Publications

JOINTLY: interpretable joint clustering of single-cell transcriptomes
A.F. Møller, J.G.S. Madsen
Nature Communications (2023)

Automatic quality control of single-cell and single-nucleus RNA-seq using valiDrops
G. Kavaliauskaite, J.G.S. Madsen
NAR Genomics and Bioinformatics (2023)

Rare variant association analysis in 51,256 type 2 diabetes cases and 370,487 controls informs the spectrum of pathogenicity of monogenic diabetes genes
P. Schroeder, R. Mandla, A. Huerta-Chagoya, A. Alkanak, D. Nagy, L. Szczerbinski, J.G.S. Madsen, J.B. Cole, B. Porneala, K. Westerman, J.H. Li, T.I. Pollin, J.C. Florez, A.L. Gloyn, I. Cebola, A. Manning, A. Leong, M. Udler, J.M. Mercader
medRxiv (2023)

Lipolysis regulates major transcriptional programs in brown adipocytes
L.K. Markussen, E.A. Rondini, O.S. Johansen, J.G.S. Madsen, E.G. Sustarsic, A-B. Marcher, J.B. Hansen, Z. Gerhart-Hines, J.G. Granneman, S. Mandrup
Nature Communications (2022)

Glucolipotoxicity promotes the capacity of the glycerolipid/NEFA cycle supporting the secretory response of pancreatic beta cells
L. Oberhauser, C. Jiménez-Sánchez, J.G.S. Madsen, D. Duhamel, S. Mandrup, T. Brun, P. Maechler
Diabetologia (2022)

Analysis of Enhancers and Transcriptional Networks in Thermogenic Adipocytes
A. Loft, M.W. Andersen, J.G.S. Madsen, S. Mandrup
Methods in Molecular Biology (2022)

Isolation of nuclei from mouse white adipose tissues for single-nucleus genomics
E.L. Van Hauwaert, E. Gammelmark, A.K. Sarvari, L. Larsen, R. Nielsen, J.G.S. Madsen, S. Mandrup
STAR Protocols (2021)

Plasticity of Epididymal Adipose Tissue in Response to Diet-Induced Obesity at Single-Nucleus Resolution
A.K. Sarvari^*, E.L. Van Hauwaert^*, L.K. Markussen, E. Gammelmark, R. Nielsen, J.G.S. Madsen^#, S. Mandrup^#
Cell Metabolism (2020)

AMPK profiling in rodent and human pancreatic beta-cells under nutrient-rich metabolic stress
T. Brun, C. Jiménez-Sánchez, J.G.S. Madsen, N. Hadadi, D. Duhamel, C. Bartley, L. Oberhauser, M. Trajkovski, S. Mandrup, P. Maechler
International Journal of Molecular Sciences (2020)

Highly connected enhancer communities’ control adipogenesis in human mesenchymal stem cells
J.G.S. Madsen, M.S. Madsen^*, A. Rauch^*, S. Traynor^*, E.L. Van Hauwaert, A.K. Haakonsson, B.M. Javierre, M. Larsen, P. Fraser, S. Mandrup
Nature Genetics (2020)

Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis
A. Rauch, A.K. Haakonsson, J.G.S. Madsen, M. Larsen, R. Nielsen, B.D. Larsen, C. Wiwie, R. Röttger, J. Baumbach, M.R. Madsen, E.L. Van Hauwaert, M. Kassem, S.Mandrup
Nature Genetics (2019)

Integrated analysis of motif activity and gene expression changes of transcription factors
J.G.S. Madsen^*, A. Rauch^*, E.L. Van Hauwaert, S.F. Schmidt, M. Winnefeld, S. Mandrup
Genome Research (2017)

Dynamic rewiring of promoter-anchored chromatin loops during adipocyte differentiation
R. Siersbæk^*, J.G.S. Madsen^*, B.M. Javierre^*, R. Nielsen^*, E.K. Bagge, J. Cairns, S.W. Wingett, S. Traynor, M. Spivakov, P. Fraser, S. Mandrup
Molecular Cell (2017)

The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiation
A.B. Brier, A. Loft, J.G.S. Madsen, T. Rosengran, R. Nielsen, S.F. Schmidt, Z. Liu, Q. Yan, H. Gronemeyer, S. Mandrup
Nucleic Acid Research (2016)

Integrative genomics outlines a biphasic glucose re-sponse and a ChREBP-RORγ axis regulating proliferation in β-cells
S.F. Schmidt^*, J.G.S. Madsen^*, K.Ø. Frafjord, L.L.C. Poulsen, S. Salö, M. Boergesen, A. Loft, B.D. Larsen, M.S. Madsen, J.J. Holst, L.T. Dalgaard, S. Mandrup
Cell Reports (2016)

RNA-Seq and Mass-Spectrometry-based lipidomics reveal extensive changes of glycerolipid pathways in brown adipose tissue in response to cold
A.-B. Marcher^*, A. Loft^*, R. Nielsen, T. Vihervaara, J.G.S. Madsen, M. Sysi-Aho, K. Ekroos, S. Mandrup
Cell Reports (2015)

Acute TNF-induced repres-sion of cell identity genes is mediated by NFκB-directed redistribution of cofactors from super-enhancers
S.F. Schmidt^*, B.D. Larsen^*, A. Loft, R. Nielsen, J.G.S. Madsen, S. Mandrup
Genome Research (2015)

iRNA-seq: A novel computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data
J.G.S. Madsen^*, S.F. Schmidt^*, B.D. Larsen, A. Loft, R. Nielsen, S. Mandrup
Nucleic Acid Research (2015)

Browning of human adipocytes requires KLF11 and reprogramming of PPARγ super-enhancers
A. Loft, I. Forss^*, M.S. Siersbæk^*, S.F. Schmidt, A-S. B. Larsen, J.G.S. Madsen, D. Pisani, R. Nielsen, M.M. Aagaard. A. Mathison, M.J. Neville, R. Urrutia, F. Karpe, E.-Z. Amri, S. Mandrup
Genes and Development (2015)