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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Identificação

Identificação pessoal

Nome completo: Rute Andreia Rodrigues da Fonseca

Nomes de citação

Rute R da Fonseca
Rute da Fonseca

Identificadores de autor

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

Domínios de atuação

Ciências Naturais - Ciências Biológicas - Biologia da Evolução das Espécies
Ciências Naturais - Ciências Biológicas - Bioquímica
Ciências Naturais - Ciências Biológicas - Biologia Marinha

Idiomas

Idioma	Conversação	Leitura	Escrita	Compreensão
Inglês	Utilizador proficiente (C1)	Utilizador proficiente (C1)	Utilizador proficiente (C1)	Utilizador proficiente (C1)
Italiano	Utilizador independente (B1)	Utilizador independente (B1)	Utilizador elementar (A1)	Utilizador independente (B1)
Português (Idioma materno)

Formação

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

Percurso profissional

Ciência

	Categoria Profissional Instituição de acolhimento	Empregador
2002/02/01 - 2002/02/01	Investigador (Investigação)	Universidade do Porto Departamento de Química e Bioquímica, Portugal

Docência no Ensino Superior

	Categoria Profissional Instituição de acolhimento	Empregador
2018/05/01 - Atual	Professor Associado (Docente Universitário)	Københavns Universitet, Dinamarca

2014/03/01 - 2018/02/28	Assistente (Docente Universitário)	København Universitet Bioinformatiok-centret, Dinamarca

Outros

	Categoria Profissional Instituição de acolhimento	Empregador
2011/03/01 - 2014/02/28	Marie Curie Postdoctoral fellow	Københavns Universitet Statens Naturhistoriske Museum, Dinamarca

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, Estados Unidos

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

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

Projetos

Bolsa

	Designação	Financiadores
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 Bolseiro de Pós-Doutoramento	Fundação para a Ciência e a Tecnologia Concluído
2006 - 2008	EMBO fellowship: Positive selection on apoptosis related genes – implications for carcinogenesis EMBO long -term fellowship Bolseiro de Pós-Doutoramento	Gesellschaft zur Förderung der Lebenswissenschaften Heidelberg GmbH Concluído
2002 - 2006	Computational studies on cytochrome P450 1A2 Computational studies on cytochrome P450 1A2 Bolseiro de Doutoramento	Associação para a Inovação e Desenvolvimento da FCT Concluído

Projeto

	Designação	Financiadores
2019/10/01 - 2023/09/30	Plant-microbiome interactions in modern and ancient barley 9040-00314A Investigador Københavns Universitet, Dinamarca	Danmarks Frie Forskningsfond Natur og Univers Em curso
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 Em curso
2017 - 2019	Comparative opioid receptor expression and reptilian neuroanatomy NNF16OC0023494 Investigador Københavns Universitet, Dinamarca	Novo Nordisk Fonden Em curso
2014 - 2017	Characterizing the differences and similarities between the genomes of industrially relevant microorganisms originating from extreme environments VKR023446 Investigador responsável Københavns Universitet, Dinamarca	Villum Fonden Concluído
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 Concluído
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 Concluído
2011/04/01 - 2014/06/30	Caracterização do conjunto de enzimas involvidas no metabolism de toxinas e poluentes em invertebrados marinhos PTDC/MAR/115347/2009 Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal	Fundação para a Ciência e a Tecnologia Concluído
2011 - 2014	Characterization of the enzymes involved in the metabolism of toxins and pollutants in marine invertebrates PTDC/MAR/115347/2009 Investigador responsável	Fundação para a Ciência e a Tecnologia Concluído
2011 - 2014	The evolution of retinoid and thyroid hormone signaling pathways, and their modulation by endocrine disrupting chemicals in invertebrates PTDC/MAR/115199/2009 Investigador
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 Concluído
2011 - 2013	MaizeKey Marie Curie IEF 272927 Bolseiro de Pós-Doutoramento	European Commission Seventh Framework Programme for Research and Technological Development Concluído
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 Investigador	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 Concluído
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 Concluído

Produções

Publicações

Artigo em revista

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
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
"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

Tese / Dissertação

Fonseca, Rute A. Rodrigues da. "Computational studies on cytochromes P450". Doutoramento, 2006. http://hdl.handle.net/10216/64285.

