    10.1111/lam.13294
  16. Amaral CRL; Chaves ACS; Borges Júnior VNT; Pereira F; Silva BM; Silva DA; Amorim A; Carvalho EF; Rocha CFD. "Correction: Amphibians on the hotspot: Molecular biology and conservation in the South American Atlantic Rainforest.". PloS one (2020): http://europepmc.org/abstract/med/31940396.
    10.1371/journal.pone.0227329
  17. Amaral, Cesar R. L.; Chaves, Anna C. S.; Borges Júnior, Vitor N. T.; Pereira, Filipe; Silva, Bruna M.; Silva, Dayse A.; Amorim, António; Carvalho, Elizeu F.; Rocha, Carlos F. D.. "Amphibians on the hotspot: Molecular biology and conservation in the South American Atlantic Rainforest". PLOS ONE 14 10 (2019): e0224320. http://dx.doi.org/10.1371/journal.pone.0224320.
    10.1371/journal.pone.0224320
  18. Brooke E Hjelm; Brandi Rollins; Ling Morgan; Adolfo Sequeira; Firoza Mamdani; Filipe Pereira; Joana Damas; et al. "Splice-Break: exploiting an RNA-seq splice junction algorithm to discover mitochondrial DNA deletion breakpoints and analyses of psychiatric disorders". Nucleic Acids Research (2019): https://doi.org/10.1093/nar/gkz164.
    10.1093/nar/gkz164
  19. Girão, Mariana; Ribeiro, Inês; Ribeiro, Tiago; Azevedo, Isabel C.; Pereira, Filipe; Urbatzka, Ralph; Leão, Pedro N.; Carvalho, Maria F.. "Actinobacteria Isolated From Laminaria ochroleuca: A Source of New Bioactive Compounds". Frontiers in Microbiology 10 (2019): http://dx.doi.org/10.3389/fmicb.2019.00683.
    10.3389/fmicb.2019.00683
  20. Rocha, Miguel; Antas, Paulo; Castro, L. Filipe C.; Campos, Alexandre; Vasconcelos, Vítor; Pereira, Filipe; Cunha, Isabel. "Comparative Analysis of the Adhesive Proteins of the Adult Stalked Goose Barnacle Pollicipes pollicipes (Cirripedia: Pedunculata)". Marine Biotechnology 21 1 (2018): 38-51. http://dx.doi.org/10.1007/s10126-018-9856-y.
    10.1007/s10126-018-9856-y
  21. Diogo Pratas; Morteza Hosseini; Gonçalo Grilo; Armando Pinho; Raquel Silva; Tânia Caetano; João Carneiro; Filipe Pereira. "Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard". Genes 9 9 (2018): 445-445. https://doi.org/10.3390/genes9090445.
    10.3390/genes9090445
  22. Chiara Santos; Filipe Pereira. Corresponding author: Filipe Pereira. "Identification of plant species using variable length chloroplast DNA sequences". Forensic Science International: Genetics 36 (2018): 1-12. https://doi.org/10.1016/j.fsigen.2018.05.009.
    10.1016/j.fsigen.2018.05.009
  23. Alexandrino, Diogo A.M.; Ribeiro, Inês; Pinto, Luís M.; Cambra, Rafael; Oliveira, Rui S.; Pereira, Filipe; Carvalho, Maria F.. "Biodegradation of mono-, di- and trifluoroacetate by microbial cultures with different origins". New Biotechnology 43 (2018): 23-29. http://dx.doi.org/10.1016/j.nbt.2017.08.005.
    10.1016/j.nbt.2017.08.005
  24. Cátia Castro; Maria Amorim; Filipa Moreira; Filipe Pereira. Corresponding author: Filipe Pereira. "A method to assemble DNA fragments mimicking junctions of transgenic elements: Application to the AquAdvantage salmon". Food Control 82 (2017): 179-183. https://doi.org/10.1016/j.foodcont.2017.06.037.
    10.1016/j.foodcont.2017.06.037
  25. Marks CA; Malcolm Clark; David Obendorf; Graham P. Hall; Inês Soares; Filipe Pereira; Marks, Clive A.; et al. "Trends in anecdotal fox sightings in Tasmania accounted for by psychological factors". Conservation biology : the journal of the Society for Conservation Biology 31 6 (2017): 1450-1458. http://europepmc.org/abstract/AGR/IND605856478.
    10.1111/cobi.12944
  26. Miguel Arenas; Keith A. Crandall; Filipe Pereira; Manuela Oliveira; Nadia Pinto; Alexandra M. Lopes; Veronica Gomes; Angel Carracedo; Antonio Amorim. "Forensic genetics and genomics: Much more than just a human affair". PLOS Genetics (2017): https://doi.org/10.1371/journal.pgen.1006960.
    10.1371/journal.pgen.1006960
  27. Amaral, Cesar R. L.; Pereira, Filipe; Silva, Dayse A.; Amorim, António; de Carvalho, Elizeu F.. "The mitogenomic phylogeny of the Elasmobranchii (Chondrichthyes)". Mitochondrial DNA Part A 29 6 (2017): 867-878. http://dx.doi.org/10.1080/24701394.2017.1376052.
    10.1080/24701394.2017.1376052
  28. Filipa Moreira; João Carneiro; Pereira, Filipe. Corresponding author: Pereira, Filipe. "A proposal for standardization of transgenic reference sequences used in food forensics". Forensic Science International: Genetics (2017): http://dx.doi.org/10.1016/j.fsigen.2017.04.022.
    10.1016/j.fsigen.2017.04.022
  29. Chiara Santos; Filipe Pereira. Corresponding author: Filipe Pereira. "Design and evaluation of PCR primers for amplification of four chloroplast DNA regions in plants". Conservation Genetics Resources (2017): https://doi.org/10.1007%2Fs12686-016-0605-0.
    10.1007/s12686-016-0605-0
