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Community assessmen...
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
- Article/chapterEnglish2019
Publisher, publication year, extent ...
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2019-06-17
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Springer Science and Business Media LLC,2019
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LIBRIS-ID:oai:prod.swepub.kib.ki.se:141113030
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http://kipublications.ki.se/Default.aspx?queryparsed=id:141113030URI
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https://doi.org/10.1038/s41467-019-09799-2DOI
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Language:English
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Summary in:English
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca’s large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.
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Wang, D
(author)
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Mason, MJ
(author)
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Szalai, B
(author)
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Bulusu, KC
(author)
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Guan, YF
(author)
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Yu, T
(author)
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Kang, J
(author)
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Jeon, M
(author)
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Wolfinger, R
(author)
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Nguyen, T
(author)
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Zaslavskiy, M
(author)
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Jang, IS
(author)
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Ghazoui, Z
(author)
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Ahsen, ME
(author)
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Vogel, R
(author)
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Neto, EC
(author)
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Norman, T
(author)
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Tang, EKY
(author)
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Garnett, MJ
(author)
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Di Veroli, GY
(author)
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Fawell, S
(author)
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Stolovitzky, G
(author)
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Guinney, J
(author)
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Dry, JR
(author)
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Saez-Rodriguez, J
(author)
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Abante, J
(author)
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Abecassis, BS
(author)
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Aben, N
(author)
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Aghamirzaie, D
(author)
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Aittokallio, T
(author)
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Akhtari, FS
(author)
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Al-lazikani, B
(author)
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Alam, T
(author)
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Allam, A
(author)
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Allen, C
(author)
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de Almeida, MP
(author)
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Altarawy, D
(author)
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Alves, V
(author)
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Amadoz, A
(author)
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Anchang, B
(author)
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Antolin, AA
(author)
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Ash, JR
(author)
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Aznar, VR
(author)
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Ba-alawi, W
(author)
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Bagheri, M
(author)
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Bajic, V
(author)
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Ball, G
(author)
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Ballester, PJ
(author)
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Baptista, D
(author)
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Bare, C
(author)
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Bateson, M
(author)
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Bender, A
(author)
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Bertrand, D
(author)
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Wijayawardena, B
(author)
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Boroevich, KA
(author)
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Bosdriesz, E
(author)
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Bougouffa, S
(author)
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Bounova, G
(author)
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Brouwer, T
(author)
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Bryant, B
(author)
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Calaza, M
(author)
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Calderone, A
(author)
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Calza, S
(author)
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Capuzzi, S
(author)
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Carbonell-Caballero, J
(author)
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Carlin, D
(author)
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Carter, H
(author)
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Castagnoli, L
(author)
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Celebi, R
(author)
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Cesareni, G
(author)
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Chang, H
(author)
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Chen, GC
(author)
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Chen, HR
(author)
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Chen, HY
(author)
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Cheng, LJ
(author)
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Chernomoretz, A
(author)
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Chicco, D
(author)
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Cho, KH
(author)
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Cho, S
(author)
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Choi, D
(author)
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Choi, J
(author)
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Choi, K
(author)
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Choi, M
(author)
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De Cock, M
(author)
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Coker, E
(author)
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Cortes-Ciriano, I
(author)
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Cserzo, M
(author)
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Cubuk, C
(author)
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Curtis, C
(author)
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Van Daele, D
(author)
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Dang, CC
(author)
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Dijkstra, T
(author)
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Dopazo, J
(author)
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Draghici, S
(author)
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Drosou, A
(author)
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Dumontier, M
(author)
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Ehrhart, F
(author)
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Eid, FE
(author)
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ElHefnawi, M
(author)
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Elmarakeby, H
(author)
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van Engelen, B
(author)
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Engin, HB
(author)
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de Esch, I
(author)
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Evelo, C
(author)
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Falcao, AO
(author)
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Farag, S
(author)
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Fernandez-Lozano, C
(author)
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Fisch, K
(author)
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Flobak, A
(author)
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Fornari, C
(author)
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Foroushani, ABK
(author)
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Fotso, DC
(author)
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Fourches, D
(author)
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Friend, S
(author)
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Frigessi, A
(author)
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Gao, F
(author)
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Gao, XT
(author)
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Gerold, JM
(author)
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Gestraud, P
(author)
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Ghosh, S
(author)
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Gillberg, J
(author)
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Godoy-Lorite, A
