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R. D. da Fonseca · SciRah

Researcher profile · Semantic Scholar

R. D. da Fonseca

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R. D. da Fonseca — researcher profile on SciRah

h-index: 32
Works: 107
Citations: 7,490

Most-cited papers

Whole-genome analyses resolve early branches in the tree of life of modern birds
E. Jarvis, S. Mirarab, A. Aberer, Bo Li +101 more
2014Science1,818 citations Open access
Semantic Scholar
Comparative genomics reveals insights into avian genome evolution and adaptation
Guojie Zhang, Cai Li, Qi-Ye Li, Bo Li +102 more
2014Science989 citations Open access
Semantic Scholar
Patterns of Positive Selection in Six Mammalian Genomes
C. Kosiol, T. Vinař, R. D. da Fonseca, M. Hubisz +3 more
2008PLoS Genetics585 citations Open access
Semantic Scholar
The adaptive evolution of the mammalian mitochondrial genome
R. D. da Fonseca, Warren E. Johnson, S. J. O’Brien, M. J. Ramos +1 more
2008BMC Genomics419 citations Open access
Semantic Scholar
Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits
Lei Chen, Q. Qiu, Yu Jiang, Kun Wang +48 more
2019Science391 citations
Semantic Scholar
Dense sampling of bird diversity increases power of comparative genomics
Shaohong Feng, Josefin Stiller, Yuan Deng, J. Armstrong +146 more
2020Nature379 citations Open access
Semantic Scholar
Complexity of avian evolution revealed by family-level genomes
Josefin Stiller, Shaohong Feng, Al-Aabid Chowdhury, Iker Rivas-González +48 more
2024Nature250 citations Open access
Semantic Scholar
Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins.
E. Cappellini, L. Jensen, D. Szklarczyk, A. Ginolhac +8 more
2012Journal of Proteome Research220 citations Open access
Semantic Scholar
Next-generation biology: Sequencing and data analysis approaches for non-model organisms.
R. D. da Fonseca, A. Albrechtsen, G. E. Themudo, Jazmín Ramos-Madrigal +6 more
2016Marine Genomics174 citations Open access
Semantic Scholar
The origin and evolution of maize in the Southwestern United States
R. D. da Fonseca, Bruce D. Smith, N. Wales, E. Cappellini +16 more
2015Nature Plants159 citations Open access
Semantic Scholar
Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution
A. Tanner, D. Fuchs, Inger Winkelmann, M. Gilbert +8 more
2017Proceedings of the Royal Society of London. Biological Sciences137 citations Open access
Semantic Scholar
Positive selection on the killer whale mitogenome
A. Foote, P. Morin, J. Durban, R. Pitman +4 more
2011Biology Letters135 citations Open access
Semantic Scholar
Natural selection shaped the rise and fall of passenger pigeon genomic diversity
G. Murray, André E. R. Soares, Ben J. Novak, Nathan K. Schaefer +20 more
2017Science120 citations Open access
Semantic Scholar
Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution
E. Willerslev, M. T. P. Gilbert, Jonas Binladen, Simon Y. W. Ho +10 more
2009BMC Evolutionary Biology113 citations Open access
Semantic Scholar
Ancient genomics
C. Der Sarkissian, M. Allentoft, M. Ávila-Arcos, Ross Barnett +22 more
2015Philosophical Transactions of the Royal Society B: Biological Sciences105 citations Open access
Semantic Scholar
The Elusive Nature of Adaptive Mitochondrial DNA Evolution of an Arctic Lineage Prone to Frequent Introgression
J. Melo-Ferreira, J. Vilela, Miguel M. Fonseca, R. D. da Fonseca +2 more
2014Genome Biology and Evolution102 citations Open access
Semantic Scholar
Comparative genomics provides insights into the aquatic adaptations of mammals
Yuan Yuan, Yaolei Zhang, Pei-Jun Zhang, Chang Liu +37 more
2021Proceedings of the National Academy of Sciences of the United States of America97 citations Open access