  30. Alves, C.; Pereira, R.; Prieto, L.; Aler, M.; Amaral, C.R.L.; Arévalo, C.; Berardi, G.; et al. Corresponding author: Pereira, F.. "Species identification in forensic samples using the SPInDel approach: A GHEP-ISFG inter-laboratory collaborative exercise". Forensic Science International: Genetics 28 (2017): 219-224. http://www.scopus.com/inward/record.url?eid=2-s2.0-85015396612&partnerID=MN8TOARS.
    10.1016/j.fsigen.2017.03.003
  31. Carneiro, J.; Resende, A.; Pereira, F.; Pereira, Filipe. Corresponding author: Pereira, F.. "The HIV oligonucleotide database (HIVoligoDB)". Database 2017 1 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85016066677&partnerID=MN8TOARS.
    10.1093/database/bax005
  32. 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.". (2016): http://europepmc.org/abstract/med/27122135.
  33. Carneiro, J.; Pereira, F.; Carneiro J; Pereira F. Corresponding author: Pereira F. "EbolaID: An Online Database of Informative Genomic Regions for Ebola Identification and Treatment". PLoS Neglected Tropical Diseases 10 7 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84980319963&partnerID=MN8TOARS.
    10.1371/journal.pntd.0004757
  34. Pereira, F.; Duarte-Pereira, S.; Silva, R.M.; Da Costa, L.T.; 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 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-85003583805&partnerID=MN8TOARS.
    10.1038/srep38383
  35. Resende, A.; Gonçalves, J.; Muigai, A.W.T.; Pereira, F.; Resende A; Gonçalves J; Muigai AW; Pereira F. Corresponding author: Pereira F. "Mitochondrial DNA variation of domestic sheep (Ovis aries) in Kenya". Animal Genetics 47 3 (2016): 377-381. http://www.scopus.com/inward/record.url?eid=2-s2.0-84954306846&partnerID=MN8TOARS.
    10.1111/age.12412
  36. Joana Gonçalves; Clive A. Marks; David Obendorf; António Amorim; Filipe Pereira. Corresponding author: Filipe Pereira. "Reply to Sarre et al. Defining specificity in DNA detection of wildlife". Forensic Science International: Genetics 16 (2015): e1-e2. https://doi.org/10.1016/j.fsigen.2014.10.024.
    10.1016/j.fsigen.2014.10.024
  37. Damas, J.; Samuels, D.C.; Carneiro, J.; Amorim, A.; Pereira, F.. Corresponding author: Pereira, F.. "Mitochondrial DNA Rearrangements in Health and Disease-A Comprehensive Study". Human Mutation 35 1 (2014): 1-14. http://www.scopus.com/inward/record.url?eid=2-s2.0-84890797290&partnerID=MN8TOARS.
    10.1002/humu.22452
  38. Marks, C.A.; Obendorf, D.; Pereira, F.; Edwards, I.; Hall, G.P.. "Opportunistically acquired evidence is unsuitable data to model fox (Vulpes vulpes) distribution in Tasmania". Wildlife Society Bulletin 38 4 (2014): 757-766. http://www.scopus.com/inward/record.url?eid=2-s2.0-84904444655&partnerID=MN8TOARS.
    10.1002/wsb.448
  39. Moreira, C.; Van Asch, B.; Fonseca, L.; Pereira-Castro, I.; Silva, R.; Azevedo, L.; Mota, M.; et al. Corresponding author: Pereira, F.. "The mitochondrial genome of the pinewood nematode (Bursaphelenchus xylophilus) lineage introduced in Europe". Mitochondrial DNA 25 6 (2014): 420-421. http://www.scopus.com/inward/record.url?eid=2-s2.0-84902453456&partnerID=MN8TOARS.
    10.3109/19401736.2013.809438
  40. Gonçalves, J.; Marks, C.A.; Obendorf, D.; Amorim, A.; Pereira, F.. Corresponding author: Pereira, F.. "A multiplex PCR assay for identification of the red fox (Vulpes vulpes) using the mitochondrial ribosomal RNA genes". Conservation Genetics Resources 7 1 (2014): 45-48. http://www.scopus.com/inward/record.url?eid=2-s2.0-84922607571&partnerID=MN8TOARS.
    10.1007/s12686-014-0343-0
  41. Marks, C.A.; Edwards, I.; Obendorf, D.; Pereira, F.; Hall, G.P.. "Did 'precautionary' 1080 baiting have a realistic potential to eradicate Red Fox (Vulpes vulpes) in Tasmania without in situ monitoring data?". Ecological Management and Restoration (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84906398685&partnerID=MN8TOARS.
    10.1111/emr.12121
  42. Dong, D.W.; Pereira, F.; Barrett, S.P.; Kolesar, J.E.; Cao, K.; Damas, J.; Yatsunyk, L.A.; Johnson, F.B.; Kaufman, B.A.. "Association of G-quadruplex forming sequences with human mtDNA deletion breakpoints". BMC Genomics 15 1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84906922263&partnerID=MN8TOARS.
    10.1186/1471-2164-15-677
  43. Gonçalves, J.; Marks, C.A.; 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 11 1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84901923037&partnerID=MN8TOARS.
    10.1016/j.fsigen.2014.03.009
  44. Marks, C.A.; Obendorf, D.; Pereira, F.; Edwards, I.; Hall, G.P.. "The dispersion and detection patterns of mtDNA-assigned red fox Vulpes vulpes scats in Tasmania are anomalous". Journal of Applied Ecology 51 4 (2014): 1033-1040. http://www.scopus.com/inward/record.url?eid=2-s2.0-84904418784&partnerID=MN8TOARS.
