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  • 2020

    Illuminating the dark side of the human transcriptome with long read transcript sequencing

    Kuo, R., Cheng, Y., Zhang, R., Brown, J. W. S., Smith, J., Archibald, A. & Burt, D., 30 Oct 2020, In: BMC Genomics. 751 (2020) .

    Research output: Contribution to journalArticlepeer-review

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  • Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0)

    Salavati, M., Caulton, A., Clark, R., Gazova, I., Smith, T. P. L., Worley, K. C., Cockett, N. E., Archibald, A., Clarke, S. M., Murdoch, B. & Clark, E., 23 Oct 2020, (E-pub ahead of print) In: Frontiers in genetics.

    Research output: Contribution to journalArticlepeer-review

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  • Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication

    Dutta, P., Talenti, A., Young, R., Jayaraman, S., Callaby, R., Jadhav, S. K., Dhanikachalam, V., Manikandan, M., Biswa, B. B., Low, W. Y., Williams, J. L., Cook, E., Toye, P., Wall, E., Djikeng, A., Marshall, K., Archibald, A., Gokhale, S., Hume, D. & Prendergast, J., 21 Sep 2020, (E-pub ahead of print) In: Nature Communications. 11, 13 p., 4739 (2020).

    Research output: Contribution to journalArticlepeer-review

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  • Open Access
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  • An improved pig reference genome sequence to enable pig genetics and genomics research

    Warr, A., Affara, N., Aken, B., Beiki, H., Bickhart, D. M., Billis, K., Chow, W., Eory, L., Finlayson, H. A., Flicek, P., Girón, C. G., Griffin, D. K., Hall, R., Hannum, G., Hourlier, T., Howe, K., Hume, D. A., Izuogu, O., Kim, K., Koren, S. & 20 others, Liu, H., Manchanda, N., Martin, F. J., Nonneman, D. J., O'Connor, R. E., Phillippy, A. M., Rohrer, G. A., Rosen, B. D., Rund, L. A., Sargent, C. A., Schook, L. B., Schroeder, S. G., Schwartz, A. S., Skinner, B. M., Talbot, R., Tseng, E., Tuggle, C. K., Watson, M., Smith, T. P. L. & Archibald, A. L., 16 Jun 2020, (E-pub ahead of print) In: GigaScience. 9, 6, p. 1-14 14 p.

    Research output: Contribution to journalArticlepeer-review

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  • Correction to: Genome-wide SNP data unveils the globalization of domesticated pigs

    Yang, B., Cui, L., Perez-Enciso, M., Traspov, A., Crooijmans, R. P. M. A., Zinovieva, N., Schook, L. B., Archibald, A., Gatphayak, K., Knorr, C., Triantafyllidis, A., Alexandri, P., Semiadi, G., Hanotte, O., Dias, D., Dovč, P., Uimari, P., Iacolina, L., Scandura, M., Groenen, M. A. M. & 2 others, Huang, L. & Megens, H-J., 4 Jun 2020, In: Genetics Selection Evolution. 52, 1, p. 30

    Research output: Contribution to journalArticlepeer-review

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  • Metagenomic sequencing of clinical samples reveals a single widespread clone of Lawsonia intracellularis responsible for porcine proliferative enteropathy.

    Bengtsson, R., Wee, B., Yebra, G., Bacigalupe, R., Watson, E., Guedes, R. M. C., Jacobson, M., Stadejek, T., Archibald, A., Fitzgerald, R. & Ait-Ali, T., 2 Apr 2020, In: Microbial Genomics.

    Research output: Contribution to journalArticlepeer-review

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  • Functional annotation of the transcriptome of the pig, Sus scrofa, based upon network analysis of an RNAseq transcriptional atlas

    Summers, K., Bush, S., Wu, C., Su, A., Muriuki, C., Clark, E., Finlayson, H., Eory, L., Waddell, L., Talbot, R., Archibald, A. & Hume, D., 14 Feb 2020, In: Frontiers in genetics.

    Research output: Contribution to journalArticlepeer-review

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  • 2021

    Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions

    Salavati, M., Woolley, S., Cortés Araya, Y., Halstead, M., Stenhouse, C., Johnsson, M., Ashworth, C., Archibald, A., Donadeu, X., Hassan, M. & Clark, E., 13 Dec 2021, (E-pub ahead of print) In: G3: Genes | Genomes | Genetics.

