Rute Andreia Rodrigues da Fonseca

2019

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

Ribeiro, Â. M., Puetz, L., Pattinson, N. B., Dalén, L., Deng, Y., Zhang, G., da Fonseca, R. R., Smit, B. & Gilbert, M. T. P., 1 Aug 2019, In: Molecular Ecology. 28, 16, p. 3709-3721 13 p.

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

6 Citations (Scopus)

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-H. S., Rasmussen, M. H., Iversen, M. R., Bertelsen, M. F., Campos, P. F., da Fonseca, R., Ruivo, R. & Castro, L. F. C., 1 Jun 2019, In: MOLECULAR BIOLOGY AND EVOLUTION . 36, 6, p. 1270-1280

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

11 Citations (Scopus)

7 Downloads (Pure)

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

da Fonseca, R. R., Urena, I., Afonso, S., Pires, A. E., Jørsboe, E., Chikhi, L. & Ginja, C., 3 May 2019, In: BMC Genomics. 20, p. 1-13 334.

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

4 Citations (Scopus)

31 Downloads (Pure)

Identifying loci under positive selection in complex population histories

Refoyo-Martínez, A., da Fonseca, R. R., Halldórsdóttir, K., Árnason, E., Mailund, T. & Racimo, F., 2019, In: Genome Research. 29, 9, p. 1506-1520

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

11 Citations (Scopus)

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

Chen, L., Qin, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Bibi, F., Yang, Y., Wang, J., Nie, W., Su, W., Liu, G., Li, Q., Fu, W., Pan, X., Liu, C., Yang, J., Zhang, C., Yin, Y., Wang, Y., & 32 othersZhao, Y., Zhang, C., Wang, Z., Qin, Y., Liu, W., Wang, B., Ren, Y., Zhang, R., Zeng, Y., da Fonseca, R. R., Wei, B., Li, R., Wan, W., Zhao, R., Zhu, W., Wang, Y., Duan, S., Gao, Y., Zhang, Y. E., Chen, C., Hvilsom, C., Epps, C. W., Chemnick, L. G., Doug, Y., Mirarab, S., Siegismund, H. R., Ryder, O. A., Gilbert, M. T. P., Lewin, H. A., Zhang, G., Heller, R. & Wang, W., 21 Jun 2019, In: Science. 364, 6446, p. 1152-

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

60 Citations (Scopus)

Population genomic footprints of environmental pollution pressure in natural populations of the Mediterranean mussel

Ribeiro, Â. M., Canchaya, C. A., Penaloza, F., Galindo, J. & da Fonseca, R. R., Jun 2019, In: Marine Genomics. 45, p. 11-15

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

2018

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., da Fonseca, R. R. & 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

3 Citations (Scopus)

111 Downloads (Pure)

Genome sequence and effectorome of Moniliophthora perniciosa and Moniliophthora roreri subpopulations

Barbosa, C. S., Rodrigues da Fonseca, R. A., 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

7 Citations (Scopus)

54 Downloads (Pure)

"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, B., Felicio, M., Campos, P. F., Fonseca, E., Bandarra, N., Lopes-Marques, M., Ferraz, R., Ruivo, R., Fonseca, M. M., Jentoft, S., Monroig, Ó., da Fonseca, R. R. & Castro, L. F. C., 9 Oct 2018, In: Genes. 9, 10, p. 1-13 485.

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

16 Citations (Scopus)

82 Downloads (Pure)

2017

Marine genomics: news and views

Oliveira Ribeiro, Â. M., Foote, A. D., Kupczok, A., Frazão, B., Limborg, M. T., Piñeiro, R., Abalde, S., Rocha, S. & Rodrigues da Fonseca, R. A., 1 Feb 2017, In: Marine Genomics. 31, p. 1-8 8 p.

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

9 Citations (Scopus)

Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution

Tanner, A. R., Fuchs, D., Winkelmann, I. E. H., Gilbert, T., Pankey, M. S., Oliveira Ribeiro, Â. M., Kocot, K. M., Halanych, K. M., Oakley, T. H., Rodrigues da Fonseca, R. A., Pisani, D. & Vinther, J., 15 Mar 2017, In: Proceedings of the Royal Society B: Biological Sciences. 284, 1850, 7 p., 20162818.

