Rute Andreia Rodrigues da Fonseca (9411-AA14-5DBC)

Curriculum Vitae

Rute Andreia Rodrigues da Fonseca

Rute R da Fonseca is currently an Associate Professor at the University of Copenhagen in Denmark. Published 55 peer-reviewed papers, including 11 as corresponding author and 11 as first author. Currently supervising/co-supervising 4 PhD students. She has extensive experience using genomic data to study evolution in non-model organisms and is interested in exploring the limits of the information that can be retrieved from sequence data, and how the quality of the data affects that information. Since 2011, has been using next-generation sequencing data in both in population and comparative genomics studies, and her work with ancient DNA was referred to as ‘pioneering work‘, and setting the current ‘state-of-the-art in palaeo-population genomics’. She has also participated in projects that were at the forefront of comparative genomics, namely within the B10K consortium. A lot her recent research has focused on marine organisms, and she has recently published the best cephalopod genome currently available, that of the giant squid. Teaching in Denmark: contributions to several courses at the University of Copenhagen. International teaching: Organized and taught two 5-day workshops on NGS data analysis and Comparative Genomics, University of Santa Cruz, Brazil. Received 8 awards/individual grants, was a main PI in 2 projects and co-PI in 4 projects (total of funds raised > 2.2 million euro). Good leadership skills developed by supervising multiple students and interacting with a large network of international collaborators (co-authored papers with 566 collaborators). Several of her research papers have captured a lot of international attention including two first-authored papers, one in Nature Plants (altmetric score of 128) and a recent paper describing the genome of a giant squid (altmetric score of 501 in just 2 weeks, half of the references are from members of the public).

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Identification

Personal identification

Full name: Rute Andreia Rodrigues da Fonseca

Citation names

Rute R da Fonseca
Rute da Fonseca

Author identifiers

Ciência ID: 9411-AA14-5DBC
ORCID iD: 0000-0002-2805-4698
Google Scholar ID: PULmEX4AAAAJ
Researcher Id: F-9143-2013
Scopus Author Id: 15724255000

Knowledge fields

Natural sciences - Biological Sciences - Evolutionary Biology
Natural sciences - Biological Sciences - Biochemistry
Natural sciences - Biological Sciences - Marine Biology

Languages

Language	Speaking	Reading	Writing	Listening
English	Advanced (C1)	Advanced (C1)	Advanced (C1)	Advanced (C1)
Italian	Intermediate (B1)	Intermediate (B1)	Beginner (A1)	Intermediate (B1)
Portuguese (Mother tongue)

Education

	Degree	Classification
2014 - 2015 Concluded	Formal Pedagogic Training: Teaching and Learning in Higher Education program (Especialização pós-licenciatura) Københavns Universitet, Denmark
2006/11/06 Concluded	Química (Doutoramento) Universidade do Porto Faculdade de Ciências, Portugal "COMPUTATIONAL STUDIES ON CYTOCHROMES P450" (THESIS/DISSERTATION)	aprovada por unanimidade
2000/09/22 Concluded	Bioquímica (Licenciatura) Universidade do Porto Faculdade de Ciências, Portugal	15

Affiliation

Science

	Category Host institution	Employer
2002/02/01 - 2002/02/01	Researcher (Research)	Universidade do Porto Departamento de Química e Bioquímica, Portugal

Teaching in Higher Education

	Category Host institution	Employer
2018/05/01 - Current	Associate Professor (University Teacher)	Københavns Universitet, Denmark

2014/03/01 - 2018/02/28	Assistant (University Teacher)	København Universitet Bioinformatiok-centret, Denmark

Others

	Category Host institution	Employer
2011/03/01 - 2014/02/28	Marie Curie Postdoctoral fellow	Københavns Universitet Statens Naturhistoriske Museum, Denmark

2008/12/01 - 2011/02/28	Postdoctoral research assistant	Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal

2008/05/01 - 2008/11/30	Postdoctoral research assistant	University of California Berkeley, United States

2006/09/01 - 2008/04/30	Postdoctoral research assistant	Københavns Universitet Biologisk Institut, Denmark

2006/02/01 - 2006/08/31	Postdoctoral research assistant	Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal

2002/02/01 - 2006/02/28	Doutoramento em Química	Universidade do Porto Departamento de Química e Bioquímica, Portugal

Projects

Grant

	Designation	Funders
2008 - 2010	FCT Postdoctoral grant: Application of novel comparative genomic annotation techniques to characterize patterns of molecular evolution among related mammalian species. FCT Postdoctoral grant Post-doc Fellow	Fundação para a Ciência e a Tecnologia Concluded
2006 - 2008	EMBO fellowship: Positive selection on apoptosis related genes – implications for carcinogenesis EMBO long -term fellowship Post-doc Fellow	Gesellschaft zur Förderung der Lebenswissenschaften Heidelberg GmbH Concluded
2002 - 2006	Computational studies on cytochrome P450 1A2 Computational studies on cytochrome P450 1A2 PhD Student Fellow	Associação para a Inovação e Desenvolvimento da FCT Concluded

