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FältnamnIndikatorerMetadata
00023212naa a2201825 4500
001oai:DiVA.org:kth-330088
003SwePub
008230626s2023 | |||||||||||000 ||eng|
009oai:lup.lub.lu.se:13c6b992-22aa-4bcc-b353-dbd6f2f72642
024a https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3300882 URI
024a https://doi.org/10.1038/s41587-022-01520-x2 DOI
024a https://lup.lub.lu.se/record/13c6b992-22aa-4bcc-b353-dbd6f2f726422 URI
040 a (SwePub)kthd (SwePub)lu
041 a engb eng
042 9 SwePub
072 7a ref2 swepub-contenttype
072 7a art2 swepub-publicationtype
100a Allesøe, Rosa Lundbyeu Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark; Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark4 aut
2451 0a Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models
264 c 2023-01-02
264 1b Springer Nature,c 2023
338 a print2 rdacarrier
500 a Correction in DOI  10.1038/s41587-023-01805-9QC 20230626
520 a 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 integration and inference a non-trivial task. We developed a deep-learning-based framework, multi-omics variational autoencoders (MOVE), to integrate such data and applied it to a cohort of 789 people with newly diagnosed type 2 diabetes with deep multi-omics phenotyping from the DIRECT consortium. Using in silico perturbations, we identified drug–omics associations across the multi-modal datasets for the 20 most prevalent drugs given to people with type 2 diabetes with substantially higher sensitivity than univariate statistical tests. From these, we among others, identified novel associations between metformin and the gut microbiota as well as opposite molecular responses for the two statins, simvastatin and atorvastatin. We used the associations to quantify drug–drug similarities, assess the degree of polypharmacy and conclude that drug effects are distributed across the multi-omics modalities.
650 7a NATURVETENSKAPx Biologix Bioinformatik och systembiologi0 (SwePub)106102 hsv//swe
650 7a NATURAL SCIENCESx Biological Sciencesx Bioinformatics and Systems Biology0 (SwePub)106102 hsv//eng
650 7a MEDICIN OCH HÄLSOVETENSKAPx Klinisk medicinx Endokrinologi och diabetes0 (SwePub)302052 hsv//swe
650 7a MEDICAL AND HEALTH SCIENCESx Clinical Medicinex Endocrinology and Diabetes0 (SwePub)302052 hsv//eng
653 a Deep learning
653 a Learning systems
653 a Patient treatment
653 a 'omics'
653 a Auto encoders
653 a In-silico
653 a Learning models
653 a Multi-modal data
653 a Multi-modal dataset
653 a Non-trivial tasks
653 a Omics technologies
653 a Phenotyping
653 a Type-2 diabetes
653 a Modal analysis
700a Lundgaard, Agnete Troenu Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 aut
700a Hernández Medina, Ricardou Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark4 aut
700a Aguayo-Orozco, Alejandrou Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 aut
700a Johansen, Joachimu Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 aut
700a Nissen, Jakob Nybou Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark4 aut
700a Brorsson, Carolineu Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 aut
700a Mazzoni, Gianlucau Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 aut
700a Niu, Liliu Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark4 aut
700a Biel, Jorge Hernansanzu Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 aut
700a Brasas, Valentasu Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark4 aut
700a Webel, Henryu Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark4 aut
700a Benros, Michael Eriksenu Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark4 aut
700a Pedersen, Anders Gormu Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 aut
700a Chmura, Piotr Jaroslawu Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 aut
700a Jacobsen, Ulrik Plesneru Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 aut
700a Mari, Andreau C.N.R. Institute of Neuroscience, Padova, Italy4 aut
700a Koivula, Robertu Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK4 aut
700a Mahajan, Anubhau Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK4 aut
700a Vinuela, Anau Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK4 aut
700a Tajes, Juan Fernandezu Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK4 aut
700a Sharma, Sapnau Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany, Bavaria; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany, Bavaria; Chair of Food Chemistry and Molecular and Sensory Science, Technical University of Munich, Freising, Germany4 aut
700a Haid, Marku Metabolomics and Proteomics Core, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany4 aut
700a Hong, Mun-Gwanu KTH,Science for Life Laboratory, SciLifeLab,Proteinvetenskap4 aut0 (Swepub:kth)u19gmsru
700a Musholt, Petra B.u Research and Development Global Development, Translational Medicine and Clinical Pharmacology, Sanofi-Aventis Deutschland, Frankfurt, Germany4 aut
700a De Masi, Federicou Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 aut