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

47 Citations (Scopus)

79 Downloads (Pure)

Natural selection shaped the rise and fall of passenger pigeon genomic diversity

Murray, G. G. R., Soares, A. E. R., Novak, B. J., Schaefer, N. K., Cahill, J. A., Baker, A. J., Demboski, J. R., Doll, A., Rodrigues da Fonseca, R. A., Fulton, T. L., Gilbert, T., Heintzman, P. D., Letts, B., McIntosh, G., O'Connell, B. L., Peck, M., Pipes, M-L., Rice, E. S., Santos, K. M., Sohrweide, A. G., & 4 othersVohr, S. H., Corbett-Detig, R. B., Green, R. E. & Shapiro, B., 17 Nov 2017, In: Science. 358, 6365, p. 951-954 4 p.

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

43 Citations (Scopus)

2016

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, R. A., Hall, N. E., Norman, M., Finn, J. & Cooke, I. R., 2 Sept 2016, In: Journal of Proteome Research. 15, 9, p. 3284-3297 14 p.

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

15 Citations (Scopus)

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, R. A., Bernatchez, L. & Hansen, M. M., 1 Feb 2016, In: Molecular Phylogenetics and Evolution. 95, p. 161-170 10 p.

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

32 Citations (Scopus)

Next-generation biology: sequencing and data analysis approaches for non-model organisms

Rodrigues da Fonseca, R. A., Albrechtsen, A., Themudo, G. E. C., Ramos Madrigal, J., Sibbesen, J. A., Sørensen, L. M., Zepeda Mendoza, M. L., Campos, P., Heller, R. & Pereira, R., 1 Dec 2016, In: Marine Genomics. 30, p. 3-13

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

70 Citations (Scopus)

131 Downloads (Pure)

2015

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 othersSchubert, M., Seguin-Orlando, A., Wales, N., Gilbert, M. T. P., Willerslev, E. & Orlando, L. A. A., 19 Jan 2015, In: Philosophical Transactions of the Royal Society B: Biological Sciences. 370, 1660, 12 p., 20130387.

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

68 Citations (Scopus)

749 Downloads (Pure)

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

Ribeiro, Â. M., Zepeda Mendoza, M. L., Bertelsen, M. F., Kristensen, A. T., Jarvis, E. D., Gilbert, M. T. P. & Rodrigues da Fonseca, R. A., 30 Jun 2015, In: B M C Evolutionary Biology. 15, 8 p., 124.

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

9 Citations (Scopus)

519 Downloads (Pure)

Phylogenomic analyses data of the avian phylogenomics project

Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., Suh, A., Weber, C. C., Rodrigues da Fonseca, R. A., Alfaro Nuñez, L. A., Narula, N., Liu, L., Burt, D., Ellegren, H., Edwards, S. V., Stamatakis, A., & 7 othersMindell, D. P., Cracraft, J., Braun, E. L., Warnow, T., Wang, J., Gilbert, M. T. P. & Zhang, G., 12 Feb 2015, In: GigaScience. 4, 9 p., 4.

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

38 Citations (Scopus)

75 Downloads (Pure)

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

Azevedo, C. C., Guzman-Guillen, R., Martins, J. C., Osório, H., Vasconcelos, V., Rodrigues da Fonseca, R. A. & Campos, A., 1 Sept 2015, In: Marine Environmental Research. 110, p. 152-161 10 p.

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

14 Citations (Scopus)

Shotgun analysis of the marine mussel Mytilus edulis hemolymph proteome and mapping the innate immunity elements

Campos, A., Apraiz, I., Rodrigues da Fonseca, R. A. & Cristobal, S., 1 Dec 2015, In: Proteomics. 15, 23-24, p. 4021-4029 9 p.

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

23 Citations (Scopus)

The origin and evolution of maize in the Southwestern United States

Rodrigues da Fonseca, R. A., Smith, B. D., Wales, N., Cappellini, E., Skoglund, P., Fumagalli, M., Samaniego Castruita, J. A., Carøe, C., Avila Arcos, M. D. C., Hufnagel, D. E., Korneliussen, T. S., Garrett Vieira, F. J., Jakobsson, M., Arriaza, B., Willerslev, E., Nielsen, R., Hufford, M. B., Albrechtsen, A., Ross-Ibarra, J. & Gilbert, M. T. P., 8 Jan 2015, In: Nature Plants. 1, 5 p., 14003.

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

83 Citations (Scopus)

2014

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 othersMark, 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., Mar 2014, In: Invertebrate Neuroscience. 14, 1, p. 13-36 24 p.

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

81 Citations (Scopus)

53 Downloads (Pure)

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 othersHu, 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, R. A., Alfaro Nuñez, L. A., Schubert, M., 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, M. F., 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, E., Graves, G. R., Alström, P., Fjeldså, J., Mindell, D. P., Edwards, S. V., Braun, E. L., Rahbek, C., Burt, D. W., Houde, P., Zhang, Y., Yang, H., Wang, J., Jarvis, E. D., Gilbert, M. T. P. & Wang, J., 2014, In: Science. 346, 6215, p. 1311-1320 10 p.

