Filipe Jorge Garrett Vieira

Filipe Jorge Garrett Vieira

Research Consultant

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    ORCID: 0000-0002-8464-7770

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    1. Published

      Parallel adaptation of rabbit populations to myxoma virus

      Alves, J. M., Carneiro, M., Cheng, J. Y., Matos, A. L. D., Rahman, M. M., Loog, L., Campos, P. F., Wales, N., Eriksson, A., Manica, A., Strive, T., Graham, S. C., Afonso, S., Bell, D. J., Belmont, L., Day, J. P., Fuller, S. J., Marchandeau, S., Palmer, W. J., Queney, G. & 8 others, Surridge, A. K., Vieira, Filipe Garrett, McFadden, G., Nielsen, Rasmus, Gilbert, M Thomas P, Esteves, P. J., Ferrand, N. & Jiggins, F. M., 2019, In: Science. 363, 6433

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

    2. Published

      Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens

      Barnett, R., Westbury, M. V., Sandoval-Velasco, M., Vieira, F. G., Jeon, S., Zazula, G., Martin, M. D., Ho, S. Y. W., Mather, N., Gopalakrishnan, S., Ramos-Madrigal, J., de Manuel, M., Zepeda-Mendoza, M. L., Antunes, A., Baez, A. C., De Cahsan, B., Larson, G., O’Brien, S. J., Eizirik, E., Johnson, W. E. & 11 others, Koepfli, K., Wilting, A., Fickel, J., Dalén, L., Lorenzen, Eline, Marques-Bonet, T., Hansen, Anders Johannes, KU, thw266, Bhak, J., Yamaguchi, N. & Gilbert, M Thomas P, 2020, In: Current Biology. 30, p. 5018-5025

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

    3. Published

      No longer locally extinct? Tracing the origins of a lion (Panthera leo) living in Gabon

      Barnett, R., Sinding, M. S., Vieira, Filipe Garrett, Mendoza, M. L. Z., Bonnet, M., Araldi, A., Kienast, I., Zambarda, A., Yamaguchi, N., Henschel, P. & Gilbert, M Thomas P, 2018, In: Conservation Genetics. 19, 3, p. 611-618 8 p.

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

    4. Published

      Genomic and proteomic identification of Late Holocene remains: setting baselines for Black Sea odontocetes

      Biard, V., Gol'din, P., Gladilina, E., Vishnyakova, K., McGrath, K., Vieira, Filipe Garrett, Wales, N., Fontaine, M. C., Speller, C. & Olsen, Morten Tange, Oct 2017, In: Journal of Archaeological Science: Reports. 15, p. 262-271 10 p.

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

    5. Published

      Palaeoproteomics identifies beaver fur in Danish high-status Viking Age burials - direct evidence of fur trade

      Brandt, Luise Ørsted, Taurozzi, Alberto John, Mackie, Meaghan, Sinding, Mikkel Holger Strander, Vieira, Filipe Garrett, Schmidt, A. L., Rimstad, C., Collins, Matthew James & Mannering, U., 2022, In: PLoS ONE. 17, 7, 14 p., e0270040.

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

    6. Published

      Ancient DNA analysis of Scandinavian medieval drinking horns and the horn of the last aurochs bull

      Bro-Jørgensen, M. H., Carøe, C., Vieira, Filipe Garrett, Nestor, S., Hallström, A., Gregersen, K. M., Etting, V., Gilbert, M Thomas P & Sinding, Mikkel Holger Strander, 1 Nov 2018, In: Journal of Archaeological Science. 99, p. 47-54 8 p.

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

    7. Published

      Evolution of genes and genomes on the Drosophila phylogeny. Drosophila 12 Genomes Consortium

      Clark, A. G., Eisen, M. B., Smith, D. R., Bergman, C. M., Oliver, B., Markow, T. A., Kaufman, T. C., Kellis, M., Gelbart, W., Iyer, V. N., Pollard, D. A., Sackton, T. B., Larracuente, A. M., Singh, N. D., Abad, J. P., Abt, D. N., Adryan, B., Aguade, M., Akashi, H., Anderson, W. W. & 31 others, Aquadro, C. F., Ardell, D. H., Arguello, R., Artieri, C. G., Barbash, D. A., Barker, D., Barsanti, P., Batterham, P., Batzoglou, S., Begun, D., Bhutkar, A., Blanco, E., Bosak, S. A., Bradley, R. K., Brand, A. D., Brent, M. R., Brooks, A. N., Brown, R. H., Butlin, R. K., Caggese, C., Calvi, B. R., Bernardo de Carvalho, A., Caspi, A., Castrezana, S., Celniker, S. E., Chang, J. L., Garcia, A. C. L., Nielsen, Rasmus, Pedersen, Jakob Skou, Vieira, Filipe Garrett & Drosophila 12 Genomes Consortium, D. 1. G. C., 2007, In: Nature. 450, 7167, p. 203-18 15 p.