Contract

	Designation	Funders
2023/03/01 - 2026/02/28	The variation of Iberian sheep under domestication: an archaeogenetics study 2022.04843.PTDC 10.54499/2022.04843.PTDC Universidade de Lisboa Centro de Investigação Interdisciplinar em Sanidade Animal, Portugal Universidade de Lisboa Centro de Arqueologia, Portugal Instituto Nacional de Investigação Agrária e Veterinária, Portugal Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2019/10/01 - 2025/09/30	Plant-microbiome interactions in modern and ancient barley 9040-00314A Researcher Københavns Universitet, Denmark	Danmarks Frie Forskningsfond Natur og Univers Ongoing
2023/07/01 - 2024/12/31	Avaliação dos números de referência pré-exploração e dinâmica populacional da Sardinha-europeia Sardina pilchardus Walbaum, 1792 usando paleogenómica 2022.03142.PTDC 10.54499/2022.03142.PTDC Co-Principal Investigator (Co-PI) Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2020/01/01 - 2024/12/31	Centro Interdisciplinar de Investigação Marinha e Ambiental UIDB/04423/2020 10.54499/UIDB/04423/2020 Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2020/01/01 - 2023/12/31	Research Network in Biodiversity and Evolutionary Biology UIDB/50027/2020 10.54499/UIDB/50027/2020 UID/BIA/50027/2019 LA/P/0048/2020 10.54499/LA/P/0048/2020 UIDP/50027/2020 10.54499/UIDP/50027/2020 Universidade de Lisboa Instituto Superior de Agronomia, Portugal Fundação Gaspar Frutuoso, Portugal Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal Universidade dos Açores, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2018/09/01 - 2021/08/31	Caracterização genética de populações de bovinos para uma performance optimizada em ecossistemas Africanos LEAPAgri/0003/2017 Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2017 - 2019	Comparative opioid receptor expression and reptilian neuroanatomy NNF16OC0023494 Researcher Københavns Universitet, Denmark	Novo Nordisk Fonden Ongoing
2014 - 2017	Characterizing the differences and similarities between the genomes of industrially relevant microorganisms originating from extreme environments VKR023446 Principal investigator Københavns Universitet, Denmark	Villum Fonden Concluded
2012/05/03 - 2015/09/30	Guerra biológica: decifrando a genómica de venenos naturais e os mecanismos de resistência natural a venenos PTDC/AAC-AMB/121301/2010 Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2011/04/01 - 2014/09/30	Estudo da modelação das vias de sinalização dos retinóides e das hormonas da tiróide, por disruptores endócrinos, em invertebrados PTDC/MAR/115199/2009 Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2011 - 2014	Characterization of the enzymes involved in the metabolism of toxins and pollutants in marine invertebrates PTDC/MAR/115347/2009 Principal investigator	Fundação para a Ciência e a Tecnologia Concluded
2011 - 2014	The evolution of retinoid and thyroid hormone signaling pathways, and their modulation by endocrine disrupting chemicals in invertebrates PTDC/MAR/115199/2009 Researcher
2010/05/01 - 2013/10/31	Genómica evolutiva de cianobactérias tóxicas e estudo dos mecanismos moleculares de detoxificação de cianotoxinas em metazoários PTDC/AAC-AMB/104983/2008 Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2011 - 2013	MaizeKey Marie Curie IEF 272927 Post-doc Fellow	European Commission Seventh Framework Programme for Research and Technological Development Concluded
2010/05/01 - 2013	Evolutionary genomic analyses of toxic cyanobacteria and study of the molecular mechanisms for detoxification of cyanotoxins across metazoan species info:eu-repo/grantAgreement/FCT/5876-PPCDTI/104983/PT Researcher	Fundação para a Ciência e a Tecnologia
2007/12/01 - 2010/06/30	APPLICATION OF NOVEL COMPARATIVE GENOMIC ANNOTATION TECHNIQUES TO CHARACTERIZE PATTERNS OF MOLECULAR EVOLUTION AMONG RELATED MAMMALIAN SPECIES SFRH/BPD/26769/2006 Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2002/02/01 - 2006/01/31	ESTUDO DO MECANISMO DA REACÇÃO DO CITOCROMO P450 1A2 HUMANO SFRH/BD/7089/2001 Universidade do Porto Faculdade de Ciências, Portugal	Fundação para a Ciência e a Tecnologia Concluded