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

483 Citations (Scopus)

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

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

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

4 Citations (Scopus)

2868 Downloads (Pure)

Proteomic Profiling of Cytosolic Glutathione Transferases from Three Bivalve Species: Corbicula fluminea, Mytilus galloprovincialis and Anodonta cygnea

Martins, J. C., Campos, A., Osorio, H., Rodrigues da Fonseca, R. A. & Vasconcelos, V., 27 Jan 2014, In: International Journal of Molecular Sciences (Online). 15, 2, p. 1887-1900 14 p.

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

18 Citations (Scopus)

49 Downloads (Pure)

The elusive nature of adaptive mitochondrial DNA evolution of an Arctic lineage prone to frequent introgression

Melo-Ferreira, J., Vilela, J., Fonseca, M. M., Rodrigues da Fonseca, R. A., Boursot, P. & Alves, P. C., Apr 2014, In: Genome Biology and Evolution. 6, 4, p. 886-896 11 p.

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

54 Citations (Scopus)

911 Downloads (Pure)

Whole-genome analyses resolve early branches in the tree of life of modern birds

Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., Suh, A., Weber, C. C., Rodrigues da Fonseca, R. A., Li, J., Zhang, F., Li, H., Zhou, L., Narula, N., Liu, L., Ganapathy, G., & 85 othersBoussau, B., Bayzid, M. S., Zavidovych, V., Subramanian, S., Gabaldón, T., Capella-Gutiérrez, S., Huerta-Cepas, J., Rekepalli, B., Terkelsen, K. M., Schierup, M. H., Lindow, B. E. K., Warren, W. C., Ray, D., Green, R. E., Bruford, M. W., Zhan, X., Dixon, A., Li, S., Li, N., Huang, Y., Derryberry, E. P., Bertelsen, M. F., Sheldon, F. H., Brumfield, R. T., Mello, C. V., Lovell, P. V., Wirthlin, M., Schneider, M. P. C., Prosdocimi, F., Samaniego Castruita, J. A., Velazquez, A. M. V., Alfaro Nuñez, L. A., Campos, P., Petersen, B., Sicheritz-Ponten, T., Pas, A., Bailey, T., Scofield, P., Bunce, M., Lambert, D. M., Zhou, Q., Perelman, P., Driskell, A. C., Shapiro, B., Xiong, Z., Zeng, Y., Liu, S., Li, Z., Liu, B., Wu, K., Xiao, J., Yinqi, X., Zheng, Q., Zhang, Y., Yang, H., Wang, J., Smeds, L., Rheindt, F. E., Braun, M., Fjeldså, J., Orlando, L. A. A., Barker, F. K., Jønsson, K. A., Johnson, W., Koepfli, K. P., O'Brien, S., Haussler, D., Ryder, O. A., Rahbek, C., Willerslev, E., Graves, G. R., Glenn, T. C., McCormack, J., Burt, D., Ellegren, H., Alström, P., Edwards, S. V., Stamatakis, A., Mindell, D. P., Cracraft, J., Braun, E. L., Warnow, T., Wang, J., Gilbert, M. T. P. & Zhang, G., 2014, In: Science. 346, 6215, p. 1320-1331 12 p.

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

958 Citations (Scopus)

2012

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 othersSchwarz, 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

42 Citations (Scopus)

63 Downloads (Pure)

Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins

Cappellini, E., Jensen, L. J., Szklarczyk, D. M., Ginolhac, A., da Fonseca, R. A. R., Stafford jr., T., Holen, S. R., Collins, M. J., Orlando, L. A. A., Willerslev, E., Gilbert, T. & Olsen, J. V., 3 Feb 2012, In: Journal of Proteome Research. 11, 2, p. 917-926 10 p.

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

126 Citations (Scopus)

2011

Positive selection on the killer whale mitogenome

Foote, A. D., Morin, P. A., Durban, J. W., Pitman, R. L., Wade, P., Willerslev, E., Gilbert, T. & Rodrigues da Fonseca, R. A., 23 Feb 2011, In: Biology Letters. 7, 1, p. 116-118 3 p.

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

79 Citations (Scopus)

2010

Positive selection on apoptosis related genes

Rodrigues da Fonseca, R. A., Kosiol, C., Vinař, T., Siepel, A. & Nielsen, R., 5 Feb 2010, In: FEBS Letters. 584, 3, p. 469-476 8 p.

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

30 Citations (Scopus)

Rute Andreia Rodrigues da Fonseca

Research output

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