    10.1111/1365-2664.12278
  45. Damas, J.; Carneiro, J.; Amorim, A.; Pereira, F.. "MitoBreak: The mitochondrial DNA breakpoints database". Nucleic Acids Research 42 D1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84891787763&partnerID=MN8TOARS.
    10.1093/nar/gkt982
  46. Pereira, F.; Moreira, C.; Fonseca, L.; van Asch, B.; Mota, M.; Abrantes, I.; Amorim, A.. Corresponding author: Pereira, F.. "New Insights into the Phylogeny and Worldwide Dispersion of Two Closely Related Nematode Species, Bursaphelenchus xylophilus and Bursaphelenchus mucronatus". PLoS ONE 8 2 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84873646517&partnerID=MN8TOARS.
    10.1371/journal.pone.0056288
  47. Carneiro, J.; Pereira, F.; Amorim, A.. Corresponding author: Pereira, F.. "SPInDel: A multifunctional workbench for species identification using insertion/deletion variants". Molecular Ecology Resources 12 6 (2012): 1190-1195. http://www.scopus.com/inward/record.url?eid=2-s2.0-84867506608&partnerID=MN8TOARS.
    10.1111/1755-0998.12011
  48. 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 42 (2012): 10480-10485. http://www.scopus.com/inward/record.url?eid=2-s2.0-84867806242&partnerID=MN8TOARS.
    10.1021/jf3029896
  49. Damas, J.; Carneiro, J.; Gonçalves, J.; Stewart, J.B.; Samuels, D.C.; Amorim, A.; Pereira, F.. Corresponding author: Pereira, F.. "Mitochondrial DNA deletions are associated with non-B DNA conformations". Nucleic Acids Research 40 16 (2012): 7606-7621. http://www.scopus.com/inward/record.url?eid=2-s2.0-84869477659&partnerID=MN8TOARS.
    10.1093/nar/gks500
  50. Van Asch, B.; Pereira, F.; Santos, L.S.; Carneiro, J.; Santos, N.; Amorim, A.. "Mitochondrial lineages reveal intense gene flow between Iberian wild boars and South Iberian pig breeds". Animal Genetics 43 1 (2012): 35-41. http://www.scopus.com/inward/record.url?eid=2-s2.0-84855642252&partnerID=MN8TOARS.
    10.1111/j.1365-2052.2011.02222.x
  51. 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 13 (2011): 6920-6926. http://www.scopus.com/inward/record.url?eid=2-s2.0-79960067625&partnerID=MN8TOARS.
    10.1021/jf201283r
  52. Pereira, Filipe; Carneiro, João; Barbara van Asch. "A guide for mitochondrial DNA analysis in non-human forensic investigations". Open Forensic Science Journal 3 (2010): 33-44. https://benthamopen.com/ABSTRACT/TOFORSJ-3-33.
    Published
  53. Pereira, F.; Carneiro, J.; Matthiesen, R.; Van Asch, B.; Pinto, N.; Gusmão, L.; Amorim, A.. Corresponding author: Pereira, F.. "Identification of species by multiplex analysis of variable-length sequences". Nucleic Acids Research 38 22 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-78650444073&partnerID=MN8TOARS.
    10.1093/nar/gkq865
  54. 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 2 (2010): 68-72. http://www.scopus.com/inward/record.url?eid=2-s2.0-73249138577&partnerID=MN8TOARS.
    10.1016/j.fsigen.2009.05.003
  55. 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 2 (2010): 303-308. http://www.scopus.com/inward/record.url?eid=2-s2.0-74549162840&partnerID=MN8TOARS.
    10.1002/elps.200900389
  56. Pereira, F.; Queirós, S.; Gusmão, L.; Nijman, I.J.; Cuppen, E.; Lenstra, J.A.; Consortium, E.; et al. Corresponding author: Pereira, F.. "Tracing the history of goat pastoralism: New clues from mitochondrial and y chromosome DNA in North Africa". Molecular Biology and Evolution 26 12 (2009): 2765-2773. http://www.scopus.com/inward/record.url?eid=2-s2.0-70450231699&partnerID=MN8TOARS.
    10.1093/molbev/msp200
  57. 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 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-67650927396&partnerID=MN8TOARS.
    10.1186/1471-2164-10-266
  58. 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 2 (2009): 417-423. http://www.scopus.com/inward/record.url?eid=2-s2.0-63649095695&partnerID=MN8TOARS.
    10.1002/elps.200800307
  59. Chessa, B.; Pereira, F.; Arnaud, F.; Amorim, A.; Goyache, F.; Mainland, I.; Kao, R.R.; et al. "Revealing the history of sheep domestication using retrovirus integrations". Science 324 5926 (2009): 532-536. http://www.scopus.com/inward/record.url?eid=2-s2.0-65449129292&partnerID=MN8TOARS.
    10.1126/science.1170587
  60. Pereira, F.; Carneiro, J.; Amorim, A.; Pereira F; Carneiro J; Amorim A. Corresponding author: Pereira, F.. "Identification of species with DNA-based technology: Current progress and challenges". Recent Patents on DNA and Gene Sequences 2 3 (2008): 187-200. http://www.scopus.com/inward/record.url?eid=2-s2.0-70350236393&partnerID=MN8TOARS.
    10.2174/187221508786241738