Outputs

Publications

Edited book	Genomic characterization of animal genetic resources. 2023. 10.4060/cc3079en
Journal article	Mai Duy Luu Trinh; Davide Visintainer; Jan Günther; Jeppe Thulin Østerberg; Rute R. da Fonseca; Sara Fondevilla; Max William Moog; et al. "Site-directed genotype screening for elimination of antinutritional saponins in quinoa seeds identifies TSARL1 as a master controller of saponin biosynthesis selectively in seeds". Plant Biotechnology Journal (2024): https://doi.org/10.1111/pbi.14340. 10.1111/pbi.14340 Yujing Yan; Rute R. da Fonseca; Carsten Rahbek; Michael K. Borregaard; Charles C. Davis. "A new nuclear phylogeny of the tea family (Theaceae) unravels rapid radiations in genus Camellia". Molecular Phylogenetics and Evolution (2024): http://dx.doi.org/10.1016/j.ympev.2024.108089. 10.1016/j.ympev.2024.108089 Nikolaj L. Kindtler; Sanea Sheikh; Jesper Richardy; Emilie Krogh; Lorrie Maccario; Mette Vestergård; Rute R. da Fonseca; Flemming Ekelund; Kristian H. Laursen. "Fertilizer regime and cultivar affect barley growth and rhizobiome composition". Applied Soil Ecology (2024): http://dx.doi.org/10.1016/j.apsoil.2024.105384. 10.1016/j.apsoil.2024.105384 Josefin Stiller; Shaohong Feng; Al-Aabid Chowdhury; Iker Rivas-González; David A. Duchêne; Qi Fang; Yuan Deng; et al. "Complexity of avian evolution revealed by family-level genomes". Nature (2024): http://dx.doi.org/10.1038/s41586-024-07323-1. 10.1038/s41586-024-07323-1 Xiaodong Liu; Long Lin; Mikkel-Holger S. Sinding; Laura Bertola; Kristian Hanghøj; Liam Quinn; Genís Garcia-Erill; et al. "Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations". Nature Communications (2024): http://dx.doi.org/10.1038/s41467-024-47015-y. 10.1038/s41467-024-47015-y Rute R. da Fonseca; Paula F. Campos; Alba Rey-Iglesia; Gustavo V. Barroso; Lucie A. Bergeron; Manuel Nande; Fernando Tuya; et al. "Population Genomics Reveals the Underlying Structure of the Small Pelagic European Sardine and Suggests Low Connectivity within Macaronesia". Genes (2024): https://doi.org/10.3390/genes15020170. 10.3390/genes15020170 Catarina Ginja; Silvia Guimarães; Rute R da Fonseca; Rita Rasteiro; Ricardo Rodríguez-Varela; Luciana G Simões; Cindy Sarmento; et al. "Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle". iScience 26 7 (2023): https://research-information.bris.ac.uk/en/publications/8a415239-4e3e-459f-95bd-8702df1d7dcf. 10.1016/j.isci.2023.107196 André M. Machado; André Gomes-dos-Santos; Miguel M. Fonseca; Rute R. da Fonseca; Ana Veríssimo; Mónica Felício; Ricardo Capela; et al. "A genome assembly of the Atlantic chub mackerel (Scomber colias): a valuable teleost fishing resource". Gigabyte (2022): https://doi.org/10.46471/gigabyte.40. 10.46471/gigabyte.40 Kasper Thorup; Lykke Pedersen; Rute R. da Fonseca; Babak Naimi; David Nogués-Bravo; Mario Krapp; Andrea Manica; et al. "Response of an Afro-Palearctic bird migrant to glaciation cycles". Proceedings of the National Academy of Sciences 118 52 (2021): e2023836118-e2023836118. https://doi.org/10.1073/pnas.2023836118. 10.1073/pnas.2023836118 Emily L. Cavill; Shyam Gopalakrishnan; Lara C. Puetz; Ângela M. Ribeiro; Sarah S. T. Mak; Rute R. da Fonseca; George Pacheco; et al. "Conservation genomics of the endangered Seychelles Magpie-Robin ( Copsychus sechellarum ): a unique insight into the history of a precious endemic bird". Ibis (2021): https://doi.org/10.1111/ibi.13023. 10.1111/ibi.13023 "Comparative genomics provides insights into the aquatic adaptations of mammals". Proceedings of the National Academy of Sciences 118 37 (2021): e2106080118-e2106080118. http://dx.doi.org/10.1073/pnas.2106080118. 10.1073/pnas.2106080118 André Gomes-dos-Santos; Manuel Lopes-Lima; André M Machado; António Marcos Ramos; Ana Usié; Ivan N Bolotov; Ilya V Vikhrev; et al. "The Crown Pearl: a draft genome assembly of the European freshwater pearl musselMargaritifera margaritifera(Linnaeus, 1758)". DNA Research (2021): http://dx.doi.org/10.1093/dnares/dsab002. 10.1093/dnares/dsab002 "High genetic diversity and low differentiation reflect the ecological versatility of the African leopard". Current Biology 31 9 (2021): 1862-1871.e5. http://dx.doi.org/10.1016/j.cub.2021.01.064. 10.1016/j.cub.2021.01.064 Josefin Stiller; Rute R. Fonseca; Michael E. Alfaro; Brant C. Faircloth; Nerida G. Wilson; Greg W. Rouse. "Using ultraconserved elements to track the influence of sea-level change on leafy seadragon populations". Molecular Ecology (2020): https://doi.org/10.1111/mec.15744. 10.1111/mec.15744 André M. Machado; Antonio Muñoz-Merida; Elza Fonseca; Ana Veríssimo; Rui Pinto; Mónica Felício; Rute R. da Fonseca; Elsa Froufe; L. Filipe C. Castro. "Liver transcriptome resources of four commercially exploited teleost species". Scientific Data 7 1 (2020): https://doi.org/10.1038/s41597-020-0565-9. 10.1038/s41597-020-0565-9 Gonçalo Espregueira Themudo; Alba Rey-Iglesia; Lucía Robles Tascón; Annette Bruun Jensen; Rute R. da Fonseca; Paula F. Campos. "Declining genetic diversity of European honeybees along the twentieth century". Scientific Reports (2020): https://doi.org/10.1038/s41598-020-67370-2. 