(author)
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Godynyuk, L
(author)
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Godzik, A
(author)
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Goldenberg, A
(author)
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Gomez-Cabrero, DKarolinska Institutet
(author)
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Gonen, M
(author)
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de Graaf, C
(author)
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Gray, H
(author)
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Grechkin, M
(author)
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Guimera, R
(author)
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Guney, E
(author)
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Haibe-Kains, B
(author)
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Han, Y
(author)
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Hase, T
(author)
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He, D
(author)
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He, LY
(author)
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Heath, LS
(author)
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Hellton, KH
(author)
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Helmer-Citterich, M
(author)
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Hidalgo, MR
(author)
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Hidru, D
(author)
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Hill, SM
(author)
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Hochreiter, S
(author)
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Hong, S
(author)
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Hovig, E
(author)
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Hsueh, YC
(author)
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Hu, ZY
(author)
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Huang, JK
(author)
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Huang, RS
(author)
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Hunyady, L
(author)
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Hwang, J
(author)
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Hwang, TH
(author)
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Hwang, W
(author)
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Hwang, Y
(author)
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Isayev, O
(author)
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Walk, OBD
(author)
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Jack, J
(author)
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Jahandideh, S
(author)
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Ji, JD
(author)
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Jo, Y
(author)
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Kamola, PJ
(author)
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Kanev, GK
(author)
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Karacosta, L
(author)
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Karimi, M
(author)
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Kaski, S
(author)
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Kazanov, M
(author)
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Khamis, AM
(author)
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Khan, SA
(author)
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Kiani, NAKarolinska Institutet
(author)
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Kim, A
(author)
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Kim, J
(author)
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Kim, J
(author)
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Kim, K
(author)
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Kim, K
(author)
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Kim, S
(author)
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Kim, Y
(author)
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Kim, Y
(author)
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Kirk, PDW
(author)
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Kitano, H
(author)
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Klambauer, G
(author)
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Knowles, D
(author)
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Ko, M
(author)
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Kohn-Luque, A
(author)
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Kooistra, AJ
(author)
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Kuenemann, MA
(author)
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Kuiper, M
(author)
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Kurz, C
(author)
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Kwon, M
(author)
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van Laarhoven, T
(author)
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Laegreid, A
(author)
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Lederer, S
(author)
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Lee, H
(author)
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Lee, J
(author)
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Lee, YW
(author)
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Leppaho, E
(author)
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Lewis, R
(author)
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Li, J
(author)
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Li, L
(author)
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Liley, J
(author)
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Lim, WK
(author)
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Lin, C
(author)
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Liu, YY
(author)
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Lopez, Y
(author)
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Low, J
(author)
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Lysenko, A
(author)
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Machado, D
(author)
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Madhukar, N
(author)
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De Maeyer, D
(author)
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Malpartida, AB
(author)
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Mamitsuka, H
(author)
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Marabita, FKarolinska Institutet
(author)
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Marchal, K
(author)
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Marttinen, P
(author)
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Mason, D
(author)
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Mazaheri, A
(author)
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Mehmood, A
(author)
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Mehreen, A
(author)
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Michaut, M
(author)
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Miller, RA
(author)
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Mitsopoulos, C
(author)
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Modos, D
(author)
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Van Moerbeke, M
(author)
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Moo, K
(author)
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Motsinger-Reif, A
(author)
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Movva, R
(author)
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Muraru, S
(author)
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Muratov, E
(author)
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Mushthofa, M
(author)
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Nagarajan, N
(author)
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Nakken, S
(author)
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Nath, A
(author)
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Neuvial, P
(author)
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Newton, R
(author)
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Ning, Z
(author)
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De Niz, C
(author)
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Oliva, B
(author)
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Olsen, C
(author)
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Palmeri, A
(author)
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Panesar, B
(author)
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Papadopoulos, S
(author)
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Park, J
(author)
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Park, S
(author)
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Park, S
(author)
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Pawitan, Y
(author)
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Peluso, D
(author)
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Pendyala, S
(author)
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Peng, J
(author)
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Perfetto, L
(author)
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Pirro, S
(author)
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Plevritis, S
(author)
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Politi, R
(author)
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Poon, H
(author)
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Porta, E
(author)
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Prellner, I
(author)
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Preuer, K
(author)
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Pujana, MA