Semantic Scholar
Phylogenomic analyses data of the avian phylogenomics project
Erich D. Jarvis, S. Mirarab, A. Aberer, Bo Li +24 more
2015GigaScience94 citations Open access
Semantic Scholar
Molecular evolution and the role of oxidative stress in the expansion and functional diversification of cytosolic glutathione transferases
R. D. da Fonseca, W. Johnson, S. O'Brien, V. Vasconcelos +1 more
2010BMC Evolutionary Biology83 citations Open access
Semantic Scholar
Declining genetic diversity of European honeybees along the twentieth century
Gonçalo Espregueira Themudo, A. Rey-Iglesia, Lucía Robles Tascón, Annette Bruun-Jensen +2 more
2020Scientific Reports66 citations Open access
Semantic Scholar
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.).
M. Jacobsen, R. D. da Fonseca, L. Bernatchez, M. Hansen
2016Molecular Phylogenetics and Evolution64 citations
Semantic Scholar
High genetic diversity and low differentiation reflect the ecological versatility of the African leopard.
P. Pečnerová, Genís Garcia-Erill, Xiao-Dong Liu, Casia Nursyifa +15 more
2021Current Biology62 citations Open access
Semantic Scholar
Cephalopod genomics: A plan of strategies and organization
C. Albertin, L. Bonnaud, C. T. Brown, Wendy J. Crookes-Goodson +22 more
2012Standards in Genomic Sciences62 citations Open access
Semantic Scholar
Identifying loci under positive selection in complex population histories
Alba Refoyo-Martínez, R. D. da Fonseca, Katrín Halldórsdóttir, E. Árnason +2 more
2018bioRxiv42 citations Open access
Semantic Scholar
Shotgun analysis of the marine mussel Mytilus edulis hemolymph proteome and mapping the innate immunity elements
A. Campos, I. Apraiz, R. D. da Fonseca, S. Cristobal
2015Proteomics42 citations Open access
Semantic Scholar
Positive selection on apoptosis related genes
R. D. da Fonseca, C. Kosiol, T. Vinař, A. Siepel +1 more
2010FEBS Letters41 citations
Semantic Scholar
“Out of the Can”: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus
A. Machado, O. K. Tørresen, N. Kabeya, Alvarina Couto +13 more
2018Genes40 citations Open access
Semantic Scholar
Complete Inactivation of Sebum-Producing Genes Parallels the Loss of Sebaceous Glands in Cetacea
M. Lopes-Marques, A. Machado, L. Alves, Miguel M. Fonseca +9 more
2019Molecular biology and evolution39 citations Open access
Semantic Scholar
A draft genome sequence of the elusive giant squid, Architeuthis dux
R. D. da Fonseca, Alvarina Couto, A. Machado, Broňa Brejová +40 more
2020GigaScience38 citations Open access
Semantic Scholar
Comparative genomics reveals insights into avian genome evolution and adaptation
Guo-Jie Zhang, Cai Li, Qi-Ye Li, B. Li +115 more
201435 citations
Semantic Scholar
Combined Transcriptomic and Proteomic Analysis of the Posterior Salivary Gland from the Southern Blue-Ringed Octopus and the Southern Sand Octopus.
Brooke L. Whitelaw, J. Strugnell, P. Faou, R. D. da Fonseca +4 more
2016Journal of Proteome Research33 citations Open access
Semantic Scholar
Losing Genes: The Evolutionary Remodeling of Cetacea Skin
Gonçalo Espregueira Themudo, L. Alves, A. Machado, M. Lopes-Marques +4 more
2020Frontiers in Marine Science32 citations Open access
Semantic Scholar
Response of an Afro-Palearctic bird migrant to glaciation cycles
K. Thorup, Lykke Pedersen, R. D. da Fonseca, B. Naimi +15 more
2021Proceedings of the National Academy of Sciences of the United States of America31 citations Open access
Semantic Scholar
Structural divergence and adaptive evolution in mammalian cytochromes P450 2C.
R. D. da Fonseca, Agostinho Antunes, A. Melo, M. Ramos
2007Gene29 citations
