The Islet Cartography project will shed new light on the regulatory and functional architecture of the human pancreatic Islets of Langerhans with the aim of further-ing the understanding of how it contributes to health and disease, most notably to diabetes. The Islet Cartography project aims to collect, integrate, and jointly analyse highly resolved molecular datasets from multiple modalities with new data science me-thods to build a comprehensive map of the human islet. The map will be made publicly available for other researchers to pave the way for new insight that could lead to prevention, diagnosis and treatment of diabetes and other pancreas-related diseases.
The Madsen group is a partner in the Human Gene Regulation Map (HGRM), a part of the new Novo Nordisk Foundation Center for Genomic Mechanisms of Dis-ease (NNFC). The aim of HGRM is to build comprehensive maps of gene regulation in the human genome as a resource for un-covering biological mechanisms on common genetic diseases, with an initial focus on cell types relevant to cardiometabolic diseases including type 2 diabetes. We aim to combine recent advances in genomics, molecular biology, single-cell analysis, and stem cell models with approaches in computational biology and machine learning to identify fundamental rules of gene regulation.
The Madsen group is a partner in the Center for Functional Genomics and Tissue Plasticity (ATLAS). The aim of ATLAS is to obtain systems-level, mechanistic and cell type-resolved understanding of adipose and hepatic tissue plasticity in response to diet-induced obesity and regres-sion in mouse models; and to translate this for in-depth under-standing of the functional chan-ges in human adipose and hepatic tissues in response to severe obesity and reversal. The center applies a combination of functional genomics approaches including single cell sequencing, mouse models, proteomics, in vivo targeting, computational biology, and clinical studies.
Plasticity of Epididymal Adipose Tissue in Reponse to Diet-Induced Obesity at Single-Nucleus Resolution
Sárvári and Van Hauwaert et al. (2020): Cell Metabolism
We created an atlas of epididymal white adipose tissue from lean and obese mice at single nucleus resolution and charted it to discover wide-spread transcriptional and compositional reprogramming of cell types and subtypes in obesity.
Highly interconnected enhancer communities control lineage-determining gens in human mesenchymal stem cells.
Madsen et al. (2020): Nature Genetics
We performed enhancer-capture Hi-C during adipogenesis and osteogenesis of human mesenchymal stem cells and found that enhancers form communities in 3D, which are intimately linked with gene regulation during differentiation.
Integrated analysis of motif activity and gene expression changes of transcription factors.
Madsen et al. (2018): Genome Research.
We created a novel statistical learning method for prediction of causal transcription factors and benchmarked it against alternative to show that our method outperforms existing methods in finding known factors.
| Shad Haval Omer Hassan | Individual project |
| Gabriel Elmazi | Bachelor project |
| Tereza Faitová | Master student | 2020 |
| Kari Østerli Frafjord | PhD student | 2022 |
| Jacob Fredegaard Hansen | Master student | 2022 |
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