Rute Andreia Rodrigues da Fonseca

Rute Andreia Rodrigues da Fonseca

Associate Professor

ORCID: 0000-0002-2805-4698

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  1. Published

    "Out of the Can": A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus

    Machado, A. M., Tørresen, O. K., Kabeya, N., Couto, A., Petersen, Bent, Felicio, M., Campos, P. F., Fonseca, E., Bandarra, N., Lopes-Marques, M., Ferraz, R., Ruivo, R., Fonseca, M. M., Jentoft, S., Monroig, Ó., Rodrigues da Fonseca, Rute Andreia & Castro, L. F. C., 2018, In: Genes. 9, 10, p. 1-13 485.

    Research output: Contribution to journal › Journal article › Research › peer-review

  2. Published

    31º South: The physiology of adaptation to arid conditions in a passerine bird

    Ribeiro, Â. M., Puetz, Lara Christine, Pattinson, N. B., Dalén, L., Deng, Y., KU, thw266, Rodrigues da Fonseca, Rute Andreia, Smit, B. & Gilbert, M Thomas P, 2019, In: Molecular Ecology. 28, 16, p. 3709-3721 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  3. Published

    A draft genome sequence of the elusive giant squid, Architeuthis dux

    da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, Â. M., Barrio-Hernandez, I., Hoving, H-J., Tafur-Jimenez, R., Chu, C., Frazão, B., Petersen, B., Peñaloza, F., Musacchia, F., Alexander, G. C. & 24 others, Osório, H., Winkelmann, I., Simakov, O., Rasmussen, Simon, Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., KU, thw266, Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Pontén, Thomas, Nielsen, Rasmus & Gilbert, M Thomas P, 2020, In: GigaScience. 9, 1, 12 p., giz152.

    Research output: Contribution to journal › Journal article › Research › peer-review

  4. Published

    A refined model of the genomic basis for phenotypic variation in vertebrate hemostasis

    Ribeiro, Â. M., Zepeda Mendoza, M. L., Bertelsen, Mads Frost, Kristensen, Annemarie T., Jarvis, E. D., Gilbert, M Thomas P & Rodrigues da Fonseca, Rute Andreia, 2015, In: B M C Evolutionary Biology. 15, 8 p., 124.

    Research output: Contribution to journal › Journal article › Research › peer-review

  5. Published

    A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias

    Machado, A. M., Felício, M., Fonseca, E., Rodrigues da Fonseca, Rute Andreia & Castro, L. F. C., 2018, In: Data in Brief. 18, p. 276-284 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  6. Published

    Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss

    Whitelaw, B. L., Cooke, I. R., Finn, J., Rodrigues da Fonseca, Rute Andreia, Ritschard, E. A., Gilbert, M Thomas P, Simakov, O. & Strugnell, J. M., 2020, In: GigaScience. 9, 11, 15 p., giaa120.

    Research output: Contribution to journal › Journal article › Research › peer-review

  7. Published

    Ancient genomics

    Der Sarkissian, C., Allentoft, M. E., Avila Arcos, M. D. C., Barnett, R., Campos, P. F., Cappellini, E., Ermini, L., Fernandez Garcia, R., Rodrigues da Fonseca, R. A., Ginolhac, A., Hansen, A. J., Jónsson, H., Korneliussen, T. S., Margaryan, A., Martin, M. D., Moreno Mayar, J. V., Raghavan, M., Rasmussen, M., Sandoval Velasco, M., Schroeder, H. & 6 others, Schubert, Mikkel, Seguin-Orlando, A., Wales, N., Gilbert, M Thomas P, Willerslev, Eske & Orlando, L. A. A., 2015, In: Philosophical Transactions of the Royal Society B: Biological Sciences. 370, 1660, 12 p., 20130387.

    Research output: Contribution to journal › Review › Research › peer-review

  8. Published

    Cartilaginous fishes offer unique insights into the evolution of the nuclear receptor gene repertoire in gnathostomes

    Fonseca, E., Machado, A. M., Vilas-Arrondo, N., Gomes-dos-Santos, A., Verissimo, A., Esteves, P., Almeida, T., Themudo, G., Ruivo, R., Perez, M., Rodrigues da Fonseca, Rute Andreia, Santos, M. M., Froufe, E., Roman-Marcote, E., Venkatesh, B. & Castro, L. F. C., 2020, In: General and Comparative Endocrinology. 295, 10 p., 113527.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. Published

    Cephalopod genomics: a plan of strategies and organization

    Albertin, C. B., Bonnaud, L., Brown, C. T., Crookes-Goodson, W. J., Rodrigues da Fonseca, R. A., Di Cristo, C., Dilkes, B. P., Edsinger-Gonzales, E., Freeman, Jr., R. M., Hanlon, R. T., Koenig, K. M., Lindgren, A. R., Martindale, M. Q., Minx, P., Moroz, L. L., Nödl, M-T., Nyholm, S. V., Ogura, A., Pungor, J. R., Rosenthal, J. J. C. & 6 others, Schwarz, E. M., Shigeno, S., Strugnell, J. M., Wollesen, T., Zhang, G. & Ragsdale, C. W., 2012, In: Standards in Genomic Sciences. 7, p. 175-188 14 p., 1.

