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Comparative perform...
Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data
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- Romagnoni, A (author)
- Centre de recherche sur l’inflammation UMR 1149, Inserm - Université Paris Diderot, Paris, France; Data Team, Département d’informatique de l’ENS, École normale supérieure, CNRS, PSL Research University, Paris, France
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Jegou, S (author)
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Van Steen, K (author)
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show more...
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Wainrib, G (author)
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Hugot, JP (author)
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Peyrin-Biroulet, L (author)
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Chamaillard, M (author)
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Colombel, JF (author)
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Cottone, M (author)
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- D'Amato, M (author)
- Karolinska Institutet
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D'Inca, R (author)
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- Halfvarson, Jonas, 1970- (author)
- Örebro universitet,Institutionen för medicinska vetenskaper
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Henderson, P (author)
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Karban, A (author)
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Kennedy, NA (author)
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Khan, MA (author)
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Lemann, M (author)
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Levine, A (author)
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Massey, D (author)
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Milla, M (author)
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Ng, SME (author)
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Oikonomou, I (author)
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Peeters, H (author)
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Proctor, DD (author)
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Rahier, JF (author)
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Rutgeerts, P (author)
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Seibold, F (author)
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Stronati, L (author)
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Taylor, KM (author)
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- Torkvist, L (author)
- Karolinska Institutet
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Ublick, K (author)
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Van Limbergen, J (author)
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Van Gossum, A (author)
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Vatn, MH (author)
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Zhang, H (author)
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Zhang, W (author)
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Andrews, JM (author)
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Bampton, PA (author)
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Barclay, M (author)
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Florin, TH (author)
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Gearry, R (author)
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Krishnaprasad, K (author)
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Lawrance, IC (author)
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Mahy, G (author)
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Montgomery, GW (author)
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Radford-Smith, G (author)
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Roberts, RL (author)
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Simms, LA (author)
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Hanigan, K (author)
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Croft, A (author)
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Amininijad, L (author)
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Cleynen, I (author)
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Dewit, O (author)
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Franchimont, D (author)
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Georges, M (author)
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Laukens, D (author)
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Theatre, E (author)
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Vermeire, S (author)
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Aumais, G (author)
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Baidoo, L (author)
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Barrie, AM (author)
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Beck, K (author)
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Bernard, EJ (author)
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Binion, DG (author)
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Bitton, A (author)
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Brant, SR (author)
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Cho, JH (author)
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Cohen, A (author)
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Croitoru, K (author)
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Daly, MJ (author)
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Datta, LW (author)
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Deslandres, C (author)
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Duerr, RH (author)
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Dutridge, D (author)
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Ferguson, J (author)
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Fultz, J (author)
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Goyette, P (author)
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Greenberg, GR (author)
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Haritunians, T (author)
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Jobin, G (author)
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Katz, S (author)
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Lahaie, RG (author)
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McGovern, DP (author)
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Nelson, L (author)
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Ng, SM (author)
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Ning, K (author)
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- Pare, P (author)
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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Regueiro, MD (author)
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Rioux, JD (author)
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Ruggiero, E (author)
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Schumm, LP (author)
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Schwartz, M (author)
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Scott, R (author)
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Sharma, Y (author)
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Silverberg, MS (author)
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Spears, D (author)
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Steinhart, AH (author)
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Stempak, JM (author)
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Swoger, JM (author)
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Tsagarelis, C (author)
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Zhang, C (author)
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Zhao, HY (author)
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Aerts, J (author)
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Ahmad, T (author)
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Arbury, H (author)
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Attwood, A (author)
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Auton, A (author)
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Ball, SG (author)
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Balmforth, AJ (author)
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Barnes, C (author)
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Barrett, JC (author)
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Barroso, I (author)
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Barton, A (author)
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Bennett, AJ (author)
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Bhaskar, S (author)
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Blaszczyk, K (author)
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Bowes, J (author)
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Brand, OJ (author)
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Braund, PS (author)
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Bredin, F (author)
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Breen, G (author)
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Brown, MJ (author)
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Bruce, IN (author)
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Bull, J (author)
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Burren, OS (author)
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Burton, J (author)
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Byrnes, J (author)
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Caesar, S (author)
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Cardin, N (author)
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Clee, CM (author)
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Coffey, AJ (author)
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Mc Connell, J (author)
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Conrad, DF (author)
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Cooper, JD (author)
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Dominiczak, AF (author)
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Downes, K (author)
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Drummond, HE (author)
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Dudakia, D (author)
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Dunham, A (author)
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Ebbs, B (author)
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Eccles, D (author)
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Edkins, S (author)
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Edwards, C (author)
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Elliot, A (author)
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Emery, P (author)
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Evans, DM (author)
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Evans, G (author)
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Eyre, S (author)
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Farmer, A (author)
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Ferrier, IN (author)
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Flynn, E (author)
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Forbes, A (author)
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Forty, L (author)
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Franklyn, JA (author)
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Frayling, TM (author)
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Freathy, RM (author)
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Giannoulatou, E (author)
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Gibbs, P (author)
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Gilbert, P (author)
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Gordon-Smith, K (author)
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Gray, E (author)
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Green, E (author)
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Groves, CJ (author)
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Grozeva, D (author)
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Gwilliam, R (author)
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Hall, A (author)
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Hammond, N (author)