Semantic Scholar
Proteomic Profiling of Cytosolic Glutathione Transferases from Three Bivalve Species: Corbicula fluminea, Mytilus galloprovincialis and Anodonta cygnea
J. Martins, A. Campos, H. Osório, R. D. da Fonseca +1 more
2014International Journal of Molecular Sciences28 citations Open access
Semantic Scholar
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.
Catarina C Azevedo, R. Guzmán-Guillén, J. Martins, H. Osório +3 more
2015Marine Environmental Research27 citations
Semantic Scholar
The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)
A. Gomes-dos-Santos, M. Lopes‐Lima, A. Machado, António Marcos Ramos +13 more
2020bioRxiv25 citations Open access
Semantic Scholar
Genome sequence and effectorome of Moniliophthora perniciosa and Moniliophthora roreri subpopulations
Ceslaine Santos Barbosa, R. D. da Fonseca, T. Batista, M. Barreto +10 more
2018BMC Genomics25 citations Open access
Semantic Scholar
Using UCEs to track the influence of sea-level change on leafy seadragon populations.
Josefin Stiller, R. D. da Fonseca, M. Alfaro, B. Faircloth +2 more
2020Molecular Ecology24 citations Open access
Semantic Scholar
Population Genomics Reveals the Underlying Structure of the Small Pelagic European Sardine and Suggests Low Connectivity within Macaronesia
R. D. da Fonseca, Paula F. Campos, A. Rey-Iglesia, G. Barroso +14 more
2024Genes22 citations Open access
Semantic Scholar
Cartilaginous fishes offer unique insights into the evolution of the nuclear receptor gene repertoire in gnathostomes.
Elza Fonseca, A. Machado, Nair Vilas-Arrondo, A. Gomes-dos-Santos +12 more
2020General and Comparative Endocrinology22 citations Open access
Semantic Scholar
Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle
R. D. da Fonseca, Irene Ureña, S. Afonso, A. E. Pires +3 more
2018BMC Genomics21 citations Open access
Semantic Scholar
Adaptive evolution of the Retinoid X receptor in vertebrates.
S. Philip, L. F. Castro, R. D. da Fonseca, M. Reis-Henriques +3 more
2012Genomics21 citations Open access
Semantic Scholar
Iron age genomic data from Althiburos – Tunisia renew the debate on the origins of African taurine cattle
Catarina Ginja, Sílvia Guimarães, R. D. da Fonseca, R. Rasteiro +14 more
2023iScience19 citations Open access
Semantic Scholar
A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias
Andr é M. Machado, M. Felício, Elza Fonseca, R. D. da Fonseca +1 more
2018Data in Brief19 citations Open access
Semantic Scholar
Site‐directed genotype screening for elimination of antinutritional saponins in quinoa seeds identifies TSARL1 as a master controller of saponin biosynthesis selectively in seeds
Mai Duy Luu Trinh, Davide Visintainer, Jan Günther, J. T. Østerberg +12 more
2024Plant Biotechnology Journal18 citations Open access
Semantic Scholar
Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss
Brooke L. Whitelaw, I. Cooke, J. Finn, R. D. da Fonseca +4 more
2020GigaScience18 citations Open access
Semantic Scholar
Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations
Xiaodong Liu, Long Lin, Mikkel-Holger S. Sinding, L. Bertola +24 more
2024Nature Communications17 citations Open access
Semantic Scholar
A refined model of the genomic basis for phenotypic variation in vertebrate hemostasis
Â. Ribeiro, M. Lisandra Zepeda-Mendoza, Mads F. Bertelsen, A. Kristensen +3 more
2015BMC Evolutionary Biology17 citations Open access
Semantic Scholar
The Vertebrate Genomes Project Phase I: A global reference genome resource
G. Formenti, Dominic E. Absolon, L. Abueg, Francine Ackerman +166 more
2026bioRxiv16 citations Open access
Semantic Scholar

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