10.1038/s41598-020-67370-2 Brooke L Whitelaw; Ira R Cooke; Julian Finn; Rute R da Fonseca; Elena A Ritschard; M T P Gilbert; Oleg Simakov; Jan M Strugnell. "Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss". GigaScience (2020): https://doi.org/10.1093/gigascience/giaa120. 10.1093/gigascience/giaa120 Pinto, Daniela; da Fonseca, Rute R. "Evolution of the extracytoplasmic function s factor protein family". NAR Genomics and Bioinformatics 2 1 (2020): http://dx.doi.org/10.1093/nargab/lqz026. 10.1093/nargab/lqz026 Rute R da Fonseca; Alvarina Couto; Andre M Machado; Brona Brejova; Carolin B Albertin; Filipe Silva; Paul Gardner; et al. "A draft genome sequence of the elusive giant squid, Architeuthis dux". GigaScience 9 1 (2020): https://doi.org/10.1093/gigascience/giz152. 10.1093/gigascience/giz152 Fonseca, E.; Machado, A.M.; Vilas-Arrondo, N.; Gomes-dos-Santos, A.; Veríssimo, A.; Esteves, P.; Almeida, T.; et al. "Cartilaginous fishes offer unique insights into the evolution of the nuclear receptor gene repertoire in gnathostomes". General and Comparative Endocrinology 295 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85086574669&partnerID=MN8TOARS. 10.1016/j.ygcen.2020.113527 Espregueira Themudo, G.; Alves, L.Q.; Machado, A.M.; Lopes-Marques, M.; da Fonseca, R.R.; Fonseca, M.; Ruivo, R.; Castro, L.F.C.. "Losing Genes: The Evolutionary Remodeling of Cetacea Skin". Frontiers in Marine Science 7 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85095809889&partnerID=MN8TOARS. 10.3389/fmars.2020.592375 Moreta, L.S.; da Fonseca, R.R.. "Link Your Sites (LYS) Scripts: Automated Search of Protein Structures and Mapping of Sites Under Positive Selection Detected by PAML". Evolutionary Biology 47 3 (2020): 240-245. http://www.scopus.com/inward/record.url?eid=2-s2.0-85087371351&partnerID=MN8TOARS. 10.1007/s11692-020-09507-9 Feng, S.; Stiller, J.; Deng, Y.; Armstrong, J.; Fang, Q.; Reeve, A.H.; Xie, D.; et al. "Dense sampling of bird diversity increases power of comparative genomics". Nature 587 7833 (2020): 252-257. http://www.scopus.com/inward/record.url?eid=2-s2.0-85095836366&partnerID=MN8TOARS. 10.1038/s41586-020-2873-9 Rute R. da Fonseca; Irene Ureña; Sandra Afonso; Ana Elisabete Pires; Emil Jørsboe; Lounès Chikhi; Catarina Ginja. "Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle". BMC Genomics (2019): https://doi.org/10.1186/s12864-019-5685-2. 10.1186/s12864-019-5685-2 Alba Refoyo-Martínez; Rute R. da Fonseca; Katrín Halldórsdóttir; Einar Árnason; Thomas Mailund; Fernando Racimo. "Identifying loci under positive selection in complex population histories". Genome Research (2019): https://doi.org/10.1101/gr.246777.118. 10.1101/gr.246777.118 Ribeiro, Ângela M.; Puetz, Lara; Pattinson, Nicholas B.; Dalén, Love; Deng, Yuan; Zhang, Guojie; Fonseca, Rute R.; Smit, Ben; Gilbert, M. Thomas P.. "31° South: The physiology of adaptation to arid conditions in a passerine bird". Molecular Ecology 28 16 (2019): 3709-3721. http://dx.doi.org/10.1111/mec.15176. 10.1111/mec.15176 Rute R da Fonseca. "Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits". Science (2019): http://dx.doi.org/10.1126/science.aav6202. 10.1126/science.aav6202 Ribeiro, Ângela M.; Canchaya, Carlos A.; Penaloza, Fernando; Galindo, Juan; da Fonseca, Rute R.. "Population genomic footprints of environmental pollution pressure in natural populations of the Mediterranean mussel". Marine Genomics 45 (2019): 11-15. http://dx.doi.org/10.1016/j.margen.2018.10.009. 10.1016/j.margen.2018.10.009 Lopes-Marques, Mónica; Machado, André M; Alves, Luís Q; Fonseca, Miguel M; Barbosa, Susana; Sinding, Mikkel-Holger S; Rasmussen, Marianne Helene; et al. "Complete inactivation of sebum-producing genes parallels the loss of sebaceous glands in Cetacea". Molecular Biology and Evolution (2019): http://dx.doi.org/10.1093/molbev/msz068. 10.1093/molbev/msz068 André M. Machado; Ole Kristian Tørresen; Naoki Kabeya; Alvarina Couto; Bent Petersen; Mónica Felício; Paula F. Campos; et al. "“Out of the Can”: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus". Genes (2018): http://www.mdpi.com/2073-4425/9/10/485. 10.3390/genes9100485 Machado, A.M.; Felício, M.; Fonseca, E.; da Fonseca, R.R.; Castro, L.F.C.. "A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias". Data in Brief 18 (2018): 276-284. http://www.scopus.com/inward/record.url?eid=2-s2.0-85044114889&partnerID=MN8TOARS. 10.1016/j.dib.2018.03.013 Barbosa, C.S.; da Fonseca, R.R.; Batista, T.M.; Barreto, M.A.; Argolo, C.S.; de Carvalho, M.R.; do Amaral, D.O.J.; et al. "Genome sequence and effectorome of Moniliophthora perniciosa and Moniliophthora roreri subpopulations". BMC Genomics 19 1 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85049473762&partnerID=MN8TOARS. 10.1186/s12864-018-4875-7 Gemma G. R. Murray; André E. R. Soares; Ben J. Novak; Nathan K. Schaefer; James A. Cahill; Allan J. Baker; John R. Demboski; et al. "Natural selection shaped the rise and fall of passenger pigeon genomic diversity". Science (2017): https://doi.org/10.1126/science.aao0960. 10.1126/science.aao0960 Alastair R. Tanner; Dirk Fuchs; Inger E. Winkelmann; M. Thomas P. Gilbert; M. Sabrina Pankey; Ângela M. Ribeiro; Kevin M. Kocot; et al. "Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution". Proceedings of the Royal Society B: Biological Sciences 284 1850 (2017): 20162818-20162818. https://doi.org/10.1098%2Frspb.2016.2818. 