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Hardy, M (author)
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Harrison, P (author)
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Hassanali, N (author)
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Hebaishi, H (author)
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Hines, S (author)
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Hinks, A (author)
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Hitman, GA (author)
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Hocking, L (author)
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Holmes, C (author)
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Howard, E (author)
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Howard, P (author)
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Howson, JMM (author)
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Hughes, D (author)
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Hunt, S (author)
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Isaacs, JD (author)
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Jain, M (author)
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Jewell, DP (author)
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Johnson, T (author)
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Jolley, JD (author)
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Jones, IR (author)
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Jones, LA (author)
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Kirov, G (author)
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Langford, CF (author)
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Lango-Allen, H (author)
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Lathrop, GM (author)
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Lee, J (author)
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Lee, KL (author)
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Lees, C (author)
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Lewis, K (author)
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Lindgren, CM (author)
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Maisuria-Armer, M (author)
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Maller, J (author)
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Mansfield, J (author)
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Marchini, JL (author)
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Martin, P (author)
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Massey, DCO (author)
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McArdle, WL (author)
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McGuffin, P (author)
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McLay, KE (author)
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McVean, G (author)
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Mentzer, A (author)
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Mimmack, ML (author)
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Morgan, AE (author)
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Morris, AP (author)
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Mowat, C (author)
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Munroe, PB (author)
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Myers, S (author)
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Newman, W (author)
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Nimmo, ER (author)
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O'Donovan, MC (author)
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Onipinla, A (author)
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Ovington, NR (author)
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Owen, MJ (author)
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Palin, K (author)
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Palotie, A (author)
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Parnell, K (author)
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Pearson, R (author)
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Pernet, D (author)
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Perry, JRB (author)
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Phillips, A (author)
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Plagnol, V (author)
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Prescott, NJ (author)
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Prokopenko, I (author)
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Quail, MA (author)
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Rafelt, S (author)
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Rayner, NW (author)
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Reid, DM (author)
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Renwick, A (author)
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Ring, SM (author)
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Robertson, N (author)
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Robson, S (author)
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Russell, E (author)
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St Clair, D (author)
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Sambrook, JG (author)
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Sanderson, JD (author)
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Sawcer, SJ (author)
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Schuilenburg, H (author)
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Scott, CE (author)
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Scott, R (author)
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Seal, S (author)
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Shaw-Hawkins, S (author)
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Shields, BM (author)
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Simmonds, MJ (author)
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Smyth, DJ (author)
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Somaskantharajah, E (author)
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Spanova, K (author)
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Steer, S (author)
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Stephens, J (author)
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Stevens, HE (author)
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Stirrups, K (author)
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Stone, MA (author)
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Strachan, DP (author)
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Su, Z (author)
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Symmons, DPM (author)
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Thompson, JR (author)
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Thomson, W (author)
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Tobin, MD (author)
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Travers, ME (author)
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Turnbull, C (author)
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Vukcevic, D (author)
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Wain, L (author)
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Walker, M (author)
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Walker, NM (author)
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Wallace, C (author)
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Warren-Perry, M (author)
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Watkins, NA (author)
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Webster, J (author)
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Weedon, MN (author)
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Wilson, AG (author)
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Woodburn, M (author)
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Wordsworth, BP (author)
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Yau, C (author)
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Young, AH (author)
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Zeggini, E (author)
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Brown, MA (author)
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Burton, PR (author)
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Caulfield, MJ (author)
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Compston, A (author)
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Farrall, M (author)
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Gough, SCL (author)
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Hall, AS (author)
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Hattersley, AT (author)
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Hill, AVS (author)
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Mathew, CG (author)
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Pembrey, M (author)
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Satsangi, J (author)
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Stratton, MR (author)
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Worthington, J (author)
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Hurles, ME (author)
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Duncanson, A (author)
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Ouwehand, WH (author)
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Parkes, M (author)
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Rahman, N (author)
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Todd, JA (author)
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Samani, NJ (author)
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Kwiatkowski, DP (author)
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McCarthy, M (author)
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Craddock, N (author)
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Deloukas, P (author)
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Donnelly, P (author)
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Blackwell, JM (author)
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Bramon, E (author)
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Casas, JP (author)
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Corvin, A (author)
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Jankowski, J (author)
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Markus, HS (author)
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Palmer, CNA (author)
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Plomin, R (author)
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Rautanen, A (author)
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Trembath, RC (author)
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Viswanathan, AC (author)
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Wood, NW (author)
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Spencer, CCA (author)
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Band, G (author)
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Bellenguez, C (author)
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Freeman, C (author)
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Hellenthal, G (author)
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Pirinen, M (author)
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Strange, A (author)
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Blackburn, H (author)
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Bumpstead, SJ (author)
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Dronov, S (author)
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Gillman, M (author)
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Jayakumar, A (author)
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McCann, OT (author)
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Liddle, J (author)
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Potter, SC (author)
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Ravindrarajah, R (author)
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Ricketts, M (author)
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Waller, M (author)
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Weston, P (author)
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Widaa, S (author)
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Whittaker, P (author)
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(creator_code:org_t)
- 2019-07-17
- 2019
- English.