    Research output: Contribution to journal › Journal article › Research › peer-review

  10. Published

    Cephalopods in neuroscience: regulations, research and the 3Rs

    Fiorito, G., Affuso, A., Anderson, D. B., Basil, J., Bonnaud, L., Botta, G., Cole, A., D'Angelo, L., De Girolamo, P., Dennison, N., Dickel, L., Di Cosmo, A., Di Cristo, C., Gestal, C., Rodrigues da Fonseca, R. A., Grasso, F., Kristiansen, T., Kuba, M., Maffucci, F., Manciocco, A. & 15 others, Mark, F. C., Melillo, D., Osorio, D., Palumbo, A., Perkins, K., Ponte, G., Raspa, M., Shashar, N., Smith, J., Smith, D., Sykes, A., Villanueva, R., Tublitz, N., Zullo, L. & Andrews, P., 2014, In: Invertebrate Neuroscience. 14, 1, p. 13-36 24 p.

    Research output: Contribution to journal › Review › Research › peer-review

  11. Published

    Combined transcriptomic and proteomic analysis of the posterior salivary gland from the southern blue-ringed octopus and the southern sand octopus

    Whitelaw, B. L., Strugnell, J. M., Faou, P., Rodrigues da Fonseca, Rute Andreia, Hall, N. E., Norman, M., Finn, J. & Cooke, I. R., 2016, In: Journal of Proteome Research. 15, 9, p. 3284-3297 14 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  12. Published

    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.)

    Jacobsen, M. W., Rodrigues da Fonseca, Rute Andreia, Bernatchez, L. & Hansen, M. M., 2016, In: Molecular Phylogenetics and Evolution. 95, p. 161-170 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  13. Published

    Comparative genomics provides insights into the aquatic adaptations of mammals

    Yuan, Y., Zhang, Y., Zhang, P., Liu, C., Wang, J., Gao, H., Rus Hoelzel, A., Seim, I., Lv, M., Lin, M., Dong, L., Gao, H., Yang, Z., Caruso, F., Lin, W., Da Fonseca, R. R., Wang, D., Wang, X., Rasmussen, M. H., Liu, M. & 21 others, Zheng, J., Zhao, L., Campos, P. F., Kang, H., Iversen, M., Song, Y., Guo, X., Guo, J., Qin, Y., Pan, S., Xu, Q., Meng, L., A, Y., Liu, S., Ming-Yuen Lee, S., Liu, X., Xu, X., Yang, H., Fan, G., Wang, K. & Li, S., 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 37, 9 p., e2106080118.

    Research output: Contribution to journal › Journal article › Research › peer-review

  14. Published

    Comparative genomics reveals insights into avian genome evolution and adaptation

    Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., Storz, J. F., Antunes, A., Greenwold, M. J., Meredith, R. W., Ödeen, A., Cui, J., Zhou, Q., Xu, L., Pan, H., Wang, Z., Jin, L., Zhang, P., Hu, H., Yang, W. & 85 others, Hu, J., Xiao, J., Yang, Z., Liu, Y., Xie, Q., Yu, H., Lian, J., Wen, P., Zhang, F., Li, H., Zeng, Y., Xiong, Z., Liu, S., Zhou, L., Huang, Z., An, N., Wang, J., Zheng, Q., Xiong, Y., Wang, G., Wang, B., Wang, J., Fan, Y., Rodrigues da Fonseca, Rute Andreia, Alfaro Nuñez, L. A., Schubert, Mikkel, Orlando, L. A. A., Mourier, T., Howard, J. T., Ganapathy, G., Pfenning, A., Whitney, O., Rivas, M. V., Hara, E., Smith, J., Farré, M., Narayan, J., Slavov, G., Romanov, M. N., Borges, R., MacHado, J. P., Khan, I., Springer, M. S., Gatesy, J., Hoffmann, F. G., Opazo, J. C., Håstad, O., Sawyer, R. H., Kim, H., Kim, K. W., Kim, H. J., Cho, S., Li, N., Huang, Y., Bruford, M. W., Zhan, X., Dixon, A., Bertelsen, Mads Frost, Derryberry, E., Warren, W., Wilson, R. K., Li, S., Ray, D. A., Green, R. E., O'Brien, S. J., Griffin, D., Johnson, W. E., Haussler, D., Ryder, O. A., Willerslev, Eske, Graves, G. R., Alström, P., Fjeldså, Jon, Mindell, D. P., Edwards, S. V., Braun, E. L., Rahbek, Carsten, Burt, D. W., Houde, P., Zhang, Y., Yang, H., Wang, J., Jarvis, E. D., Gilbert, M Thomas P & Wang, J., 2014, In: Science. 346, 6215, p. 1311-1320 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  15. Published