(author)
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Ramnarine, R
(author)
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Reid, JE
(author)
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Reyal, F
(author)
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Richardson, S
(author)
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Ricketts, C
(author)
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Rieswijk, L
(author)
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Rocha, M
(author)
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Rodriguez-Gonzalvez, C
(author)
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Roell, K
(author)
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Rotroff, D
(author)
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de Ruiter, JR
(author)
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Rukawa, P
(author)
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Sadacca, B
(author)
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Safikhani, Z
(author)
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Safitri, F
(author)
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Sales-Pardo, M
(author)
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Sauer, S
(author)
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Schlichting, M
(author)
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Seoane, JA
(author)
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Serra, J
(author)
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Shang, MMKarolinska Institutet
(author)
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Sharma, A
(author)
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Sharma, H
(author)
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Shen, Y
(author)
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Shiga, M
(author)
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Shin, M
(author)
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Shkedy, Z
(author)
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Shopsowitz, K
(author)
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Sinai, S
(author)
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Skola, D
(author)
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Smirnov, P
(author)
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Soerensen, IF
(author)
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Soerensen, P
(author)
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Song, JH
(author)
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Song, SO
(author)
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Soufan, O
(author)
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Spitzmueller, A
(author)
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Steipe, B
(author)
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Suphavilai, C
(author)
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Tamayo, SP
(author)
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Tamborero, DKarolinska Institutet
(author)
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Tang, J
(author)
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Tanoli, ZUR
(author)
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Tarres-Deulofeu, M
(author)
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Tegner, JKarolinska Institutet
(author)
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Thommesen, L
(author)
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Tonekaboni, SAM
(author)
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Tran, H
(author)
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De Troyer, E
(author)
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Truong, A
(author)
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Tsunoda, T
(author)
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Turu, G
(author)
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Tzeng, GY
(author)
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Verbeke, L
(author)
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Videla, S
(author)
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Vis, D
(author)
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Voronkov, A
(author)
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Votis, K
(author)
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Wang, A
(author)
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Wang, HQH
(author)
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Wang, PW
(author)
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Wang, S
(author)
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Wang, W
(author)
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Wang, XC
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Wang, X
(author)
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Wennerberg, K
(author)
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Wernisch, L
(author)
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Wessels, L
(author)
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van Westen, GJP
(author)
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Westerman, BA
(author)
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White, SR
(author)
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Willighagen, E
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Wurdinger, T
(author)
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Xie, L
(author)
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Xie, SL
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Xu, H
(author)
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Yadav, B
(author)
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Yau, C
(author)
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Yeerna, H
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Yin, JW
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Yu, M
(author)
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Yu, M
(author)
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Yun, SJ
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Zakharov, A
(author)
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Zamichos, A
(author)
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Zanin, M
(author)
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Zeng, L
(author)
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Zenil, H
(author)
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Zhang, F
(author)
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Zhang, PY
(author)
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Zhang, W
(author)
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Zhao, HY
(author)
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Zhao, L
(author)
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Zheng, WJ
(author)
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Zoufir, A
(author)
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Zucknick, M
(author)
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In:Nature communications: Springer Science and Business Media LLC10:1, s. 2674-2041-1723
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Menden, MP
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Wang, D
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Mason, MJ
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Szalai, B
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Bulusu, KC
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Guan, YF
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Yu, T
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Kang, J
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Jeon, M
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Zaslavskiy, M
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Jang, IS
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Neto, EC
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Garnett, MJ
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Al-lazikani, B
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Alam, T
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Allam, A
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Allen, C
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de Almeida, MP
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Alves, V
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Anchang, B
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Antolin, AA
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Ash, JR
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Ba-alawi, W
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Ball, G
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Boroevich, KA
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Bougouffa, S
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Bounova, G
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Chen, GC
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Chen, HR
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Chen, HY
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Cheng, LJ
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Chernomoretz, A
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Chicco, D
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Cho, KH
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Cho, S
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Choi, D
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Choi, J
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Choi, K
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Choi, M
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De Cock, M
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Coker, E
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Cortes-Ciriano, ...