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In: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1, s. 10351-
- Related links:
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https://www.nature.c...
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https://doi.org/10.1...
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http://kipublication...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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Abstract
Subject headings
Close
- Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Publication and Content Type
- ref (subject category)
- art (subject category)
Find in a library
To the university's database
- By the author/editor
-
Romagnoni, A
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Jegou, S
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Van Steen, K
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Wainrib, G
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Hugot, JP
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Peyrin-Biroulet, ...
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show more...
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Chamaillard, M
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Colombel, JF
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Cottone, M
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D'Amato, M
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D'Inca, R
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Halfvarson, Jona ...
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Henderson, P
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Karban, A
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Kennedy, NA
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Khan, MA
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Lemann, M
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Levine, A
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Massey, D
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Milla, M
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Ng, SME
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Oikonomou, I
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Peeters, H
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Proctor, DD
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Rahier, JF
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Rutgeerts, P
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Seibold, F
-
Stronati, L
-
Taylor, KM
-
Torkvist, L
-
Ublick, K
-
Van Limbergen, J
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Van Gossum, A
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Vatn, MH
-
Zhang, H
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Zhang, W
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Andrews, JM
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Bampton, PA
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Barclay, M
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Florin, TH
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Gearry, R
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Krishnaprasad, K
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Lawrance, IC
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Mahy, G
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Montgomery, GW
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Radford-Smith, G
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Roberts, RL
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Simms, LA
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Hanigan, K
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Croft, A
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Amininijad, L
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Cleynen, I
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Dewit, O
-
Franchimont, D
-
Georges, M
-
Laukens, D
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Theatre, E
-
Vermeire, S
-
Aumais, G
-
Baidoo, L
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Barrie, AM
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Beck, K
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Bernard, EJ
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Binion, DG
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Bitton, A
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Brant, SR
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Cho, JH
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Cohen, A
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Croitoru, K
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Daly, MJ
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Datta, LW
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Deslandres, C
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Duerr, RH
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Dutridge, D
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Ferguson, J
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Fultz, J
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Goyette, P
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Greenberg, GR
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Haritunians, T
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Jobin, G
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Katz, S
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Lahaie, RG
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McGovern, DP
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Nelson, L
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Ng, SM
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Ning, K
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Pare, P
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Regueiro, MD
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Rioux, JD
-
Ruggiero, E
-
Schumm, LP
-
Schwartz, M
-
Scott, R
-
Sharma, Y
-
Silverberg, MS
-
Spears, D
-
Steinhart, AH
-
Stempak, JM
-
Swoger, JM
-
Tsagarelis, C
-
Zhang, C
-
Zhao, HY
-
Aerts, J
-
Ahmad, T
-
Arbury, H
-
Attwood, A
-
Auton, A
-
Ball, SG
-
Balmforth, AJ
-
Barnes, C
-
Barrett, JC
-
Barroso, I
-
Barton, A
-
Bennett, AJ
-
Bhaskar, S
-
Blaszczyk, K
-
Bowes, J
-
Brand, OJ
-
Braund, PS
-
Bredin, F
-
Breen, G
-
Brown, MJ
-
Bruce, IN
-
Bull, J
-
Burren, OS
-
Burton, J
-
Byrnes, J
-
Caesar, S
-
Cardin, N
-
Clee, CM
-
Coffey, AJ
-
Mc Connell, J
-
Conrad, DF
-
Cooper, JD
-
Dominiczak, AF
-
Downes, K
-
Drummond, HE
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Dudakia, D
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Dunham, A
-
Ebbs, B
-
Eccles, D
-
Edkins, S
-
Edwards, C
-
Elliot, A
-
Emery, P
-
Evans, DM
-
Evans, G
-
Eyre, S
-
Farmer, A
-
Ferrier, IN
-
Flynn, E
-
Forbes, A
-
Forty, L
-
Franklyn, JA
-
Frayling, TM
-
Freathy, RM
-
Giannoulatou, E
-
Gibbs, P
-
Gilbert, P
-
Gordon-Smith, K
-
Gray, E
-
Green, E
-
Groves, CJ
-
Grozeva, D
-
Gwilliam, R
-
Hall, A
-
Hammond, N
-
Hardy, M
-
Harrison, P
-
Hassanali, N
-
Hebaishi, H
-
Hines, S
-
Hinks, A
-
Hitman, GA
-
Hocking, L
-
Holmes, C
-
Howard, E
-
Howard, P
-
Howson, JMM
-
Hughes, D
-
Hunt, S
-
Isaacs, JD
-
Jain, M
-
Jewell, DP
-
Johnson, T
-
Jolley, JD
-
Jones, IR
-
Jones, LA
-
Kirov, G
-
Langford, CF
-
Lango-Allen, H
-
Lathrop, GM
-
Lee, J
-
Lee, KL
-
Lees, C
-
Lewis, K
-
Lindgren, CM
-
Maisuria-Armer, ...
