ArticleNature biotechnology2023
Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models.
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Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 55 papers, 2 of them syntheses that pooled it.
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55citing papers in PubMed, 2 pooled it
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Who cites it
55 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Sources of Heterogeneity in the Efficacy of Statins for Primary Prevention of Cardiovascular Diseases: A Systematic Review with Meta-Regression and Meta-Analysis of Within-Study Subgroup Differences.Cardiovascular drugs and therapy · 2026Pooled it
- Multi-omics time-series analysis in microbiome research: a systematic review.Briefings in bioinformatics · 2025Pooled it
- Endocrine-Metabolic Crosstalk Between Diabetes Mellitus and Hypothyroidism: From Network Mechanisms to Translational Stratification.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Review
- Distinct multi-omics signatures of clinical subgroups of type 2 diabetes define heterogeneous responses to an insulin sensitizer.Nature communications · 2026Article
- DIVAS: an R package for identifying shared and individual variations of multiomics data.Bioinformatics (Oxford, England) · 2026Article
- Translating genome-wide association studies at multiple scales: Drug target prioritization, cellular architectures, and organ imaging.Cell genomics · 2026Review
- MIND: multimodal integration with neighbourhood-aware distributions.Nature communications · 2026Article
- Improving metagenome binning by integrating intrinsic features and taxonomy.Nature biotechnology · 2026Article
- Precision oncology in the age of AI: lessons from AI-driven drug discovery and clinical translation.BJC reports · 2026Review
- Deep learning-based stratification of Schizophrenia Spectrum Disorder from real-world data reveals distinct profiles of common and rare variant genetic signal.medRxiv : the preprint server for health sciences · 2026Article
- Mapping whole-organism genetic comorbidities across model Species using unified ontologies.Genetics · 2026Article
- Artificial intelligence-assisted spatial omics-based biomimetic nanoplatform for intelligent and precise intervention in the immunosuppressive core region of ovarian cancer.NPJ precision oncology · 2026Review
- Multiomics: the intersection of personalized nutrition in cardiometabolic diseases.Journal of translational medicine · 2026Review
- Precision phenotyping of type 2 diabetes in chinese populations using a variational autoencoder-informed tree model.Nature communications · 2026Article
- Organ cross-talk: molecular mechanisms, biological functions, and therapeutic interventions for diseases.Signal transduction and targeted therapy · 2026Review
- MRI-based multi-organ clocks for healthy aging and disease assessment.Nature medicine · 2026Article
- Ophthalmic drug discovery and development using artificial intelligence and digital health technologies.NPJ digital medicine · 2025Review
- Article
- Generative artificial intelligence in diabetes healthcare.iScience · 2025Review
- Multitarget Generate Electrolyte Additive for Lithium Metal Batteries.Advanced materials (Deerfield Beach, Fla.) · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
70 authors.
Rosa Lundbye AllesøeNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Agnete Troen LundgaardNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0001-7447-6560
Ricardo Hernández MedinaNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0001-6373-2362
Alejandro Aguayo-OrozcoNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Joachim JohansenNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0001-7052-1870
Jakob Nybo NissenNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Caroline BrorssonNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Gianluca MazzoniNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Lili NiuNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0003-4571-4368
Jorge Hernansanz BielNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-3125-2951
Cristina Leal RodríguezNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-3133-0630
Valentas BrasasNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Henry WebelNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Michael Eriksen BenrosCopenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark.ORCID http://orcid.org/0000-0003-4939-9465
Anders Gorm PedersenDepartment of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.ORCID http://orcid.org/0000-0001-9650-8965
Piotr Jaroslaw ChmuraNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Ulrik Plesner JacobsenNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0001-9181-6854
Andrea MariC.N.R. Institute of Neuroscience, Padova, Italy.
Robert KoivulaWellcome Centre for Human Genetics, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-1646-4163
Anubha MahajanWellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
Ana VinuelaDepartment of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.ORCID http://orcid.org/0000-0003-3771-8537
Juan Fernandez TajesWellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
Sapna SharmaResearch Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany.