  61. Pereira, F.; Soares, P.; Carneiro, J.; Pereira, L.; Richards, M.B.; Samuels, D.C.; Amorim, A.. Corresponding author: Pereira, F.. "Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region". Molecular Biology and Evolution 25 12 (2008): 2759-2770. http://www.scopus.com/inward/record.url?eid=2-s2.0-56449124495&partnerID=MN8TOARS.
    10.1093/molbev/msn225
  62. Pereira, F.; Carneiro, J.; Soares, P.; Maciel, S.; Nejmeddine, F.; Lenstra, J.A.; Gusmão, L.; Amorim, A.. Corresponding author: Pereira, F.. "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 2 (2008): 663-668. http://www.scopus.com/inward/record.url?eid=2-s2.0-55149091106&partnerID=MN8TOARS.
    10.1016/j.ympev.2008.08.026
  63. van Asch, B.; Alves, C.; Pereira, F.; Gusmão, L.; Amorim, A.. "A new autosomal STR multiplex for canine genotyping". Forensic Science International: Genetics Supplement Series 1 1 (2008): 628-629. http://www.scopus.com/inward/record.url?eid=2-s2.0-50349084059&partnerID=MN8TOARS.
    10.1016/j.fsigss.2007.10.043
  64. Arnaud, F.; Caporale, M.; Varela, M.; Biek, R.; Chessa, B.; Alberti, A.; Golder, M.; et al. "A paradigm for virus-host coevolution: Sequential counter-adaptations between endogenous and exogenous retroviruses". PLoS Pathogens 3 11 (2007): 1716-1729. http://www.scopus.com/inward/record.url?eid=2-s2.0-37349005478&partnerID=MN8TOARS.
    10.1371/journal.ppat.0030170
  65. Pereira, Filipe; Meirinhos, José; Amorim, António; Pereira, Luísa. Corresponding author: Pereira, Filipe. "Analysis of inter-specific mitochondrial DNA diversity for accurate species identification". International Congress Series 1288 (2006): 103-105. http://dx.doi.org/10.1016/j.ics.2005.09.125.
    10.1016/j.ics.2005.09.125
  66. Pereira, F.; Davis, S.J.M.; Pereira, L.; McEvoy, B.; Bradley, D.G.; Amorim, A.. Corresponding author: Pereira, F.. "Genetic signatures of a Mediterranean influence in Iberian Peninsula sheep husbandry". Molecular Biology and Evolution 23 7 (2006): 1420-1426. http://www.scopus.com/inward/record.url?eid=2-s2.0-33745623627&partnerID=MN8TOARS.
    10.1093/molbev/msl007
  67. Frigi, S.; Pereira, F.; Pereira, L.; Yacoubi, B.; Gusmão, L.; Alves, C.; Khil, H.K.e.; et al. "Data for Y-chromosome haplotypes defined by 17 STRs (AmpFLSTR® Yfiler™) in two Tunisian Berber communities". Forensic Science International 160 1 (2006): 80-83. http://www.scopus.com/inward/record.url?eid=2-s2.0-33745234085&partnerID=MN8TOARS.
    10.1016/j.forsciint.2005.05.007
  68. Alonso, A; Albarran, C; Martin, P; Garcia, P; Capilla, J; Garcia, O; de la Rua, C; et al. "Usefulness of microchip electrophoresis for the analysis of mitochondrial DNA in forensic and ancient DNA studies". Electrophoresis 27 24 (2006): 5101-5109.
    10.1002/elps.200600331
  69. Pereira, F.; Pereira, L.; Van Asch, B.; Bradley, D.G.; Amorim, A.. Corresponding author: Pereira, F.. "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 8 (2005): 2313-2318. http://www.scopus.com/inward/record.url?eid=2-s2.0-21244460361&partnerID=MN8TOARS.
    10.1111/j.1365-294X.2005.02594.x
  70. 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 (2005): http://www.scopus.com/inward/record.url?eid=2-s2.0-26444602094&partnerID=MN8TOARS.
    10.1186/1471-2156-6-37
Online resource
  1. Chiara Santos; João Carneiro; Filipe Pereira. Corresponding author: Filipe Pereira. A web-based platform of nucleotide sequence alignments of plants. 2019. https://doi.org/10.1101/617035.
    10.1101/617035
  2. Pereira, Filipe. PlantAligDB: A database of curated nucleotide sequence alignments for plants. 2018. http://plantaligdb.portugene.com/.
  3. Pereira, Filipe. Catalogue of reference sequences for transgenic elements (GMORefSeq). 2017. http://portugene.com/GMOTables/cgi-bin/GMOTablesHome.cgi.
  4. Pereira, Filipe. EbolaID Database Project (EbolaID). 2016. http://ebolaid.portugene.com/.
  5. Pereira, Filipe. The mitochondrial DNA breakpoints database (MitoBreak). 2014. http://mitobreak.portugene.com.
Preprint
  1. Okiemute B. Omoru; Filipe Pereira; Sarath Chandra Janga; Amirhossein Manzourolajdad. "Evidence for a long-range RNA-RNA interaction between ORF8 and Spike of SARS-CoV-2". 2021. https://doi.org/10.1101/2021.11.09.467911.
    10.1101/2021.11.09.467911
  2. Nijman IJ; Rosen BD; Zheng Z; Jiang Y; Cumer T; Daly KG; Bâlteanu VA; et al. "Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats". 2020. http://europepmc.org/abstract/PPR/PPR113423.
    10.1101/2020.02.17.952051
Thesis / Dissertation
  1. Pereira, Filipe. "Genetic diversity and structural organization of the mammalian mtDNA: functional and phylogenetic implications". PhD, Universidade do Porto Faculdade de Ciências, 2009.

