Pedro Alexandre Soares (291F-4B5A-2CD4)

Curriculum Vitae

Pedro Alexandre Soares

Pedro Alexandre Soares completed his Licenciatura in Biology in 2003 at the Faculty of Sciences of the University of Porto. He obtained his Doctor of Philosophy through the Marie Curie PhD programme Early Stage Training in Advanced Genetic Analysis (AGAPE) in 2009 at the University of Leeds, United Kingdom. Following his PhD and a one-year postdoctoral contract, Pedro returned to Portugal to join IPATIMUP (Porto), where he continued his research in human genetics and evolutionary genomics. Seeking to combine research with a stronger involvement in teaching and to apply his transversal expertise in genomics and bioinformatics across diverse biological questions, he later joined the Centre of Molecular and Environmental Biology (CBMA) at the University of Minho in Braga. Pedro currently holds the position of Assistant Professor at the University of Minho lecturing Genetics, Biological Anthropology and Bioinformatics, where he conducts research at CBMA. Pedro has an established academic record, with several influential articles, book chapters, and a forthcoming book to be published by Oxford University Press. His publications, particularly in the fields of human genetics and archaeogenetics, have accumulated more than 5,200 citations in Scopus. Throughout his career, he has supervised six PhD students who successfully completed their degrees and currently supervises four PhD theses while co-supervising another two. In addition, he has supervised or co-supervised more than 30 MSc dissertations, primarily in Molecular Genetics and Bioinformatics. Pedro has served as Principal Investigator in three competitive research projects and as co-Principal Investigator in another project focusing on human genetics and genomics. Overall, he has secured approximately €1 million in competitive funding as Principal Investigator. He has also contributed as a team member in nearly twenty research projects spanning multiple areas, including ecology, biotechnology, and health sciences. In addition, he has been Principal Investigator in one project and co-Principal Investigator in two projects related to advanced computational resources. Pedro’s main research interests lie in genetics and heredity, human genetics, evolutionary biology, and bioinformatics, with a particular focus on population genomics and the reconstruction of human evolutionary history using genomic data. He currently serves as Head of the GEB Lab (Genomics, Evolution and Bioinformatics Laboratory) at the Institute of Bio-sustainability (IBS). In addition to his academic activities, Pedro is also a partner and Scientific Advisor at the biotechnology company ÉonGenetics.

Read full resume ↓

Identification

Personal identification

Full name: Pedro Alexandre Soares

Citation names

Soares, Pedro

Author identifiers

Ciência ID: 291F-4B5A-2CD4
ORCID iD: 0000-0002-2807-690X
Google Scholar ID: M7LWYTkAAAAJ
Researcher Id: G-9422-2011
Scopus Author Id: 15061713600

Addresses

Centre of Molecular and Environmental Biology (CBMA) Biology Department, University of Minho, 4710-057 , Gualtar, Braga, Portugal (Professional)

Websites

https://scholar.google.pt/citations?user=M7LWYTkAAAAJ&hl=en (Scholar)

Languages

Language	Speaking	Reading	Writing	Listening	Peer-review
Portuguese (Mother tongue)
English	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)

Education

	Degree	Classification
1999/09/15 - 2013/07/20 Concluded	Biology (Licenciatura) Major in Biology Universidade do Porto Faculdade de Ciências, Portugal	15
2005/05/01 - 2009/09/15 Concluded	Marie-Curie PhD programme “Early Stage Training in Advanced Genetic Analysis” (AGAPE) (Doctor of Philosophy) Major in Genetics University of Leeds School of Biology, United Kingdom "Phylogenetics and Phylogeography of Human mtDNA in Island Southeast Asia" (THESIS/DISSERTATION)	Concluded

Affiliation

Teaching in Higher Education

	Category Host institution	Employer
2022/03/01 - Current	Assistant Professor (University Teacher)	Universidade do Minho, Portugal
	Universidade do Minho Escola de Ciências, Portugal

Projects

Grant

	Designation	Funders
2022/01/01 - 2024/12/31	Fine-scale study of ancestry, mobility and diet in the Copper Age-Bronze Age transition in northern Portugal PTDC/HAR-ARQ/3286/2021 Principal investigator Universidade do Minho, Portugal Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2018/02/01 - 2023/01/31	Australasian Colonization Research: Origins of Seafaring to Sahul info:eu-repo/grantAgreement/EC/H2020/759677/EU Researcher University of Southampton, United Kingdom	European Commission
2018/10 - 2022/09	Abordagens omicas para a exploração industrial de Torulaspora delbrueckii: elucidação das bases moleculares de fenótipos complexos Provided by PTCRIS: PTDC/BIA-MIC/32059/2017	Fundação para a Ciência e a Tecnologia
2018/10 - 2022/09	Surto de dengue na Madeira: ferramenta para pesquisar fatores do hospedeiro envolvidos na infecão assintomática Provided by PTCRIS: PTDC/SAU-INF/30440/2017	Fundação para a Ciência e a Tecnologia
2018/09 - 2022/08	De Portugal para África: revelando a origem africana da população portuguesa atual Provided by PTCRIS: PTDC/SOC-ANT/30316/2017	Fundação para a Ciência e a Tecnologia
2019/04/01 - 2022/03/31	Efficient computational solutions for integrated DNA barcoding, metabarcoding and associated high-throughput sequencing data analysis POCI-01-0145-FEDER-029626 Researcher Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal	Fundação para a Ciência e a Tecnologia Cancelled
2018/09/01 - 2021/08/31	From Portugal back to Africa: uncovering the african roots of present-day Portuguese PTDC/SOC-ANT/30316/2017 Principal investigator Universidade da Madeira, Portugal Universidade do Minho, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2018/09/01 - 2021/08/31	Omics approaches towards the industrial exploitation of Torulaspora delbrueckii: Elucidation of the molecular basis underlying complex cellular traits PTDC/BIA-MIC/32059/2017 Researcher Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2018/09/01 - 2021/08/31	Madeira Dengue Outbreak: a tool for searching host factors involved in asymptomatic infection PTDC/SAU-INF/30440/2017 Researcher Universidade da Madeira, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2015/09/01 - 2020/08/31	Leverhulme Doctoral Scholarship Centre for Evolutionary Genomics - Researcher University of Huddersfield, United Kingdom	Leverhulme Trust Ongoing
2016/05 - 2020/08	Origens da Cultura Campaniforme: Testando a hipotética expansão Neolítica a partir da Península Ibérica usando genomas mitocondriais actuais e antigos Provided by PTCRIS: PTDC/EPH-ARQ/4164/2014	Fundação para a Ciência e a Tecnologia
2016/01/01 - 2020/05/31	EcoAgriFood: Innovative Green Products and Processes to Promote Agri-Food Bioeconomy NORTE-01-0145-FEDER-000009 Researcher	Programa Operacional Regional do Norte Ongoing
2014/05 - 2019/04	Archaeogenetics of Southeast Asia and the Pacific: from whole-mtDNA genomes to complete human genomes Provided by PTCRIS: IF/01641/2013/CP1158/CT0015	Fundação para a Ciência e a Tecnologia
2016/01 - 2018/12	Beaker origins: Testing the hypothesis of late Neolithic dispersals from Iberia using both ancient and contemporary mitochondrial genomes Provided by PTCRIS: 142795 Principal investigator	Fundação para a Ciência e a Tecnologia, I.P.
2012/01 - 2016/12	Dengue research Framework for Resisting Epidemics in Europe 282378 Researcher Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal	European Commission
2011/11/01 - 2015/10/31	A Marie Curie Initial Training Network on the History, Archaeology and New Genetics of the Transatlantic Slave Trade 290344 Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal	European Union Concluded
2013/01/01 - 2015/06/30	Microenvironment, metabolism and cancer - Researcher Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal	Programa Operacional Regional do Norte
2013/06 - 2015/05	Genetic history and population structure in Southeast Asia 132046 Principal investigator	Fundação para a Ciência e a Tecnologia, I.P.
2011/03 - 2014/06	Genetic and chronological characterisation of the European settlement by modern humans in the Upper Palaeolithic 113832 Researcher	Fundação para a Ciência e a Tecnologia, I.P.
2011/03 - 2014/06	Caracterização genética e cronológica do povoamento europeu pelo Homem Moderno no Paleolítico Superior Provided by PTCRIS: PTDC/CS-ANT/113832/2009	Fundação para a Ciência e a Tecnologia
2012/02/01 - 2013/12/31	L and U6 mtDNA lineages in Southern and Western Iberia: migratory links between Africa and Europe - Researcher Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal	Concluded
2010/01 - 2013/04	COMPLETE MTDNA GENOME ANALYSIS AND THE MODERN HUMAN SETTLEMENT OF ANATOLIA Provided by PTCRIS: SFRH/BPD/64233/2009	Fundação para a Ciência e a Tecnologia
2008/05/01 - 2009/04/30	Using mitochondrial DNA to investigate the prehistoric settlement of Myanmar Pyay (Burma) BARDA-48208 Post-doc Fellow University of Leeds Faculty of Biological Sciences, United Kingdom	The British Academy

