Ensembl and enabling genetics and genomics research in farmed animal species

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    Analyses of pig genomes provide insight into porcine demography and evolution

    Groenen, M. A. M., Archibald, A. L., Uenishi, H., Tuggle, C. K., Takeuchi, Y., Rothschild, M. F., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H-J., Li, S., Larkin, D. M., Kim, H., Frantz, L. A. F., Caccamo, M., Ahn, H., Aken, B. L., Anselmo, A., Anthon, C., Auvil, L. & 116 others, Badaoui, B., Beattie, C. W., Bendixen, C., Berman, D., Blecha, F., Blomberg, J., Bolund, L., Bosse, M., Botti, S., Zhan Bujie, N. V., Bystrom, M., Capitanu, B., Carvalho-Silva, D., Chardon, P., Chen, C., Cheng, R., Choi, S-H., Chow, W., Clark, R. C., Clee, C., Crooijmans, R. P. M. A., Dawson, H. D., Dehais, P., De Sapio, F., Dibbits, B., Drou, N., Du, Z-Q., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G., Fowler, K. E., Fredholm, M., Fritz, E., Gilbert, J. G. R., Giuffra, E., Gorodkin, J., Griffin, D. K., Harrow, J. L., Hayward, A., Howe, K., Hu, Z-L., Humphray, S. J., Hunt, T., Hornshoj, H., Jeon, J-T., Jern, P., Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Kim, J., Kim, J-H., Kim, K-W., Kim, T-H., Larson, G., Lee, K., Lee, K-T., Leggett, R., Lewin, H. A., Li, Y., Liu, W., Loveland, J. E., Lu, Y., Lunney, J. K., Ma, J., Madsen, O., Mann, K., Matthews, L., McLaren, S., Morozumi, T., Murtaugh, M. P., Narayan, J., Dinh Truong Nguyen, N. V., Ni, P., Oh, S-J., Onteru, S., Panitz, F., Park, E-W., Park, H-S., Pascal, G., Paudel, Y., Perez-Enciso, M., Ramirez-Gonzalez, R., Reecy, J. M., Rodriguez-Zas, S., Rohrer, G. A., Rund, L., Sang, Y., Schachtschneider, K., Schraiber, J. G., Schwartz, J., Scobie, L., Scott, C., Searle, S., Servin, B., Southey, B. R., Sperber, G., Stadler, P., Sweedler, J. V., Tafer, H., Thomsen, B., Wali, R., Wang, J., Wang, J., White, S., Xu, X., Yerle, M., Zhang, G., Zhang, J., Zhang, J., Zhao, S., Rogers, J., Churcher, C. & Schook, L. B., 15 Nov 2012, In: Nature. 491, 7424, p. 393-398 6 p.

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  • Avianbase: a community resource for bird genomics

    Eory, L., Gilbert, M. T. P., Li, C., Li, B., Archibald, A., Aken, B. L., Zhang, G., Jarvis, E., Flicek, P. & Burt, D. W., 29 Jan 2015, In: Genome Biology. 16, 1, 21.

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  • Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

    The FAANG Consortium, 1 Dec 2015, In: Genome Biology. 16, 1, 57.

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  • Epithelial, metabolic and innate immunity transcriptomic signatures differentiating the rumen from other sheep and mammalian gastrointestinal tract tissues

    Xiang, R., Oddy, V. H., Archibald, A. L., Vercoe, P. E. & Dalrymple, B. P., 8 Mar 2016, In: PeerJ. 4, e1762.

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  • Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome

    Robert, C., Kapetanovic, R., Beraldi, D., Watson, M., Archibald, A. L. & Hume, D. A., 20 Nov 2015, In: BMC Genomics. 16, 1, p. 970

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  • Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly

    O'Connor, R. E., Fonseka, G., Frodsham, R., Archibald, A. L., Lawrie, M., Walling, G. A. & Griffin, D. K., Aug 2017, In: Animal Genetics. 48, 4, p. 395-403

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  • Strong signatures of selection in the domestic pig genome

    Rubin, C-J., Megens, H-J., Barrio, A. M., Maqbool, K., Sayyab, S., Schwochow, D., Wang, C., Carlborg, O., Jern, P., Jorgensen, C. B., Archibald, A. L., Fredholm, M., Groenen, M. A. M. & Andersson, L., 27 Nov 2012, In: Proceedings of the National Academy of Sciences. 109, 48, p. 19529-19536 8 p.

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  • Structural and functional annotation of the porcine immunome

    Dawson, H. D., Loveland, J. E., Pascal, G., Gilbert, J. G. R., Uenishi, H., Mann, K. M., Sang, Y., Zhang, J., Carvalho-Silva, D., Hunt, T., Hardy, M., Hu, Z., Zhao, S-H., Anselmo, A., Shinkai, H., Chen, C., Badaoui, B., Berman, D., Amid, C., Kay, M. & 30 others, Lloyd, D., Snow, C., Morozumi, T., Cheng, R. P-Y., Bystrom, M., Kapetanovic, R., Schwartz, J. C., Kataria, R., Astley, M., Fritz, E., Steward, C., Thomas, M., Wilming, L., Toki, D., Archibald, A. L., Bed'Hom, B., Beraldi, D., Huang, T-H., Ait-Ali, T., Blecha, F., Botti, S., Freeman, T. C., Giuffra, E., Hume, D. A., Lunney, J. K., Murtaugh, M. P., Reecy, J. M., Harrow, J. L., Rogel-Gaillard, C. & Tuggle, C. K., 15 May 2013, In: BMC Genomics. 14, 16 p., ARTN 332.

