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, N. N., Brunak, S., Chmura, P. J., De Masi, F., Dermitzakis, E. T., Fernandez-Tajes, J. J., Forgie, I. M., Franks, P. W., Giordano, G. N., Haid, M., Hansen, T., Hansen, T. H., Harms, P. P., Hattersley, A. T., Hong, M. G., Jacobsen, U. P. & Jones, A. G. & 20 others, Koivula, R. W., Kokkola, T., Mahajan, A., Mari, A., McCarthy, M. I., McDonald, T. J., Musholt, P. B., Pavo, I., Pearson, E. R., Pedersen, O., Ruetten, H., Rutters, F., Schwenk, J. M., Sharma, S., T Hart, L. M., Vestergaard, H., Walker, M., Viñuela, A., Cordell, H. J. & The IMI DIRECT Consortium, 2025, In: PLOS Genetics. 21, 7, 20 p., e1011776.

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Glucocorticoid-induced changes of the gut microbiota and metabolic markers in healthy young men: Outcome of a randomized controlled trial

Lyu, L., Fan, Y., Bryrup, T., Clos-Garcia, M., Brix, S., Eiken, M., Stankevic, E., Lund, A. B., Knop, F. K., Jørgensen, N. R., Vestergaard, H., Hansen, T., Hansen, T., Nielsen, T. & Pedersen, O., 2025, In: Cell Reports Medicine. 6, 11, 18 p., 102426.

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The dynamics of the gut microbiota in prediabetes during a four-year follow-up among European patients—an IMI-DIRECT prospective study

Lyu, L., Fan, Y., Vogt, J. K., Clos-Garcia, M., Bonnefond, A., Pedersen, H. K., Dutta, A., Koivula, R., Sharma, S., Allin, K. H., Brorsson, C., Cederberg, H., Chabanova, E., De Masi, F., Dermitzakis, E., Elders, P. J., Blom, M. T., Hollander, M., Eriksen, R. & Forgie, I. & 35 others, Frost, G., Giordano, G. N., Grallert, H., Haid, M., Hansen, T. H., Jablonka, B., Kokkola, T., Mahajan, A., Mari, A., McDonald, T. J., Musholt, P. B., Pavo, I., Prehn, C., Ridderstråle, M., Ruetten, H., Hart, L. M. ‘., Schwenk, J. M., Stankevic, E., Thomsen, H. S., Vangipurapu, J., Vestergaard, H., Viñuela, A., Walker, M., Hansen, T., Linneberg, A., Nielsen, H. B., Brunak, S., McCarthy, M. I., Froguel, P., Adamski, J., Franks, P. W., Laakso, M., Beulens, J. W. J., Pearson, E. & Pedersen, O., 2025, In: Genome Medicine. 17, 1, 23 p., 78.

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Characterization of the gut bacterial and viral microbiota in latent autoimmune diabetes in adults

Poulsen, C. S., Hesse, D., Fernandes, G. R., Hansen, T. H., Kern, T., Linneberg, A., Van Espen, L., Jørgensen, T., Nielsen, T., Alibegovic, A. C., Matthijnssens, J., Pedersen, O., Vestergaard, H., Hansen, T. & Andersen, M. K., 2024, In: Scientific Reports. 14, 1, 11 p., 8315.

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Alteration of Gut Microbiome in Patients With Schizophrenia Indicates Links Between Bacterial Tyrosine Biosynthesis and Cognitive Dysfunction

Thirion, F., Speyer, H., Hansen, T. H., Nielsen, T., Fan, Y., Le Chatelier, E., Fromentin, S., Berland, M., Plaza Oñate, F., Pons, N., Galleron, N., Levenez, F., Markó, L., Birkner, T., Jørgensen, T., Forslund, S. K., Vestergaard, H., Hansen, T., Nordentoft, M. & Mors, O. & 3 others, Benros, M. E., Pedersen, O. & Ehrlich, S. D., 2023, In: Biological Psychiatry Global Open Science. 3, 2, p. 283-291 9 p.

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Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models: [with Author Correction]

Allesøe, R. L., Lundgaard, A. T., Hernández Medina, R., Aguayo-Orozco, A., Johansen, J., Nissen, J. N., Brorsson, C., Mazzoni, G., Niu, L., Biel, J. H., Brasas, V., Webel, H., Benros, M. E., Pedersen, A. G., Chmura, P. J., Jacobsen, U. P., Mari, A., Koivula, R., Mahajan, A. & Vinuela, A. & 31 others, Tajes, J. F., Sharma, S., Haid, M., Hong, M.-G., Musholt, P. B., De Masi, F., Vogt, J., Pedersen, H. K., Gudmundsdottir, V., Jones, A., Kennedy, G., Bell, J., Thomas, E. L., Frost, G., Thomsen, H., Hansen, E., Hansen, T. H., Vestergaard, H., Muilwijk, M., Blom, M. T., 't Hart, L. M., Pattou, F., Raverdy, V., Brage, S., Ridderstråle, M., Pedersen, O., Hansen, T., Banasik, K., Rasmussen, S., Brunak, S. & IMI-DIRECT consortium, 2023, In: Nature Biotechnology. 41, 3, p. 399–408 18 p.