Contract

	Designation	Funders
2023/05/01 - 2027/04/30	A Multi-Pillar Framework to address childhood obesity by building on an EU biobank, micro-moments and mobile recommendation systems. 101080718 Researcher Universidade do Minho, Portugal	Ongoing
2021/01/01 - 2025/12/31	ARNET - Aquatic Research Network LA/P/0069/2020 10.54499/LA/P/0069/2020 Universidade do Minho, Portugal Universidade do Algarve, Portugal Instituto Politécnico de Leiria, Portugal Instituto Universitário de Ciências Psicológicas Sociais e da Vida, Portugal Universidade Nova de Lisboa, Portugal FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal Universidade de Coimbra, Portugal Universidade de Lisboa Faculdade de Ciências, Portugal Universidade de Évora, Portugal Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação, Portugal Universidade Nova de Lisboa Associação para a Inovação e Desenvolvimento da FCT, Portugal Centro de Ciências do Mar e do Ambiente, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2020/08/24 - 2024/04/23	A-FISH-DNA-SCAN: Cutting-edge DNA-based approaches for improved monitoring and management of fisheries resources along Magellan-Elcano´s Atlantic route CIRCNA/BRB/0156/2019 Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal Universidade do Minho, Portugal Instituto Português do Mar e da Atmosfera, Portugal Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal Centro de Ciências do Mar, Portugal	Fundação para a Ciência e a Tecnologia Ongoing

Other

	Designation	Funders
2021/01/01 - 2025/12/31	Aquatic Research Infrastructure Network LA/P/0069/2020 10.54499/LA/P/0069/2020 Universidade do Minho, Portugal Universidade do Algarve, Portugal Instituto Politécnico de Leiria, Portugal Instituto Universitário de Ciências Psicológicas Sociais e da Vida, Portugal Universidade Nova de Lisboa, Portugal FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal Universidade de Coimbra, Portugal Universidade de Lisboa Faculdade de Ciências, Portugal Universidade de Évora, Portugal Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação, Portugal Universidade Nova de Lisboa Associação para a Inovação e Desenvolvimento da FCT, Portugal Centro de Ciências do Mar e do Ambiente, Portugal	Fundação para a Ciência e a Tecnologia Ongoing