10.1098/rspb.2016.2818 Ângela M. Ribeiro; Andrew D. Foote; Anne Kupczok; Bárbara Frazão; Morten T. Limborg; Rosalía Piñeiro; Samuel Abalde; Sara Rocha; Rute R. da Fonseca. "Marine genomics: News and views". Marine Genomics 31 (2017): 1-8. https://doi.org/10.1016%2Fj.margen.2016.09.002. 10.1016/j.margen.2016.09.002 Rute R. da Fonseca; Anders Albrechtsen; Gonçalo Espregueira Themudo; Jazmín Ramos-Madrigal; Jonas Andreas Sibbesen; Lasse Maretty; M. Lisandra Zepeda-Mendoza; et al. "Next-generation biology: Sequencing and data analysis approaches for non-model organisms". Marine Genomics 30 (2016): 3-13. http://dx.doi.org/10.1016/j.margen.2016.04.012. 10.1016/j.margen.2016.04.012 Magnus W. Jacobsen; Rute R. da Fonseca; Louis Bernatchez; Michael M. Hansen. "Comparative analysis of complete mitochondrial genomes suggests that relaxed purifying selection is driving high nonsynonymous evolutionary rate of the NADH2 gene in whitefish (Coregonus ssp.)". Molecular Phylogenetics and Evolution 95 (2016): 161-170. http://dx.doi.org/10.1016/j.ympev.2015.11.008. 10.1016/j.ympev.2015.11.008 Whitelaw, B.L.; Strugnell, J.M.; Faou, P.; Da Fonseca, R.R.; Hall, N.E.; Norman, M.; Finn, J.; Cooke, I.R.. "Combined Transcriptomic and Proteomic Analysis of the Posterior Salivary Gland from the Southern Blue-Ringed Octopus and the Southern Sand Octopus". Journal of Proteome Research 15 9 (2016): 3284-3297. http://www.scopus.com/inward/record.url?eid=2-s2.0-84985961692&partnerID=MN8TOARS. 10.1021/acs.jproteome.6b00452 Alexandre Campos; Itxaso Apraiz; Rute R. da Fonseca; Susana Cristobal. "Shotgun analysis of the marine mussel Mytilus edulis hemolymph proteome and mapping the innate immunity elements". Proteomics 15 23-24 (2015): 4021-4029. http://dx.doi.org/10.1002/pmic.201500118. 10.1002/pmic.201500118 Catarina C. Azevedo; Remédios Guzmán-Guillén; José C. Martins; Hugo Osório; Vitor Vasconcelos; Rute R. da Fonseca; Alexandre Campos. "Proteomic profiling of gill GSTs in Mytilus galloprovincialis from the North of Portugal and Galicia evidences variations at protein isoform level with a possible relation with water quality". Marine Environmental Research 110 (2015): 152-161. http://dx.doi.org/10.1016/j.marenvres.2015.08.008. 10.1016/j.marenvres.2015.08.008 Ângela M. Ribeiro; M. Lisandra Zepeda-Mendoza; Mads F. Bertelsen; Annemarie T. Kristensen; Erich D. Jarvis; M. Thomas P. Gilbert; Rute R. da Fonseca. "A refined model of the genomic basis for phenotypic variation in vertebrate hemostasis". BMC Evol Biol 15 1 (2015): http://dx.doi.org/10.1186/s12862-015-0409-y. 10.1186/s12862-015-0409-y Rute R. da Fonseca; Bruce D. Smith; Nathan Wales; Enrico Cappellini; Pontus Skoglund; Matteo Fumagalli; José Alfredo Samaniego; et al. "The origin and evolution of maize in the Southwestern United States". NPLANTS 1 1 (2015): 14003-14003. http://dx.doi.org/10.1038/nplants.2014.3. 10.1038/nplants.2014.3 Rute R. da Fonseca; Bruce D. Smith; Nathan Wales; Enrico Cappellini; Pontus Skoglund; Matteo Fumagalli; José Alfredo Samaniego; et al. "Erratum: The origin and evolution of maize in the Southwestern United States". NPLANTS (2015): 15007-15007. http://dx.doi.org/10.1038/nplants.2015.7. 10.1038/nplants.2015.7 Jarvis, E.D.; Mirarab, S.; Aberer, A.J.; Li, B.; Houde, P.; Li, C.; Ho, S.Y.W.; et al. "Phylogenomic analyses data of the avian phylogenomics project". GigaScience 4 1 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84929606489&partnerID=MN8TOARS. 10.1186/s13742-014-0038-1 Sarkissian, Clio Der; Allentoft, Morten E.; Avila-Arcos, Maria C.; Barnett, Ross; Campos, Paula F.; Cappellini, Enrico; Ermini, Luca; et al. "Ancient genomics". Philosophical Transactions of the Royal Society B-Biological Sciences 370 1660 (2015): 10.1098/rstb.2013.0387 J. Melo-Ferreira; J. Vilela; M. M. Fonseca; R. R. da Fonseca; P. Boursot; P. C. Alves. "The Elusive Nature of Adaptive Mitochondrial DNA Evolution of an Arctic Lineage Prone to Frequent Introgression". Genome Biology and Evolution 6 4 (2014): 886â¿¿896-886â¿¿896. http://dx.doi.org/10.1093/gbe/evu059. 10.1093/gbe/evu059 Fiorito, Graziano; Affuso, Andrea; Anderson, David B.; Basil, Jennifer; Bonnaud, Laure; Botta, Giovanni; Cole, Alison; et al. "Cephalopods in neuroscience: regulations, research and the 3Rs". Invertebrate Neuroscience 14 1 (2014): 13-36. http://dx.doi.org/10.1007/s10158-013-0165-x. 10.1007/s10158-013-0165-x Martins, J.C.; Campos, A.; Osório, H.; da Fonseca, R.; Vasconcelos, V.. "Proteomic profiling of cytosolic glutathione transferases from three bivalve species: Corbicula fluminea, Mytilus galloprovincialis and Anodonta cygnea". International Journal of Molecular Sciences 15 2 (2014): 1887-1900. http://www.scopus.com/inward/record.url?eid=2-s2.0-84893116829&partnerID=MN8TOARS. 10.3390/ijms15021887 Jarvis, Erich D.; Mirarab, Siavash; Aberer, Andre J.; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon Y. W.; et al. "Whole-genome analyses resolve early branches in the tree of life of modern birds". Science 346 6215 (2014): 1320-1331. 10.1126/science.1253451 Zepeda Mendoza, Marie; Nygaard, Sanne; da Fonseca, Rute R. "DivA: detection of non-homologous and very divergent regions in protein sequence alignments". BMC Research Notes 7 1 (2014): 806. http://dx.doi.org/10.1186/1756-0500-7-806. 