    Research output: Contribution to journalArticlepeer-review

    Open Access
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  • Characterisation of autophagy disruption in the ileum of pigs infected with Lawsonia intracellularis

    Salvesen, H. A., Sargison, F. A., Archibald, A. L. & Ait-Ali, T., 20 Oct 2021, (E-pub ahead of print) In: Veterinary Research Communications.

    Research output: Contribution to journalArticlepeer-review

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  • Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

    Grapotte, M., Saraswat, M., Bessière, C., Menichelli, C., Ramilowski, J. A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-sueki, H., Frith, M., Abugessaisa, I., Aitken, S. & 471 others, Aken, B. L., Alam, I., Alam, T., Alasiri, R., Alhendi, A. M. N., Alinejad-rokny, H., Alvarez, M. J., Andersson, R., Arakawa, T., Araki, M., Arbel, T., Archer, J., Archibald, A. L., Arner, E., Arner, P., Asai, K., Ashoor, H., Astrom, G., Babina, M., Baillie, J. K., Bajic, V. B., Bajpai, A., Baker, S., Baldarelli, R. M., Balic, A., Bansal, M., Batagov, A. O., Batzoglou, S., Beckhouse, A. G., Beltrami, A. P., Beltrami, C. A., Bertin, N., Bhattacharya, S., Bickel, P. J., Blake, J. A., Blanchette, M., Bodega, B., Bonetti, A., Bono, H., Bornholdt, J., Bttcher, M., Bougouffa, S., Boyd, M., Breda, J., Brombacher, F., Brown, J. B., Bult, C. J., Burroughs, A. M., Burt, D. W., Busch, A., Caglio, G., Califano, A., Cameron, C. J., Cannistraci, C. V., Carbone, A., Carlisle, A. J., Carninci, P., Carter, K. W., Cesselli, D., Chang, J., Chen, J. C., Chen, Y., Chierici, M., Christodoulou, J., Ciani, Y., Clark, E. L., Coskun, M., Dalby, M., Dalla, E., Daub, C. O., Davis, C. A., De Hoon, M. J. L., De Rie, D., Denisenko, E., Deplancke, B., Detmar, M., Deviatiiarov, R., Di Bernardo, D., Diehl, A. D., Dieterich, L. C., Dimont, E., Djebali, S., Dohi, T., Dostie, J., Drablos, F., Edge, A. S. B., Edinger, M., Ehrlund, A., Ekwall, K., Elofsson, A., Endoh, M., Enomoto, H., Enomoto, S., Faghihi, M., Fagiolini, M., Farach-carson, M. C., Faulkner, G. J., Favorov, A., Fernandes, A. M., Ferrai, C., Forrest, A. R. R., Forrester, L. M., Forsberg, M., Fort, A., Francescatto, M., Freeman, T. C., Frith, M., Fukuda, S., Funayama, M., Furlanello, C., Furuno, M., Furusawa, C., Gao, H., Gazova, I., Gebhard, C., Geier, F., Geijtenbeek, T. B. H., Ghosh, S., Ghosheh, Y., Gingeras, T. R., Gojobori, T., Goldberg, T., Goldowitz, D., Gough, J., Greco, D., Gruber, A. J., Guhl, S., Guigo, R., Guler, R., Gusev, O., Gustincich, S., Ha, T. J., Haberle, V., Hale, P., Hallstrom, B. M., Hamada, M., Handoko, L., Hara, M., Harbers, M., Harrow, J., Harshbarger, J., Hase, T., Hasegawa, A., Hashimoto, K., Hatano, T., Hattori, N., Hayashi, R., Hayashizaki, Y., Herlyn, M., Hettne, K., Heutink, P., Hide, W., Hitchens, K. J., Sui, S. H., ’t Hoen, P. A. C., Hon, C. C., Hori, F., Horie, M., Horimoto, K., Horton, P., Hou, R., Huang, E., Huang, Y., Hugues, R., Hume, D., Ienasescu, H., Iida, K., Ikawa, T., Ikemura, T., Ikeo, K., Inoue, N., Ishizu, Y., Ito, Y., Itoh, M., Ivshina, A. V., Jankovic, B. R., Jenjaroenpun, P., Johnson, R., Jorgensen, M., Jorjani, H., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kajiyama, K., Kaliyaperumal, R., Kaminuma, E., Kanaya, T., Kaneda, H., Kapranov, P., Kasianov, A. S., Kasukawa, T., Katayama, T., Kato, S., Kawaguchi, S., Kawai, J., Kawaji, H., Kawamoto, H., Kawamura, Y. I., Kawasaki, S., Kawashima, T., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L., Kiryu, H., Kishima, M