Outputs

Publications

Book	Martin B. Richards; Pedro Soares. DNA and ancestry - an introduction to archaeogenetics. Oxford, United Kingdom: Oxford University Press. 2027. Accepted
Book chapter	Rito, Teresa; Inlamea, Osvaldo; Oliveira, Olena; Duarte, Raquel; Soares, Pedro; Correia-Neves, Margarida. "Evolution and Molecular Characteristics of Mycobacterium tuberculosis and Mycobacterium bovis". In Integrated Science, 847-865. Springer International Publishing, 2023. 10.1007/978-3-031-15955-8_41 Rezaei, Nima; Hosseini, Nastaran-Sadat; Saghazadeh, Amene; Fateh, Abolfazl; Duse, Adriano; Ahmad, Aijaz; Braley, Alexander E.; et al. "Tuberculosis: Integrated Studies for a Complex Disease 2050". In Integrated Science, 1063-1098. Springer International Publishing, 2023. 10.1007/978-3-031-15955-8_51 Soares, P.; Mormina, M.; Rito, T.; Richards, M.B.. "THE ARCHAEOGENETICS OF SOUTHEAST ASIA". 70-91. 2022. Vieira, Daniel; Almeida, Mafalda; Richards, Martin B.; Soares, Pedro. "An Efficient and User-Friendly Implementation of the Founder Analysis Methodology". In Practical Applications of Computational Biology and Bioinformatics, 13th International Conference, 121-128. Springer International Publishing, 2019. 10.1007/978-3-030-23873-5_15 Marina Silva; Katharina Dulias; Gonzalo Oteo-Garcia; Francesca Gandini; Ceiridwen Edwards; Maria Pala; Soares, Pedro; Jim Wilson; Martin B. Richards. "Once upon a time in the West: The archaeogenetics of Celtic origins". In Exploring Celtic Origins: New Ways Forward in Archaeology, Genetics and Linguistics, edited by John Koch; Barry Cunliffe, 153-191. Oxbow Books, 2019. Published Martin B. Richards; Antonio Torroni; Pedro Soares. "Phylogeography". In The International Encyclopedia of Biological Anthropology, edited by Wenda Trevathan. 2018. Published Soares, Pedro; Rito, Teresa; Pereira, Luísa; Richards, Martin B.. "A Genetic Perspective on African Prehistory". In Vertebrate Paleobiology and Paleoanthropology, edited by Sacha C. Jones; Brian A. Stewart, 383-405. Springer Netherlands, 2016. 10.1007/978-94-017-7520-5_18 Maria Pala; Pedro Soares; Gyaneshwer Chaubey; Martin B. Richards; Graeme Barker; Candice Goucher. "Archaeogenetics". In The Cambridge World History, 26-54. Cambridge University Press, 2015. Published • 10.1017/cbo9780511978807.003 Maria Pala; Gyaneshwer Chaubey; Pedro Soares; Martin B Richards. "The Archaeogenetics of European Ancestry". In Encyclopedia of Life Science (eLS). John Wiley and Sons, Chichester, 2014. Published Alves, Marco; Alves, Joãd; Camacho, Rui; Soares, Pedro; Pereira, Luísa. "From Networks to Trees". In 6th International Conference on Practical Applications of Computational Biology & Bioinformatics, 129-136. Springer Berlin Heidelberg, 2012. 10.1007/978-3-642-28839-5_15
Conference paper	Sousa-Silva, M.; Vieira, Daniel; Ribas, David Manuel Nogueira; Soares, Pedro; Casal, Margarida; Soares-Silva, Isabel João; Silva, Maria Antónia Sousa Correia. "Exploring the Cyberlindnera jadinii yeast transportome to uncover novel carboxylate transporters for biotechnological applications". 2019. Ribas, David Manuel Nogueira; Soares-Silva, Isabel João; Vieira, Daniel; Silva, Maria Antónia Sousa Correia; Sá-Pessoa, Joana; Silva, João Pedro Azevedo; Viegas, Sandra; et al. "The Ady2 “NPAPLGL(M/S)” motif is critical for acetate uptake and binding". 2018. 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". 2005. 10.1016/j.ics.2005.09.173
Conference poster	Ribeiro, Fabiana M; Rito, Teresa; Soares, Pedro; Silva, Ana Maria. "Socioeconomic Determinants as Risk Factors for Tuberculosis Infection in the Past: Historical an Skeletal Evidence". Paper presented in 29th Annual Meeting of the European Association of Archaeologists, 2023. Torre, C.; Vieira, D; Sousa, M.J.; Soares, P.; Franco-Duarte, R.. "Torulaspora delbrueckii genomic data: bioinformatic analysis towards elucidation of its fermentation capacity and application in wine industry". Paper presented in MICROBIOTEC’19, 2019. Sousa-Silva, M.; Vieira, D.; Ribas, D; Soares, Pedro; Casal, Margarida; Soares-Silva, I.. "Exploring the Cyberlindnera jadinii transportome for the identification of novel carboxylate transporters". Paper presented in MICROBIOTEC’19, 2019. Almeida M, Brandão A, Vieira D, Cavadas B, Matos E, Rito T, Oppenheimer S, Pereira L, Richards MB,; Soares, Pedro. "Recovering the genetic history of the Pacific using mitochondrial DNA and genome-wide data". Paper presented in XV Encontro Nacional de Biologia Evolutiva, 2019. Foody MG, Ditchfield PW, Ambrose SH, Eakin JE, Almeida M, Vieira D, Brandão A, Rito T, Hackland J, Aguon LB, Blas RFY; Pala M, Hunter-Anderson RL, Richards MB, Oppenheimer SJ, Soares P, Edwards CJ. "Ancient DNA and isotopic analysis of archaeological remains from two individuals from Guam". Paper presented in 8th International Symposium on Biomolecular Archaeology ISBA 2018, Jena, Germany, 2018. Donzella L, Almeida D, Soares P, Morrissey JP, Sousa MJ. "Enhancing Yeast Sugar Transport Capacity Under Stress Conditions". Paper presented in 36th Small Meeting on Yeast Transport and Energetics (SMYTE), 2018. Vieira D, Soares-Silva I, Ribas D, Azevedo-Silva J, Casal M, Soares P. "A tool for the extraction of relevant and representative homologues of a given gene: the example of a transmembrane protein from Eukaryotic and Prokaryotic genomes". Paper presented in MICROBIOTEC´17, 2017. Silva M, Oliveira M, Vieira D, Gandini F, Dulias K, Fichera A; Foody G, Oteo-Garcia G, Yau B, Edwards C, Pala M, Koch J; Wilson JF, Pereira L, Richards MB, Soares P. "A genetic chronology for the Indian Subcontinent". Paper presented in Human Evolution: Fossils, Ancient and Modern Genomes, Cambridge, UK., 2017. Fichera A, Tamm E, Gandini F, Silva M, Dulias K, Foody G,; Yau B, Oteo-Garcia G, Metspalu M, Metspalu E, Edwards C, Soares P. "Mitochondrial haplogroup HV expansion through the Mediterranean region: a founder analysis approach". Paper presented in Human Evolution: Fossils, Ancient and Modern Genomes, Cambridge, UK, 2017. Branco C, Guimarães J, Vieira D, Silva M, Richards MB, Soares P. "Testing the time of female-associated migrations within Europe using mitochondrial DNA haplogroup U clades and a founder analysis approach". Paper presented in XLI Portuguese Genetics Conference, Aveiro, Portugal, 2017. Dulias K, Fichera A, Silva M, Gandini F, Rito T, Edwards CJ, Pala M, Soares P, Richards MB. "Disentangling the expansion of major European mitochondrial DNA lineages". Paper presented in UK Archaeological Science Conference 2017, London, UK, 2017. Ferreira J, Cavadas B, Soares P, Pereira L.. "Inference of viral infection in human cancer samples from TCGA database". Paper presented in Bioinformatics Open Days 2017, 2017. Ferreira, Joana; Cavadas, Bruno; Soares, Pedro; Pereira, Luisa. "Viral infections in Cancer – Evaluation in omics datasets". Paper presented in 5th I3S Annual Meeting, 2016. Sierra, Beatriz; Triska, Petr; Soares, Pedro; Garcia, G; Perez, AB; Aguirre, E; Oliveira, Marisa; et al. "Lipid/Cholesterol Metabolism Is Involved in Viral Replication and Immune Response to Protection for African-Ancestry against Dengue Hemorrhagic Fever". Paper presented in 35th Annual Meeting of the American Society for Virology, 2016. Brandão A, Cavadas B, Pereira L, Richards M, Soares P. "Complex genetic structure of Southeast Asian populations using genome-wide data". Paper presented in 19ª Reunião Anual da Sociedade Portuguesa de Genética Humana, Porto, Portugal, 2015. Cavadas B, Soares P, Samuels DC, Pereira L. "Heteroplasmic germline inherited mtDNA mutations – an empirical dataset for evaluation of selection on pathogenic mutations". Paper presented in The Genomics of Common Diseases 