Intellectual property

Patent
  1. Pereira, Filipe. 2006. "Process for animal species identification in samples with genetic material based on mitochondrial DNA size variation". Portugal.
    Granted/Issued
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2019 Species identification in routine casework samples using the SPInDel kit. 28th International Congress of International Society for Forensic Genetics (ISFG). 9 -13 September 2019, Prague, Czech Republic
2018 Variations of the mitogenome's control region in domestic sheep of the State of Mexico. 4° Congreso de Ciencia, Educación Y Tecnología. National Autonomous University of Mexico ,19-22 June 2018, Mexico.
2018 Mitochondrial DNA evolutionary breakpoints are associated with non-B DNA conformations Portugaliæ Genetica, 18 edition, 22-23 March 2018, Porto, Portugal
2018 Mitochondrial DNA mutations in health and disease MitoXT meeting, Coimbra, Portugal,
2018 Mitochondrial DNA rearrangements in health and disease MitoPorto. International symposium. Porto, Portugal.
2018 When secondary comes first: the role of DNA secondary structures in mitochondrial genomes Portugaliæ Genetica, 18 edition, Porto, Portugal
2018 Aplicações da genética forense não humana XIX Jornadas de Biologia Aplicada, Braga, Portugal
2018 Development of a genetic assay for detection of transgenic fishes in food and environmental samples Institut Pasteur, Paris, France. EMBRIC Transnational Access Workshop.
2017 The archaeogenetics of Estonian sheep – what do we know so far? EAA Annual Meeting 2017. Maastricht, Netherlands, 30.08.–03.09.2017
2017 Diversity of Actinomycetes from a Coastal Marine Sediment in Northern Portugal IJUP 2017 –10º Edição Encontro de Investigação Jovem, Porto, Portugal, 8-10 de Fevereiro de 2017.
2017 Development of DNA-based tests for detection of wild and transgenic species Marine Scotland Science (MSS), Aberdeen, UK
2017 New genetic assays for the identification of wild, domestic and transgenic species Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Crete, Greece.
2017 Construção de bases de dados de livre acesso na Internet para deteção e tratamento de doenças: o caso do EbolaID Ciência 2017 - Encontro com a Ciência e Tecnologia em Portugal, Lisboa, Portugal
2016 The archaeogenetics of domestic sheep and goats Institute of History and Archaeology. University of Tartu, Estonia
2016 Genotoxicidade: o teste dos micronúcleos Externato S. Miguel de Refojos, Cabeceiras de Basto
2016 Genética e Evolução Escola Secundária Garcia de Orta
2015 Results of the GHEP-ISFG collaborative exercise for the taxonomic identi¿cation of forensic samples using the SPInDel method 26th Congress of the International Society for Forensic Genetics, 31 August – 5 September, 2015, Krakow, Poland
2015 Identification of HIV-1, HCV and HBV using multiplex PCR XXXIX Portuguese Genetics Conference, 25-27 May, 2015, Braga, Portugal
2015 A new method for the detection of genetically modified plants using multiplex PCR IJUP 2015 - 8º Encontro de Jovens Investigadores da U.PORTO, 13-15 May, 2015, Portugal
2015 Identification of transgenic fishes using multiplex PCR. IJUP 2015 - 8º Encontro de Jovens Investigadores da U.PORTO, 13-15 May, 2015, Portugal
2015 Characterization of Pollicipes pollicipes cement protein genes IJUP 2015 - 8º Encontro de Jovens Investigadores da U.PORTO, 13-15 May, 2015, Portugal
2014 Non-B DNA conformations, genomic rearrangements and disease II AEICBAS Biomedical Congress
2014 Genética, genómica e evolução Lycée Français International de Porto
2010 A new method for detection of compositional strand asymmetries in vertebrate mitochondrial genomes Portugaliae Genética, 13 edition, 19-19 March, 2010, Porto. Portugal
2010 The mitochondrial genome of Bursaphelenchus xylophilus, the pinewood nematode 30th International ESN Symposium. 19-23 September 2010, Vienna, Austria
2009 Secondary structures in mitochondrial DNA: inferring functional constraints from evolutionary patterns III Encontro Ciência em Portugal – Ciência 2009, 30 July 2009, Lisboa, Portugal
2009 Detecção, identificação e quantificação do nemátode-da-madeira-do-pinheiro, Bursaphelenchus xylophilus 6º Congresso Nacional Florestal Nacional, 6-9 October 2009, Ponta Delgada, Açores, Portugal
2008 Revealing the history of animal domestication and migrations using endogenous retroviruses Cold Spring Harbor Retroviruses meeting. 19-24 May 2008, New York, USA
2008 A comparative approach to the evolution of mitochondrial DNA: the animal control region paradigm Portugaliæ Genetica, 11 edition, 27-28 March 2008, Porto, Portugal
2008 A utilidade da Genética na investigação forense Secondary school Colégio de Nossa Senhora da Apresentação. Calvão, Aveiro, Portugal
2007 Mitochondrial DNA haplotyping in Portuguese pig breeds and applications in the traceability of processed products 6th Symposium on Mediterranean Pig. 11-13 October 2007, Capo d’Orlando, Sicília, Itália
2007 SPecies IDentification multiplex: a process for animal species identification in samples with genetic material based on mitochondrial DNA size variation Academy Day. i-techpartner North of Portugal, 2 October 2007, Porto, Portugal
2007 CANIplex: a PCR multiplex system for canine DNA profiling Academy Day. i-techpartner North of Portugal, 2 October 2007, Porto, Portugal
2006 Determinação dos padrões de diversidade genética do DNA mitocondrial e sua aplicabilidade na identificação de espécies animais IV Encontro de Marcadores Moleculares. 23-24 November 2006, Vila Real, Portugal
2006 Novo método para a identificação de espécies baseado em diferenças de tamanho de segmentos do DNA mitocondrial. I Encontro Nacional de Pós-Graduação em Ciências Biológicas. 2-4 May 2006. Aveiro, Portugal
2006 A highly conserved hexanucleotide motif triggers the formation of tandem repeats in the mammalian mitochondrial DNA control region Portugaliæ Genetica, 9th edition, 16-18 March 2006, Porto, Portugal
2005 Linhagens mitocondriais de Canis lupus: diversidade e filogeografia II Congresso Luso-Espanhol do Lobo Ibérico, ESA-IPCB, 10-13 November 2005, Castelo Branco, Portugal
2005 Mitochondrial DNA lineages in five Portuguese dog breeds and a mixed-breed population: does diversity reveal different artificial selection pressures? 9ª Reunião Anual da Sociedade Portuguesa de Genética Humana, 10-12 November 2005, Cascais, Portugal
2005 Mitochondrial DNA lineages in five Portuguese dog breeds and a mixed-breed population: does diversity reveal different artificial selection pressures? 9ª Reunião Anual da Sociedade Portuguesa de Genética Humana, 10-12 November 2005, Cascais, Portugal
2005 The Origin and Diversity of Portuguese Sheep Breeds XV Congresso de Zootecnia e I Congresso Ibero-Americano de Zootecnia, 3-4 November, Vila Real, Portugal
2005 Analysis of inter-specific mitochondrial DNA diversity for accurate species identification 21st International Congress of the International Society for Forensic Genetics, 13-17 September 2005, Ponta Delgada, Portugal
2005 Relative Y-STR mutation rates estimated from the variance inside SNP defined lineages 21st International Congress of the International Society for Forensic Genetics, 13-17 September 2005, Ponta Delgada, Portugal
2005 Extensive conservation of secondary structures in the human mtDNA control region Portugaliæ Genetica, 8th edition, 17-19 March 2005, Porto, Portugal
2005 Genetics Secondary school Escola da Ponte. Vila das Aves, Portugal. Semana da Ciência e Tecnologia, Ciência Viva.

