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Reposted by Martina Braun

Til Steinicke @til-steinicke.bsky.social · 16d

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

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.

www.nature.com

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Reposted by Martina Braun

Saez-Rodriguez Group @saezlab.bsky.social · 24d

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

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Reposted by Martina Braun

Trevor Graham @trevorgraham.bsky.social · 29d

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...

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.

www.nature.com

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Reposted by Martina Braun

Jamie Blundell @jamie-blundell.bsky.social · Jul 3

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...

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Reposted by Martina Braun

bioRxiv Genomics @biorxiv-genomic.bsky.social · Jun 28

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

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Reposted by Martina Braun

Lars Velten @larsplus.bsky.social · May 31

🇦🇹: 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)

„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 ...

science.orf.at

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Reposted by Martina Braun

Charlie Pugh @cwjpugh.bsky.social · May 26

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...

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...

www.biorxiv.org

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Reposted by Martina Braun

Nature @nature.com · May 21

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

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

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.

go.nature.com

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Reposted by Martina Braun

Alejo Rodriguez-Fraticelli @alejofraticelli.bsky.social · May 21

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!

Lars Velten @larsplus.bsky.social · May 21

Out @nature.com: Clonal tracing with somatic epimutations

🧬 Single cell methylome encodes cell state & clonal identity

🔨 EPI-Clone reads out both (+mutations, +RNA) at scale

🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations

doi.org/10.1038/s415...
🧵

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 th...

doi.org

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Martina Braun @martinabraun.bsky.social · May 21

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

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Martina Braun @martinabraun.bsky.social · May 21

🚀 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.

Lars Velten @larsplus.bsky.social · May 21

Out @nature.com: Clonal tracing with somatic epimutations

🧬 Single cell methylome encodes cell state & clonal identity

🔨 EPI-Clone reads out both (+mutations, +RNA) at scale

🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations

doi.org/10.1038/s415...
🧵

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 th...

doi.org

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Reposted by Martina Braun

Michael Scherer @scherermich.bsky.social · May 21

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.

Lars Velten @larsplus.bsky.social · May 21

Out @nature.com: Clonal tracing with somatic epimutations

🧬 Single cell methylome encodes cell state & clonal identity

🔨 EPI-Clone reads out both (+mutations, +RNA) at scale

🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations

doi.org/10.1038/s415...
🧵

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 th...

doi.org

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Reposted by Martina Braun

Michael Scherer @scherermich.bsky.social · May 21

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...

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Reposted by Martina Braun

IRB Barcelona @irbbarcelona.org · May 21

🔬‘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

⬇️ ⬇️

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Reposted by Martina Braun

Shalin H. Naik @shalinhnaik.bsky.social · May 16

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...

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…

www.sciencedirect.com

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Martina Braun @martinabraun.bsky.social · May 14

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...

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Reposted by Martina Braun

Erik van Nimwegen @erikvannimwegen.bsky.social · May 9

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...

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...

www.biorxiv.org

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Martina Braun @martinabraun.bsky.social · May 8

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

Lars Velten @larsplus.bsky.social · May 8

Out in Cell @cp-cell.bsky.social: Design principles of cell-state-specific enhancers in hematopoiesis
🧬🩸 screen of fully synthetic enhancers in blood progenitors
🤖 AI that creates new cell state specific enhancers
🔍 negative synergies between TFs lead to specificity!
www.cell.com/cell/fulltex...
🧵

Design principles of cell-state-specific enhancers in hematopoiesis

Screen of minimalistic enhancers in blood progenitor cells demonstrates widespread dual activator-repressor function of transcription factors (TFs) and enables the model-guided design of cell-state-sp...

www.cell.com

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Reposted by Martina Braun

Michael Scherer @scherermich.bsky.social · Apr 22

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/

Single Cell Genomics Day

section.section { padding: 0.25rem; padding-bottom: 0.5rem } div.iframe-wrapper { position: relative; margin: 0 auto; width: 50%; /* Reduced from 72% */ height: 50%; /* Reduced from 72% */ padding-bot...

satijalab.org

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Alejo Rodriguez-Fraticelli @alejofraticelli.bsky.social · Feb 25

🔥 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

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Martina Braun @martinabraun.bsky.social · Dec 18

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!

Michael Scherer @scherermich.bsky.social · Dec 18

Our EPI-Clone preprint was mentioned by a @naturemethods.bsky.social editorial, and listed as a "Method to Watch"! We'll keep you posted.
www.nature.com/articles/s41...

Mapping cell history and fates - Nature Methods

New experimental and computational methods illuminate the history of cell differentiation and its molecular underpinnings.

www.nature.com

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Reposted by Martina Braun

Michael Scherer @scherermich.bsky.social · Dec 3

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)

GitHub - CompEpigen/epiCHAOS

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

github.com

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Martina Braun @martinabraun.bsky.social · Nov 25

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

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Martina Braun @martinabraun.bsky.social · Nov 23

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

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Martina Braun @martinabraun.bsky.social · Nov 22

🌟 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. 🧬✨🚀

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.

www.nature.com

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