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

    8. Published

      Evolutionary genomics and conservation of the endangered Przewalski's horse

      Der Sarkissian, C., Ermini, L., Schubert, M., Yang, M. A., Sanz, P. L., Fumagalli, M., Jónsson, H., Bar-Gal, G. K., Albrechtsen, A., Garrett Vieira, F. J., Petersen, B., Ginolhac, A., Seguin-Orlando, A., Magnussen, K., Fages, A. A., Gamba, C., Lorente-Galdos, B., Polani, S., Steiner, C., Neuditschko, M. & 17 others, Jagannathan, V., Feh, C., Greenblatt, C. L., Ludwig, A., Abramson, N. I., Zimmermann, W., Schafberg, R., Tikhonov, A., Sicheritz-Ponten, T., Willerslev, Eske, Marques-Bonet, T., Ryder, O. A., McCue, M., Rieder, S., Leeb, T., Slatkin, M. & Orlando, L. A. A., 2015, In: Current Biology. 25, 19, p. 2577-2583 7 p.

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

    9. Published

      Genome-culture coevolution promotes rapid divergence of killer whale ecotypes

      Foote, A. D., Vijay, N., Avila Arcos, M. D. C., Baird, R. W., Durban, J. W., Fumagalli, M., Gibbs, R. A., Hanson, M. B., Korneliussen, Thorfinn Sand, Martin, M. D., Robertson, K. M., Sousa, V. C., Vieira, Filipe Garrett, Vinař, T., Wade, P., Worley, K. C., Excoffier, L., Morin, P. A., Gilbert, M Thomas P & Wolf, J. B. W., May 2016, In: Nature Communications. 7, 12 p., 11693.

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

    10. Published

      ngsLD: evaluating linkage disequilibrium using genotype likelihoods

      Fox, E. A., Wright, A. E., Fumagalli, M. & Vieira, Filipe Garrett, 1 Oct 2019, In: Bioinformatics (Oxford, England). 35, 19, p. 3855-3856 2 p.

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

    11. Published

      ngsTools : methods for population genetics analyses from next-generation sequencing data

      Fumagalli, M., Vieira, Filipe Garrett, Linderoth, T. & Nielsen, Rasmus, 2014, In: Bioinformatics. 30, 10, p. 1486-1487 2 p.

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

    12. Published

      Quantifying population genetic differentiation from next-generation sequencing data

      Fumagalli, M., Vieira, Filipe Garrett, Korneliussen, Thorfinn Sand, Linderoth, T., Huerta-Sánchez, E., Albrechtsen, Anders & Nielsen, Rasmus, Nov 2013, In: Genetics. 195, 3, p. 979-992 14 p.

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

    13. Published

      A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data

      Gabrielaite, M., Torp, M., Rasmussen, M., Andreu-Sánchez, S., Vieira, Filipe Garrett, Pedersen, C., Kinalis, S., Madsen, M., Yde, C., Rønn, O. L., Marvig, R., Østrup, O., Rossing, Caroline Maria, Nielsen, Finn Cilius, Winther, Ole & Bagger, F. O., 2021, bioRxiv, 29 p.

      Research output: Working paper › Preprint › Research

    14. Published

      A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data

      Gabrielaite, M., Torp, M. H., Rasmussen, Malthe Sebro, Andreu-Sánchez, S., Vieira, Filipe Garrett, Pedersen, C. B., Kinalis, S., Madsen, M. B., Kodama, M., Demircan, G. S., Simonyan, A., Yde, C. W., Olsen, L. R., Marvig, R. L., Østrup, O., Rossing, Caroline Maria, Nielsen, Finn Cilius, Winther, Ole & Bagger, F. O., 2021, In: Cancers. 13, 24, 6283.

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

    15. Published

      Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation

      Vieira, Filipe Garrett, Fumagalli, M., Albrechtsen, Anders & Nielsen, Rasmus, 2013, In: Genome Research. 23, p. 1852-1861 10 p.

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

    16. Published

      Estimating IBD tracts from low coverage NGS data

      Vieira, Filipe Garrett, Albrechtsen, Anders & Nielsen, Rasmus, 2016, In: Bioinformatics. 32, 14, p. 2096-2102 7 p.