    Complete Inactivation of Sebum-Producing Genes Parallels the Loss of Sebaceous Glands in Cetacea

    Lopes-Marques, M., Machado, A. M., Alves, L. Q., Fonseca, M. M., Barbosa, S., Sinding, M. S., Rasmussen, M. H., Iversen, M. R., Bertelsen, Mads Frost, Campos, P. F., Rodrigues da Fonseca, Rute Andreia, Ruivo, R. & Castro, L. F. C., 2019, In: MOLECULAR BIOLOGY AND EVOLUTION . 36, 6, p. 1270-1280

    Research output: Contribution to journal › Journal article › Research › peer-review

  16. Published

    Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle

    Rodrigues da Fonseca, Rute Andreia, Urena, I., Afonso, S., Pires, A. E., Jørsboe, E., Chikhi, L. & Ginja, C., 2019, In: BMC Genomics. 20, p. 1-13 334.

    Research output: Contribution to journal › Journal article › Research › peer-review

  17. Published

    Conservation genomics of the endangered Seychelles Magpie-Robin (Copsychus sechellarum): a unique insight into the history of a precious endemic bird

    Cavill, Emily Louisa, Gopalakrishnan, Shyam, Puetz, Lara Christine, Ribeiro, Â. M., Mak, Sarah Siu Tze, Rodrigues da Fonseca, Rute Andreia, Antunes Pacheco, George, Dunlop, B., Accouche, W., Shah, N., Zora, A., Calabrese, L., Genner, M., Jones, G., Guo, C., KU, thw266 & Gilbert, M Thomas P, 2022, In: Ibis. 164, 2, p. 396-410 15 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  18. Published

    Declining genetic diversity of European honeybees along the twentieth century

    Themudo, G. E., Rey de la Iglesia, Alba, Tascón, L. R., Jensen, Annette Bruun, Rodrigues da Fonseca, Rute Andreia & Campos, P. F., 29 Jun 2020, In: Scientific Reports. 10, 12 p., 10520.

    Research output: Contribution to journal › Journal article › Research › peer-review

  19. Published

    Dense sampling of bird diversity increases power of comparative genomics

    Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q., Hart Reeve, A., Xie, D., Chen, G., Guo, C., Faircloth, B. C., Petersen, B., Wang, Z., Zhou, Q., Diekhans, M., Chen, W., Andreu-Sánchez, S., Margaryan, A., Howard, J. T., Parent, C., Pacheco, G. & 130 others, Sinding, Mikkel Holger Strander, Puetz, Lara Christine, Cavill, Emily Louisa, Ribeiro, Â. M., Eckhart, L., Fjeldså, Jon, Hosner, Peter Andrew, Brumfield, R. T., Christidis, L., Bertelsen, Mads Frost, Sicheritz-Pontén, Thomas, Tietze, D. T., Robertson, B. C., Song, G., Borgia, G., Claramunt, S., Lovette, I. J., Cowen, S. J., Njoroge, P., Dumbacher, J. P., Ryder, O. A., Fuchs, J., Bunce, M., Burt, D. W., Cracraft, J., Meng, G., Hackett, S. J., Ryan, P. G., Jønsson, Knud Andreas, Jamieson, I. G., Rodrigues da Fonseca, Rute Andreia, Braun, E. L., Houde, P., Mirarab, S., Suh, A., Hansson, B., Ponnikas, S., Sigeman, H., Stervander, M., Frandsen, P. B., van der Zwan, H., van der Sluis, R., Visser, C., Balakrishnan, C. N., Clark, A. G., Fitzpatrick, J. W., Bowman, R., Chen, N., Cloutier, A., Sackton, T. B., Edwards, S. V., Foote, D. J., Shakya, S. B., Sheldon, F. H., Vignal, A., Soares, A. E. R., Shapiro, B., González-Solís, J., Ferrer-Obiol, J., Rozas, J., Riutort, M., Tigano, A., Friesen, V., Dalén, L., Urrutia, A. O., Székely, T., Liu, Y., Campana, M. G., Corvelo, A., Fleischer, R. C., Rutherford, K. M., Gemmell, N. J., Dussex, N., Mouritsen, H., Thiele, N., Delmore, K., Liedvogel, M., Franke, A., Hoeppner, M. P., Krone, O., Fudickar, A. M., Milá, B., Ketterson, E. D., Fidler, A. E., Friis, G., Parody-Merino, Á. M., Battley, P. F., Cox, M. P., Lima, N. C. B., Prosdocimi, F., Parchman, T. L., Schlinger, B. A., Loiselle, B. A., Blake, J. G., Lim, H. C., Day, L. B., Fuxjager, M. J., Baldwin, M. W., Braun, M. J., Wirthlin, M., Dikow, R. B., Ryder, T. B., Camenisch, G., Keller, L. F., Dacosta, J. M., Hauber, M. E., Louder, M. I. M., Witt, C. C., McGuire, J. A., Mudge, J., Megna, L. C., Carling, M. D., Wang, B., Taylor, S. A., Del-Rio, G., Aleixo, A., Vasconcelos, A. T. R., Mello, C. V., Weir, J. T., Haussler, D., Li, Q., Yang, H., Wang, J., Lei, F., Rahbek, Carsten, Gilbert, M Thomas P, Graves, G. R., Jarvis, E. D., Paten, B. & KU, thw266, 2020, In: Nature. 587, 7833, p. 252-257