700a Vogt, Josefu Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark4 aut
700a Pedersen, Helle Kroghu Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark4 aut
700a Gudmundsdottir, Valborgu Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 aut
700a Jones, Angusu University of Exeter Medical School, Exeter, UK4 aut
700a Kennedy, Gwenu The Immunoassay Biomarker Core Laboratory, School of Medicine, University of Dundee, Dundee, UK4 aut
700a Bell, Jimmyu Research Centre for Optimal Health, Department of Life Sciences, University of Westminster, London, UK4 aut
700a Thomas, E. Louiseu Research Centre for Optimal Health, Department of Life Sciences, University of Westminster, London, UK4 aut
700a Frost, Garyu Section for Nutrition Research, Faculty of Medicine, Imperial College London, London, UK4 aut
700a Thomsen, Henriku Department of Radiology, Copenhagen University Hospital Herlev-Gentofte, Herlev, Denmark4 aut
700a Hansen, Elizavetau Department of Radiology, Copenhagen University Hospital Herlev-Gentofte, Herlev, Denmark4 aut
700a Hansen, Tue Haldoru Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark4 aut
700a Vestergaard, Henriku Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark4 aut
700a Ridderstråle, M.u Lund University,Lunds universitet,Genomik, diabetes och endokrinologi,Forskargrupper vid Lunds universitet,Genomics, Diabetes and Endocrinology,Lund University Research Groups4 aut0 (Swepub:lu)endo-mri
700a Blom, Marieke T.u Department of General Practice, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands4 aut
700a ‘t Hart, Leen M.u Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Department of Biomedical Data Science, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands; Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands4 aut
700a Pattou, Francoisu Inserm, Univ Lille, CHU Lille, Lille Pasteur Institute, EGID, Lille, France4 aut
700a Raverdy, Violetau Inserm, Univ Lille, CHU Lille, Lille Pasteur Institute, EGID, Lille, France4 aut
700a Brage, Sorenu MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK4 aut
700a Kokkola, Tarjau Department of Medicine, University of Eastern Finland, Kuopio, Finland4 aut
700a Heggie, Alisonu Institute of Cellular Medicine, Newcastle University, Newcastle, UK4 aut
700a McEvoy, Donnau Diabetes Research Network, Royal Victoria Infirmary, Newcastle, UK4 aut
700a Klintenberg, M.u Lund University,Lunds universitet,Genomik, diabetes och endokrinologi,Forskargrupper vid Lunds universitet,Genomics, Diabetes and Endocrinology,Lund University Research Groups4 aut0 (Swepub:lu)med-mk1
700a Kaye, Janeu Centre for Health, Law and Emerging Technologies (HeLEX), Faculty of Law, University of Oxford, Oxford, UK4 aut
700a Hattersley, Andrewu University of Exeter Medical School, Exeter, UK4 aut
700a McDonald, Timothyu University of Exeter Medical School, Exeter, UK4 aut
700a Ridderstråle, Martinu Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Malmö, Sweden4 aut
700a Walker, Marku Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK4 aut
700a Forgie, Ianu Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK4 aut
700a Giordano, G.N.u Lund University,Lunds universitet,Genetisk och molekylär epidemiologi,Forskargrupper vid Lunds universitet,Genetic and Molecular Epidemiology,Lund University Research Groups4 aut0 (Swepub:lu)med-geg
700a Pavo, Imreu Eli Lilly Regional Operations, Vienna, Austria4 aut
700a Ruetten, Hartmutu Research and Development Global Development, Translational Medicine and Clinical Pharmacology, Sanofi-Aventis Deutschland, Frankfurt, Germany4 aut
700a Pedersen, Olufu Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark4 aut
700a Hansen, Torbenu Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark4 aut
700a Dermitzakis, Emmanouilu Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland4 aut
700a Franks, P.W.u Lund University,Lunds universitet,Genetisk och molekylär epidemiologi,Forskargrupper vid Lunds universitet,Genetic and Molecular Epidemiology,Lund University Research Groups4 aut0 (Swepub:lu)med-plf
700a Schwenk, Jochen M.u KTH,Science for Life Laboratory, SciLifeLab,Affinitets-proteomik4 aut0 (Swepub:kth)u1h7wtme
700a Adamski, Jerzyu Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia4 aut
700a McCarthy, Mark I.u Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK; Genentech, South San Francisco, CA, USA4 aut
700a Pearson, Ewanu Division of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK4 aut
700a Banasik, Karinau Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 aut
700a Rasmussen, Simonu Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark4 aut
700a Brunak, Sørenu Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 aut
700a Froguel, Philippeu Inserm, Univ Lille, CHU Lille, Lille Pasteur Institute, EGID, Lille, France; Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK4 aut
700a Thomas, Cecilia Engelu KTH,Affinitets-proteomik,Science for Life Laboratory, SciLifeLab,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 aut0 (Swepub:kth)u1ja1scu