2015, Hinxton, Cambridge, UK, 2015. Soares, Pedro. "Genetic trace of postglacial and Neolithic movements in Southeast Asia". Paper presented in The European Human Genetics Conference 2015, Glasgow, United Kingdom, 2015. Silva M, Alshamali F, Pereira L, Soares P. "Phylogeography of mtDNA haplogroup L2: 60,000 years interactions between Central and Eastern Africa". Paper presented in XXXIX Portuguese Genetics Conference, Braga, Portugal, 2015. Brandão A, Richards MB, Soares P, Pereira L. "Genetic trace of postglacial and Neolithic movements in Southeast Asia". Paper presented in XXXIX Portuguese Genetics Conference, Braga, Portugal, 2015. Silva M, Alshamali F, Pereira L, Soares P. "Phylogeography of mtDNA haplogroup L2: insights into some African population movements". Paper presented in X Encontro Nacional de Biologia Evolutiva, 2014. Cavadas, Bruno; Soares, Pedro; Camacho, Rui; Samuels, DC; Pereira, Luisa. "Heteroplasmic germinal and somatic mtDNA mutations evaluated in NGS data – implications in cancer". Paper presented in 4th I3S Annual Meeting, 2014. Silva M, Alshamali F, Pereira L, Soares P. "Bidirectional gene flow between Central and Eastern Africa in the Early Holocene and low genetic input of East African mtDNA lineages into Bantu populations before their expansion South". Paper presented in ESHE - 4th Annual Meeting of the European Society for the study of Human Evolution (ESHE), 2014. Ribeiro J, Triska P, Soares P, Pereira L. "Phylogeny of OAS genes and association with dengue fever". Paper presented in IJUP 2014, 2014. Fernandes V, Machado A, Soares P, Richards M, Pereira L. "The African genetic input in the Arabian Peninsula: evaluating between pre-historic and historic migrations". Paper presented in XXXVIII Portuguese Genetics Conference, 2013. van der Waerden A, Triska P, Rito T, Soares P, Pereira L. "Evaluating selection in human nuclear-encoded genes for proteins intervening at the mitochondrial oxidative phosphorylation pathway". Paper presented in 16ª Reunião Anual da Sociedade Portuguesa de Genética Humana, 2012. Soares P, Ermini L, Richards M. "Re-evaluation of the complete mitochondrial DNA genome chronology". Paper presented in II Encontro nacional de Pós-graduação em Ciências Biológicas, 2007. Pereira F, Soares P, Amorim A, Pereira L. "Análise das estruturas secundárias da região de controlo do DNA mitocondrial". Paper presented in 8ª Reunião Anual da Sociedade Portuguesa de Genética Humana, 2004.
Journal article	Marina Silva; Leonardo García Sanjuán; Alessandro Fichera; Gonzalo Oteo-García; M.George B. Foody; Luis Efrén Fernández Rodríguez; Verónica Navarrete Pendón; et al. "Genetic and historical perspectives on the early medieval inhumations from the Menga dolmen, Antequera (Spain)". Journal of Archaeological Science: Reports (2026): https://doi.org/10.1016/j.jasrep.2025.105559. 10.1016/j.jasrep.2025.105559 Erica Olund-Matos; Ricardo Franco-Duarte; André Santa-Cruz; Maria Nogueira; Margarida Correia-Neves; Diana Lopes; Rui Jorge Silva; et al. "Hospital-Based Genomic Surveillance of Klebsiella pneumoniae: Trends in Resistance and Infection". Biology (2025): https://www.mdpi.com/2079-7737/14/12/1795. 10.3390/biology14121795 William Pomat; Maria Pala; Antonio Torroni; Martin Brian Richards; Ceiridwen Jane Edwards; Helen Farr; Stephen Oppenheimer; et al. "Genomic evidence supports the “long chronology” for the peopling of Sahul". Science Advances (2025): https://www.science.org/doi/10.1126/sciadv.ady9493. 10.1126/sciadv.ady9493 Pedro Fernandes; Bernardo Pinho; Bárbara Miguéis; João B. Almeida; Teresa Rito; Pedro Soares. "Analysis of Selective Pressure on Ancient Human Mitochondrial Genomes Reveals the Presence of Widespread Sequencing Artefacts". International Journal of Molecular Sciences (2025): https://doi.org/10.3390/ijms26167739. 10.3390/ijms26167739 Fabiana M. Ribeiro; Pedro Soares; Teresa Rito; Ana Maria Silva. "Tuberculosis in Portugal: Intertwining History and Public Health Development". World (2025): https://doi.org/10.3390/world6020061. 10.3390/world6020061 Franco-Duarte, R.; Fernandes, T.; Sousa, M.J.; Sampaio, P.; Rito, T.; Soares, P.. "Phylogenomics and functional annotation of 530 non-Saccharomyces yeasts from winemaking environments reveals their fermentome and flavorome". Studies in Mycology (2025): https://doi.org/10.3114/sim.2025.111.01. 10.3114/sim.2025.111.01 Osório, C.; Fernandes, T.; Rito, T.; Soares, P.; Franco-Duarte, R.; Sousa, M.J.. "Adaptive Laboratory Evolution Uncovers Potential Role of a DNA Helicase Mutation in Torulaspora delbrueckii Increased Sulphite Resistance". Environmental Microbiology 27 2 (2025): https://www.scopus.com/inward/record.url?eid=2-s2.0-85216520518&partnerID=MN8TOARS. 10.1111/1462-2920.70038 Franco-Duarte, R.; Saati-Santamaría, Z.; Choowong, P.; Dharmarathne, G.; Menéndez, E.; Soares, P.; Rito, T.; et al. "Oral-associated bacteria in the gut microbiome of individuals with type 2 diabetes: a secondary analysis of metagenomic data". BMC Oral Health 25 1 (2025): https://www.scopus.com/inward/record.url?eid=2-s2.0-105025109924&partnerID=MN8TOARS. 10.1186/s12903-025-07285-4 Almeida, M.; Gandini, F.; Rito, T.; Foody, M.G.; Brandão, A.; Oliveira, M.; Olivieri, A.; et al. "Leveraging known Pacific colonisation times to test models for the ancestry of Southeast Asians". Scientific Reports 15 1 (2025): https://www.scopus.com/inward/record.url?eid=2-s2.0-105019493212&partnerID=MN8TOARS. 10.1038/s41598-025-20856-3 Fontes, J.T.; Mokhtar-Jamaï, K.; Nchioua, Z.; Durand, J.-D.; Landi, M.; Meira, J.; Machado, L.; et al. "Phylogeography of the widely distributed John Dory (Zeus faber, Actinopterygii: Zeiformes) reaffirms the prevalence of at least two deeply divergent clades". Journal of Fish Biology (2025): https://www.scopus.com/inward/record.url?eid=2-s2.0-105018500306&partnerID=MN8TOARS. 10.1111/jfb.70245 João T. Fontes; Kazutaka Katoh; Rui Pires; Pedro Soares; Filipe O. Costa. "Benchmarking the discrimination power of commonly used markers and amplicons in marine fish (e)DNA (meta)barcoding". Metabarcoding and Metagenomics (2024): https://doi.org/10.3897/mbmg.8.128646. 10.3897/mbmg.8.128646 Chopra, A.; Franco-Duarte, R.; Rajagopal, A.; Choowong, P.; Soares, P.; Rito, T.; Eberhard, J.; Jayasinghe, T.N.. "Exploring the presence of oral bacteria in non-oral sites of patients with cardiovascular diseases using whole metagenomic data". Scientific Reports 14 1 (2024): https://www.scopus.com/inward/record.url?eid=2-s2.0-85182442795&partnerID=MN8TOARS. 10.1038/s41598-023-50891-x Henriques, Paulo; Rosa, Alexandra; Caldeira-Araújo, Helena; Soares, Pedro; Vigário, Ana Margarida. "Flying under the radar – impact and factors influencing asymptomatic DENV infections". Frontiers in Cellular and Infection Microbiology 13 (2023): http://dx.doi.org/10.3389/fcimb.2023.1284651. 10.3389/fcimb.2023.1284651 Santos-Pereira, Cátia; Sousa, Joana; Costa, Ângela M. A.; Santos, Andréia O.; Rito, Teresa; Soares, Pedro; Franco-Duarte, Ricardo; Silvério, Sara C.; Rodrigues, Lígia R.. "Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples". Applied Microbiology and Biotechnology 107 17 (2023): 5379-5401. http://dx.doi.org/10.1007/s00253-023-12627-9. 10.1007/s00253-023-12627-9 Teresa Rito; Pedro Fernandes; Raquel Duarte; Pedro Soares. "Evaluating Data Sharing of SARS-CoV-2 Genomes for Molecular Epidemiology across the COVID-19 Pandemic". Viruses (2023): https://doi.org/10.3390/v15020560. 10.3390/v15020560 Alves, J.; Sousa-Silva, M.; Soares, P.; Sauer, M.; Casal, M.; Soares-Silva, I.. "Structural characterization of the Aspergillus niger citrate transporter CexA uncovers the role of key residues S75, R192 and Q196". Computational and Structural Biotechnology Journal 21 (2023): 2884-2898. http://dx.doi.org/10.1016/j.csbj.2023.04.025. 