Feels like this paper on protein-templated DNA synthesis by a natural enzyme warrants some comment. So here's a 🧵. /1 www.science.org/doi/10.1126/...

1/ A PhD milestone 👏 My work on comparing neighbor preference methods for spatial data analysis is out in Nature Communications. We compared 9+ neighbor preference methods and propose a new approach that combines the most relevant analysis features: COZI. Read more: www.nature.com/articles/s41...

The main project of my PhD 🧬🔬 is out: we developed single-cell lentiMPRA, a lentivirus-based method to measure enhancer activity and transcriptomes at single-cell resolution. We then applied sc-lentiMPRA to fully synthetic enhancers 🧩... 🔗 doi.org/10.64898/202...

INTERESTED IN SINGLE-CELL LINEAGE TRACING? Check our new review @naturerevgenet.bsky.social from the @alejofraticelli.bsky.social lab 🎉🎉 nature.com/articles/s41... With Victoria Parreno, we tried to update the modern manual for genetic tracing and clonal analysis. Read link: rdcu.be/e50gy

Super interesting!

ISCO (Innovations in Single-Cell OMICS) will be back in beautiful Barcelona! 🗓️ 28th/29th of May 2026 📍Barcelona Biomedical Research Park @prbb.org (beachfront!) Keynotes: @bartdeplancke.bsky.social and @bocklab.bsky.social Submit your abstract and present your research! www.isco-conference.eu

Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp.... genzplyr is dplyr, but bussin fr fr no cap.

I’m thrilled to share my postdoc work and the first paper from the McKinley Lab! 🎉 @karalmckinley.bsky.social We built the first transgenic model of menstruation in mice. We used it to uncover how the endometrium organizes and sheds during menstruation. 🧪 www.biorxiv.org/content/10.1... 🧵

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

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

🇦🇹: 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)

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...

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!

🚀 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 ⬇️ ⬇️

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...

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!

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)

🌟 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. 🧬✨🚀