Martina Braun

Rapid epigenomic classification of acute leukemia - Nature Genetics The authors present a molecular classification of acute leukemia using 5-methylcytosine signatures, together with a neural network-based classifier for clinical use.

Epigenetic diagnosis of acute leukemia within two hours from sample receipt 🚀

Very happy to share the results of a great collaboration between @hovestadt.bsky.social and Griffin Labs, I co-led with @sbenfatto.bsky.social, published today in @natgenet.nature.com
📄 www.nature.com/articles/s41...
🧵1/n

Introducing ParTIpy, a python package for Pareto Task Inference that scales to large-scale datasets, including single-cell and spatial transcriptomics.
🔗 Manuscript: www.biorxiv.org/content/10.1...
💻 Code: partipy.readthedocs.io

Fluctuating DNA methylation tracks cancer evolution at clinical scale - Nature Cancer evolutionary dynamics are quantitatively inferred using a method, EVOFLUx, applied to fluctuating DNA methylation.

Studying cancer evolution needs multi-region or single cell seq for phylogenetics, right? Amazingly (I think!) we found single-sample bulk methylation suffices, via analysis of "fluctuating methylation". In @nature.com today led by brilliant @calumgabbutt.bsky.social www.nature.com/articles/s41...

Delighted to share our latest on longitudinal methylation dynamics preceding cancer. Epigenetic signs of AML appear in blood DECADES before Dx.
👉 Early cancer detection
👉 Methylation drivers
👉 Epimutation rates
👉 CpG lineage tracing

www.biorxiv.org/content/10.1...

Methylation dynamics in the decades preceding acute myeloid leukaemia https://www.biorxiv.org/content/10.1101/2025.06.26.661643v1

„Blutbarcodes“ könnten Alterung verlangsamen Auch das Blut altert: Ab 50 Jahren verringert sich die Vielfalt der Stammzellen, die Blut produzieren. Ein Forschungsteam hat nun ein „Barcodesystem“ entwickelt, das die verschiedenen Blutstammzellen ...

🇦🇹: Austrian ORF covered both the blood ageing context and the DNA methylation discovery in two minutes on the radio after interviewing @martinabraun.bsky.social and me. Real quality science journalism. science.orf.at/stories/3230... (5/n)

From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models Generative models trained on natural sequences are increasingly used to predict the effects of genetic variation, enabling progress in therapeutic design, disease risk prediction, and synthetic biolog...

New preprint in collaboration with @paulinanunezv.bsky.social supervised by @jonnyfrazer.bsky.social and Mafalda Dias – we propose a simple approach to improving zero-shot variant effect prediction in pre-existing protein and genome language models: 🧶 1/n

www.biorxiv.org/content/10.1...

Clonal tracing with somatic epimutations reveals dynamics of blood ageing - Nature The discovery that DNA methylation of different CpG sites can serve as digital barcodes of clonal identity led to the development of EPI-Clone, an algorithm that enables single-cell lineage tracing through cellular differentiation at scale.

Nature research paper: Clonal tracing with somatic epimutations reveals dynamics of blood ageing

https://go.nature.com/43NOe1R

Our work on lineage tracing with somatic epimutations is finally out in @nature.com!

Check out the thread by @larsplus.bsky.social below.

EPI-clone is a revolutionary technique for lineage tracing and it will immediately impact how we trace clones everywhere.

Detailed protocols coming out soon!

Huge thanks to the rest of the amazing team @scherermich.bsky.social, @indrasingh.bsky.social, Chelsea, and @alejofraticelli.bsky.social

🚀 Our Nature paper on EPI-Clone is live

I loved analyzing the human data - we discovered that after age 50, blood production shifts to an oligoclonal pattern, and these expansions aren’t driven by CH mutations!

Dive into @larsplus.bsky.social thread for the full story & visuals.

It is finally out! EPI-Clone is a powerful tool for analyzing clonal dynamics in blood ageing. Thanks to everyone involved, especially @indrasingh.bsky.social, @martinabraun.bsky.social, Chelsea, and @alejofraticelli.bsky.social. Have a look at the thread by @larsplus.bsky.social.

Bislang gab es keine Methoden, mit denen man sich die klonale Entwicklung von Blutzellen anschauen konnte. Mit EPI-Clone haben wir nun eine solche Methode, die es ermöglicht, klonale Diversität - eine wichtige Eigenschaft eines gesunden Blutsystems - zu untersuchen. doi.org/10.1038/s415...

🔬‘Barcodes’ written into our DNA reveal how blood ages

Naturally occurring methylation patterns reveal changes in blood which are detectable at age 50 and almost universal by 60

📰 Published in @nature.com by #IRBBarcelona & @crg.eu

Read the news ➡️ bit.ly/4jZHQeB

⬇️ ⬇️

LoxCode in vivo barcoding reveals epiblast clonal fate bias to fetal organs Much remains to be learned about the clonal fate of mammalian epiblast cells. Here, we develop high-diversity Cre recombinase-driven LoxCode barcoding…

A triumph of perseverance from twitterless Tom Weber, Christine Biben and the team, our in vivo barcoding "LoxCode mouse" used to resolve epiblast fate to fetal organs is finally published in @cellpress.bsky.social and available through @jacksonlab.bsky.social www.sciencedirect.com/science/arti...

What an inspiring ISCO 2025! Thanks to the organisers & community. Thrilled to have won the 'People’s Choice Best Talk' for my presentation on clonal tracing using epimutations in human hematopoiesis 🌟

Check out our preprint for more. Full paper coming soon! www.biorxiv.org/content/10.1...

Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...

Huge congrats to the whole team for this exciting paper! Can’t wait to see where it takes us!

Honored to be able to speak among such an amazing line-up of speakers. Check out the Single Cell Genomics Day 2025 if you want to learn more about DNA methylation based lineage tracing: satijalab.org/scgd25/

🔥 New Fraticelli lab publication🔥

“Pre-existing stem cell heterogeneity dictates clonal responses to the acquisition of leukemia driver mutations”

Now at Cell Stem Cell, with two new figures, in vivo, and sequential mutagenesis data.

Performed with the support of Cris Cancer and @erc.europa.eu

Excited to see our EPI-Clone work recognized as a „Method to Watch“ by @naturemethods.bsky.social! Proud to contribute alongside such a fantastic team. Stay tuned for updates!

GitHub - CompEpigen/epiCHAOS Contribute to CompEpigen/epiCHAOS development by creating an account on GitHub.

In single-cell epigenomics, comparative analyses have traditionally been performed between cell-type clusters. With epiCHAOS the very talented Katherine Kelly presented the first method to quantify single-cell epigenomic heterogeneity from any type of epigenomic data. doi.org/10.1186/s130... (1/2)

Thanks for making this!
Would love to be added :)

Super helpful! Thanks for the great work.
Would love to join

Analyzing single-cell bisulfite sequencing data with MethSCAn - Nature Methods This work highlights the technical issues in previous approaches and introduces a preprocessing approach along with a software package, MethSCAn, for single-cell bisulfite sequencing data analysis.

🌟 Highlighting a milestone from earlier this year: Proud to be the second author! My contributions focused on the detection of differential methylation. Big thanks to my mentors for their support. 🌱
www.nature.com/articles/s41...

Looking forward to sharing more thoughts with the community. 🧬✨🚀

Thanks for creating this list. Super helpful! Would be great to be added as well.

Thanks for creating this list, super helpful! 😊
Would be happy to be added as well.