10.1016/j.csbj.2023.04.025 Dulias, Katharina; Foody, M. George B.; Justeau, Pierre; Silva, Marina; Martiniano, Rui; Oteo-García, Gonzalo; Fichera, Alessandro; et al. "Ancient DNA at the edge of the world: Continental immigration and the persistence of Neolithic male lineages in Bronze Age Orkney". Proceedings of the National Academy of Sciences 119 8 (2022): http://dx.doi.org/10.1073/pnas.2108001119. 10.1073/pnas.2108001119 Sousa-Silva, Maria; Soares, Pedro; Alves, João; Vieira, Daniel; Casal, Margarida; Soares-Silva, Isabel. "Uncovering Novel Plasma Membrane Carboxylate Transporters in the Yeast Cyberlindnera jadinii". Journal of Fungi 8 1 (2022): 51. http://dx.doi.org/10.3390/jof8010051. 10.3390/jof8010051 Franco-Duarte, R.; Cadež, N.; Rito, T.; Drumonde-Neves, J.; Reyes Dominguez, Y.; Pais, C.; Sousa, M.J.; Soares, P.. "Whole-Genome Sequencing and Annotation of the Yeast Clavispora santaluciae Reveals Important Insights about Its Adaptation to the Vineyard Environment". Journal of Fungi 8 1 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85122315030&partnerID=MN8TOARS. 10.3390/jof8010052 Silva, M.; Pontes, A.; Franco-Duarte, R.; Soares, P.; Sampaio, J.P.; Sousa, M.J.; Brito, P.H.. "A glimpse at an early stage of microbe domestication revealed in the variable genome of Torulaspora delbrueckii, an emergent industrial yeast". Molecular Ecology (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85127231383&partnerID=MN8TOARS. 10.1111/mec.16428 Sá, L.; Almeida, M.; Azonbakin, S.; Matos, E.; Franco-Duarte, R.; Gómez-Carballa, A.; Salas, A.; et al. "Phylogeography of Sub-Saharan Mitochondrial Lineages Outside Africa Highlights the Roles of the Holocene Climate Changes and the Atlantic Slave Trade". International Journal of Molecular Sciences 23 16 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85137125154&partnerID=MN8TOARS. 10.3390/ijms23169219 Sousa-Silva, M.; Vieira, D.; Soares, P.; Casal, M.; Soares-Silva, I.. "Expanding the knowledge on the skillful yeast cyberlindnera jadinii". Journal of Fungi 7 1 (2021): 1-19. http://www.scopus.com/inward/record.url?eid=2-s2.0-85099849781&partnerID=MN8TOARS. 10.3390/jof7010036 Fontes, J.T.; Vieira, P.E.; Ekrem, T.; Soares, P.; Costa, F.O.. "BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries". Molecular Ecology Resources 21 2 (2021): 573-583. http://www.scopus.com/inward/record.url?eid=2-s2.0-85094624838&partnerID=MN8TOARS. 10.1111/1755-0998.13262 Silva, M.; Oteo-García, G.; Martiniano, R.; Guimarães, J.; von Tersch, M.; Madour, A.; Shoeib, T.; et al. "Biomolecular insights into North African-related ancestry, mobility and diet in eleventh-century Al-Andalus". Scientific Reports 11 1 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85114864613&partnerID=MN8TOARS. 10.1038/s41598-021-95996-3 Santiago, C.; Rito, T.; Vieira, D.; Fernandes, T.; Pais, C.; Sousa, M.J.; Soares, P.; Franco-Duarte, R.. "Improvement of torulaspora delbrueckii genome annotation: Towards the exploitation of genomic features of a biotechnologically relevant yeast". Journal of Fungi 7 4 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85104939809&partnerID=MN8TOARS. 10.3390/jof7040287 Fernandes, T.; Silva-Sousa, F.; Pereira, F.; Rito, T.; Soares, P.; Franco-Duarte, R.; Sousa, M.J.. "Biotechnological importance of torulaspora delbrueckii: From the obscurity to the spotlight". Journal of Fungi 7 9 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85114321282&partnerID=MN8TOARS. 10.3390/jof7090712 Teresa Rito; MARTIN RICHARDS; Maria Pala; Margarida Correia-Neves; Pedro Soares. "Phylogeography of 27,000 SARS-CoV-2 Genomes: Europe as the Major Source of the COVID-19 Pandemic". Microorganisms (2020): https://www.mdpi.com/2076-2607/8/11/1678. 10.3390/microorganisms8111678 Alves, R.; Sousa-Silva, M.; Vieira, D.; Soares, P.; Chebaro, Y.; Lorenz, M.C.; Casal, M.; Soares-Silva, I.; Paiva, S.. "Carboxylic acid transporters in candida pathogenesis". mBio 11 3 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85084552559&partnerID=MN8TOARS. 10.1128/mBio.00156-20 Inlamea, O.F.; Soares, P.; Ikuta, C.Y.; Heinemann, M.B.; Achá, S.J.; Machado, A.; Neto, J.S.F.; Correia-Neves, M.; Rito, T.. "Evolutionary analysis of mycobacterium bovis genotypes across africa suggests co-evolution with livestock and humans". PLoS Neglected Tropical Diseases 14 3 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85082098474&partnerID=MN8TOARS. 10.1371/journal.pntd.0008081 Vieira, D.; Esteves, S.; Santiago, C.; Conde-Sousa, E.; Fernandes, T.; Pais, C.; Soares, P.; Franco-Duarte, R.. "Population analysis and evolution of saccharomyces cerevisiae mitogenomes". Microorganisms 8 7 (2020): 1-22. http://www.scopus.com/inward/record.url?eid=2-s2.0-85090711549&partnerID=MN8TOARS. 10.3390/microorganisms8071001 Ribas, D.; Soares-Silva, I.; Vieira, D.; Sousa-Silva, M.; Sá-Pessoa, J.; Azevedo-Silva, J.; Viegas, S.C.; et al. "The acetate uptake transporter family motif “NPAPLGL(M/S)” is essential for substrate uptake". Fungal Genetics and Biology 122 (2019): 1-10. http://www.scopus.com/inward/record.url?eid=2-s2.0-85055317896&partnerID=MN8TOARS. 10.1016/j.fgb.2018.10.001 Macaulay, V.; Soares, P.; Richards, M.B.. "Rectifying long-standing misconceptions about the ¿ statistic for molecular dating". PLoS ONE 14 2 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85061852660&partnerID=MN8TOARS. 10.1371/journal.pone.0212311 Silva, M.; Justeau, P.; Rodrigues, S.; Oteo-Garcia, G.; Dulias, K.; Foody, G.; Fichera, A.; et al. "Untangling Neolithic and Bronze Age mitochondrial lineages in South Asia". Annals of Human Biology 46 2 (2019): 140-144. http://www.scopus.com/inward/record.url?eid=2-s2.0-85068616086&partnerID=MN8TOARS. 10.1080/03014460.2019.1623319 Brucato, N.; Fernandes, V.; Kusuma, P.; Cerny, V.; Mulligan, C.J.; Soares, P.; Rito, T.; et al. "Evidence of Austronesian Genetic Lineages in East Africa and South Arabia: Complex Dispersal from Madagascar and Southeast Asia". Genome Biology and Evolution 11 3 (2019): 748-758. http://www.scopus.com/inward/record.url?eid=2-s2.0-85063277878&partnerID=MN8TOARS. 10.1093/gbe/evz028 Olalde, I.; Mallick, S.; Patterson, N.; Rohland, N.; Villalba-Mouco, V.; Silva, M.; Dulias, K.; et al. "The genomic history of the Iberian Peninsula over the past 8000 years". Science 363 6432 (2019): 1230-1234. http://www.scopus.com/inward/record.url?eid=2-s2.0-85063000762&partnerID=MN8TOARS. 10.1126/science.aav4040 Rito, T.; Vieira, D.; Silva, M.; Conde-Sousa, E.; Pereira, L.; Mellars, P.; Richards, M.B.; Soares, P.. "A dispersal of Homo sapiens from southern to eastern Africa immediately preceded the out-of-Africa migration". Scientific Reports 9 1 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85063327488&partnerID=MN8TOARS. 10.1038/s41598-019-41176-3 Vieira, P.E.; Desiderato, A.; Holdich, D.M.; Soares, P.; Creer, S.; Carvalho, G.R.; Costa, F.O.; Queiroga, H.. "Deep segregation in the open ocean: Macaronesia as an evolutionary hotspot for low dispersal marine invertebrates". Molecular Ecology 28 7 (2019): 1784-1800. http://www.scopus.com/inward/record.url?eid=2-s2.0-85064525493&partnerID=MN8TOARS. 10.1111/mec.15052 Silva, M.; Koch, J.T.; Pala, M.; Edwards, C.J.; Soares, P.; Richards, M.B.. "On Methodological issues in the Indo-European debate By Michel Danino". Journal of Biosciences 44 3 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85068734509&partnerID=MN8TOARS. 10.1007/s12038-019-9890-6 Rito, T.; Ferreira, J.; Cavadas, B.; Soares, P.; Oliveira, O.; Richards, M.B.; Duarte, R.; Pereira, L.; Correia-Neves, M.. "Association of leukotriene A4 hydrolase with tuberculosis susceptibility using genomic data in Portugal". Microorganisms 7 12 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85078610005&partnerID=MN8TOARS. 