NetAllergen, a random forest model integrating MHC-II presentation propensity for improved allergenicity prediction.

Autor: Li, Yuchen¹, Sackett, Peter Wad¹, Nielsen, Morten^1,2, Barra, Carolina¹ carolet@dtu.dk

Publikováno v: Bioinformatics Advances. 2023, Vol. 3 Issue 1, p1-10. 10p.

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Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models

Autor: Allesøe, Rosa Lundbye, Lundgaard, Agnete Troen, Hernández Medina, Ricardo, Aguayo-Orozco, Alejandro, Johansen, Joachim, Nissen, Jakob Nybo, Brorsson, Caroline, Mazzoni, Gianluca, Niu, Lili, Biel, Jorge Hernansanz, Brasas, Valentas, Webel, Henry, Benros, Michael Eriksen, Pedersen, Anders Gorm, Chmura, Piotr Jaroslaw, Jacobsen, Ulrik Plesner, Mari, Andrea, Koivula, Robert, Mahajan, Anubha, Vinuela, Ana, Tajes, Juan Fernandez, Sharma, Sapna, Haid, Mark, Hong, Mun-Gwan, Musholt, Petra B., de Masi, Federico, Vogt, Josef, Pedersen, Helle Krogh, Gudmundsdottir, Valborg, Jones, Angus, Kennedy, Gwen, Bell, Jimmy, Thomas, E. Louise, Frost, Gary, Thomsen, Henrik, Hansen, Elizaveta, Hansen, Tue Haldor, Vestergaard, Henrik, Muilwijk, Mirthe, Blom, Marieke T., ‘t Hart, Leen M., Pattou, Francois, Raverdy, Violeta, Brage, Soren, Kokkola, Tarja, Heggie, Alison, McEvoy, Donna, Mourby, Miranda, Kaye, Jane, Hattersley, Andrew, McDonald, Timothy, Ridderstråle, Martin, Walker, Mark, Forgie, Ian, Giordano, Giuseppe N., Pavo, Imre, Ruetten, Hartmut, Pedersen, Oluf, Hansen, Torben, Dermitzakis, Emmanouil, Franks, Paul W., Schwenk, Jochen M., Adamski, Jerzy, McCarthy, Mark I., Pearson, Ewan, Banasik, Karina, Rasmussen, Simon, Brunak, S. ren, Froguel, Philippe, Thomas, Cecilia Engel, Haussler, Ragna, Beulens, Joline, Rutters, Femke, Nijpels, Giel, van Oort, Sabine, Groeneveld, Lenka, Elders, Petra, Giorgino, Toni, Rodriquez, Marianne, Nice, Rachel, Perry, Mandy, Bianzano, Susanna, Graefe-Mody, Ulrike, Hennige, Anita, Grempler, Rolf, Baum, Patrick, Stærfeldt, Hans-Henrik, Shah, Nisha, Teare, Harriet, Ehrhardt, Beate, Tillner, Joachim, Dings, Christiane, Lehr, Thorsten, Scherer, Nina, Sihinevich, Iryna, Cabrelli, Louise, Loftus, Heather, Bizzotto, Roberto, Tura, Andrea, Dekkers, Koen, van Leeuwen, Nienke, Groop, Leif, Slieker, Roderick, Ramisch, Anna, Jennison, Christopher, McVittie, Ian, Frau, Francesca, Steckel-Hamann, Birgit, Adragni, Kofi, Thomas, Melissa, Pasdar, Naeimeh Atabaki, Fitipaldi, Hugo, Kurbasic, Azra, Mutie, Pascal, Pomares-Millan, Hugo, Bonnefond, Amelie, Canouil, Mickael, Caiazzo, Robert, Verkindt, Helene, Holl, Reinhard, Kuulasmaa, Teemu, Deshmukh, Harshal, Cederberg, Henna, Laakso, Markku, Vangipurapu, Jagadish, Dale, Matilda, Thorand, Barbara, Nicolay, Claudia, Fritsche, Andreas, Hill, Anita, Hudson, Michelle, Thorne, Claire, Allin, Kristine, Arumugam, Manimozhiyan, Jonsson, Anna, Engelbrechtsen, Line, Forman, Annemette, Dutta, Avirup, Sondertoft, Nadja, Fan, Yong, Gough, Stephen, Robertson, Neil, McRobert, Nicky, Wesolowska-Andersen, Agata, Brown, Andrew, Davtian, David, Dawed, Adem, Donnelly, Louise, Palmer, Colin, White, Margaret, Ferrer, Jorge, Whitcher, Brandon, Artati, Anna, Prehn, Cornelia, Adam, Jonathan, Grallert, Harald, Gupta, Ramneek, Sackett, Peter Wad, Nilsson, Birgitte, Tsirigos, Konstantinos, Eriksen, Rebeca, Jablonka, Bernd, Uhlen, Mathias, Gassenhuber, Johann, Baltauss, Tania, de Preville, Nathalie, Klintenberg, Maria, Abdalla, Moustafa

