Assistant Professor @ Sect. for Functional Genomics and Metabolism @ Dept. of Biochemistry and Molecular Biology @ University of Southern Denmark.
Odense, Danmark
Joined June 2015
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📢 PREPRINT ALERT 📢 Clustering cells is a key step in most scRNA-seq analysis workflows. It's hard, and harder with batch effects.
Our take on the problem, JOINTLY, use a hybrid linear and non-linear NMF. The non-linearity gives performance, the linearity gives interpretability
Jesper Madsen retweeted
@IsabellVSE @jespergrud @NATsdu
Single-nucleus multiomics identifies a β-cell subpopulation mounting an early interferon-driven inflammatory response to a high-fat diet, with traces of this signature detected in human diabetes.
hubs.la/Q04wf2Xp0
Jesper Madsen retweeted
Single-nucleus multiomics reveals an early inflammatory response to a high-fat diet in a subset of pancreatic β-cells, implicating inflammation in the loss of β-cell identity during metabolic stress.
@IsabellVSE @jespergrud @NATsdu
hubs.la/Q04wdNTB0
Jesper Madsen retweeted
This is my very first research paper, finally published, please check it out! @LSAjournal @GenomicsUnit @SyddanskUni
Single-nucleus multiomics reveals an early inflammatory response to a high-fat diet in a subset of pancreatic β-cells, implicating inflammation in the loss of β-cell identity during metabolic stress.
@IsabellVSE @jespergrud @NATsdu
hubs.la/Q04wdNTB0
Jesper Madsen retweeted
Single-cell-resolved transcriptional dynamics of human subcutaneous adipose tissue during lifestyle- and bariatric surgery-induced weight loss dlvr.it/TQJnyR
Jesper Madsen retweeted
This study was led by the brilliant Anne Lietzke together with outstanding collaborators @maria_mcoronel,
@jespergrud, Sub Pennathur, Lonnie Shea among many others! We are so grateful for support of the editor, reviewers, and @BreakthroughT1D to complete this work!
Excited to share DeepDive, a generative model for disentangling covariate effects in snATAC-seq developed by the amazing @afmoeller. DeepDive enables deeper understanding of a dataset by separating the effects of known and unknown covariates. Here are some highlights. 1/6
You can find many more details in the preprint biorxiv.org/content/10.1101/…. You can also try out DeepDive on your own data. You can find a tutorial on how to get started here: deepdive-tutorial.readthedoc…. Reach out if you have questions or something does not work. 5/6
Shoutout to funders and collaborators without whom this work would not have been possible @novonordiskfond @GrundforskFond @GenomicsUnit Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at the Broad Institute of MIT and Harvard 6/6
Jesper Madsen retweeted
New from us! We found that targeting mitochondrial programming promoted the formation and maturation of stem cell-derived beta cells. Mitos - more than a powerhouse! #T1D
biorxiv.org/content/10.1101/…
Jesper Madsen retweeted
Currently at #EISG2024 in Helsinki 🧬
I presented my PhD research, conducted in @susmandrup ‘s lab and co-supervised by @jespergrud at @GenomicsUnit @NATsdu , in a poster session.
Last photo by @Hazemibrahimi - who has posted more photos of the conference. Check them out!
Our watching party getting ready to dive into what will sure be an excellent talk by @MelinaClaussnit 🤯 at the V2F symposium hosted by @novonordiskfond Center @broadinstitute
Jesper Madsen retweeted
🧵: How do you design a network that can optimize (edit, transform, ...) the weights of another neural network?
Our latest answer to that question: *Universal* Neural Functionals (UNFs) that can process the weights of *any* deep architecture.
Jesper Madsen retweeted
The commentary I wrote is now live at Nature Biotech: nature.com/articles/s41587-0… (free version rdcu.be/dwSSy).
Jesper Madsen retweeted
Extremely excited to open the registration for the 2nd Annual Variant to Function Symposium hosted by the @novonordiskfond Center @broadinstitute co-Chaired by @MelinaClaussnit. A stellar (!!) lineup of speakers & virtual+physical attendance. Please share! broadinstitute.swoogo.com/V2…
Jesper Madsen retweeted
Very excited to share a new work on AUPRC, AUROC, and class imbalance: arxiv.org/abs/2401.06091
The short of it? Despite widespread belief, AUPRC is not superior to AUROC under general class imbalance and it can exacerbate biases towards subpopulations with higher prevalence.
Jesper Madsen retweeted
@afmoeller @jespergrud present JOINTLY, a hybrid linear and non-linear NMF-based algorithm, providing interpretable and robust cell clustering across batches against over-integration. @NatureComms #singlecell #BiotechNatureComms
nature.com/articles/s41467-0…