10.3390/microorganisms7120650 Dulias, K.; Birch, S.; Wilson, J.F.; Justeau, P.; Gandini, F.; Flaquer, A.; Soares, P.; et al. "Maternal relationships within an Iron Age burial at the High Pasture Cave, Isle of Skye, Scotland". Journal of Archaeological Science 110 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85072012574&partnerID=MN8TOARS. 10.1016/j.jas.2019.104978 Vieira, Pedro; Soares, Pedro; Queiroga, Henrique; Costa, Filipe. "Evolutionary insights derived from comprehensive analyses of DNA barcoding diversity in marine members of the superorder Peracarida (Crustacea: Malacostraca)". Frontiers in Marine Science 6 (2019): http://dx.doi.org/10.3389/conf.fmars.2019.08.00058. Published • 10.3389/conf.fmars.2019.08.00058 Marina Silva; Marisa Oliveira; Daniel Vieira; Andreia Brandão; Teresa Rito; Joana B. Pereira; Ross M. Fraser; et al. "A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals". BMC Evolutionary Biology 17 1 (2017): https://doi.org/10.1186%2Fs12862-017-0936-9. 10.1186/s12862-017-0936-9 Sahakyan, H.; Kashani, B.H.; Tamang, R.; Kushniarevich, A.; Francis, A.; Costa, M.D.; Pathak, A.K.; et al. "Origin and spread of human mitochondrial DNA haplogroup U7". Scientific Reports 7 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85017234632&partnerID=MN8TOARS. 10.1038/srep46044 Olivieri, A.; Sidore, C.; Achilli, A.; Angius, A.; Posth, C.; Furtwängler, A.; Brandini, S.; et al. "Mitogenome Diversity in Sardinians: A Genetic Window onto an Island's Past". Molecular Biology and Evolution 34 5 (2017): 1230-1239. http://www.scopus.com/inward/record.url?eid=2-s2.0-85019115396&partnerID=MN8TOARS. 10.1093/molbev/msx082 Sierra, B.; Triska, P.; Soares, P.; Garcia, G.; Perez, A.B.; Aguirre, E.; Oliveira, M.; et al. "OSBPL10, RXRA and lipid metabolism confer African-ancestry protection against dengue haemorrhagic fever in admixed CUBANS". PLoS Pathogens 13 2 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85014104562&partnerID=MN8TOARS. 10.1371/journal.ppat.1006220 Pereira, J.B.; Costa, M.D.; Vieira, D.; Pala, M.; Bamford, L.; Harich, N.; Cherni, L.; et al. "Reconciling evidence from ancient and contemporary genomes: A major source for the European Neolithic within Mediterranean Europe". Proceedings of the Royal Society B: Biological Sciences 284 1851 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85016117668&partnerID=MN8TOARS. 10.1098/rspb.2016.1976 L. M. Oliveira; T. Knebelsberger; M. Landi; P. Soares; M. J. Raupach; F. O. Costa. "Assembling and auditing a comprehensive DNA barcode reference library for European marine fishes". Journal of Fish Biology (2016): http://dx.doi.org/10.1111/jfb.13169. 10.1111/jfb.13169 Gandini, F.; Achilli, A.; Pala, M.; Bodner, M.; Brandini, S.; Huber, G.; Egyed, B.; et al. "Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes". Scientific Reports 6 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84966320652&partnerID=MN8TOARS. 10.1038/srep25472 Brandão, A.; Eng, K.K.; Rito, T.; Cavadas, B.; Bulbeck, D.; Gandini, F.; Pala, M.; et al. "Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia". Human Genetics 135 4 (2016): 363-376. http://www.scopus.com/inward/record.url?eid=2-s2.0-84957947895&partnerID=MN8TOARS. 10.1007/s00439-016-1640-3 Soares, P.A.; Trejaut, J.A.; Rito, T.; Cavadas, B.; Hill, C.; Eng, K.K.; Mormina, M.; et al. "Resolving the ancestry of Austronesian-speaking populations". Human Genetics 135 3 (2016): 309-326. http://www.scopus.com/inward/record.url?eid=2-s2.0-84958777413&partnerID=MN8TOARS. 10.1007/s00439-015-1620-z Richards, M.B.; Soares, P.; Torroni, A.. "Palaeogenomics: Mitogenomes and migrations in Europe's past". Current Biology 26 6 (2016): R243-R246. http://www.scopus.com/inward/record.url?eid=2-s2.0-84962590921&partnerID=MN8TOARS. 10.1016/j.cub.2016.01.044 Gomes, V.; Pala, M.; Salas, A.; Álvarez-Iglesias, V.; Amorim, A.; Gómez-Carballa, A.; Carracedo, Á.; et al. "Mosaic maternal ancestry in the Great Lakes region of East Africa". Human Genetics 134 9 (2015): 1013-1027. http://www.scopus.com/inward/record.url?eid=2-s2.0-84938953750&partnerID=MN8TOARS. 10.1007/s00439-015-1583-0 Fernandes, V.; Triska, P.; Pereira, J.B.; Alshamali, F.; Rito, T.; Machado, A.; Fajkošová, Z.; et al. "Genetic stratigraphy of key demographic events in Arabia". PLoS ONE 10 3 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84928905713&partnerID=MN8TOARS. 10.1371/journal.pone.0118625 Triska, P.; Soares, P.; Patin, E.; Fernandes, V.; Cerny, V.; Pereira, L.. "Extensive admixture and selective pressure across the sahel belt". Genome Biology and Evolution 7 12 (2015): 3484-3495. http://www.scopus.com/inward/record.url?eid=2-s2.0-84982150804&partnerID=MN8TOARS. 10.1093/gbe/evv236 Silva, M.; Alshamali, F.; Silva, P.; Carrilho, C.; Mandlate, F.; Jesus Trovoada, M.; Cerny, V.; Pereira, L.; Soares, P.. "60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2". Scientific Reports 5 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84938117675&partnerID=MN8TOARS. 10.1038/srep12526 Cavadas, B.; Soares, P.; Camacho, R.; Brandão, A.; Costa, M.D.; Fernandes, V.; Pereira, J.B.; et al. "Fine Time Scaling of Purifying Selection on Human Nonsynonymous mtDNA Mutations Based on the Worldwide Population Tree and Mother-Child Pairs". Human Mutation 36 11 (2015): 1100-1111. http://www.scopus.com/inward/record.url?eid=2-s2.0-84944036873&partnerID=MN8TOARS. 10.1002/humu.22849 Hernández, C.L.; Soares, P.; Dugoujon, J.M.; Novelletto, A.; Rodríguez, J.N.; Rito, T.; Oliveira, M.; et al. "Early holocenic and historic mtDNA African signatures in the Iberian Peninsula: The Andalusian region as a paradigm". PLoS ONE 10 10 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84949845601&partnerID=MN8TOARS. 10.1371/journal.pone.0139784 Pereira, L.; Soares, P.; Triska, P.; Rito, T.; Van Der Waerden, A.; Li, B.; Radivojac, P.; Samuels, D.C.. "Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential". Scientific Reports 4 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84923322985&partnerID=MN8TOARS. 10.1038/srep07155 Rito, T.; Richards, M.B.; Fernandes, V.; Alshamali, F.; Cerny, V.; Pereira, L.; Soares, P.. "The first modern human dispersals across Africa". PLoS ONE 8 11 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84893421368&partnerID=MN8TOARS. 10.1371/journal.pone.0080031 Podgorná, E.; Soares, P.; Pereira, L.; Cerný, V.. "The genetic impact of the lake chad basin population in north africa as documented by mitochondrial diversity and internal variation of the L3e5 haplogroup". Annals of Human Genetics 77 6 (2013): 513-523. http://www.scopus.com/inward/record.url?eid=2-s2.0-84892979417&partnerID=MN8TOARS. 10.1111/ahg.12040 Soares, P.; Abrantes, D.; Rito, T.; Thomson, N.; Radivojac, P.; Li, B.; Macaulay, V.; Samuels, D.C.; Pereira, L.. "Evaluating Purifying Selection in the Mitochondrial DNA of Various Mammalian Species". PLoS ONE 8 3 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84875280073&partnerID=MN8TOARS. 10.1371/journal.pone.0058993 Mellars, P.; Gori, K.C.; Carr, M.; Soares, P.A.; Richards, M.B.. "Genetic and archaeological perspectives on the initial modern human colonization of southern Asia". Proceedings of the National Academy of Sciences of the United States of America 110 26 (2013): 10699-10704. http://www.scopus.com/inward/record.url?eid=2-s2.0-84879512750&partnerID=MN8TOARS. 10.1073/pnas.1306043110 Martins, R.G.; Nunes, J.B.; Máximo, V.; Soares, P.; Peixoto, J.; Catarino, T.; Rito, T.; et al. "A founder SDHB mutation in Portuguese paraganglioma patients". Endocrine-Related Cancer 20 6 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84891402383&partnerID=MN8TOARS. 