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

    17. Published

      Improving the estimation of genetic distances from Next-Generation Sequencing data

      Vieira, Filipe Garrett, Lassalle, F., Korneliussen, Thorfinn Sand & Fumagalli, M., 2016, In: Biological Journal of the Linnean Society. 117, 1, p. 139-149 11 p.

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

    18. Published

      The population genomic legacy of the second plague pandemic

      Gopalakrishnan, S., Ebenesersdóttir, S. S., Lundstrøm, I. K. C., Turner-Walker, G., Moore, K. H. S., Luisi, P., Margaryan, A., Martin, M. D., Ellegaard, M. R., Magnússon, Ó., Sigurðsson, Á., Snorradóttir, S., Magnúsdóttir, D. N., Laffoon, J. E., van Dorp, L., Liu, X., Moltke, I., Ávila-Arcos, M. C., Schraiber, J. G., Rasmussen, S. & 40 others, Juan, D., Gelabert, P., de-Dios, T., Fotaki, Anna Katerina, Iraeta Orbegozo, Miren, Vågene, Åshild Joanne, Denham, S. D., Christophersen, A., Stenøien, H. K., Vieira, Filipe Garrett, Liu, Shanlin, Günther, T., Kivisild, T., Moseng, O. G., Skar, B., Cheung, C., Sandoval-Velasco, Marcela, Wales, N., Schroeder, Hannes, Campos, P. F., Guðmundsdóttir, V. B., Sicheritz-Pontén, Thomas, Petersen, Bent, Halgunset, J., Gilbert, E., Cavalleri, G. L., Hovig, E., Kockum, I., Olsson, T., Alfredsson, L., Hansen, Thomas Folkmann, Werge, Thomas, Willerslev, Eske, Balloux, F., Marques-Bonet, T., Lalueza-Fox, C., Nielsen, Rasmus, Stefánsson, K., Helgason, A. & Gilbert, M Thomas P, 2022, In: Current Biology. 32, 21, p. 4743-4751.e6

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

    19. Published

      Interspecific Gene Flow Shaped the Evolution of the Genus Canis

      Gopalakrishnan, S., Sinding, M. H. S., Ramos-Madrigal, J., Niemann, J., Samaniego Castruita, J. A., Vieira, F. G., Carøe, C., Montero, M. D. M., Kuderna, L., Serres, A., González-Basallote, V. M., Liu, Y. H., Wang, G. D., Marques-Bonet, T., Mirarab, S., Fernandes, C., Gaubert, P., Koepfli, K. P., Budd, J., Rueness, E. K. & 7 others, Heide-Jørgensen, M. P., Petersen, Bent, Sicheritz-Ponten, T., Bachmann, L., Wiig, Ø., Hansen, Anders Johannes & Gilbert, M. T. P., 2018, In: Current Biology. 28, 21, p. 3441-3449

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

    20. Published

      Genomic insights into the Ixodes scapularis tick vector of Lyme disease

      Gulia-Nuss, M., Nuss, A. B., Meyer, J. M., Sonenshine, D. E., Roe, R. M., Waterhouse, R. M., Sattelle, D. B., de la Fuente, J., Ribeiro, J. M., Megy, K., Thimmapuram, J., Miller, J. R., Walenz, B. P., Koren, S., Hostetler, J. B., Thiagarajan, M., Joardar, V. S., Hannick, L. I., Bidwell, S., Hammond, M. P. & 73 others, Young, S., Zeng, Q., Abrudan, J. L., Almeida, F. C., Ayllón, N., Bhide, K., Bissinger, B. W., Bonzon-Kulichenko, E., Buckingham, S. D., Caffrey, D. R., Caimano, M. J., Croset, V., Driscoll, T., Gilbert, D., Gillespie, J. J., Giraldo-Calderón, G. I., Grabowski, J. M., Jiang, D., Khalil, S. M. S., Kim, D., Kocan, K. M., Koči, J., Kuhn, R. J., Kurtti, T. J., Lees, K., Lang, E. G., Kennedy, R. C., Kwon, H., Perera, R., Qi, Y., Radolf, J. D., Sakamoto, J. M., Sánchez-Gracia, A., Severo, M. S., Silverman, N., Šimo, L., Tojo, M., Tornador, C., Van Zee, J. P., Vázquez, J., Vieira, Filipe Garrett, Villar, M., Wespiser, A. R., Yang, Y., Zhu, J., Arensburger, P., Pietrantonio, P. V., Barker, S. C., Shao, R., Zdobnov, E. M., Hauser, Frank, Grimmelikhuijzen, Cornelis (Cok), Park, Y., Rozas, J., Benton, R., Pedra, J. H. F., Nelson, D. R., Unger, M. F., Tubio, J. M. C., Tu, Z., Robertson, H. M., Shumway, M., Sutton, G., Wortman, J. R., Lawson, D., Wikel, S. K., Nene, V. M., Fraser, C. M., Collins, F. H., Birren, B., Nelson, K. E., Caler, E. & Hill, C. A., 2016, In: Nature Communications. 7, 13 p., 10507.