Mark HaidMetabolomics and Proteomics Core, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany.ORCID http://orcid.org/0000-0001-6118-1333
Mun-Gwan HongAffinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden.ORCID http://orcid.org/0000-0001-8603-8293
Petra B MusholtResearch and Development Global Development, Translational Medicine and Clinical Pharmacology, Sanofi-Aventis Deutschland, Frankfurt, Germany.
Federico De MasiNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Josef VogtNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Helle Krogh PedersenDepartment of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.
Valborg GudmundsdottirNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Angus JonesUniversity of Exeter Medical School, Exeter, UK.
Gwen KennedyThe Immunoassay Biomarker Core Laboratory, School of Medicine, University of Dundee, Dundee, UK.ORCID http://orcid.org/0000-0002-9856-3236
Jimmy BellResearch Centre for Optimal Health, Department of Life Sciences, University of Westminster, London, UK.
E Louise ThomasResearch Centre for Optimal Health, Department of Life Sciences, University of Westminster, London, UK.ORCID http://orcid.org/0000-0003-4235-4694
Gary FrostSection for Nutrition Research, Faculty of Medicine, Imperial College London, London, UK.ORCID http://orcid.org/0000-0003-0529-6325
Henrik ThomsenDepartment of Radiology, Copenhagen University Hospital Herlev-Gentofte, Herlev, Denmark.
Elizaveta HansenDepartment of Radiology, Copenhagen University Hospital Herlev-Gentofte, Herlev, Denmark.
Tue Haldor HansenNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0001-5948-8993
Henrik VestergaardNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Mirthe MuilwijkDepartment of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
Marieke T BlomDepartment of General Practice, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
Leen M 't HartDepartment of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
Francois PattouInserm, Univ Lille, CHU Lille, Lille Pasteur Institute, EGID, Lille, France.
Violeta RaverdyInserm, Univ Lille, CHU Lille, Lille Pasteur Institute, EGID, Lille, France.
Soren BrageMRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK.
Tarja KokkolaDepartment of Medicine, University of Eastern Finland, Kuopio, Finland.
Alison HeggieInstitute of Cellular Medicine, Newcastle University, Newcastle, UK.
Donna McEvoyDiabetes Research Network, Royal Victoria Infirmary, Newcastle, UK.
Miranda MourbyCentre for Health, Law and Emerging Technologies (HeLEX), Faculty of Law, University of Oxford, Oxford, UK.
Jane KayeCentre for Health, Law and Emerging Technologies (HeLEX), Faculty of Law, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-7311-4725
Andrew HattersleyUniversity of Exeter Medical School, Exeter, UK.ORCID http://orcid.org/0000-0001-5620-473X
Timothy McDonaldUniversity of Exeter Medical School, Exeter, UK.
Martin RidderstråleLund University Diabetes Centre, Department of Clinical Sciences, Lund University, Malmö, Sweden.ORCID http://orcid.org/0000-0002-3270-9167
Mark WalkerTranslational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
Ian ForgieDivision of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK.
Giuseppe N GiordanoGenetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, CRC, Lund University, SUS, Malmö, Sweden.
Imre PavoEli Lilly Regional Operations, Vienna, Austria.
Hartmut RuettenResearch and Development Global Development, Translational Medicine and Clinical Pharmacology, Sanofi-Aventis Deutschland, Frankfurt, Germany.
Oluf PedersenNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-3321-3972
Torben HansenNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0001-8748-3831
Emmanouil DermitzakisDepartment of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
Paul W FranksLund University Diabetes Centre, Department of Clinical Sciences, Lund University, Malmö, Sweden.
Jochen M SchwenkAffinity Proteomics, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden.ORCID http://orcid.org/0000-0001-8141-8449
Jerzy AdamskiInstitute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
Mark I McCarthyWellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
Ewan PearsonDivision of Population Health & Genomics, School of Medicine, University of Dundee, Dundee, UK.
Karina BanasikNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Simon RasmussenNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. simon.rasmussen@cpr.ku.dk.ORCID http://orcid.org/0000-0001-6323-9041
Søren BrunakNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. soren.brunak@cpr.ku.dk.ORCID http://orcid.org/0000-0003-0316-5866
IMI DIRECT Consortium
Funding
Medical Research Council MC_UU_00006/4
Abstract
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.
Indexed as
Deep LearningDiabetes Mellitus, Type 2AlgorithmsHumans
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LicenceCC BY
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.