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2018 - 2023 Unravelling the role of topoisomerases in mitochondrial DNA rearrangements.
Supervisor of Filipa Isabel Menezes Moreira
 Ciências Biomédicas (PhD)
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2018 - 2022 Assessing the impact of fluoroacetic acid on mitochondrial function using Neurospora crassa as a model organism
Supervisor of João Pedro Silva Monteiro
 Ciências Biomédicas (PhD)
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2018 - 2022 Maternal genetic diversity in Mexican domestic ovine contemporary criollos and novohispanic: bases to sustentainable production
Co-supervisor of Victoria Campos
Producción y de la Salud Animal (PhD)
Universidad Nacional Autónoma de México, Mexico
2017 - 2021 Biodegradation of widely used fluorinated pesticides
Co-supervisor of Diogo Alves da Mota Alexandrino
 Contaminação e Toxicologia Ambientais (PhD)
Universidade do Porto Faculdade de Ciências, Portugal
2017 - 2018 Investigation of the microbial community associated with the fluoracetate-producing plant Dichapetalum cymosum and of the presence of fluorinase gene in its microbiome
Co-supervisor of Sandra Vicente
 Genética Forense (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2014 - 2018 Development of new tools for the identification of plants using chloroplast DNA sequences
Supervisor of Chiara Gabriele Santos
 Biologia (PhD)
Universidade do Porto Faculdade de Ciências, Portugal
2016 - 2017 The mtDNA of Mexican domestic sheep
Co-supervisor of Victoria Campos
 Maestría en Ciencias de la Producción y de la Salud Animal (Master)
Universidad Nacional Autónoma de México, Mexico
2015 - 2016 Marine Actinobacteria from the Northern Portuguese Coast: isolation, identification and investigation of their bioactive potential
Co-supervisor
 Toxicologia e Contaminação Ambientais (Master)
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2015 - 2016 Study of the microbiome of the fluoroacetate producing plant Dichapetalum cymosum: Investigation of microbial community
Co-supervisor of Zita Diana Marinho Couto
 Genética Forense (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2015 - 2016 Desenvolvimento de métodos moleculares para identificação de peixes transgénicos
Supervisor
 Genética Forense (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2015 - 2015 In vitro detection of non-canonical mitochondrial DNA conformations
Supervisor
 Genética Forense (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2015 - 2015 Development of multiplex PCR assays for the detection of genetically modified plants
Supervisor of Filipa Isabel Menezes Moreira
 Genética Forense (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2014 - 2015 Supervision of Research internship in Biochemistry
Supervisor
 Bioquímica (Degree)
Universidade do Porto Faculdade de Ciências, Portugal
2014 - 2015 Supervision of Research internship in Applied Statistics
Supervisor
 Estatística Aplicada (Degree)
Universidade do Minho, Portugal
2014 - 2015 Molecular targets involved in the goose barnacle Pollicipes pollicipes (Cirripedia) larvae metamorphosis and settlement
Co-supervisor
 Biologia Celular e Molecular (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2014 - 2015 In vitro detection of non-canonical mitochondrial DNA conformations
Supervisor of João Pedro Silva Monteiro
 Genética Forense (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2014 - 2015 Development of multiplex PCR assays for the detection of genetically modified plants
Supervisor
 Genética Forense (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2013 - 2014 New method for the simultaneous identification of pathogenic human viruses using multiplex PCR
Supervisor
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2012 - 2013 Identification of plant species using variable length chloroplast DNA sequences
Supervisor
 Genética Forense (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2011 - 2012 Supervision of Research internship in Biology
Supervisor
 Biologia (Degree)
Universidade do Porto Faculdade de Ciências, Portugal
2006 - 2007 Supervision of research internship in Biology
Supervisor
 Biologia (Degree)
Universidade do Porto Faculdade de Ciências, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2015 - 2017 Coordination of an inter-laboratory collaborative exercise for evaluation of the Species Identi¿cation by Insertions/Deletions (SPInDel) method. The exercise was organized by the Working Commission of the Spanish and Portuguese-Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) and included 24 participating laboratories from 10 countries. The results were described in Alves et al. Forensic Science International: Genetics. 28(2017) 219–224. (2015 - 2017)
Other (Co-organisor)
2010/03/18 - 2010/03/19 Portugaliæ Genética, 13th edition. (2010/03/18 - 2010/03/19)
Congress (Co-organisor)
 Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2007/07/04 - 2007/07/06 II Encontro Nacional de Pós-Graduação em Ciências Biológicas Biblioteca Municipal Almeida Garrett, Porto (2007/07/04 - 2007/07/06)
Congress (Co-organisor)