-
Maller, J
-
Mansfield, J
-
Marchini, JL
-
Martin, P
-
Massey, DCO
-
McArdle, WL
-
McGuffin, P
-
McLay, KE
-
McVean, G
-
Mentzer, A
-
Mimmack, ML
-
Morgan, AE
-
Morris, AP
-
Mowat, C
-
Munroe, PB
-
Myers, S
-
Newman, W
-
Nimmo, ER
-
O'Donovan, MC
-
Onipinla, A
-
Ovington, NR
-
Owen, MJ
-
Palin, K
-
Palotie, A
-
Parnell, K
-
Pearson, R
-
Pernet, D
-
Perry, JRB
-
Phillips, A
-
Plagnol, V
-
Prescott, NJ
-
Prokopenko, I
-
Quail, MA
-
Rafelt, S
-
Rayner, NW
-
Reid, DM
-
Renwick, A
-
Ring, SM
-
Robertson, N
-
Robson, S
-
Russell, E
-
St Clair, D
-
Sambrook, JG
-
Sanderson, JD
-
Sawcer, SJ
-
Schuilenburg, H
-
Scott, CE
-
Seal, S
-
Shaw-Hawkins, S
-
Shields, BM
-
Simmonds, MJ
-
Smyth, DJ
-
Somaskantharajah ...
-
Spanova, K
-
Steer, S
-
Stephens, J
-
Stevens, HE
-
Stirrups, K
-
Stone, MA
-
Strachan, DP
-
Su, Z
-
Symmons, DPM
-
Thompson, JR
-
Thomson, W
-
Tobin, MD
-
Travers, ME
-
Turnbull, C
-
Vukcevic, D
-
Wain, L
-
Walker, M
-
Walker, NM
-
Wallace, C
-
Warren-Perry, M
-
Watkins, NA
-
Webster, J
-
Weedon, MN
-
Wilson, AG
-
Woodburn, M
-
Wordsworth, BP
-
Yau, C
-
Young, AH
-
Zeggini, E
-
Brown, MA
-
Burton, PR
-
Caulfield, MJ
-
Compston, A
-
Farrall, M
-
Gough, SCL
-
Hall, AS
-
Hattersley, AT
-
Hill, AVS
-
Mathew, CG
-
Pembrey, M
-
Satsangi, J
-
Stratton, MR
-
Worthington, J
-
Hurles, ME
-
Duncanson, A
-
Ouwehand, WH
-
Parkes, M
-
Rahman, N
-
Todd, JA
-
Samani, NJ
-
Kwiatkowski, DP
-
McCarthy, M
-
Craddock, N
-
Deloukas, P
-
Donnelly, P
-
Blackwell, JM
-
Bramon, E
-
Casas, JP
-
Corvin, A
-
Jankowski, J
-
Markus, HS
-
Palmer, CNA
-
Plomin, R
-
Rautanen, A
-
Trembath, RC
-
Viswanathan, AC
-
Wood, NW
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Spencer, CCA
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Band, G
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Bellenguez, C
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Freeman, C
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Hellenthal, G
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Pirinen, M
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Strange, A
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Blackburn, H
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Bumpstead, SJ
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Dronov, S
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Gillman, M
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Jayakumar, A
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McCann, OT
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Liddle, J
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Potter, SC
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Ravindrarajah, R
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Ricketts, M
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Waller, M
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Weston, P
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Widaa, S
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Whittaker, P
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- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Medical Genetics
- Articles in the publication
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Scientific repor ...
- By the university
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Karolinska Institutet
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Örebro University