10.1530/ERC-12-0399 Costa, M.D.; Pereira, J.B.; Pala, M.; Fernandes, V.; Olivieri, A.; Achilli, A.; Perego, U.A.; et al. "A substantial prehistoric european ancestry amongst ashkenazi maternal lineages". Nature Communications 4 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84885452665&partnerID=MN8TOARS. 10.1038/ncomms3543 Fernandes, V.; Alshamali, F.; Alves, M.; Costa, M.D.; Pereira, J.B.; Silva, N.M.; Cherni, L.; et al. "The Arabian cradle: Mitochondrial relicts of the first steps along the Southern route out of Africa". American Journal of Human Genetics 90 2 (2012): 347-355. http://www.scopus.com/inward/record.url?eid=2-s2.0-84857046912&partnerID=MN8TOARS. 10.1016/j.ajhg.2011.12.010 Soares, P.; Alshamali, F.; Pereira, J.B.; Fernandes, V.; Silva, N.M.; Afonso, C.; Costa, M.D.; et al. "The expansion of mtDNA haplogroup L3 within and out of Africa". Molecular Biology and Evolution 29 3 (2012): 915-927. http://www.scopus.com/inward/record.url?eid=2-s2.0-84857059207&partnerID=MN8TOARS. 10.1093/molbev/msr245 Al-Abri, A.; Podgorná, E.; Rose, J.I.; Pereira, L.; Mulligan, C.J.; Silva, N.M.; Bayoumi, R.; Soares, P.; Cerný, V.. "Pleistocene-Holocene boundary in Southern Arabia from the perspective of human mtDNA variation". American Journal of Physical Anthropology 149 2 (2012): 291-298. http://www.scopus.com/inward/record.url?eid=2-s2.0-84866345742&partnerID=MN8TOARS. 10.1002/ajpa.22131 Pereira, L.; Soares, P.; Máximo, V.; Samuels, D.C.. "Somatic mitochondrial DNA mutations in cancer escape purifying selection and high pathogenicity mutations lead to the oncocytic phenotype: Pathogenicity analysis of reported somatic mtDNA mutations in tumors". BMC Cancer 12 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84856420412&partnerID=MN8TOARS. 10.1186/1471-2407-12-53 Pala, M.; Olivieri, A.; Achilli, A.; Accetturo, M.; Metspalu, E.; Reidla, M.; Tamm, E.; et al. "Mitochondrial DNA signals of late glacial recolonization of europe from near eastern refugia". American Journal of Human Genetics 90 5 (2012): 915-924. http://www.scopus.com/inward/record.url?eid=2-s2.0-84860740251&partnerID=MN8TOARS. 10.1016/j.ajhg.2012.04.003 Achilli, A.; Olivieri, A.; Soares, P.; Lancioni, H.; Kashani, B.H.; Perego, U.A.; Nergadze, S.G.; et al. "Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication". Proceedings of the National Academy of Sciences of the United States of America 109 7 (2012): 2449-2454. http://www.scopus.com/inward/record.url?eid=2-s2.0-84857124895&partnerID=MN8TOARS. 10.1073/pnas.1111637109 Soares, P.; Rito, T.; Trejaut, J.; Mormina, M.; Hill, C.; Tinkler-Hundal, E.; Braid, M.; et al. "Ancient voyaging and polynesian origins". American Journal of Human Genetics 88 2 (2011): 239-247. http://www.scopus.com/inward/record.url?eid=2-s2.0-79851514728&partnerID=MN8TOARS. 10.1016/j.ajhg.2011.01.009 Pereira, L.; Soares, P.; Radivojac, P.; Li, B.; Samuels, D.C.. "Comparing phylogeny and the predicted pathogenicity of protein variations reveals equal purifying selection across the global human mtDNA diversity". American Journal of Human Genetics 88 4 (2011): 433-439. http://www.scopus.com/inward/record.url?eid=2-s2.0-79953706954&partnerID=MN8TOARS. 10.1016/j.ajhg.2011.03.006 Musilová, E.; Fernandes, V.; Silva, N.M.; Soares, P.; Alshamali, F.; Harich, N.; Cherni, L.; et al. "Population history of the Red Sea-genetic exchanges between the Arabian Peninsula and East Africa signaled in the mitochondrial DNA HV1 haplogroup". American Journal of Physical Anthropology 145 4 (2011): 592-598. http://www.scopus.com/inward/record.url?eid=2-s2.0-79960153689&partnerID=MN8TOARS. 10.1002/ajpa.21522 Erný, V.; Pereira, L.; Musilová, E.; Kujanová, M.; Vašíková, A.; Blasi, P.; Garofalo, L.; et al. "Genetic structure of pastoral and farmer populations in the African Sahel". Molecular Biology and Evolution 28 9 (2011): 2491-2500. http://www.scopus.com/inward/record.url?eid=2-s2.0-80052146246&partnerID=MN8TOARS. 10.1093/molbev/msr067 Chaubey, G.; Metspalu, M.; Choi, Y.; Mägi, R.; Romero, I.G.; Soares, P.; Van Oven, M.; et al. "Population genetic structure in indian austroasiatic speakers: The role of landscape barriers and sex-specific admixture". Molecular Biology and Evolution 28 2 (2011): 1013-1024. http://www.scopus.com/inward/record.url?eid=2-s2.0-78751529248&partnerID=MN8TOARS. 10.1093/molbev/msq288 Pereira, L.; Silva, N.M.; Franco-Duarte, R.; Fernandes, V.; Pereira, J.B.; Costa, M.D.; Martins, H.; et al. "Population expansion in the North African Late Pleistocene signalled by mitochondrial DNA haplogroup U6". BMC Evolutionary Biology 10 1 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-78650287512&partnerID=MN8TOARS. 10.1186/1471-2148-10-390 Soares, P.; Achilli, A.; Semino, O.; Davies, W.; Macaulay, V.; Bandelt, H.-J.; Torroni, A.; Richards, M.B.. "The Archaeogenetics of Europe". Current Biology 20 4 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-76749111003&partnerID=MN8TOARS. 10.1016/j.cub.2009.11.054 Dhandapany, P.S.; Sadayappan, S.; Xue, Y.; Powell, G.T.; Rani, D.S.; Nallari, P.; Rai, T.S.; et al. "A common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia". Nature Genetics 41 2 (2009): 187-191. http://www.scopus.com/inward/record.url?eid=2-s2.0-59149087665&partnerID=MN8TOARS. 10.1038/ng.309 Soares, P.; Ermini, L.; Thomson, N.; Mormina, M.; Rito, T.; Röhl, A.; Salas, A.; et al. "Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock". American Journal of Human Genetics 84 6 (2009): 740-759. http://www.scopus.com/inward/record.url?eid=2-s2.0-66749153836&partnerID=MN8TOARS. 10.1016/j.ajhg.2009.05.001 Ermini, L.; Olivieri, C.; Rizzi, E.; Corti, G.; Bonnal, R.; Soares, P.; Luciani, S.; et al. "Complete Mitochondrial Genome Sequence of the Tyrolean Iceman". Current Biology 18 21 (2008): 1687-1693. http://www.scopus.com/inward/record.url?eid=2-s2.0-55549099553&partnerID=MN8TOARS. 10.1016/j.cub.2008.09.028 Pereira, F.; Soares, P.; Carneiro, J.; Pereira, L.; Richards, M.B.; Samuels, D.C.; Amorim, A.. "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 Pereira, F.; Carneiro, J.; Soares, P.; Maciel, S.; Nejmeddine, F.; Lenstra, J.A.; 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 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 Soares, P.; Trejaut, J.A.; Loo, J.-H.; Hill, C.; Mormina, M.; Lee, C.-L.; Chen, Y.-M.; et al. "Climate change and postglacial human dispersals in Southeast Asia". Molecular Biology and Evolution 25 6 (2008): 1209-1218. http://www.scopus.com/inward/record.url?eid=2-s2.0-44649179942&partnerID=MN8TOARS. 10.1093/molbev/msn068 Hill, C.; Soares, P.; Mormina, M.; Macaulay, V.; Clarke, D.; Blumbach, P.B.; Vizuete-Forster, M.; et al. "A mitochondrial stratigraphy for Island Southeast Asia". American Journal of Human Genetics 80 1 (2007): 29-43. http://www.scopus.com/inward/record.url?eid=2-s2.0-33846004483&partnerID=MN8TOARS. 10.1086/510412 Azevedo, L.; Soares, P.A.; Quental, R.; Vilarinho, L.; Teles, E.L.; Martins, E.; Diogo, L.; et al. "Mutational spectrum and linkage disequilibrium patterns at the ornithine transcarbamylase gene (OTC)". Annals of Human Genetics 70 6 (2006): 797-801. http://www.scopus.com/inward/record.url?eid=2-s2.0-33749539324&partnerID=MN8TOARS. 10.1111/j.1469-1809.2006.00283.x Hill, C.; Soares, P.; Mormina, M.; Macaulay, V.; Meehan, W.; Blackburn, J.; Clarke, D.; et al. "Phylogeography and ethnogenesis of aboriginal Southeast Asians". Molecular Biology and Evolution 23 12 (2006): 2480-2491. http://www.scopus.com/inward/record.url?eid=2-s2.0-33750933354&partnerID=MN8TOARS. 10.1093/molbev/msl124