., Kitajima, H., Kitamura, T., Kitano, H., Klaric, E., Klepper, K., Klinken, S. P., Kloppmann, E., Knox, A. J., Kodama, Y., Kogo, Y., Kojima, M., Kojima, S., Komatsu, N., Komiyama, H., Kono, T., Koseki, H., Koyasu, S., Kratz, A., Kukalev, A., Kulakovskiy, I., Kundaje, A., Kunikata, H., Kuo, R., Kuo, T., Kuraku, S., Kuznetsov, V. A., Kwon, T. J., Larouche, M., Lassmann, T., Law, A., Le-cao, K., Lecellier, C., Lee, W., Lenhard, B., Lennartsson, A., Li, K., Li, R., Lilje, B., Lipovich, L., Lizio, M., Lopez, G., Magi, S., Mak, G. K., Makeev, V., Manabe, R., Mandai, M., Mar, J., Maruyama, K., Maruyama, T., Mason, E., Mathelier, A., Matsuda, H., Medvedeva, Y. A., Meehan, T. F., Mejhert, N., Meynert, A., Mikami, N., Minoda, A., Miura, H., Miyagi, Y., Miyawaki, A., Mizuno, Y., Morikawa, H., Morimoto, M., Morioka, M., Morishita, S., Moro, K., Motakis, E., Motohashi, H., Mukarram, A. K., Mummery, C. L., Mungall, C. J., Murakawa, Y., Muramatsu, M., Murata, M., Nagasaka, K., Nagase, T., Nakachi, Y., Nakahara, F., Nakai, K., Nakamura, K., Nakamura, Y., Nakamura, Y., Nakazawa, T., Nason, G. P., Nepal, C., Nguyen, Q. H., Nielsen, L. K., Nishida, K., Nishiguchi, K. M., Nishiyori, H., Nitta, K., Noguchi, S., Noma, S., Notredame, C., Ogishima, S., Ohkura, N., Ohno, H., Ohshima, M., Ohtsu, T., Okada, Y., Okada-hatakeyama, M., Okazaki, Y., Oksvold, P., Orlando, V., Ow, G. S., Ozturk, M., Pachkov, M., Paparountas, T., Parihar, S. P., Park, S., Pascarella, G., Passier, R., Persson, H., Philippens, I. H., Piazza, S., Plessy, C., Pombo, A., Ponten, F., Poulain, S., Poulsen, T. M., Pradhan, S., Prezioso, C., Pridans, C., Qin, X., Quackenbush, J., Rackham, O., Ramilowski, J., Ravasi, T., Rehli, M., Rennie, S., Rito, T., Rizzu, P., Robert, C., Roos, M., Rost, B., Roudnicky, F., Roy, R., Rye, M. B., Sachenkova, O., Saetrom, P., Sai, H., Saiki, S., Saito, M., Saito, A., Sakaguchi, S., Sakai, M., Sakaue, S., Sakaue-sawano, A., Sandelin, A., Sano, H., Sasamoto, Y., Sato, H., Saxena, A., Saya, H., Schafferhans, A., Schmeier, S., Schmidl, C., Schmocker, D., Schneider, C., Schueler, M., Schultes, E. A., Schulze-tanzil, G., Semple, C. A., Seno, S., Seo, W., Sese, J., Severin, J., Sheng, G., Shi, J., Shimoni, Y., Shin, J. W., Simonsanchez, J., Sivertsson, A., Sjostedt, E., Soderhall, C., Laurent, G. S., Stoiber, M. H., Sugiyama, D., Summers, K. M., Suzuki, A. M., Suzuki, H., Suzuki, K., Suzuki, M., Suzuki, N., Suzuki, T., Swanson, D. J., Swoboda, R. K., Tagami, M., Taguchi, A., Takahashi, H., Takahashi, M., Takamochi, K., Takeda, S., Takenaka, Y., Tam, K. T., Tanaka, H., Tanaka, R., Tanaka, Y., Tang, D., Taniuchi, I., Tanzer, A., Tarui, H., Taylor, M. S., Terada, A., Terao, Y., Testa, A. C., Thomas, M., Thongjuea, S., Tomii, K., Triglia, E. T., Toyoda, H., Tsang, H. G., Tsujikawa, M., Uhlén, M., Valen, E., Van De Wetering, M., Van Nimwegen, E., Velmeshev, D., Verardo, R., Vitezic, M., Vitting-seerup, K., Von Feilitzen, K., Voolstra, C. R., Vorontsov, I. E., Wahlestedt, C., Wasserman, W. W., Watanabe, K., Watanabe, S., Wells, C. A., Winteringham, L. N., Wolvetang, E., Yabukami, H., Yagi, K., Yamada, T., Yamaguchi, Y., Yamamoto, M., Yamamoto, Y., Yamamoto, Y., Yamanaka, Y., Yano, K., Yasuzawa, K., Yatsuka, Y., Yo, M., Yokokura, S., Yoneda, M., Yoshida, E., Yoshida, Y., Yoshihara, M., Young, R., Young, R. S., Yu, N. Y., Yumoto, N., Zabierowski, S. E., Zhang, P. G., Zucchelli, S., Zwahlen, M., Chatelain, C., Carninci, P., De Hoon, M. J. L., Wasserman, W. W., Bréhélin, L. & Lecellier, C., 2 Jun 2021, In: Nature Communications. 12, 1