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

    21. Published

      Germline RET Leu56Met Variant Is Likely Not Causative of Multiple Endocrine Neoplasia Type 2

      Hansen, A. R., Borgwardt, L., Rasmussen, Å. K., Godballe, C., Poulsen, M. M., Vieira, Filipe Garrett, Mathiesen, J. S. & Rossing, Caroline Maria, 2021, In: Frontiers in Endocrinology. 12, 764512.

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

    22. Published

      Conservation genetics of the critically endangered Siamese rosewood (Dalbergia cochinchinensis): recommendations for management and sustainable use

      Hartvig, Ida, So, T., Changtragoon, S., Tran, H. T., Bouamanivong, S., Ogden, R., Senn, H., Vieira, Filipe Garrett, Turner, F., Talbot, R., Theilade, Ida, Nielsen, Lene Rostgaard & Kjær, Erik Dahl, 2020, In: Conservation Genetics. 21, p. 677-692

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

    23. Published

      BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines

      Hernandez, Y., Bernstein, R., Pagan, P., Vargas, L., McCaig, W., Ramrattan, G., Akther, S., Larracuente, A., Di, L., Vieira, Filipe Garrett & Qiu, W., 2 Mar 2018, In: B M C Bioinformatics. 19, 7 p., 76.

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

    24. Published

      Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes

      Iwanycki Ahlstrand, N., Gopalakrishnan, S., Vieira, F. G., Bieker, V. C., Meudt, H. M., Dunbar-Co, S., Rothfels, C. J., Martinez-Swatson, K. A., Maldonado, C., Hassemer, G., Shipunov, A., Bowers, M. D., Gardner, E., Xu, M., Ghorbani, A., Amano, M., Grace, O. M., Pringle, J. S., Bishop, M., Manzanilla, V. & 18 others, Cotrim, H., Blaney, S., Zubov, D., Choi, H., Yesil, Y., Bennett, B., Vimolmangkang, S., El-Seedi, H. R., Staub, P. O., Li, Z., Boldbaatar, D., Hislop, M., Caddy, L. J., Muasya, A. M., Saslis-Lagoudakis, C. H., Gilbert, M Thomas P, Zerega, N. J. C. & Rønsted, Nina, 2022, In: Frontiers in Plant Science. 13, 16 p., 838166.

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

    25. Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle

      Kirkness, E. F., Haas, B. J., Sun, W., Braig, H. R., Perotti, M. A., Clark, J. M., Lee, S. H., Robertson, H. M., Kennedy, R. C., Elhaik, E., Gerlach, D., Kriventseva, E. V., Elsik, C. G., Graur, D., Hill, C. A., Veenstra, J. A., Walenz, B., Tubío, J. M. C., Ribeiro, J. M. C., Rozas, J. & 51 others, Johnston, J. S., Reese, J. T., Popadic, A., Tojo, M., Raoult, D., Reed, D. L., Tomoyasu, Y., Krause, E., Mittapalli, O., Margam, V. M., Li, H. M., Meyer, J. M., Johnson, R. M., Romero-Severson, J., VanZee, J. P., Alvarez-Ponce, D., Vieira, Filipe Garrett, Aguadé, M., Guirao-Rico, S., Anzola, J. M., Yoon, K. S., Strycharz, J. P., Unger, M. F., Christley, S., Lobo, N. F., Seufferheld, M. J., Wang, N. K., Dasch, G. A., Struchiner, C. J., Madey, G., Hannick, L. I., Bidwell, S., Joardar, V., Caler, E., Shao, R., Barker, S. C., Cameron, S., Bruggner, R. V., Regier, A., Johnson, J., Viswanathan, L., Utterback, T. R., Sutton, G. G., Lawson, D., Waterhouse, R. M., Venter, J. C., Strausberg, R. L., Berenbaum, M. R., Collins, F. H., Zdobnov, E. M. & Pittendrigh, B. R., 6 Jul 2010, In: Proceedings of the National Academy of Sciences of the United States of America. 107, 27, p. 12168-12173 6 p.

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

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    ID: 105377460