    Research output: Contribution to journal › Journal article › Research › peer-review

  20. Published

    DivA: detection of non-homologous and very divergent regions in protein sequence alignments

    Zepeda Mendoza, M. L., Nygaard, S. & Rodrigues da Fonseca, Rute Andreia, 2014, In: BMC Research Notes. 7, 806, 6 p., 806.

    Research output: Contribution to journal › Journal article › Research › peer-review

  21. Published

    Evolution of the extracytoplasmic function σ factor protein family

    Pinto, D. & Rodrigues da Fonseca, Rute Andreia, 2020, In: NAR Genomics and Bioinformatics. 2, 1, 13 p., lqz026.

    Research output: Contribution to journal › Journal article › Research › peer-review

  22. Published

    Fertilizer regime and cultivar affect barley growth and rhizobiome composition

    Kindtler, Nikolaj Lunding, Sheikh, Sanea, Richardy, J., Krogh, E., Maccario, Lorrie, Vestergård, M., Rodrigues da Fonseca, Rute Andreia, Ekelund, Flemming & Laursen, Kristian Holst, 2024, In: Applied Soil Ecology. 198, 13 p., 105384.

    Research output: Contribution to journal › Journal article › Research › peer-review

  23. Published

    Genome sequence and effectorome of Moniliophthora perniciosa and Moniliophthora roreri subpopulations

    Barbosa, C. S., Rodrigues da Fonseca, Rute Andreia, Batista, T. M., Barreto, M. A., Argolo, C. S., de Carvalho, M. R., Jordao do Amaral, D. O., de Andrade Silva, E. M., Arevalo-Gardini, E., Hidalgo, K. S., Franco, G. R., Pirovani, C. P., Micheli, F. & Gramacho, K. P., 3 Jul 2018, In: BMC Genomics. 19, 12 p., 509.

    Research output: Contribution to journal › Journal article › Research › peer-review

  24. Published

    High genetic diversity and low differentiation reflect the ecological versatility of the African leopard

    Chrzanová Pecnerová, Patrícia, Garcia Erill, Genís, Liu, Xiaodong, Nursyifa, Casia, Waples, R. K., Santander, Cindy, Quinn, Liam James Elgaard, Frandsen, P., Meisner, Jonas, Stæger, Frederik Filip Vinggaard, Rasmussen, Malthe Sebro, Brüniche-Olsen, Anna, Jørgensen, C. H. F., Rodrigues da Fonseca, Rute Andreia, Siegismund, Hans Redlef, Albrechtsen, Anders, Heller, Rasmus, Moltke, Ida & Hanghøj, Kristian Ebbesen, 2021, In: Current Biology. 31, 9, p. 1862-1871, e1-e5

    Research output: Contribution to journal › Journal article › Research › peer-review

  25. Published

    Identifying loci under positive selection in complex population histories

    Refoyo Martínez, Alba, Rodrigues da Fonseca, Rute Andreia, Halldórsdóttir, K., Árnason, E., Mailund, T. & Racimo, Fernando, 2019, In: Genome Research. 29, 9, p. 1506-1520

    Research output: Contribution to journal › Journal article › Research › peer-review

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ID: 33270633