    Research output: Contribution to journalArticlepeer-review

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  • A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas

    Penaloza, C., Gutierrez Silva, A., Eory, L., Wang, S., Guo, X., Archibald, A., Bean, T. & Houston, R., 25 Mar 2021, (E-pub ahead of print) In: GigaScience. 10, 3

    Research output: Contribution to journalArticlepeer-review

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  • 2022

    Stem cell-derived porcine macrophages as a new platform for studying host-pathogen interactions

    Meek, S., Watson, T., Eory, L., McFarlane, G., Wynne, F. J., McCleary, S., Dunn, L. E. M., Charlton, E. M., Craig, C., Shih, B., Regan, T., Taylor, R., Sutherland, L., Gossner, A., Chintoan-Uta, C., Fletcher, S., Beard, P. M., Hassan, M. A., Grey, F., Hope, J. C. & 16 others, Stevens, M. P., Nowak-Imialek, M., Niemann, H., Ross, P. J., Tait-Burkard, C., Brown, S. M., Lefevre, L., Thomson, G., McColl, B. W., Lawrence, A. B., Archibald, A. L., Steinbach, F., Crooke, H. R., Gao, X., Liu, P. & Burdon, T., 14 Jan 2022, In: BMC Biology. 20, 1, 14 p.

    Research output: Contribution to journalArticlepeer-review

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  • Stem cell-derived macrophages as a new platform for studying host-pathogen interactions in livestock

    Meek, S., Watson, T., Eory, L., McFarlane, G., Wynne, F. J., McCleary, S., Dunn, L. E. M., Charlton, E., Criag, C., Shih, B., Regan, T., Taylor, R., Sutherland, L., Gossner, A., Chintoan-Uta, C., Fletcher, S., Beard, P., Hassan, M., Grey, F., Hope, J. & 16 others, Stevens, M., Nowak-Imialek, M., Niemann, H., Ross, P. J., Tait-Burkard, C., Brown, S., Lefevre, L., Thomson, G., McColl, B. W., Lawrence, A. B., Archibald, A., Steinbach, F., Crooke, H. R., Gao, X., Liu, P. & Burdon, T., 10 Jan 2022, bioRxiv, at Cold Spring Harbor Laboratory.

    Research output: Working paper

    Open Access
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