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Page 1
Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models.
Allesøe RL, Lundgaard AT, Hernández Medina R, Aguayo-Orozco A, Johansen J, Nissen JN, Brorsson C, Mazzoni G, Niu L, Biel JH, Leal Rodríguez C, Brasas V, Webel H, Benros ME, Pedersen AG, Chmura PJ, Jacobsen UP, Mari A, Koivula R, Mahajan A, Vinuela A, Tajes JF, Sharma S, Haid M, Hong MG, Musholt PB, De Masi F, Vogt J, Pedersen HK, Gudmundsdottir V, Jones A, Kennedy G, Bell J, Thomas EL, Frost G, Thomsen H, Hansen E, Hansen TH, Vestergaard H, Muilwijk M, Blom MT, 't Hart LM, Pattou F, Raverdy V, Brage S, Kokkola T, Heggie A, McEvoy D, Mourby M, Kaye J, Hattersley A, McDonald T, Ridderstråle M, Walker M, Forgie I, Giordano GN, Pavo I, Ruetten H, Pedersen O, Hansen T, Dermitzakis E, Franks PW, Schwenk JM, Adamski J, McCarthy MI, Pearson E, Banasik K, Rasmussen S, Brunak S; IMI DIRECT Consortium. Allesøe RL, et al. Among authors: jacobsen up. Nat Biotechnol. 2023 Mar;41(3):399-408. doi: 10.1038/s41587-022-01520-x. Epub 2023 Jan 2. Nat Biotechnol. 2023. PMID: 36593394 Free PMC article.
Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits.
Brown AA, Fernandez-Tajes JJ, Hong MG, Brorsson CA, Koivula RW, Davtian D, Dupuis T, Sartori A, Michalettou TD, Forgie IM, Adam J, Allin KH, Caiazzo R, Cederberg H, De Masi F, Elders PJM, Giordano GN, Haid M, Hansen T, Hansen TH, Hattersley AT, Heggie AJ, Howald C, Jones AG, Kokkola T, Laakso M, Mahajan A, Mari A, McDonald TJ, McEvoy D, Mourby M, Musholt PB, Nilsson B, Pattou F, Penet D, Raverdy V, Ridderstråle M, Romano L, Rutters F, Sharma S, Teare H, 't Hart L, Tsirigos KD, Vangipurapu J, Vestergaard H, Brunak S, Franks PW, Frost G, Grallert H, Jablonka B, McCarthy MI, Pavo I, Pedersen O, Ruetten H, Walker M; DIRECT Consortium; Adamski J, Schwenk JM, Pearson ER, Dermitzakis ET, Viñuela A. Brown AA, et al. Nat Commun. 2023 Aug 21;14(1):5062. doi: 10.1038/s41467-023-40569-3. Nat Commun. 2023. PMID: 37604891 Free PMC article.
The influence of metformin treatment on the circulating proteome.
Connolly B, McCreight L, Slieker RC, Bedair KF, Donnelly L, de Klerk JA, Beulens JWJ, Elders PJM, Bergström G, Hong MG, Koivula RW, Franks PW, Schwenk JM, Gummesson A, Pearson ER, 't Hart LM; IMI-DIRECT; IMI-RHAPSODY. Connolly B, et al. EBioMedicine. 2025 Aug;118:105859. doi: 10.1016/j.ebiom.2025.105859. Epub 2025 Jul 19. EBioMedicine. 2025. PMID: 40684475 Free PMC article.
A Biological-Systems-Based Analyses Using Proteomic and Metabolic Network Inference Reveals Mechanistic Insights into Hepatic Lipid Accumulation: An IMI-DIRECT Study.
