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Page 1
Machine learning and deep learning applications in microbiome research.
Hernández Medina R, Kutuzova S, Nielsen KN, Johansen J, Hansen LH, Nielsen M, Rasmussen S. Hernández Medina R, et al. Among authors: rasmussen s. ISME Commun. 2022 Oct 6;2(1):98. doi: 10.1038/s43705-022-00182-9. ISME Commun. 2022. PMID: 37938690 Free PMC article. Review.
Genetic studies of abdominal MRI data identify genes regulating hepcidin as major determinants of liver iron concentration.
Wilman HR, Parisinos CA, Atabaki-Pasdar N, Kelly M, Thomas EL, Neubauer S; IMI DIRECT Consortium; Mahajan A, Hingorani AD, Patel RS, Hemingway H, Franks PW, Bell JD, Banerjee R, Yaghootkar H. Wilman HR, et al. J Hepatol. 2019 Sep;71(3):594-602. doi: 10.1016/j.jhep.2019.05.032. Epub 2019 Jun 19. J Hepatol. 2019. PMID: 31226389 Free PMC article.
A reference map of potential determinants for the human serum metabolome.
Bar N, Korem T, Weissbrod O, Zeevi D, Rothschild D, Leviatan S, Kosower N, Lotan-Pompan M, Weinberger A, Le Roy CI, Menni C, Visconti A, Falchi M, Spector TD; IMI DIRECT consortium; Adamski J, Franks PW, Pedersen O, Segal E. Bar N, et al. Nature. 2020 Dec;588(7836):135-140. doi: 10.1038/s41586-020-2896-2. Epub 2020 Nov 11. Nature. 2020. PMID: 33177712 Clinical Trial.
The ubiquitin ligase RFWD3 is required for translesion DNA synthesis.
Gallina I, Hendriks IA, Hoffmann S, Larsen NB, Johansen J, Colding-Christensen CS, Schubert L, Sellés-Baiget S, Fábián Z, Kühbacher U, Gao AO, Räschle M, Rasmussen S, Nielsen ML, Mailand N, Duxin JP. Gallina I, et al. Among authors: rasmussen s. Mol Cell. 2021 Feb 4;81(3):442-458.e9. doi: 10.1016/j.molcel.2020.11.029. Epub 2020 Dec 14. Mol Cell. 2021. PMID: 33321094 Free PMC article.
Improved metagenome binning and assembly using deep variational autoencoders.
Nissen JN, Johansen J, Allesøe RL, Sønderby CK, Armenteros JJA, Grønbech CH, Jensen LJ, Nielsen HB, Petersen TN, Winther O, Rasmussen S. Nissen JN, et al. Among authors: rasmussen s. Nat Biotechnol. 2021 May;39(5):555-560. doi: 10.1038/s41587-020-00777-4. Epub 2021 Jan 4. Nat Biotechnol. 2021. PMID: 33398153
Profiles of Glucose Metabolism in Different Prediabetes Phenotypes, Classified by Fasting Glycemia, 2-Hour OGTT, Glycated Hemoglobin, and 1-Hour OGTT: An IMI DIRECT Study.
Tura A, Grespan E, Göbl CS, Koivula RW, Franks PW, Pearson ER, Walker M, Forgie IM, Giordano GN, Pavo I, Ruetten H, Dermitzakis ET, McCarthy MI, Pedersen O, Schwenk JM, Adamski J, De Masi F, Tsirigos KD, Brunak S, Viñuela A, Mahajan A, McDonald TJ, Kokkola T, Vangipurapu J, Cederberg H, Laakso M, Rutters F, Elders PJM, Koopman ADM, Beulens JW, Ridderstråle M, Hansen TH, Allin KH, Hansen T, Vestergaard H, Mari A; IMI DIRECT Consortium. Tura A, et al. Diabetes. 2021 Sep;70(9):2092-2106. doi: 10.2337/db21-0227. Epub 2021 Jul 7. Diabetes. 2021. PMID: 34233929
SCAI promotes error-free repair of DNA interstrand crosslinks via the Fanconi anemia pathway.
Schubert L, Hendriks IA, Hertz EPT, Wu W, Sellés-Baiget S, Hoffmann S, Viswalingam KS, Gallina I, Pentakota S, Benedict B, Johansen J, Apelt K, Luijsterburg MS, Rasmussen S, Lisby M, Liu Y, Nielsen ML, Mailand N, Duxin JP. Schubert L, et al. Among authors: rasmussen s. EMBO Rep. 2022 Apr 5;23(4):e53639. doi: 10.15252/embr.202153639. Epub 2022 Feb 14. EMBO Rep. 2022. PMID: 35156773 Free PMC article.
Genome binning of viral entities from bulk metagenomics data.
Johansen J, Plichta DR, Nissen JN, Jespersen ML, Shah SA, Deng L, Stokholm J, Bisgaard H, Nielsen DS, Sørensen SJ, Rasmussen S. Johansen J, et al. Among authors: rasmussen s. Nat Commun. 2022 Feb 18;13(1):965. doi: 10.1038/s41467-022-28581-5. Nat Commun. 2022. PMID: 35181661 Free PMC article.
Critical Assessment of Metagenome Interpretation: the second round of challenges.
Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC. Meyer F, et al. Among authors: rasmussen s. Nat Methods. 2022 Apr;19(4):429-440. doi: 10.1038/s41592-022-01431-4. Epub 2022 Apr 8. Nat Methods. 2022. PMID: 35396482 Free PMC article.
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: rasmussen s. 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.
2,592 results