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  • The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

    Huang, Y., Burt, D., Li, Y., Chen, H., Zhang, Y., Qian, W., Kim, H., Gan, S., Zhao, Y., Li, J., Yi, K., Feng, H., Zhu, P., Li, B., Liu, Q., Fairley, S., Magor, K., Du, Z., Hu, X., Goodman, L. & 30 others, Tafer, H., Vignal, A., Lee, T., Kim, K-W., Sheng, Z., An, Y., Searle, S., Herrero, J., Groenen, M. A., Crooijmans, R. P., Faraut, T., Cai, Q., Webster, R., Aldridge, J., Warren, W. C., Bartschat, S., Kehr, S., Marz, M., Stadler, P., Smith, J., Kraus, R., Zhao, Y., Ren, L., Fei, J., Morisson, M., Kaiser, P., Griffin, D. K., Pitel, F., Wang, J. & Li, N., 2013, In: Nature Genetics. 45, 7, p. 776-U797

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  • The sheep genome illuminates biology of the rumen and lipid metabolism

    Jiang, Y., Xie, M., Chen, W., Talbot, R., Maddox, J. F., Faraut, T., Wu, C., Muzny, D. M., Li, Y., Zhang, W., Stanton, J-A., Brauning, R., Barris, W. C., Hourlier, T., Aken, B. L., Searle, S. M. J., Adelson, D. L., Bian, C., Cam, G. R., Chen, Y. & 53 others, Cheng, S., DeSilva, U., Dixen, K., Dong, Y., Fan, G., Franklin, I. R., Fu, S., Fuentes-Utrilla, P., Guan, R., Highland, M. A., Holder, M. E., Huang, G., Ingham, A. B., Jhangiani, S. N., Kalra, D., Kovar, C. L., Lee, S. L., Liu, W., Liu, X., Lu, C., Lv, T., Mathew, T., McWilliam, S., Menzies, M., Pan, S., Robelin, D., Servin, B., Townley, D., Wang, W., Wei, B., White, S. N., Yang, X., Ye, C., Yue, Y., Zeng, P., Zhou, Q., Hansen, J. B., Kristiansen, K., Gibbs, R. A., Flicek, P., Warkup, C. C., Jones, H. E., Oddy, V. H., Nicholas, F. W., McEwan, J. C., Kijas, J. W., Wang, J., Worley, K. C., Archibald, A. L., Cockett, N., Xu, X., Wang, W. & Dalrymple, B. P., 6 Jun 2014, In: Science. 344, 6188, p. 1168-1173 6 p.

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  • Third Report on Chicken Genes and Chromosomes 2015

    Schmid, M., Smith, J., Burt, D. W., Aken, B. L., Antin, P. B., Archibald, A. L., Ashwell, C., Blackshear, P. J., Boschiero, C., Brown, C. T., Burgess, S. C., Cheng, H. H., Chow, W., Coble, D. J., Cooksey, A., Crooijmans, R. P. M. A., Damas, J., Davis, R. V. N., De Koning, D., Delany, M. E. & 84 others, Derrien, T., Desta, T. T., Dunn, I. C., Dunn, M., Ellegren, H., Eory, L., Erb, I., Farre, M., Fasold, M., Fleming, D., Flicek, P., Fowler, K. E., Fresard, L., Froman, D. P., Garceau, V., Gardner, P. P., Gheyas, A. A., Griffin, D. K., Groenen, M. A. M., Haaf, T., Hanotte, O., Hart, A., Hasler, J., Hedges, S. B., Hertel, J., Howe, K., Hubbard, A., Hume, D. A., Kaiser, P., Kedra, D., Kemp, S., Klopp, C., Kniel, K. E., Kuo, R., Lagarrigue, S., Lamont, S. J., Larkin, D. M., Lawal, R. A., Markland, S. M., Mccarthy, F., Mccormack, H. A., Mcpherson, M. C., Motegi, A., Muljo, S. A., Munsterberg, A., Nag, R., Nanda, I., Neuberger, M., Nitsche, A., Notredame, C., Noyes, H., O''connor, R., O''hare, E. A., Oler, A. J., Ommeh, S. C., Pais, H., Persia, M., Pitel, F., Preeyanon, L., Prieto Barja, P., Pritchett, E. M., Rhoads, D. D., Robinson, C. M., Romanov, M. N., Rothschild, M., Roux, P., Schmidt, C. J., Schneider, A., Schwartz, M., Searle, S. M., Skinner, M. A., Smith, C. A., Stadler, P. F., Steeves, T. E., Steinlein, C., Sun, L., Takata, M., Ulitsky, I., Wang, Q., Wang, Y., Warren, W. C., Wood, J. M. D., Wragg, D. & Zhou, H., Aug 2015, In: Cytogenetic and Genome Research. 145, 2, p. 78-179

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