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...

Comparison and optimization of cellular neighbor preference methods for quantitative tissue analysis - Nature Communications

Schiller and colleagues present a systematic comparison of methods that quantify whether pairs of cell types preferentially co-occur in tissues, highlighting their strengths and limitations. This stud...

nature.com

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

Charting single-cell lineages with synthetic and natural barcodes - Nature Reviews Genetics

In this Review, Rodriguez-Fraticelli and Parreno discuss advances in single-cell lineage-tracing methods and how their application to diverse biological processes, such as development, ageing and canc...

nature.com

Super interesting!

bioRxiv Genomics@biorxiv-genomic.bsky.social · 7mo ago

In vivo lineage tracing across human tissues using methylation barcodes in the protocadherin gene cluster https://www.biorxiv.org/content/10.64898/2026.02.23.707349v1

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.

GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap

dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.

github.com

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... 🧵

Induction of menstruation in mice reveals the regulation of menstrual shedding

During menstruation, an inner layer of the endometrium is selectively shed, while an outer, progenitor-containing layer is preserved to support repeated regeneration. Progress in understanding this co...

biorxiv.org

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.

nature.com

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...

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.

nature.com

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)

„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

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...

biorxiv.org

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

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 · last yr.

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... 🧵

🚀 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 · last yr.

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... 🧵

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 · last yr.

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... 🧵

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...

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

Deutsches Krebsforschungszentrum (DKFZ)@dkfz.bsky.social · last yr.

Forschende vom @crg.eu, dem @irbbarcelona.org und dem DKFZ fanden heraus: Mit dem #Alter schrumpft das Reservoir an Blutstammzellen. Es wird zunehmend von Stammzellen dominiert, die entzündungsfördernde Immunzellen hervorbringen. t1p.de/ovqqp 👇

🔬‘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...

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…

sciencedirect.com

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...

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...

biorxiv.org

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

Lars Velten@larsplus.bsky.social · last yr.

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... 🧵

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!

Michael Scherer@scherermich.bsky.social · 2y ago

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...

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

🌟 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.

nature.com