700a Häussler, Ragna S.u KTH,Affinitets-proteomik,Science for Life Laboratory, SciLifeLab4 aut0 (Swepub:kth)u1izv3pd
700a Beulens, Jolineu Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands4 aut
700a Rutters, Femkeu Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands4 aut
700a Nijpels, Gielu Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands4 aut
700a van Oort, Sabineu Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands4 aut
700a Groeneveld, Lenkau Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands4 aut
700a Elders, Petrau Department of General Practice, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands4 aut
700a Giorgino, Toniu Biophysics Institute (IBF-CNR), National Research Council of Italy, Milan, Italy; Department of Biosciences, University of Milan, Milan, Italy4 aut
700a Rodriquez, Marianneu Biotech & Biomarkers Research Department, Institut de Recherches Internationales Servier, Croissy sur Seine, France4 aut
700a Nice, Rachelu Blood Sciences, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK4 aut
700a Perry, Mandyu Blood Sciences, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK4 aut
700a Bianzano, Susannau Boehringer Ingelheim International, Therapeutic Area CardioMetabolism and Respiratory Medicine, Ingelheim am Rhein, Germany4 aut
700a Graefe-Mody, Ulrikeu Boehringer Ingelheim International, Therapeutic Area CNS, Retinopathies and Emerging Areas, Ingelheim am Rhein, Germany4 aut
700a Hennige, Anitau Boehringer Ingelheim International, Medicine Cardiometabolism and Respiratory, Biberach an der Riss, Germany4 aut
700a Grempler, Rolfu Boehringer Ingelheim International, Translational Medicine & Clinical Pharmacology, Biberach an der Riss, Germany4 aut
700a Baum, Patricku Boehringer Ingelheim International, Translational Medicine & Clinical Pharmacology, Biberach an der Riss, Germany4 aut
700a Stærfeldt, Hans Henriku Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 aut
700a Shah, Nishau Centre for Health, Law and Emerging Technologies (HeLEX), Faculty of Law, University of Oxford, Oxford, UK4 aut
700a Teare, Harrietu Centre for Health, Law and Emerging Technologies (HeLEX), Faculty of Law, University of Oxford, Oxford, UK4 aut
700a Ehrhardt, Beateu Centre for Mathematics and Algorithms for Data, University of Bath, Bath, UK4 aut
700a Tillner, Joachimu Clinical Operations, Sanofi-Aventis Deutschland, Frankfurt, Germany4 aut
700a Dings, Christianeu Clinical Pharmacy, Saarland University, Saarbrücken, Germany4 aut
700a Lehr, Thorstenu Clinical Pharmacy, Saarland University, Saarbrücken, Germany4 aut
700a Scherer, Ninau Clinical Pharmacy, Saarland University, Saarbrücken, Germany4 aut
700a Sihinevich, Irynau Clinical Pharmacy, Saarland University, Saarbrücken, Germany4 aut
700a Cabrelli, Louiseu Clinical Research Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, UK, Scotland4 aut
700a Loftus, Heatheru Clinical Research Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, UK, Scotland4 aut
700a Bizzotto, Robertou C.N.R. Institute of Neuroscience, Padova, Italy4 aut
700a Tura, Andreau C.N.R. Institute of Neuroscience, Padova, Italy4 aut
700a Dekkers, Koenu Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands4 aut
700a Groop, L.u Lund University,Lunds universitet,Genomik, diabetes och endokrinologi,Forskargrupper vid Lunds universitet,Genomics, Diabetes and Endocrinology,Lund University Research Groups4 aut0 (Swepub:lu)endo-lgr
700a Pasdar, N.A.4 aut
700a Fitipaldi, H.u Lund University,Lunds universitet,Genetisk och molekylär epidemiologi,Forskargrupper vid Lunds universitet,Genetic and Molecular Epidemiology,Lund University Research Groups4 aut0 (Swepub:lu)hu3745fi
700a Kurbasic, A.u Lund University,Lunds universitet,Genetisk och molekylär epidemiologi,Forskargrupper vid Lunds universitet,Genetic and Molecular Epidemiology,Lund University Research Groups4 aut0 (Swepub:lu)mats-aku
700a Mutie, P.u Lund University,Lunds universitet,Genetisk och molekylär epidemiologi,Forskargrupper vid Lunds universitet,Genetic and Molecular Epidemiology,Lund University Research Groups4 aut0 (Swepub:lu)pa4264mu
700a Pomares-Millan, H.u Lund University,Lunds universitet,Genetisk och molekylär epidemiologi,Forskargrupper vid Lunds universitet,Genetic and Molecular Epidemiology,Lund University Research Groups4 aut0 (Swepub:lu)hu7454po
700a Abdalla, M.u University of Oxford4 aut
710a Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark; Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmarkb Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark4 org
773t Nature Biotechnologyd : Springer Natureg 41:3, s. 399-408q 41:3<399-408x 1087-0156x 1546-1696
856u https://doi.org/10.1038/s41587-022-01520-xy Fulltext
856u http://dx.doi.org/10.1038/s41587-022-01520-xx freey FULLTEXT
8564 8u https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-330088
8564 8u https://doi.org/10.1038/s41587-022-01520-x
8564 8u https://lup.lub.lu.se/record/13c6b992-22aa-4bcc-b353-dbd6f2f72642

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