10.1186/1756-0500-7-806 Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; et al. "Comparative genomics reveals insights into avian genome evolution and adaptation". Science 346 6215 (2014): 1311-1320. 10.1126/science.1251385 Philip, Siby; Castro, L. Filipe C.; da Fonseca, Rute R.; Reis-Henriques, Maria A.; Vasconcelos, Vítor; Santos, Miguel M.; Antunes, Agostinho. "Adaptive evolution of the Retinoid X receptor in vertebrates". Genomics 99 2 (2012): 81-89. http://dx.doi.org/10.1016/j.ygeno.2011.12.001. 10.1016/j.ygeno.2011.12.001 Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus; Crookes-Goodson, Wendy J.; da Fonseca, Rute R.; Di Cristo, Carlo; Dilkes, Brian P.; et al. "Cephalopod genomics: A plan of strategies and organization". Standards in Genomic Sciences 7 1 (2012): 175-188. 10.4056/sigs.3136559 Cappellini, Enrico; Jensen, Lars J.; Szklarczyk, Damian; Ginolhac, Aurelien; da Fonseca, Rute A. R.; Stafford, Thomas W., Jr.; Holen, Steven R.; et al. "Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins". Journal of Proteome Research 11 2 (2012): 917-926. 10.1021/pr200721u Maldonado, Emanuel; Dutheil, Julien Y.; Da Fonseca, Rute R.; Vasconcelos, Vitor; Antunes, Agostinho. "IMPACT: Integrated Multiprogram Platform for Analyses in ConTest". Journal of Heredity 102 3 (2011): 366-369. 10.1093/jhered/esr003 Foote, Andrew D.; Morin, Phillip A.; Durban, John W.; Pitman, Robert L.; Wade, Paul; Willerslev, Eske; Gilbert, M. Thomas P.; da Fonseca, Rute R.. "Positive selection on the killer whale mitogenome". Biology Letters 7 1 (2011): 116-118. 10.1098/rsbl.2010.0638 da Fonseca, R.R.; Kosiol, C.; Vinar, T.; Siepel, A.; Nielsen, R.. "Positive selection on apoptosis related genes". FEBS Letters 584 3 (2010): 469-476. http://www.scopus.com/inward/record.url?eid=2-s2.0-74449088364&partnerID=MN8TOARS. 10.1016/j.febslet.2009.12.022 Marques, Jose R. F.; da Fonseca, Rute R.; Drury, Brett; Melo, Andre. "Amino Acid Patterns around Disulfide Bonds". International Journal of Molecular Sciences 11 11 (2010): 4673-4686. 10.3390/ijms11114673 Ferreira Marques, Jose Rui; da Fonseca, Rute R.; Drury, Brett; Melo, Andre. "Conformational characterization of disulfide bonds: A tool for protein classification". Journal of Theoretical Biology 267 3 (2010): 388-395. 10.1016/j.jtbi.2010.09.012 da Fonseca, Rute R.; Johnson, Warren E.; O'Brien, Stephen J.; Vasconcelos, Vitor; Antunes, Agostinho. "Molecular evolution and the role of oxidative stress in the expansion and functional diversification of cytosolic glutathione transferases". Bmc Evolutionary Biology 10 (2010): 10.1186/1471-2148-10-281 Willerslev E; Gilbert MT; Binladen J; Ho SY; Campos PF; Ratan A; Tomsho LP; et al. "Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution.". (2009): http://europepmc.org/abstract/med/19432984. 10.1186/1471-2148-9-95 Kosiol, Carolin; Vinar, Tomas; da Fonseca, Rute R.; Hubisz, Melissa J.; Bustamante, Carlos D.; Nielsen, Rasmus; Siepel, Adam. "Patterns of Positive Selection in Six Mammalian Genomes". Plos Genetics 4 8 (2008): 10.1371/journal.pgen.1000144 da Fonseca, Rute R.; Johnson, Warren E.; O'Brien, Stephen J.; Ramos, Maria Joao; Antunes, Agostinho. "The adaptive evolution of the mammalian mitochondrial genome". Bmc Genomics 9 (2008): 10.1186/1471-2164-9-119 da Fonseca, R.R.; Antunes, A.; Melo, A.; Ramos, M.J.. "Structural divergence and adaptive evolution in mammalian cytochromes P450 2C". Gene 387 1-2 (2007): 58-66. http://www.scopus.com/inward/record.url?eid=2-s2.0-33845624599&partnerID=MN8TOARS. 10.1016/j.gene.2006.08.017 Joao Ramos, Maria; Iori, Francesco; Cristina Menziani, Maria; Melo, Andre; Rute da Fonseca, Bentham Science Publisher. "Molecular Interactions Between Human Cytochrome P450 1A2 and Flavone Derivatives". Medicinal Chemistry 2 4 (2006): 401-406. http://dx.doi.org/10.2174/157340606777723988. 10.2174/157340606777723988 Rute Fonseca; Michele Marini; Andre Melo; Maria Menziani; Maria Ramos. "Computational Insight into Anti-mutagenic Properties of CYP1A Flavonoid Ligands". MC 1 4 (2005): 355-360. http://dx.doi.org/10.2174/1573406054368729. 10.2174/1573406054368729 Iori, F.; Da Fonseca, R.; João Ramos, M.; Menziani, M.C.. "Theoretical quantitative structure-activity relationships of flavone ligands interacting with cytochrome P450 1A1 and 1A2 isozymes". Bioorganic and Medicinal Chemistry 13 14 (2005): 4366-4374. http://www.scopus.com/inward/record.url?eid=2-s2.0-20444481352&partnerID=MN8TOARS. 10.1016/j.bmc.2005.04.066 Da Fonseca, R.; Menziani, M. C.; Melo, A.; Ramos, M. J.. "Modelling the metabolic action of human and rat CYP1A2 and its relationship with the carcinogenicity of heterocyclic amines". Molecular Physics 101 17 (2003): 2731-2741. 10.1080/00268970310001603112
Report	ICES. 2024. Working Group on the Application of Genetics for Fisheries and Aquaculture (WGAGFA). https://ices-library.figshare.com/articles/report/Working_Group_on_the_Application_of_Genetics_for_Fisheries_and_Aquaculture_WGAGFA_/24466417. 10.17895/ICES.PUB.24466417
Thesis / Dissertation	Fonseca, Rute A. Rodrigues da. "Computational studies on cytochromes P450". PhD, 2006. http://hdl.handle.net/10216/64285.