Atabaki NN, Coral DE, Pomares-Millan H, Smith K, Behjat HH, Koivula RW, Tura A, Miller H, Pinnick K, Agudelo L, Allin KH, Brown AA, Chabanova E, Chmura PJ, Jacobsen UP, Dawed AY, Elders PJM, Fernandez-Tajes JJ, Forgie IM, Haid M, Hansen TH, Hansen EL, Jones AG, Kokkola T, Kalamajski S, Mahajan A, McDonald TJ, McEvoy D, Muilwijk M, Tsirigos KD, Vangipurapu J, van Oort S, Vestergaard H, Adamski J, Beulens JW, Brunak S, Dermitzakis ET, Giordano GN, Gupta R, Hansen T, Hart LT, Hattersley AT, Hodson L, Laakso M, Loos RJF, Merino J, Ohlsson M, Pedersen O, Ridderstråle M, Ruetten H, Rutters F, Schwenk JM, Tomlinson J, Walker M, Yaghootkar H, Karpe F, McCarthy MI, Thomas EL, Bell JD, Mari A, Pavo I, Pearson ER, Viñuela A, Franks PW. Atabaki NN, et al. Among authors: jacobsen up. medRxiv [Preprint]. 2025 Jun 2:2025.06.02.25328773. doi: 10.1101/2025.06.02.25328773. medRxiv. 2025. PMID: 40502600 Free PMC article. Preprint.
Author Correction: Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models.
Allesøe RL, Lundgaard AT, Hernández Medina R, Aguayo-Orozco A, Johansen J, Nissen JN, Brorsson C, Mazzoni G, Niu L, Biel JH, Leal Rodríguez C, Brasas V, Webel H, Benros ME, Pedersen AG, Chmura PJ, Jacobsen UP, Mari A, Koivula R, Mahajan A, Vinuela A, Tajes JF, Sharma S, Haid M, Hong MG, Musholt PB, De Masi F, Vogt J, Pedersen HK, Gudmundsdottir V, Jones A, Kennedy G, Bell J, Thomas EL, Frost G, Thomsen H, Hansen E, Hansen TH, Vestergaard H, Muilwijk M, Blom MT, 't Hart LM, Pattou F, Raverdy V, Brage S, Kokkola T, Heggie A, McEvoy D, Mourby M, Kaye J, Hattersley A, McDonald T, Ridderstråle M, Walker M, Forgie I, Giordano GN, Pavo I, Ruetten H, Pedersen O, Hansen T, Dermitzakis E, Franks PW, Schwenk JM, Adamski J, McCarthy MI, Pearson E, Banasik K, Rasmussen S, Brunak S; IMI DIRECT Consortium. Allesøe RL, et al. Among authors: jacobsen up. Nat Biotechnol. 2023 Jul;41(7):1026. doi: 10.1038/s41587-023-01805-9. Nat Biotechnol. 2023. PMID: 37130959 Free PMC article. No abstract available.
ChemProt-2.0: visual navigation in a disease chemical biology database.
Kim Kjærulff S, Wich L, Kringelum J, Jacobsen UP, Kouskoumvekaki I, Audouze K, Lund O, Brunak S, Oprea TI, Taboureau O. Kim Kjærulff S, et al. Among authors: jacobsen up. Nucleic Acids Res. 2013 Jan;41(Database issue):D464-9. doi: 10.1093/nar/gks1166. Epub 2012 Nov 26. Nucleic Acids Res. 2013. PMID: 23185041 Free PMC article.
Bayesian network imputation methods applied to multi-omics data identify putative causal relationships in a type 2 diabetes dataset containing incomplete data: An IMI DIRECT Study.
Howey R, Adam J, Adamski J, Atabaki NN, Brunak S, Chmura PJ, De Masi F, Dermitzakis ET, Fernandez-Tajes JJ, Forgie IM, Franks PW, Giordano GN, Haid M, Hansen T, Hansen TH, Harms PP, Hattersley AT, Hong MG, Jacobsen UP, Jones AG, Koivula RW, Kokkola T, Mahajan A, Mari A, McCarthy MI, McDonald TJ, Musholt PB, Pavo I, Pearson ER, Pedersen O, Ruetten H, Rutters F, Schwenk JM, Sharma S, 't Hart LM, Vestergaard H, Walker M; IMI DIRECT Consortium; Viñuela A, Cordell HJ. Howey R, et al. Among authors: jacobsen up. PLoS Genet. 2025 Jul 15;21(7):e1011776. doi: 10.1371/journal.pgen.1011776. eCollection 2025 Jul. PLoS Genet. 2025. PMID: 40663565 Free PMC article.