Outros

Outra produção

Low coverage whole genome sequencing reveals the underlying structure of European sardine populations. 2021. Rute da Fonseca; Paula Campos; Alba Rey de la Iglesia; Gustavo Barroso; Lucie Bergeron; Manuel Nande; Fernando Tuya; et al. https://doi.org/10.22541/au.161628445.52373083/v1.
10.22541/au.161628445.52373083/v1
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

Atividades

Apresentação oral de trabalho

	Título da apresentação	Nome do evento Anfitrião (Local do evento)
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, França)
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, França)
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, Estados Unidos)
2017	Introgression shaped hummingbird evolution	PAG XXV (San Diego, Estados Unidos)
2017	A high quality genome for the giant squid	PAG XXV (San Diego, Estados Unidos)
2017	Squids 2.0	CephsInAction: what next? (COST meeting) (Galway, Irlanda)
2016	Hummingbird diversification: a tale of introgression	Annual Danish Bioinformatics Conference (Odense, Dinamarca)
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, República Checa)
2014	The origin and evolution of maize from the SW of the USA	SMBE meeting (San Juan, Porto Rico)
2014	The origin and evolution of maize from the SW of the USA	ISBA6 (Basel, Suiça)
2014	The origin and evolution of maize from the SW of the USA	9th International Conference on Genomics (Shenzen, China)

Orientação

	Título / Tema Papel desempenhado	Curso (Tipo) Instituição / Organização
2018/11 - Atual	PhD: Análise da estrutura de genes e elementos regulatórios relacionados com a biossíntese de ácidos orgânicos e açúcares em Citrus spp Coorientador	Københavns Universitet, Dinamarca Universidade Estadual de Santa Cruz, Brasil
2018/08 - Atual	PhD: Out of the can: genomic resources and tools to manage the European sardine, Sardina pilchardus Coorientador	Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal Københavns Universitet Det Natur- og Biovidenskabelige Fakultet, Dinamarca
2018/07 - 2018/10	EMBO short-term fellowship. Theme: Divergent evolution and horizontal gene transfer in the extracytoplasmic function protein family Orientador	Københavns Universitet, Dinamarca
2017 - 2018	MSc student in Bioinformatics (30 ECTS): Comparative genomics using capture data Orientador	Københavns Universitet, Dinamarca
2017/05 - 2017/09	Postdoc: Transcriptomics of metazoan neuronal tissues Orientador	Københavns Universitet, Dinamarca
2017/04 - 2017/06	7.5 ECTS project in Bioinformatics: Population genetics of bees Orientador	Københavns Universitet Det Natur- og Biovidenskabelige Fakultet, Dinamarca
2016/04 - 2017/06	Research assistant: cephalopod genomics Orientador	Universidade de Vigo, Espanha
2016/09 - 2017/02	MSc student in Bioinformatics (30 ECTS): Population genomics of historical bee samples Orientador	Københavns Universitet Det Natur- og Biovidenskabelige Fakultet, Dinamarca
2016/07 - 2016/09	7.5 ECTS project in Bioinformatics: Population genomics methods Orientador	Københavns Universitet Det Natur- og Biovidenskabelige Fakultet, Dinamarca
2016/04 - 2016/06	7.5 ECTS project in Bioinformatics: Population genomics methods Orientador	Københavns Universitet Det Natur- og Biovidenskabelige Fakultet, Dinamarca
2016 - 2016	7.5 ECTS project in Bioinformatics Coorientador	København Universitet Bioinformatiok-centret, Dinamarca
2015/04 - 2015/11	Research Assistant: The evolution of high-accuracy vision in avian species Orientador	København Universitet Bioinformatiok-centret, Dinamarca
2015 - 2015	7.5 ECTS project in Bioinformatics Coorientador	København Universitet Bioinformatiok-centret, Dinamarca
2015 - 2015	Research assistant: Comparative genomics using capture data Coorientador	Københavns Universitet Statens Naturhistoriske Museum, Dinamarca
2012 - 2014	Postdoc: Population genomic footprints of environmental pollution pressure in natural populations of the Mediterranean mussel Orientador	Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2012 - 2014	Research Assistant: Proteomic profiling of gill GSTs in Mytilus galloprovincialis Orientador	Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2013 - 2013	Research assistant: Detecting highly divergent windows in multiple sequence alignments Coorientador	Københavns Universitet Statens Naturhistoriske Museum, Dinamarca

Júri de grau académico

	Tema Tipo de participação	Nome do candidato (Tipo de grau) Instituição / Organização
2019/07/02	A genome-wide study of the molecular adaptations underpinning dietary specialisations in New World leaf-nosed bats (Phyllostomidae, Chiroptera) Arguente principal	Joshua Potter (Doutoramento) Queen Mary University of London, Reino Unido
2019/04/29	Flying rats shall no longer be: A population genomic analysis of fancy and feral pigeons Presidente do júri	George Antunes Pacheco (Doutoramento) Københavns Universitet, Dinamarca
2018	Ancient DNA and novel molecular methods in modern population genomics Presidente do júri	Alba Rey (Doutoramento) Københavns Universitet, Dinamarca
2017/07	Evaluation of phylogenomic methods for species tree estimation Arguente	Diego Mallo Adán (Doutoramento) Universidade de Vigo, Espanha