Publikováno v: 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, 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, Kokkola, T, Heggie, A, McEvoy, D, Mourby, M, Kaye, J, Hattersley, A, McDonald, T, Ridderstråle, M, Walker, M, Forgie, I, Giordano, G N, Pavo, I, Ruetten, H, Pedersen, O, Hansen, T, Dermitzakis, E, Franks, P W, Schwenk, J M, Adamski, J, McCarthy, M I, Pearson, E, Banasik, K, Rasmussen, S, Brunak, S R, Froguel, P, Thomas, C E, Haussler, R, Beulens, J, Rutters, F, Nijpels, G, van Oort, S, Groeneveld, L, Elders, P, Giorgino, T, Rodriquez, M, Nice, R, Perry, M, Bianzano, S, Graefe-Mody, U, Hennige, A, Grempler, R, Baum, P, Stærfeldt, H-H, Shah, N, Teare, H, Ehrhardt, B, Tillner, J, Dings, C, Lehr, T, Scherer, N, Sihinevich, I, Cabrelli, L, Loftus, H, Bizzotto, R, Tura, A, Dekkers, K, van Leeuwen, N, Groop, L, Slieker, R, Ramisch, A, Jennison, C, McVittie, I, Frau, F, Steckel-Hamann, B, Adragni, K, Thomas, M, Pasdar, N A, Fitipaldi, H, Kurbasic, A, Mutie, P, Pomares-Millan, H, Bonnefond, A, Canouil, M, Caiazzo, R, Verkindt, H, Holl, R, Kuulasmaa, T, Deshmukh, H, Cederberg, H, Laakso, M, Vangipurapu, J, Dale, M, Thorand, B, Nicolay, C, Fritsche, A, Hill, A, Hudson, M, Thorne, C, Allin, K, Arumugam, M, Jonsson, A, Engelbrechtsen, L, Forman, A, Dutta, A, Sondertoft, N, Fan, Y, Gough, S, Robertson, N, McRobert, N, Wesolowska-Andersen, A, Brown, A, Davtian, D, Dawed, A, Donnelly, L, Palmer, C, White, M, Ferrer, J, Whitcher, B, Artati, A, Prehn, C, Adam, J, Grallert, H, Gupta, R, Sackett, P W, Nilsson, B, Tsirigos, K, Eriksen, R, Jablonka, B, Uhlen, M, Gassenhuber, J, IMI DIRECT Consortium, Baltauss, T, de Preville, N, Klintenberg, M & Abdalla, M 2023, ' Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models ', Nature Biotechnology, vol. 41, no. 3, pp. 399-408 . https://doi.org/10.1038/s41587-022-01520-x
Nature Biotechnology, 41(3), 399-408. Nature Publishing Group
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, 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, Hansen, T, Schwenk, J M, Adamski, J, McCarthy, M I, Pearson, E, Banasik, K, Rasmussen, S, Brunak, S & Franks, P W 2023, ' Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models ', Nature Biotechnology, vol. 41, no. 3, pp. 399-408 . https://doi.org/10.1038/s41587-022-01520-x
Nature Biotechnology, 41, 399-408. NATURE PORTFOLIO
Nature biotechnology, 41(3), 399-408. Nature Publishing Group

The application of multiple omics technologies in biomedical cohorts has the potential to reveal patient-level disease characteristics and individualized response to treatment. However, the scale and heterogeneous nature of multi-modal data makes int

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::94a38183b41c4b550c847aebac0cdbdf
https://research.vumc.nl/en/publications/216574f1-bee3-436a-971a-07c15cf44b94

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SAFARI: Pangenome Alignment of Ancient DNA Using Purine/Pyrimidine Encodings.

Autor: Rubin J; Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark., van Waaij J; Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark., Kraft L; Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark., Sirén J; UC Santa Cruz Genomics Institute, Santa Cruz, USA., Sackett PW; Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark., Renaud G; Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Oct 08. Date of Electronic Publication: 2024 Oct 08.