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2023/12/12 Identification and characterization of bioactive secondary metabolites from the filamentous fungus Neurospora crassa
(Thesis) Main arguer
 Patrícia Alexandra Soares Sequeira (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
2023/12/07 Development and validation of a protocol to analyse in StarQ Punch reference samples collected with a swab
(Thesis) Main arguer
 Ana Isabel Soares da Fonseca (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2021/08/25 The identification of plant DNA in metagenomic samples
(Thesis) Main arguer
 Kairi Raime (PhD)
Tartu Ulikool Molekulaar- ja Rakubioloogia Instituut, Estonia
2015/12/07 Testing the reliability of ancestral populations estimated on data from complete human genomes using different mixing algorithms
(Thesis) Main arguer
 João Daniel de Almeida Vieira (Master)
Universidade do Minho, Portugal
2013/10/30 Selective constraints and expression pattern of the ataxin-3 like 1 retrogene
(Thesis) Main arguer
 Andreia Patrícia de Sousa Pinto (Master)
Universidade do Porto Faculdade de Ciências, Portugal

Consulting

Activity description Institution / Organization
2022 - Current Consultant at DeciBio Analytics DeciBio LLC, United States
2013 - 2018 Member of the independent scientific review panel of the Tasmanian fox eradication program of the Australian government (http://www.tasmanianfox.com/).

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2023/02/01 - Current Molecular Genetics, Biotechology, Forensic Genetics, Bioinformatics Genética e Biotecnologia (Licenciatura) Universidade de Trás-os-Montes e Alto Douro, Portugal
2018 - 2021 Organismos transgénicos Engenharia Agrícola (Mestrado) Universidade de Trás-os-Montes e Alto Douro, Portugal
2018 - 2018 Workshop in Forensic Genetics. Spanish and Portuguese-Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG). Faculty of Sciences of the University of Porto, Portugal. Lecturing on “Species identification in forensics (SPInDel approach)”.
2008 - 2018 Forense genética não humana Genética Forense (Mestrado integrado) Universidade do Porto Faculdade de Ciências, Portugal
2017 - 2017 Workshop Non-human DNA, a "new" challenge!?. Laboratório da Polícia Cientifica. Lisboa, Portugal. Lecturing on real cases of forensic genetics.
2013 - 2013 Formal and Population Genetics. GABBA - Graduate Program (PhD) in Areas of Basic and Applied Biology. Biologia Básica e Aplicada (Doutoramento) Universidade do Porto Faculdade de Medicina, Portugal
2007 - 2009 Genética básica e aplicada Desenvolvimento Motor (Mestrado) Universidade do Porto Faculdade de Desporto, Portugal
2008 - 2008 Workshop “Genética populacional em Malária: Parasitas, vectores e humanos”. Instituto de Higiene e Medicina Tropical. Lisboa, Portugal. Lecturing on “Population Genetics”. Teaching on population genetics data analysis (practical lessons).
2006 - 2006 Identificação Genética. ABZ da Genética Humana da Sociedade Portuguesa de Genética Humana. (Especialização pós-licenciatura)

Interview (newspaper / magazine)

Activity description Newspaper / Forum
2017 Há um teste para detectar salmão transgénico e é português Público
2017 Investigadores do CIIMAR ganham acesso a plataformas de investigação internacionais UP
2017 Na Tasmânia, a caça à raposa não passou de uma caça aos gambozinos Público
2017 CIIMAR deteta falha no programa de erradicação da raposa na Tasmânia UP
2017 Cientistas portugueses oferecem base de dados sobre o vírus do ébola Público
2013 Cientistas da U.Porto abrem caminho no tratamento de doença dos pinheiros UP
2006 Cientistas do Porto criam teste rápido para identificação de espécies Público

Interview (tv / radio show)

Program Topic
2017 - Current RTP Jornal da Tarde Base de Dados sobre o vírus Ébola criada por investigadores da U.Porto
2017 - Current SIC - Jornal da tarde Investigadores da U.Porto desenvolvem base de dados mundial sobre o vírus Ébola
2017 - Current Antena 1 - Os Dias do Futuro Base de dados EbolaID
2017 - Current Antena 1 - Ponto de Partida Ébola: Ameaça Global?