Comissão de avaliação

	Descrição da atividade Tipo de assessoria	Instituição / Organização
2018 - 2018	Rapporteur for the Second Progress Report (PR2) of COST Action CA15112 Avaliador	European Cooperation in Science and Technology, Bélgica
2017 - 2017	Grant proposal evaluation Avaliador	Fonds zur Förderung der wissenschaftlichen Forschung, Áustria
2015 - 2015	Evaluator of COST action OC-2015-1-19443 Avaliador	European Cooperation in Science and Technology, Bélgica

Consultoria / Parecer

	Descrição da atividade	Instituição / Organização
2009 - Atual	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, Bélgica
2012 - 2012	Part of the international discussion group NESCent Catalysis meeting	National Evolutionary Synthesis Center, Estados Unidos
2012 - 2012	Part of international discussion group at Cephalopods in Research	Stazione Zoologica Anton Dohrn, Itália

Curso / Disciplina lecionado

	Disciplina	Curso (Tipo)	Instituição / Organização
2012/12/14 - Atual	Genomic Approaches in Non-model Organisms	(Master)	Københavns Universitet, Dinamarca
2017/10/23 - 2017/10/27	Comparative Genomics	(Master)	Universidade Estadual de Santa Cruz, Brasil
2016/03/18 - 2016/03/29	Introduction to Bioinformatics	Biochemistry (Bachelor)	Københavns Universitet, Dinamarca
2016/03/16 - 2016/03/16	Population genetics	Biology (Bachelor)	Københavns Universitet, Dinamarca
2016/02/16 - 2016/02/16	Statistics for Molecular Biomedicine	(Bachelor)	København Universitet Bioinformatiok-centret, Dinamarca
2016/01/08 - 2016/01/08	Genomic Approaches in Non-model Organisms	(Master)	Københavns Universitet, Dinamarca
2015/11/30 - 2015/11/30	Genome Sequence Analysis	(Master)	Københavns Universitet, Dinamarca
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, Brasil
2015/06/03 - 2015/06/03	Population Genetics	(Bachelor)	Københavns Universitet, Dinamarca
2015/03/10 - 2015/03/10	Introduction to Bioinformatics	(Bachelor)	Københavns Universitet, Dinamarca
2014/11/24 - 2014/11/24	Statistics for Molecular Biomedicine	(Master)	Københavns Universitet, Dinamarca
2014/01/07 - 2014/01/07	Genomic Approaches in Non-model Organisms	(Master)	Københavns Universitet, Dinamarca
2012/10/01 - 2012/10/01	Genomic Approaches in Non-model Organisms	(Master)	Københavns Universitet, Dinamarca

Entrevista (jornal / revista)

	Descrição da atividade	Jornal / 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

Membro de associação

	Nome da associação	Tipo de participação
2018 - Atual	The International Biogeography Society
2001 - 2010	Sociedade Portuguesa de Bioquímica

Membro de comissão

	Descrição da atividade Tipo de participação	Instituição / Organização
2014 - Atual	Part of the Bird10K advisory committee (consortium that aims at sequencing 10,000 avian genomes) Consultor	Københavns Universitet, Dinamarca
2015 - 2017	Danish partner of COST action FA1301 Membro	European Cooperation in Science and Technology, Bélgica

Outro júri / avaliação

	Descrição da atividade	Instituição / Organização
2018/11 - 2018/11	7.5 ECTS project: Alba Refoyo Martinez	Københavns Universitet, Dinamarca
2015 - 2016	Censor in Introduction to Bioinformatics. Oral examination of 54 students in 2016 and 39 students in 2015.	Københavns Universitet, Dinamarca
2015 - 2015	15 ECT project, MSc student Kristian Hanghoej	Københavns Universitet, Dinamarca
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, Dinamarca
2012 - 2012	7.5 ECTS project: Peter de Barros Damgaard, SNM, University of Copenhagen	Københavns Universitet, Dinamarca
2010 - 2010	7.5 ECTS project: Mikkel Holger Strander Sinding, SNM, University of Copenhagen	Københavns Universitet, Dinamarca

Distinções

Outra distinção

2017	DeiC computerome grant Danish e-Infrastructure Cooperation, Dinamarca
2014	Villum Young Investigator Grant
2014	SMBE Travel grant Society for Molecular Biology and Evolution, Estados Unidos
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, Alemanha
2006	Short-term fellowship Fundação Calouste Gulbenkian, Portugal
2001	FCT PhD scholarship Fundação para a Ciência e a Tecnologia, Portugal