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Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide

Andrikopoulos, P., Aron-Wisnewsky, J., Chakaroun, R., Myridakis, A., Forslund, S. K., Nielsen, T., Adriouch, S., Holmes, B., Chilloux, J., Vieira-Silva, S., Falony, G., Salem, J. E., Andreelli, F., Belda, E., Kieswich, J., Chechi, K., Puig-Castellvi, F., Chevalier, M., Le Chatelier, E. & Olanipekun, M. T. & 83 others, Hoyles, L., Alves, R., Helft, G., Isnard, R., Køber, L., Coelho, L. P., Rouault, C., Gauguier, D., Gøtze, J. P., Prifti, E., Froguel, P., Alili, R., Galijatovic, E. A. A., Barthelemy, O., Bastard, J. P., Batisse, J. P., Bel-Lassen, P., Berland, M., Bittar, R., Blottière, H., Bosquet, F., Boubrit, R., Bourron, O., Camus, M., Ciangura, C., Collet, J. P., Dietrich, A., Djebbar, M., Doré, A., Engelbrechtsen, L., Fezeu, L., Fromentin, S., Pons, N., Graine, M., Grünemann, C., Hartemann, A., Hartmann, B., Hornbak, M., Jaqueminet, S., Jørgensen, N. R., Julienne, H., Justesen, J., Kammer, J., Karup, N., Kozlowski, R., Kuhn, M., Lejard, V., Letunic, I., Levenez, F., Marko, L., Martinez-Gili, L., Massey, R., Maziers, N., Moitinho-Silva, L., Montalescot, G., Neves, A. L., Le Pavin, L. P., Pousset, F., Rodriguez-Martinez, A., Schmidt, S., Schütz, T., Silva, L., Silvain, J., Svendstrup, M., Swartz, T. D., Vanduyvenboden, T., Verger, E. O., Walther, S., Zucker, J. D., Bäckhed, F., Vestergaard, H., Hansen, T., Oppert, J. M., Blüher, M., Nielsen, J., Raes, J., Bork, P., Yaqoob, M. M., Stumvoll, M., Pedersen, O., Ehrlich, S. D., Clément, K. & Dumas, M. E., 2023, In: Nature Communications. 14, 18 p., 5843.

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Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits

Brown, A. A., Fernandez-Tajes, J. J., Hong, M. G., Brorsson, C. A., Koivula, R. W., Davtian, D., Dupuis, T., Sartori, A., Michalettou, T. D., Forgie, I. M., Adam, J., Allin, K. H., Caiazzo, R., Cederberg, H., De Masi, F., Elders, P. J. M., Giordano, G. N., Haid, M., Hansen, T. & Hansen, T. H. & 134 others, Hattersley, A. T., Heggie, A. J., Howald, C., Jones, A. G., Kokkola, T., Laakso, M., Mahajan, A., Mari, A., McDonald, T. J., McEvoy, D., Mourby, M., Musholt, P. B., Nilsson, B., Pattou, F., Penet, D., Raverdy, V., Ridderstråle, M., Romano, L., Rutters, F., Sharma, S., Teare, H., ‘t Hart, L., Tsirigos, K. D., Vangipurapu, J., Vestergaard, H., Brunak, S., Franks, P. W., Frost, G., Grallert, H., Jablonka, B., McCarthy, M. I., Pavo, I., Pedersen, O., Ruetten, H., Walker, M., Adragni, K., Allesøe, R. L. L., Artati, A. A., Arumugam, M., Atabaki-Pasdar, N., Baltauss, T., Banasik, K., Barnett, A. L., Baum, P., Bell, J. D., Beulens, J. W., Bianzano, S. B., Bizzotto, R., Bonnefond, A., Cabrelli, L., Dale, M., Dawed, A. Y., de Preville, N., Dekkers, K. F., Deshmukh, H. A., Dings, C., Donnelly, L., Dutta, A., Ehrhardt, B., Engelbrechtsen, L., Eriksen, R., Fan, Y., Ferrer, J., Fitipaldi, H., Forman, A., Fritsche, A., Froguel, P., Gassenhuber, J., Gough, S., Graefe-Mody, U., Grempler, R., Groeneveld, L., Groop, L., Gudmundsdóttir, V., Gupta, R., Hennige, A. M. H., Hill, A. V., Holl, R. W., Hudson, M., Jacobsen, U. P., Jennison, C., Johansen, J., Jonsson, A., Karaderi, T., Kaye, J., Kennedy, G., Klintenberg, M., Kuulasmaa, T., Lehr, T., Loftus, H., Lundgaard, A. T. T., Mazzoni, G., McRobert, N., McVittie, I., Nice, R., Nicolay, C., Nijpels, G., Palmer, C. N., Pedersen, H. K., Perry, M. H., Pomares-Millan, H., Prehn, C. P., Ramisch, A., Rasmussen, S., Robertson, N., Rodriquez, M., Sackett, P., Scherer, N., Shah, N., Sihinevich, I., Slieker, R. C., Sondertoft, N. B., Steckel-Hamann, B., Thomas, M. K., Thomas, C. E. E., Thomas, E. L. L., Thorand, B., Thorne, C. E., Tillner, J., Tura, A., Uhlen, M., van Leeuwen, N., van Oort, S., Verkindt, H., Vogt, J., Wad Sackett, P. W., Wesolowska-Andersen, A., Whitcher, B., White, M. W., Adamski, J., Schwenk, J. M., Pearson, E. R., Dermitzakis, E. T. & Viñuela, A., 2023, In: Nature Communications. 14, 17 p., 5062.

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