Journal scientific committee

Journal title (ISSN) Publisher
2021 - Current Journal of Translational Medicine
2021 - Current Forensic Sciences Research
2021 - Current Heliyon
2021 - Current Infection Genetics and Evolution
2021 - Current Evolutionary Bioinformatics
2021 - Current Microorganisms
2021 - Current LWT - Food Science and Technology
2021 - Current Future Virology
2021 - Current ZooKeys
2021 - Current Molecular and Cellular Probes
2021 - Current Cellular Immunology
2021 - Current Informatics in Medicine Unlocked
2021 - Current Free Radical Biology and Medicine
2021 - Current Diagnostic Microbiology & Infectious Disease
2021 - Current International Journal of Biological Macromolecules
2021 - Current Genomics
2021 - Current Vaccine
2021 - Current Gene
2021 - Current Frontiers in Virology
2021 - Current Frontiers in Microbiology
2021 - Current Journal of Biomolecular Structure & Dynamics
2021 - Current Molecular Biology Reports (MOLE)
2021 - Current Journal of Molecular Evolution
2021 - Current Viruses
2020 - Current Molecular and Cellular Probes
2020 - Current ZooKeys
2020 - Current Future Virology
2020 - Current LWT - Food Science and Technology
2020 - Current Microorganisms
2020 - Current Evolutionary Bioinformatics
2020 - Current Infection Genetics and Evolution
2020 - Current Heliyon
2020 - Current Forensic Sciences Research
2020 - Current Journal of Translational Medicine
2020 - Current Scientific African
2020 - Current Sustainability
2020 - Current Animals
2020 - Current Molecules
2019 - Current BioTechniques (1940-9818) Future Science Ltd
2019 - Current Investigative Genetics (2041-2223) Springer (Biomed Central Ltd.)
2018 - Current Animal Genetics (1365-2052) Wiley (Blackwell Publishing)
2018 - Current AFRICAN JOURNAL OF BIOTECHNOLOGY (1684-5315) Academic Journals
2018 - Current Wildlife Society Bulletin (1938-5463) Wiley (John Wiley & Sons)
2018 - Current Forensic Science International Genetics (1872-4973) Elsevier
2018 - Current Food Control (0956-7135) Elsevier
2016 - Current Small Ruminant Research (0921-4488) Elsevier
2016 - Current Biochemical Genetics (1573-4927) Springer-Verlag
2016 - Current ZOOLOGICAL SCIENCE (2212-3830) BioOne (Zoological Society of Japan)
2016 - Current African Journal of Ecology (1365-2028) Wiley (Blackwell Publishing)
2015 - Current BMC Evolutionary Biology (1471-2148) Springer (Biomed Central Ltd.)
2015 - Current International Journal of Legal Medicine (1437-1596) Springer-Verlag
2015 - Current Journal of Virological Methods (0166-0934) Elsevier
2015 - Current Mitochondrial DNA (1940-1744) Informa UK (Taylor & Francis)
2015 - Current PeerJ (2167-8359) PeerJ
2015 - Current Diagnostics (2075-4418) MDPI AG
2014 - Current Scientific Reports (2045-2322) Springer Science and Business Media LLC
2013 - Current PLoS ONE (1932-6203) Public Library of Science
2013 - Current Journal of Animal Breeding and Genetics (1439-0388) Wiley (Blackwell Publishing)
2013 - Current Biological Journal of the Linnean Society (1095-8312) Oxford University Press
2012 - Current Journal of Heredity (1471-8505) Oxford University Press
2012 - Current Livestock Science (1871-1413) Elsevier
2010 - Current Nucleic Acids Research (1362-4962) Oxford University Press
2010 - Current PLoS Genetics (1553-7404) Public Library of Science
2008 - Current Molecular Phylogenetics and Evolution (1095-9513) Elsevier
2008 - Current Molecular Genetics and Metabolism (1096-7206) Elsevier
2007 - Current Genes (2073-4425) MDPI AG
2006 - Current Invertebrate Systematics (1445-5226) CSIRO Publishing
2005 - Current Journal of Integrative Agriculture (2095-3119) Elsevier
2000 - Current The Scientific World JOURNAL (1537-744X) Hindawi (The Scientific World)

Other jury / evaluation

Activity description Institution / Organization
2021 - 2021 Martí Franquès Cofund Doctoral Programme 2021 Call. Member of the Evaluation Panel. Universitat Rovira i Virgili, Spain
2021 - 2021 PASIFIC Postdoctoral Fellowships Programme (https://pasific.pan.pl/). Member of the Evaluation Panel - Life Sciences. Polska Akademia Nauk, Poland
2021 - 2021 Call for PhD scholarships. Evaluator. Fundo Regional para a Ciência e Tecnologia, do Governo Regional dos Açores. , Portugal
2019 - 2019 Reviewer - Fundo Regional para a Ciência e Tecnologia, do Governo Regional dos Açores. Call for Postdoc scholarships in companies. Fundo Regional para a Ciência e Tecnologia, do Governo Regional dos Açores. , Portugal
2018 - 2019 Reviewer - Agência Nacional de Inovação, S.A. (ANI). Projetos de I&D Industrial à Escala Europeia e em Copromoção. Agência Nacional de Inovação, S.A. (ANI). Projetos de I&D Industrial à Escala Europeia e em Copromoção., Portugal
2017 - 2017 International Foundation for Science (IFS) research grants. Evaluator. International Foundation for Science, Sweden
2015 - 2015 The National Science Centre. Poland. Research projects. Evaluator. Polska Akademia Nauk, Poland
2014 - 2015 Member of the evaluation panel, Biological Sciences – Postdoc scholarships. Call for PhD and Postdoc scholarships 2014, 2015. Portuguese Science and Technology Foundation (FCT). Fundação para a Ciência e a Tecnologia, Portugal
2014 - 2014 Fundo Regional para a Ciência e Tecnologia, do Governo Regional dos Açores. Call for Postdoc scholarships. Evaluator. Fundo Regional para a Ciência e Tecnologia, do Governo Regional dos Açores. , Portugal
2013 - 2013 Member of the evaluation panel, Biological Sciences II. Call for PhD and Postdoc scholarships 2013 - Portuguese Science and Technology Foundation (FCT) Fundação para a Ciência e a Tecnologia, Portugal
2011 - 2011 French National Research Agency (ANR). Review of research projects. Agence nationale de la recherche, France
2009 - 2010 Projectos Pluridisciplinares para estímulo à Iniciação. Evaluator. Universidade do Porto, Portugal
Distinctions

Award

2018 Publons Peer Review Award 2018 for placing in the top 1% reviewers worldwide in Multidisciplinary area.
2018 Individual prize - Business Ignition Program. University of Porto.
Universidade do Porto Porto Business School, Portugal
2004 Young Researcher SPGH 2004 - Honorable Mention