Other

Dataset

Ricardo Franco-Duarte; Ticiana Fernandes; Maria João Sousa; Paula Sampaio; Teresa Rito; Pedro Soares. Phylogenomics and functional annotation of 530 non-Saccharomyces yeasts from winemaking environments reveals their Fermentome and Flavorome. 2024.
10.34622/datarepositorium/wphmjl

Activities

Oral presentation

	Presentation title	Event name Host (Event location)
2020/02/20	Learning Bioinformatics: Genetics and Evolution	IX Bioinformatics Open Day University of Minho (Braga, Portugal)
2019/11/14	Phylogeography of mtDNA haplogroup U records the history of modern humans in Europe	XV Encontro Nacional de Biologia Evolutiva CIIMAR (Porto, Portugal)
2019/09/09	Evolutionary insights derived from comprehensive analyses of DNA barcoding diversity in marine members of the superorder Peracarida (Crustacea: Malacostraca)	XX Iberian Symposium on Marine Biology Studies University of Minho (Braga, Portugal)
2019/09/06	A Genética Portuguesa: De onde vimos afinal?	Pint of Science (Braga, Portugal)
2019/06/26	An Efficient and User-Friendly Implementation of the Founder Analysis Methodology	13th International Conference. PACBB 2019 (Ávila, Spain)

Supervision

	Thesis Title Role	Degree Subject (Type) Institution / Organization
2022/11/01 - Current	The Portuguese genomic signature: a genomic characterization of the genetic structure and ancestry of Portugal Supervisor	Genomics (PhD) Universidade do Minho, Portugal
2021/01 - Current	The genomic ancestry of prehistoric human populations in Northern Portugal Supervisor of Pedro Fernandes	PhD Molecular and Environmental Biology (PhD) Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2020/11/01 - Current	Meta-species screening for genetic divergence and phylogeographic reconstruction in Atlantic marine fish species Co-supervisor	PhD in Molecular and Environmental Biology (PhD) Universidade do Minho, Portugal
2020/11 - Current	Bioinformatic approaches to the genomic and epidemiological study of hospital- and community-acquired Klebsiella pneumoniae infections Co-supervisor	PhD Molecular and Environmental Biology (PhD) Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2019/09/01 - Current	Mitochondrial DNA phylogeography of African lineages Supervisor	Master in Molecular Genetics (Master) Universidade do Minho, Portugal
2019/09/01 - Current	Understanding transmission chains and episodes of reinfection of tuberculosis through genetic characterization of Mycobacterium tuberculosis isolates Co-supervisor	Master in Molecular Genetics (Master) Universidade do Minho, Portugal
2019/09/01 - Current	Exploitation and annotation of Torulaspora delbrueckii genomes: comparison with biotechnological data Co-supervisor	Master in Bioinformatics (Master) Universidade do Minho, Portugal
2019/09 - Current	Mitochondrial DNA phylogeography of African lineages Supervisor	MSc Molecular Genetics (Master) Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2018/09/01 - Current	Pseudoautosomal regions in X and Y-chromosomes: boundaries and interactions Supervisor	Master in Molecular Genetics (Master)
2017/07/01 - Current	Comparing rates of evolution between different bacterial species Co-supervisor	Master in Bioinformatics (Master) Universidade do Minho, Portugal
2016/09/01 - Current	European Settlement by Modern Humans” Supervisor	Master in Molecular Genetics (Master) Universidade do Minho, Portugal
2022/11/01 - 2026/10/31	Tracking the first age of globalisation from Bronze Age to Medieval Eurasia Supervisor	Population Genetics (PhD) Universidade do Minho, Portugal
2022/09/01 - 2026/10/31	Mutations involved in albinism in the Angolan population Supervisor	Molecular and Environmental Biology (PhD) Universidade do Minho, Portugal
2024/09/01 - 2025/12/18	Characterising genetic determinants for Albinism in Angola Supervisor	Genética Molecular (Master) Universidade do Minho, Portugal
2024/09/01 - 2025/12/18	Understanding lactoferrin multifunctionality by analyzing its evolutionary history and interacting partners Supervisor	Bioinformática (Master) Universidade do Minho, Portugal
2021/11/01 - 2025/10/31	Tuberculosis in Portugal through time: A multidisciplinary approach to the understanding of TB Co-supervisor	PhD in Anthropology (PhD) Universidade de Coimbra, Portugal
2023/09/01 - 2025/01/16	Comparison of genomic and phenotypical traits on nosocomial Klebsiella pneumoniae Co-supervisor	Genética Molecular (Master) Universidade do Minho, Portugal
2019/12/01 - 2023/11/30	Archaeogenetics of New Guinea: Settlement and Population History Supervisor	Universidade do Minho, Portugal
2018/06/01 - 2022/06/05	Phylogeny of uniparental genetic markers and population migrations between Benin, Portugal, and São Tomé e Príncipe Co-supervisor	Population Genetics (PhD) Université d'Abomey-Calavi, Benin
2019/08/01 - 2020/09/30	Molecular evolution rates across the sweep of taxonomic diversity and hierarchy of marine fishes Co-supervisor	Master in Ecology (Master) Universidade do Minho, Portugal
2018/09/01 - 2020/01/31	Unravelling the maternal ancestry of the European Continent Supervisor	Master in Molecular Genetics (Master) Universidade do Minho, Portugal
2015/10/01 - 2020/01/31	Archaeogenetics and Palaeogenetics in the Atlantic Zone Co-supervisor	University of Huddersfield, United Kingdom
2017/09/01 - 2018/12/01	The genetic history of Micronesia using mitochondrial DNA and genome-wide data Supervisor	Master in Molecular Genetics (Master) Universidade do Minho, Portugal
2017/09/01 - 2018/12/01	Establishment of a detailed mitochondrial DNA phylogenetic tree of Saccharomyces cerevisiae and assessment of purifying selection profiles throughout the phylogeny Supervisor	Master in Forensic Genetics (Master) Universidade do Porto, Portugal
2017/09/01 - 2018/12/01	Selection on the mitochondrial haplogroup H in Homo sapiens and its putative role in protecting against sepsis Co-supervisor	Master in Molecular Genetics (Master) Universidade do Minho, Portugal
2017/09/01 - 2018/11/30	A comprehensive phylogenetic analysis of Mycobacterium tuberculosis protein-coding genes: insights into evolution, pathogenicity and drug-targets Co-supervisor	Master in Bioinformatics (Master) Universidade do Minho, Portugal
2016/09/01 - 2018/03/01	mtDNA diversity and the Archaeogenetics of the Iberian Peninsula Supervisor	Master in Applied Biochemistry (Master) Universidade do Minho, Portugal
2015/09/01 - 2016/12/01	Estimating recombination frequency throughout the human genome using a phylogenetic-based method Supervisor	Master in Bioinformatics (Master) Universidade do Minho, Portugal
2015/09/01 - 2016/11/01	Genomic and transcriptomic analyses in cancers related with viral infection Co-supervisor	Master in Bioinformatics (Master) Universidade do Minho, Portugal
2015/08 - 2016/11/01	Settlement and flooding of the ancient Sundaland continent Supervisor	Master in Molecular Genetics (Master) Universidade do Minho, Portugal
2013/03/01 - 2016/09/01	The genetic legacy of the Transatlantic Slave Trade in Europe Co-supervisor	Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2012/02/01 - 2016/06/01	Demography of Modern Humans in Southeast Asia (SEA): a Genetic Approach Co-supervisor	Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2014/09/01 - 2015/12/01	Testing the reliability of the estimated ancestral populations in human genome-wide data using different admixture algorithms Supervisor	Master in Bioinformatics (Master) Universidade do Minho, Portugal
2014/09/01 - 2015/12/01	DNA barcodes de peixes marinhos da Europa: compilação de uma biblioteca de referência validada e investigação de padrões de divergência genética Co-supervisor	Master in Ecology (Master) Universidade do Minho, Portugal
2013/09/01 - 2014/12/01	Phylogeography of mtDNA haplogroup L2 Supervisor	Master in Biodiversity, Genetics and Evolution (Master) Universidade do Porto, Portugal

Jury of academic degree

	Topic Role	Candidate name (Type of degree) Institution / Organization
2019/12/12	"Using omics to address questions in biomedical sciences: human and microbiome diversities in cancer susceptibility" (Thesis) Arguer	Bruno Cavadas (PhD) Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal