Kim Summers

Search results

• 2021

  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 othersAken, 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 journal › Article › peer-review

  Open Access

  File

  • Microsatellite DNA 100%
  • Transcription Initiation 100%
  • Short Tandem Repeat 100%
  • Gene Expression 33%
  • Transcription 22%

• CRISPR-Cas9 Editing of Human Histone Deubiquitinase Gene USP16 in Human Monocytic Leukemia Cell Line THP-1

  Gažová, I., Lefevre, L., Bush, S. J., Rojo, R., Hume, D. A., Lengeling, A. & Summers, K. M., 31 May 2021, In: Frontiers in Cell and Developmental Biology. 9, 679544.

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

  Open Access

  File

  • Clone 100%
  • Nested Gene 100%
  • Histone 100%
  • CRISPR/Cas9 100%
  • Wild Type 66%

• Analysis of homozygous and heterozygous Csf1r knockout in the rat as a model for understanding microglial function in brain development and the impacts of human CSF1R mutations.

  Patkar, O. L., Caruso, M., Teakle, N., Keshvari, S., Bush, S. J., Pridans, C., Belmer, A., Summers, K. M., Irvine, K. M. & Hume, D. A., 1 Apr 2021, In: Neurobiology of disease. 151, 105268.

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

  Open Access

  File

  • Brain 100%
  • Brain Development 100%
  • Microglia 50%
  • Diffusion Imaging 25%
  • Purkinje Cell 25%

• The influence of X chromosome variants on trait neuroticism

  Luciano, M., Davies, G., Summers, K. M., Hill, W. D., Hayward, C., Liewald, D. C., Porteous, D. J., Gale, C. R., McIntosh, A. M. & Deary, I. J., 28 Feb 2021, In: Molecular Psychiatry. 26, 2, p. 483-491

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

  Open Access

  File

  • X Chromosome 100%
  • Chromosome Variant 100%
  • Sample 42%
  • Single-Nucleotide Polymorphism 28%
  • Dog 28%
• 2020

  Comparative transcriptomic profiling of myxomatous mitral valve disease in the Cavalier King Charles Spaniel

  Markby, G., MacRae, V., Corcoran, B. & Summers, K., 23 Sept 2020, (E-pub ahead of print) In: BMC Veterinary Research.

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

  Open Access

  File

  • Transcriptomics 100%
  • Cavalier King Charles Spaniel 100%
  • Breed 43%
  • Breeds 43%
  • Dog 31%

• Expression of calcification and extracellular matrix genes in the cardiovascular system of the healthy domestic sheep (Ovis aries).

  Tsang, G., Clark, E., Markby, G., Bush, S., Hume, D., Corcoran, B., MacRae, V. & Summers, K., 8 Sept 2020, (E-pub ahead of print) In: Frontiers in Genetics. 11

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

  Open Access

  File

  • Extracellular Matrix 100%
  • Cardiovascular System 100%
  • Calcification 100%
  • Domestic Sheep 100%
  • Nested Gene 100%

• Species-specificity of transcriptional regulation and the response to lipopolysaccharide in mammalian macrophages.

  Bush, S., Mcculloch, M., Lisowski, Z., Muriuki, C., Clark, E., Young, R., Pridans, C., Prendergast, J., Summers, K. & Hume, D., 21 Jul 2020, (E-pub ahead of print) In: Frontiers in Cell and Developmental Biology.

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

  Open Access

  File

  • Lipopolysaccharide 100%
  • Regulatory Mechanism 100%
  • Species Difference 100%
  • Macrophage 100%
  • Species 22%

• The Transcriptional Network that Controls Growth Arrest and Macrophage Differentiation in the Human Myeloid Leukemia Cell Line THP-1

  Gazova, I., Lefevre, L., Bush, S. J., Clohisey, S., Arner, E., de Hoon, M. J., Severin, J., Duin, L. V., Andersson, R., Lengeling, A., Hume, D. & Summers, K., 3 Jul 2020, (E-pub ahead of print) In: Frontiers in Cell and Developmental Biology.

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

  Open Access

  File

  • Cell Line 100%
  • Myeloid 100%
  • Gene 100%
  • Macrophage Differentiation 100%
  • Acetate 75%

• Disease severity-associated gene expression in canine myxomatous mitral valve disease is dominated by TGFß signalling

  Markby, G., MacRae, V., Summers, K. & Corcoran, B., 27 Apr 2020, (E-pub ahead of print) In: Frontiers in Genetics.

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

  Open Access

  File

  • Chemokine 100%
  • Dog 100%
  • Tumor Necrosis Factor 100%

• 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 journal › Article › peer-review

  Open Access

  File

  • Pig 100%
  • Transcriptome 100%
  • Gene Expression 28%
  • Nested Gene 28%
  • Domestic Pig 14%
• 2019

  Analysis of the progeny of sibling matings reveals regulatory variation impacting the transcriptome of immune cells in commercial chickens

  Freem, L., Summers, K., Gheyas, A., Psifidi, A., Boulton, K., MacCallum, A., O'Dell, J., Bush, S. J. & Hume, D., 14 Nov 2019, In: Frontiers in Genetics.

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

  Open Access

  File

  • Chicken 100%
  • Immunocompetent Cell 100%
  • Transcriptome 100%
  • Mating 100%
  • Nested Gene 100%

• Evaluation of Canine 2D cell cultures as models of myxomatous mitral valve degeneration

  Tan, K., Markby, G., Muirhead, R., Blake, R., Bergeron, L., Fici, G. J., Summers, K., MacRae, V. & Corcoran, B., 15 Aug 2019, In: PLoS ONE.

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

  Open Access

  File

  • Interstitial Cell 100%
  • Mitral Valve 100%
  • Degeneration 100%
  • Cell Culture 100%
  • Evaluation Study 100%

• A Gene Expression Atlas of the Domestic Water Buffalo (Bubalus bubalis)

  Young, R., Lefevre, L., Bush, S. J., Joshi, A., Singh, S. H., Jadhav, S. K., Dhanikachalam, V., Lisowski, Z., Iamartino, D., Summers, K., Williams, J. L., Archibald, A., Gokhale, S. B., Kumar, S. & Hume, D., 24 Jul 2019, In: Frontiers in Genetics.

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

  Open Access

  File

  • Water 100%
  • Gene Expression 100%
  • Bubalus 100%
  • Water Buffalo 100%
  • Livestock Species 28%

• Phenotypic impacts of CSF1R deficiencies in humans and model organisms

  Hume, D. A., Caruso, M., Ferrari-Cestari, M., Summers, K. M., Pridans, C. & Irvine, K. M., 22 Jul 2019, (E-pub ahead of print) In: Journal of Leukocyte Biology.

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

  Open Access

  File

  • Human 100%
  • Brain 100%
  • Organisms 100%
  • Mononuclear Phagocyte 66%
  • Mouse 66%

• Visualization and analysis of RNA-Seq assembly graphs

  Wan mohamad nazarie, W. F. B., Shih, B-J., Angus, T., Barnett, M., Chen, S., Summers, K., Klein, K., Faulkner, G. J., Saini, H. K., Watson, M., Van Dongen, S., Enright, A. J. & Freeman, T., 15 Jul 2019, In: Nucleic Acids Research.

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

  Open Access

  File

  • RNA Sequencing 100%
  • Comprehension 66%
  • Nested Gene 66%
  • RNA 33%
  • Electric Potential 33%

• Erratum: Pleiotropic impacts of macrophage ands microglial deficiency on development in rats with targeted mutation of the Csf1r locus (Journal of Immunology (2019) 201 (2683-2699) DOI: 10.4049/jimmunol.1701783)

  Pridans, C., Raper, A., Davis, G. M., Alves, J., Sauter, K. A., Lefevre, L., Regan, T., Meek, S., Sutherland, L., Thomson, A. J., Clohisey, S., Bush, S. J., Rojo, R., Lisowski, Z. M., Wallace, R., Grabert, K., Upton, K. R., Tsai, Y. T., Brown, D., Smith, L. B., & 6 othersSummers, K. M., Mabbott, N. A., Piccardo, P., Cheeseman, M. T., Burdon, T. & Hume, D. A., 1 Jun 2019, In: The Journal of Immunology. 202, 11, p. 3334-3335 2 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  • 4 Iodo 2,5 Dimethoxyamphetamine 100%
  • Immunology 100%
  • Macrophage 100%
  • Mutation 100%
  • Development 100%

• Arginine to glutamine variant in olfactomedin-like 3 (OLFML3) is a candidate for severe goniodysgenesis and glaucoma in the Border Collie dog breed

  Pugh, C., Farrell, L., Carlisle, A., Bush, S., Ewing, A., Trejo-Reveles, V., Matika, O., de Kloet, A., Walsh, C., Bishop, S., Prendergast, J., Rainger, J., Schoenebeck, J. & Summers, K., 7 Mar 2019, In: G3: Genes | Genomes | Genetics. 9, 3, p. 943-954

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

  Open Access

  File

  • Dog 100%
  • Border Collie 100%

• The effect of race training on the basal gene expression of alveolar macrophages derived from Standardbred racehorses

  Karagianni, A., Summers, K., Couroucé, A., Depecker, M., McGorum, B., Hume, D. & Pirie, R., 29 Jan 2019, (E-pub ahead of print) In: Journal of equine veterinary science.

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

  Open Access

  File

  • Gene Expression 100%
  • Race 100%
  • Training 100%
  • Standardbred Horse 100%
  • Alveolar Macrophage 100%

• Characterization of Subpopulations of Chicken Mononuclear Phagocytes That Express TIM4 and CSF1R

  Hu, T., Wu, Z., Bush, S. J., Freem, L., Vervelde, L., Summers, K. M., Hume, D. A., Balic, A. & Kaiser, P., 9 Jan 2019, In: The Journal of Immunology. 202, 4, p. 1186-1199

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

  • Mononuclear Phagocyte 100%
  • Cells 100%
  • Chicken 100%
  • Kupffer Cell 50%
  • Monocyte 40%
• 2018

  Pleiotropic impacts of macrophage and microglial deficiency on development in rats with targeted mutation of the Csf1r locus

  Pridans, C., Raper, A., Davis, G. M., Alves, J., Sauter, K. A., Lefevre, L., Regan, T., Meek, S., Sutherland, L., Thomson, A. J., Clohisey, S., Bush, S. J., Rojo, R., Lisowski, Z. M., Wallace, R., Grabert, K., Upton, K. R., Tsai, Y. T., Brown, D., Smith, L. B., & 6 othersSummers, K. M., Mabbott, N. A., Piccardo, P., Cheeseman, M. T., Burdon, T. & Hume, D. A., 1 Nov 2018, In: The Journal of Immunology. 201, 9, p. 2683-2699

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

  Open Access

  File

  • Rat 100%
  • Development 100%
  • Mutation 100%
  • Macrophage 100%
  • Brain 31%

• Environmentally enriched pigs have transcriptional profiles consistent with neuroprotective effects and reduced microglial activity

  Brown, S., Bush, S., Summers, K., Hume, D. & Lawrence, A. B., 17 Sept 2018, In: Behavioural Brain Research. 350, p. 6-15

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

  Open Access

  File

  • Neuroprotective Agent 100%
  • Pig 100%
  • Rodent 40%
  • Frontal Lobe 20%
  • RNA Sequence 20%

• Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

  Bush, S. J., Freem, L., MacCallum, A. J., O'Dell, J., Wu, C., Afrasiabi, C., Psifidi, A., Stevens, M. P., Smith, J., Summers, K. M. & Hume, D. A., 7 Aug 2018, In: BMC Genomics. 19, 1, 594 (2018).

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

  Open Access

  File

  • Chicken 100%
  • Messenger RNA 100%
  • RNA Sequencing 100%
  • Tissues 41%
  • Species 16%

• An analysis of anterior segment development in the chicken eye

  Trejo-Reveles, V., McTeir, L., Summers, K. & Rainger, J., Apr 2018, In: Mechanisms of Development. 150, p. 42-49

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

  Open Access

  File

  • Chicken 100%
  • Chick 100%
  • Development 100%
  • Mouse 50%
  • Birth 16%

• Exploiting novel valve interstitial cell lines to study calcific aortic valve disease

  Tsang, H., Cui, L., Farquharson, C., Corcoran, B., Summers, K. & MacRae, V., Feb 2018, In: Molecular Medicine Reports. 17, 2, p. 2100-2106

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

  Open Access

  File

  • Interstitial Cell 100%
  • Cell Line 100%
  • Aortic Valve Disease 100%
  • Calcification 100%
  • Isotopes of Calcium 75%
• 2017

  Identification of the macrophage-specific promoter signature in FANTOM5 mouse embryo developmental time course data

  Summers, K. & Hume, D., 1 Oct 2017, (E-pub ahead of print) In: Journal of Leukocyte Biology. 102, 4, p. 1081-1092

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

  Open Access

  File

• A high resolution atlas of gene expression in the domestic sheep (Ovis aries)

  Clark, E., Bush, S., McCulloch, M., Farquhar, I., Young, R., Lefevre, L., Pridans, C., Tsang, H., Wu, C., Afrasiabi, C., Watson, M., Whitelaw, C., Freeman, T., Summers, K., Archibald, A. & Hume, D., 15 Sept 2017, In: PLoS Genetics. 13, 9, e1006997.

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

  Open Access

  File

  • Domestic Sheep 100%
  • Gene Expression 100%
  • Nested Gene 100%
  • Sheep 85%
  • Coding 28%

• FANTOM5 CAGE profiles of human and mouse samples

  Noguchi, S., Arakawa, T., Fukuda, S., Furuno, M., Hasegawa, A., Hori, F., Ishikawa-Kato, S., Kaida, K., Kaiho, A., Kanamori-Katayama, M., Kawashima, T., Kojima, M., Kubosaki, A., Manabe, R-I., Murata, M., Nagao-Sato, S., Nakazato, K., Ninomiya, N., Nishiyori-Sueki, H., Noma, S., & 158 othersSaijyo, E., Saka, A., Sakai, M., Simon, C., Suzuki, N., Tagami, M., Watanabe, S., Yoshida, S., Arner, P., Axton, R. A., Babina, M., Baillie, J. K., Barnett, T. C., Beckhouse, A. G., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Carlisle, A. J., Clevers, H. C., Davis, C. A., Detmar, M., Dohi, T., Edge, A. S. B., Edinger, M., Ehrlund, A., Ekwall, K., Endoh, M., Enomoto, H., Eslami, A., Fagiolini, M., Fairbairn, L., Farach-Carson, M. C., Faulkner, G. J., Ferrai, C., Fisher, M. E., Forrester, L. M., Fujita, R., Furusawa, J-I., Geijtenbeek, T. B., Gingeras, T., Goldowitz, D., Guhl, S., Guler, R., Gustincich, S., Ha, T. J., Hamaguchi, M., Hara, M., Hasegawa, Y., Herlyn, M., Heutink, P., Hitchens, K. J., Hume, D. A., Ikawa, T., Ishizu, Y., Kai, C., Kawamoto, H., Kawamura, Y. I., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L. M., Kitamura, T., Klein, S., Klinken, S. P., Knox, A. J., Kojima, S., Koseki, H., Koyasu, S., Lee, W., Lennartsson, A., Mackay-Sim, A., Mejhert, N., Mizuno, Y., Morikawa, H., Morimoto, M., Moro, K., Morris, K. J., Motohashi, H., Mummery, C. L., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nozaki, T., Ogishima, S., Ohkura, N., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D. A., Passier, R., Patrikakis, M., Pombo, A., Pradhan-Bhatt, S., Qin, X-Y., Rehli, M., Rizzu, P., Roy, S., Sajantila, A., Sakaguchi, S., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schmidl, C., Schneider, C., Schulze-Tanzil, G. G., Schwegmann, A., Sheng, G., Shin, J. W., Sugiyama, D., Sugiyama, T., Summers, K. M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Tomoiu, A., Toyoda, H., van de Wetering, M., van den Berg, L. M., Verardo, R., Vijayan, D., Wells, C. A., Winteringham, L. N., Wolvetang, E., Yamaguchi, Y., Yamamoto, M., Yanagi-Mizuochi, C., Yoneda, M., Yonekura, Y., Zhang, P. G., Zucchelli, S., Abugessaisa, I., Arner, E., Harshbarger, J., Kondo, A., Lassmann, T., Lizio, M., Sahin, S., Sengstag, T., Severin, J., Shimoji, H., Suzuki, M., Suzuki, H., Kawai, J., Kondo, N., Itoh, M., Daub, C. O., Kasukawa, T., Kawaji, H., Carninci, P., Forrest, A. R. R. & Hayashizaki, Y., 29 Aug 2017, In: Scientific Data. 4, 170112.

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

  Open Access

  File

  • Sample 100%
  • Mouse 100%
  • Gene Expression 100%
  • Transcription Initiation 50%
  • Sequencing 50%

• An integrated expression atlas of miRNAs and their promoters in human and mouse

  The FANTOM Consortium & de Rie, D., 21 Aug 2017, In: Nature Biotechnology. 35, 9, p. 872-878

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

  Open Access

  File

  • Mouse 100%
  • Promoter Region 100%
  • MicroRNA 100%
  • microRNA 42%
  • RNA 28%

• Comparative Transcriptomic Profiling and Gene Expression for Myxomatous Mitral Valve Disease in the Dog and Human

  Markby, G. R., Summers, K. M., MacRae, V. E. & Corcoran, B. M., 17 Jul 2017, In: Veterinary Sciences. 4, 3, 34.

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

  Open Access

  File

  • Dog 100%

• Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries

  Bush, S. J., McCulloch, M. E. B., Summers, K. M., Hume, D. A. & Clark, E. L., 13 Jun 2017, In: BMC Bioinformatics. 18, 1, p. 301

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

  Open Access

  File

  • Ribosomal RNA 100%
  • RNA Sequencing 100%
  • RNA 30%
  • Transcriptome 30%
  • Sheep 10%

• Incidence rates and risk factor analyses for owner reported vomiting and diarrhoea in Labrador Retrievers – findings from the Dogslife Cohort

  Pugh, C., Summers, K., Rose, E., Handel, I., Bronsvoort, M., Querry, D. & Clements, D., 1 May 2017, In: Preventive Veterinary Medicine.

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

  Open Access

  File

  • Dog 100%
  • Cat 12%

• Comparative transcriptome analysis of equine alveolar macrophages

  Karagianni, A. E., Kapetanovic, R., Summers, K. M., McGorum, B. C., Hume, D. A. & Pirie, R. S., May 2017, In: Equine Veterinary Journal. 49, 3, p. 375-382

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

  Open Access

  File

  • Alveolar Macrophage 100%
  • Horse 33%
  • Target Cell 8%

• Myxomatous Degeneration of the Canine Mitral Valve: From Gross Changes to Molecular Events

  Markby, G., Summers, K., MacRae, V., Del-Pozo, J. & Corcoran, B., May 2017, In: Journal of Comparative Pathology. 156, 4, p. 371-383

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

  Open Access

  File

  • Dog 100%

• Analysis of gene expression in the nervous system identifies key genes and novel candidates for health and disease

  Carpanini, S. M., Wishart, T. M., Gillingwater, T. H., Manson, J. C. & Summers, K. M., Apr 2017, In: Neurogenetics. 18, 2, p. 81-95

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

  Open Access

  File

  • Analysis 100%
  • Health 100%
  • Gene Expression 100%
  • Nervous System 100%
  • Gene 100%

• Investigating calcific aortic valve disease using novel immortalised sheep and rat valve interstitial cell lines

  Tsang, H-G., Cui, L., Farquharson, C., Corcoran, B. M., Summers, K. M. & MacRae, V. E., Apr 2017, In: Heart. 103, p. A7-A7 1 p.

  Research output: Contribution to journal › Meeting abstract › peer-review

• Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease

  Baillie, J. K., Arner, E., Daub, C., De Hoon, M., Itoh, M., Kawaji, H., Lassmann, T., Carninci, P., Forrest, A. R. R., Hayashizaki, Y., The FANTOM Consortium, Faulkner, G. J., Wells, C. A., Rehli, M., Pavli, P., Summers, K. M. & Hume, D. A., 6 Mar 2017, (E-pub ahead of print) In: PLoS Genetics. 13, 3, e1006641.

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

  Open Access

  File

  • Inflammatory Bowel Disease 100%
  • Lipopolysaccharide 100%
  • Analysis 100%
  • Transcriptome 100%
  • Etiology 100%

• Functional Annotation of the Sheep (Ovis aries) Genome

  Clark, E., Bush, S., Summers, K., Hume, D., Whitelaw, C., Watson, M., Farquhar, I. & Archibald, A., 16 Jan 2017.

  Research output: Contribution to conference › Abstract › peer-review

  • Sheep 100%
  • Domestic Sheep 100%
  • Nested Gene 100%
  • RNA Sequencing 28%
  • Gene Expression 28%
• 2016

  Vascular calcification and the cardiovascular transcriptome

  Tsang, H., Cui, L., Farquharson, C., Corcoran, B. M., Summers, K. M. & MacRae, V. E., Oct 2016, In: International Journal of Experimental Pathology. 97, 5, p. A2-A3 2 p.

  Research output: Contribution to journal › Meeting abstract › peer-review

• Macrophage colony-stimulating factor (CSF1) controls monocyte production and maturation and the steady-state size of the liver in pigs

  Sauter, K. A., Waddell, L. A., Lisowski, Z. M., Young, R., Lefevre, L., Davis, G. M., Clohisey, S. M., McCulloch, M. B., Magowan, E., Mabbott, N. A., Summers, K. M. & Hume, D. A., 9 Sept 2016, In: American Journal of Physiology - Gastrointestinal and Liver Physiology. 311, 3, p. G533-G547 15 p.

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

  Open Access

  File

  • Liver 100%
  • Macrophage Colony-Stimulating Factor 100%
  • Pig 100%
  • Steady State 100%
  • Maturation 100%

• Expression of FBN1 during adipogenesis: relevance to the lipodystrophy phenotype in Marfan syndrome and related conditions

  Davis, M. R., Arner, E., Duffy, C. R. E., De Sousa, P., Dahlman, I., Arner, P. & Summers, K., Sept 2016, In: Molecular Genetics and Metabolism. 119, 1-2, p. 174-185

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

  Open Access

  File

  • Marfan's Syndrome 100%
  • Phenotype 100%
  • Fibrillin 100%
  • FBN1 100%
  • Adipogenesis 100%

• Datasets of genes coexpressed with FBN1 in mouse adipose tissue and during human adipogenesis

  Davis, M. R., Arner, E., Duffy, C. R. E., De Sousa, P., Dahlman, I., Arner, P. & Summers, K., 5 Jul 2016, (E-pub ahead of print) In: Data in brief. 8, p. 851-857

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

  Open Access

  File

  • Mouse 100%
  • FBN1 100%
  • Nested Gene 100%
  • Adipogenesis 100%
  • Protein 42%

• Cumulative incidence and risk factors for Limber Tail in the Dogslife Labrador Retriever cohort

  Pugh, C., Bronsvoort, M., Handel, I., Querry, D., Rose, E., Summers, K. & Clements, D., 27 Jun 2016, (E-pub ahead of print) In: Veterinary Record. 179, 11, p. 275-U290

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

  Open Access

  File

  • Dog 100%
  • Working Dog 100%

• Transcriptional regulation and macrophage differentiation

  Hume, D., Summers, K. & Rehli, M., 3 Jun 2016, In: Microbiology Spectrum. 4, 3, 19 p., MCHD-0024-2015.

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

  Open Access

  File

  • Regulatory Mechanism 100%
  • Macrophage Differentiation 100%
  • Macrophage 100%
  • Monocyte 42%
  • Tissues 28%

• A deletion in the canine POMC gene is associated with weight and appetite in obesity prone Labrador retriever dogs

  Raffan, E., Dennis, R. J., O'Donovan, C. J., Becker, J. M., Scott, R. A., Smith, S. P., Withers, D. J., Wood, C. J., Conci, E., Clements, D. N., Summers, K., German, A. J., Mellersh, C. S., Arendt, M. L., Iyemere, V. P., Withers, E., Soder, J., Wernersson, S., Andersson, G., Lindblad-Toh, K., & 2 othersYeo, G. S. H. & O'Rahilly, S., 3 May 2016, In: Cell Metabolism. 23, 5, p. 893-900

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

  Open Access

  File

  • Dog 100%
  • Proopiomelanocortin 100%

• Microglial brain region−dependent diversity and selective regional sensitivities to aging

  Grabert, K., Michoel, T., Karavolos, M. H., Clohisey, S., Baillie, J. K., Stevens, M. P., Freeman, T. C., Summers, K. M. & McColl, B. W., 31 Mar 2016, In: Nature Neuroscience. 19, 3, p. 504-516 13 p.

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

  Open Access

  File

  • Microglia 100%
  • Brain 100%
  • Neurodegeneration 50%
  • Forebrain 25%
  • Neural Development 25%

• Large animal models of cardiovascular disease

  Tsang, H-G., Rashdan, N., Whitelaw, C., Corcoran, B., Summers, K. & MacRae, V., 24 Feb 2016, (E-pub ahead of print) In: Cell Biochemistry and Function. 34, 3, p. 113–132

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

  Open Access

  File

  • Cardiovascular Disease 100%
  • Animal Models 100%
  • Pathological Process 25%
  • Heart Valve 25%
  • Ossification 25%

• The sheep gene expression atlas project

  Clark, E. L., Farquhar, I. L., McCulloch, M. B., Bush, S. J., Whitelaw, C. B., Watson, M., Summers, K. M., Archibald, A. L. & Hume, D. A., 9 Jan 2016.

  Research output: Contribution to conference › Abstract

  • Gene Expression 100%
  • Sheep 100%
  • Tissues 50%
  • Cells 37%
  • Depth 25%
• 2015

  A high incidence of atypical scrapie in an inbred flock of Cheviot sheep.

  Tan, B. C., McCutcheon, S., Goldmann, W., Hunter, N., Farrell, L., Simmons, H., Summers, K. & Houston, E., 16 Apr 2015.

  Research output: Contribution to conference › Poster

• Validity of Internet-Based Longitudinal Study Data: The elephant in the virtual room

  Pugh, C., Summers, K., Bronsvoort, M., Handel, I. & Clements, D., 16 Apr 2015, In: Journal of medical Internet research. 17, 4, e96.

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

  Open Access

  File

  • Internet 100%
  • Validation 100%
  • Longitudinal Study 100%
  • Validity 100%
  • Questionnaire 66%

• Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

  Arner, E., Daub, C. O., Vitting-Seerup, K., Andersson, R., Lilje, B., Drabløs, F., Lennartsson, A., Rönnerblad, M., Hrydziuszko, O., Vitezic, M., Freeman, T. C., Alhendi, A. M. N., Arner, P., Axton, R., Baillie, J. K., Beckhouse, A., Bodega, B., Briggs, J., Brombacher, F., Davis, M., & 31 othersDetmar, M., Ehrlund, A., Endoh, M., Eslami, A., Fagiolini, M., Fairbairn, L., Faulkner, G. J., Ferrai, C., Fisher, M. E., Forrester, L., Goldowitz, D., Guler, R., Ha, T., Hara, M., Herlyn, M., Ikawa, T., Kai, C., Kawamoto, H., Khachigian, L. M., Klinken, S. P., Kojima, S., Koseki, H., Klein, S., Mejhert, N., Miyaguchi, K., Mizuno, Y., Morimoto, M., Tomoiu, A., Summers, K. M., FANTOM Consortium & Hume, D. A., 27 Feb 2015, In: Science. 347, 6225, p. 1010-1014 5 p.

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

  • Enhancer Region 100%
  • Transcription 100%
  • Mammalian Cell 100%
  • Promoter Region 60%
  • Transcription Factor 40%