Other

Dataset	Gomes-dos-Santos, André; Lopes-Lima, Manuel; Andre M. Machado; Marcos Ramos, António; Usié, Ana; Ivan N Bolotov; Ilya V Vikhrev; et al. Margaritifera margaritifera whole genome assembly and annotation. 10.6084/m9.figshare.13333841
Other output	The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758). 2020. André Gomes-dos-Santos; Manuel Lopes-Lima; André M. Machado; António Marcos Ramos; Ana Usié; Ivan N. Bolotov; Ilya V. Vikhrev; et al. https://doi.org/10.1101/2020.12.06.413450. 10.1101/2020.12.06.413450

Activities

Oral presentation

	Presentation title	Event name Host (Event location)
2020/01/09	DNA from ancient maize reveals early targets of selection during domestication diffusion routes out of Mexico	Department Seminar Alessandra Carbone/Sorbonne Université (Paris, France)
2019/11/07	Comparative genomics provides insight into the evolution of hemostasis in vertebrates	“How Nature came to be: from molecules to organisms” Max Planck Institute (MPI) for Developmental Biology
2019/10/01	Comparative genomics provides insight into the evolution of hemostasis in vertebrates	RECOMB-CG 2019 (Paris, France)
2019/02/12	The genetic diversity of Atlantic and Mediterranean populations of the European sardine	IGC Lisboa (Lisboa, Portugal)
2018	Data problems in comparative genomics	G10K meeting (New York, United States)
2017	Introgression shaped hummingbird evolution	PAG XXV (San Diego, United States)
2017	A high quality genome for the giant squid	PAG XXV (San Diego, United States)
2017	Squids 2.0	CephsInAction: what next? (COST meeting) (Galway, Ireland)
2016	Hummingbird diversification: a tale of introgression	Annual Danish Bioinformatics Conference (Odense, Denmark)
2015	Detecting positive selection using genome-wide data from non-models organism: advantages and limitations	Genome-powered perspectives in integrative physiology and evolutionary biology (SEB satellite meeting) (Prague, Czech Republic)
2014	The origin and evolution of maize from the SW of the USA	SMBE meeting (San Juan, Puerto Rico)
2014	The origin and evolution of maize from the SW of the USA	ISBA6 (Basel, Switzerland)
2014	The origin and evolution of maize from the SW of the USA	9th International Conference on Genomics (Shenzen, China)

Supervision

	Thesis Title Role	Degree Subject (Type) Institution / Organization
2024/11/15 - Current	Linking environmental impacts, habitat creation and sustainable infrastructure projects Co-supervisor	Danmarks Tekniske Universitet, Denmark
2018/11 - Current	PhD: Análise da estrutura de genes e elementos regulatórios relacionados com a biossíntese de ácidos orgânicos e açúcares em Citrus spp Co-supervisor	Københavns Universitet, Denmark Universidade Estadual de Santa Cruz, Brazil
2018/08 - Current	PhD: Out of the can: genomic resources and tools to manage the European sardine, Sardina pilchardus Co-supervisor	Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal Københavns Universitet Det Natur- og Biovidenskabelige Fakultet, Denmark
2021/01/01 - 2024/06/11	Microbiome and fertilizer interactions in old and modern barley cultivars Co-supervisor	Københavns Universitet - Nørre Campus, Denmark
2022 - 2022	Are birds what they eat? Comparative genomics of avian dietary adaptations Supervisor	Biologia (PhD) Universidade do Porto Faculdade de Ciências, Portugal
2021 - 2021	Changing seas: Unravelling the genomic diversity, connectivity and climate resilience of deep-sea habitat-forming sponges Co-supervisor	Biodiversidade, Genética e Evolução (PhD) Universidade do Porto Faculdade de Ciências, Portugal
2018/07 - 2018/10	EMBO short-term fellowship. Theme: Divergent evolution and horizontal gene transfer in the extracytoplasmic function protein family Supervisor	Københavns Universitet, Denmark
2017 - 2018	MSc student in Bioinformatics (30 ECTS): Comparative genomics using capture data Supervisor	Københavns Universitet, Denmark
2017/05 - 2017/09	Postdoc: Transcriptomics of metazoan neuronal tissues Supervisor	Københavns Universitet, Denmark
2017/04 - 2017/06	7.5 ECTS project in Bioinformatics: Population genetics of bees Supervisor	Københavns Universitet Det Natur- og Biovidenskabelige Fakultet, Denmark
2016/04 - 2017/06	Research assistant: cephalopod genomics Supervisor	Universidade de Vigo, Spain
2016/09 - 2017/02	MSc student in Bioinformatics (30 ECTS): Population genomics of historical bee samples Supervisor	Københavns Universitet Det Natur- og Biovidenskabelige Fakultet, Denmark
2016/07 - 2016/09	7.5 ECTS project in Bioinformatics: Population genomics methods Supervisor	Københavns Universitet Det Natur- og Biovidenskabelige Fakultet, Denmark
2016/04 - 2016/06	7.5 ECTS project in Bioinformatics: Population genomics methods Supervisor	Københavns Universitet Det Natur- og Biovidenskabelige Fakultet, Denmark
2016 - 2016	7.5 ECTS project in Bioinformatics Co-supervisor	København Universitet Bioinformatiok-centret, Denmark
2015/04 - 2015/11	Research Assistant: The evolution of high-accuracy vision in avian species Supervisor	København Universitet Bioinformatiok-centret, Denmark
2015 - 2015	7.5 ECTS project in Bioinformatics Co-supervisor	København Universitet Bioinformatiok-centret, Denmark
2015 - 2015	Research assistant: Comparative genomics using capture data Co-supervisor	Københavns Universitet Statens Naturhistoriske Museum, Denmark
2012 - 2014	Postdoc: Population genomic footprints of environmental pollution pressure in natural populations of the Mediterranean mussel Supervisor	Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2012 - 2014	Research Assistant: Proteomic profiling of gill GSTs in Mytilus galloprovincialis Supervisor	Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2013 - 2013	Research assistant: Detecting highly divergent windows in multiple sequence alignments Co-supervisor	Københavns Universitet Statens Naturhistoriske Museum, Denmark

Jury of academic degree

	Topic Role	Candidate name (Type of degree) Institution / Organization
2019/07/02	A genome-wide study of the molecular adaptations underpinning dietary specialisations in New World leaf-nosed bats (Phyllostomidae, Chiroptera) (Thesis) Main arguer	Joshua Potter (PhD) Queen Mary University of London, United Kingdom
2019/04/29	Flying rats shall no longer be: A population genomic analysis of fancy and feral pigeons President of the jury	George Antunes Pacheco (PhD) Københavns Universitet, Denmark
2018	Ancient DNA and novel molecular methods in modern population genomics President of the jury	Alba Rey (PhD) Københavns Universitet, Denmark
2017/07	Evaluation of phylogenomic methods for species tree estimation (Thesis) Arguer	Diego Mallo Adán (PhD) Universidade de Vigo, Spain