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Cserzo, M
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Cubuk, C
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Curtis, C
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Van Daele, D
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Dang, CC
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Dijkstra, T
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Dopazo, J
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Draghici, S
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Drosou, A
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Dumontier, M
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Ehrhart, F
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Eid, FE
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ElHefnawi, M
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Elmarakeby, H
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van Engelen, B
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Engin, HB
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de Esch, I
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Evelo, C
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Falcao, AO
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Farag, S
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Fernandez-Lozano ...
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Fisch, K
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Flobak, A
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Fornari, C
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Foroushani, ABK
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Fotso, DC
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Fourches, D
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Friend, S
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Frigessi, A
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Gao, F
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Gao, XT
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Gerold, JM
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Gestraud, P
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Ghosh, S
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Gillberg, J
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Godoy-Lorite, A
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Godynyuk, L
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Godzik, A
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Goldenberg, A
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Gomez-Cabrero, D
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Gonen, M
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de Graaf, C
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Gray, H
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Grechkin, M
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Guimera, R
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Guney, E
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Haibe-Kains, B
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Han, Y
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Hase, T
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He, D
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He, LY
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Heath, LS
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Hellton, KH
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Helmer-Citterich ...
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Hidalgo, MR
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Hidru, D
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Hill, SM
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Hochreiter, S
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Hong, S
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Hovig, E
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Hsueh, YC
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Hu, ZY
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Huang, JK
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Huang, RS
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Hunyady, L
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Hwang, J
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Hwang, TH
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Hwang, W
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Hwang, Y
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Isayev, O
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Walk, OBD
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Jack, J
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Jahandideh, S
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Ji, JD
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Jo, Y
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Kamola, PJ
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Kanev, GK
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Karacosta, L
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Karimi, M
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Kaski, S
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Kazanov, M
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Khamis, AM
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Khan, SA
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Kiani, NA
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Kim, A
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Kim, J
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Kim, K
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Kim, S
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Kim, Y
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Kirk, PDW
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Kitano, H
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Klambauer, G
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Knowles, D
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Ko, M
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Kohn-Luque, A
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Kooistra, AJ
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Kuenemann, MA
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Kuiper, M
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Kurz, C
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Kwon, M
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van Laarhoven, T
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Laegreid, A
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Lederer, S
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Lee, H
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Lee, J
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Lee, YW
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Leppaho, E
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Lewis, R
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Li, J
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Li, L
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Liley, J
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Lim, WK
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Lin, C
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Liu, YY
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Lopez, Y
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Low, J
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Lysenko, A
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Machado, D
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Madhukar, N
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De Maeyer, D
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Malpartida, AB
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Mamitsuka, H
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Marabita, F
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Marchal, K
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Marttinen, P
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Mason, D
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Mazaheri, A
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Mehmood, A
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Mehreen, A
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Michaut, M
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Miller, RA
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Mitsopoulos, C
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Modos, D
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Van Moerbeke, M
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Moo, K
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Motsinger-Reif, ...
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Movva, R
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Muraru, S
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Muratov, E
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Mushthofa, M
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Nagarajan, N
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Nakken, S
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Nath, A
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Neuvial, P
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Newton, R
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Ning, Z
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De Niz, C
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Oliva, B
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Olsen, C
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Palmeri, A
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Panesar, B
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Papadopoulos, S
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Park, J
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Park, S
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Pawitan, Y
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