Association member

	Society Organization name	Role
2018 - Current	The International Biogeography Society
2001 - 2010	Sociedade Portuguesa de Bioquímica

Committee member

	Activity description Role	Institution / Organization
2014 - Current	Part of the Bird10K advisory committee (consortium that aims at sequencing 10,000 avian genomes) Advisor / Consultant	Københavns Universitet, Denmark
2015 - 2017	Danish partner of COST action FA1301 Member	European Cooperation in Science and Technology, Belgium

Consulting

	Activity description	Institution / Organization
2009 - Current	Reviewer for international journals: Zoological Journal of the Linnean Society, Molecular Biology and Evolution, Molecular Ecology, PLoS One, Heredity, Marine Genomics, Journal of Ornithology, BMC Evolutionary Biology, Communications Biology and Current Biology.
2013 - 2013	Scientific advisor in the COST action SeqAhead	European Cooperation in Science and Technology, Belgium
2012 - 2012	Part of the international discussion group NESCent Catalysis meeting	National Evolutionary Synthesis Center, United States
2012 - 2012	Part of international discussion group at Cephalopods in Research	Stazione Zoologica Anton Dohrn, Italy

Course / Discipline taught

	Academic session	Degree Subject (Type)	Institution / Organization
2012/12/14 - Current	Genomic Approaches in Non-model Organisms	(Master)	Københavns Universitet, Denmark
2017/10/23 - 2017/10/27	Comparative Genomics	(Master)	Universidade Estadual de Santa Cruz, Brazil
2016/03/18 - 2016/03/29	Introduction to Bioinformatics	Biochemistry (Bachelor)	Københavns Universitet, Denmark
2016/03/16 - 2016/03/16	Population genetics	Biology (Bachelor)	Københavns Universitet, Denmark
2016/02/16 - 2016/02/16	Statistics for Molecular Biomedicine	(Bachelor)	København Universitet Bioinformatiok-centret, Denmark
2016/01/08 - 2016/01/08	Genomic Approaches in Non-model Organisms	(Master)	Københavns Universitet, Denmark
2015/11/30 - 2015/11/30	Genome Sequence Analysis	(Master)	Københavns Universitet, Denmark
2015/10/19 - 2015/10/23	Introduction to NGS data analyses, University of Santa Cruz, Brazil	Introduction to NGS data analyses (Master Universitario)	Universidade Estadual de Santa Cruz, Brazil
2015/06/03 - 2015/06/03	Population Genetics	(Bachelor)	Københavns Universitet, Denmark
2015/03/10 - 2015/03/10	Introduction to Bioinformatics	(Bachelor)	Københavns Universitet, Denmark
2014/11/24 - 2014/11/24	Statistics for Molecular Biomedicine	(Master)	Københavns Universitet, Denmark
2014/01/07 - 2014/01/07	Genomic Approaches in Non-model Organisms	(Master)	Københavns Universitet, Denmark
2012/10/01 - 2012/10/01	Genomic Approaches in Non-model Organisms	(Master)	Københavns Universitet, Denmark

Evaluation committee

	Activity description Role	Institution / Organization
2018 - 2018	Rapporteur for the Second Progress Report (PR2) of COST Action CA15112 Evaluator	European Cooperation in Science and Technology, Belgium
2017 - 2017	Grant proposal evaluation Evaluator	Fonds zur Förderung der wissenschaftlichen Forschung, Austria
2015 - 2015	Evaluator of COST action OC-2015-1-19443 Evaluator	European Cooperation in Science and Technology, Belgium

Interview (newspaper / magazine)

	Activity description	Newspaper / Forum
2020/01/16	https://www.publico.pt/2020/01/16/ciencia/noticia/genoma-lulagigante-nao-assim-tao-gigante-1900525	Publico
2018	https://www.publico.pt/2018/10/13/ciencia/noticia/eis-finalmente-o-genoma-da-sardinha-e-em-duplicado-1847297	Público
2017	https://www.publico.pt/2017/11/22/ciencia/noticia/martha-lembranos-como-uma-especie-com-milhoes-pode-ser-extinta-1793395al	Público

Other jury / evaluation

	Activity description	Institution / Organization
2018/11 - 2018/11	7.5 ECTS project: Alba Refoyo Martinez	Københavns Universitet, Denmark
2015 - 2016	Censor in Introduction to Bioinformatics. Oral examination of 54 students in 2016 and 39 students in 2015.	Københavns Universitet, Denmark
2015 - 2015	15 ECT project, MSc student Kristian Hanghoej	Københavns Universitet, Denmark
2012 - 2015	Censor in Genomic Approaches in Non-model Organisms. Oral examination: 8 students in 2015, 9 students in 2013, 7 students in 2012.	Københavns Universitet, Denmark
2012 - 2012	7.5 ECTS project: Peter de Barros Damgaard, SNM, University of Copenhagen	Københavns Universitet, Denmark
2010 - 2010	7.5 ECTS project: Mikkel Holger Strander Sinding, SNM, University of Copenhagen	Københavns Universitet, Denmark

Distinctions

Other distinction

2017	DeiC computerome grant Danish e-Infrastructure Cooperation, Denmark
2014	Villum Young Investigator Grant
2014	SMBE Travel grant Society for Molecular Biology and Evolution, United States
2010	Marie Curie Intra-European fellowship
2008	FCT Postdoc fellowship Fundação para a Ciência e a Tecnologia, Portugal
2006	EMBO Long-term fellowship Gesellschaft zur Förderung der Lebenswissenschaften Heidelberg GmbH, Germany
2006	Short-term fellowship Fundação Calouste Gulbenkian, Portugal
2001	FCT PhD scholarship Fundação para a Ciência e a Tecnologia, Portugal