Lars Velten

Now, synthetic enhancers with single cells - great work by @juruehle.bsky.social : www.biorxiv.org/content/10.6...

Proud of @juruehle.bsky.social for getting her PhD paper on biorxiv! In it, we take synthetic enhancer screens to the single cell level, offering new insight into how transcription factors and enhancers interact 👀

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...

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

Insightful seminar by Roderic Guigó: Figure 1 of the Craig Venter human genome paper (Science, 2001) was made by a Spanish PhD student who had no salary and earned his living serving tables in a Pizzeria.

Expansion cultures of mouse AML stem cells! Enabling large scale genetic screens in a system that's very close to "the real thing", with deep implications for drug discovery. Great work @alejofraticelli.bsky.social and @indrasingh.bsky.social

Early bird registration is closing Feb 28! We will have an AMAZING party!

Where are they from? They sing in bad Swahili or a very similar language, “I’m lighting fire, I’m lighting mama fire, and I’m bringing money”. Uganda military speaks (bad) Swahili, but does Museveni send soldiers to Ukraine?

Delighted to have our work on 🧬 resilience to 🩸cancer led by @g-agarwal.bsky.social & amazing collaborators, including @kharaslab.bsky.social, published in @science.org: www.science.org/doi/10.1126/... 🧵

There is one joker: Highly skilled technicians. Our two techs are why we can do projects that are ambitious, clear first author, no 100h weeks. Requires very strong commitment to a few projects by PI (more applicable to wetlab, and a + of 🇪🇸 is that there's no industry competing for the best people).

IMHO It’s near impossible to sustainably scale an academic research team quickly to 5-10 people. My take: Keep the bar for hiring high, keep money in the bank (allows you to scale up when things start working), and keep two full days per week free of Interruptions for hands on work.

A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines Feng et al. present the first genome-scale CRISPR interference perturbation map with scRNA-seq readout across many genetic backgrounds in human pluripotent cells, pioneering population-scale CRISPR pe...

Happy to see this out now in Cell Genomics: A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines: www.cell.com/cell-genomic...

@yusufroohani.bsky.social @rberrens.bsky.social @timcoorens.bsky.social @hsiuchuanlin.bsky.social @albarmeira.bsky.social @ferrannadeu.bsky.social @alejofraticelli.bsky.social @elimereu.bsky.social @simonhaas.bsky.social @leifludwig.bsky.social @stefaniegrosswendt.bsky.social

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

Yes, this is where you would work (the round building, not the boat)

We are looking for a postdoc to join our team! If you're interested in translating a cutting edge genomics technology (www.nature.com/articles/s41...) to real-life applications in hematology, this is for you. We offer a unique working environment ON THE BEACH: recruitment.crg.eu/content/jobs...

🗨️ Just published in Nature Biotechnology: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper here: www.nature.com/articles/s41.... Annotated walkthrough in a thread below (1/11)

Are you looking for a PhD? Join us in Barcelona! You'll dive into a community of >100 PhD students from 30 countries exploring the frontiers of biology. You can also join an online workshop on 6 November (15:00 CET) to learn how to find the right lab for you.

More info: www.crg.eu/en/content/t...

Big, beautiful trees!!

SMART-PTA for whole-genome+transcriptome on thousand of single cells from the normal human esophagus 🤯 Massively scaling up the power of scWGS to build deep phylogenies and chart somatic evolution from birth throughout life.

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

Graphic with a blue background and light green dots. The text 'call for applications' appears in green, and 'Ausschreibung' in white. A white arrow on the right points diagonally upward.

Early-career researchers: want to run your own lab? 🌟Max Planck Research Groups offer 6+ years, up to €2.7M in funding, open-topic freedom, team support & tenure-track opportunities. Intrigued? 😃Apply by Oct 14, 2025! www.mpg.de/max-planck-r...

This was a lot of fun! Thanks Daylon and @arunsharmaphd.bsky.social for being great hosts!

Is the decline of reading making politics dumber? As people read less they think less clearly, scholars fear

www.economist.com/culture/2025...

To counter this, here’s my 3 fav reads 📚 from this summer:
- The dream of the Celt by Mario Vargas Llosa
- Paradise by Abdulrazak Gurnah
- Dzhamilia by Tsjyngyz Ajtmatov

Functional phenotyping of genomic variants using joint multiomic single-cell DNA–RNA sequencing - Nature Methods This study introduces SDR-seq, a droplet-based single-cell DNA–RNA sequencing platform, enabling the study of gene expression profiles linked to both noncoding and coding variants.

New method from my former lab - combining targeted RNA-seq and DNA-seq from the same cell on the @missionbio.bsky.social platform. Congrats!
It can also be combined with targeted methylation profiling and clonal tracing.
www.nature.com/articles/s41...

A really powerful, easy and affordable method for profiling cellular interactions in the immune system. Congrats @dom60.bsky.social , @simonhaas.bsky.social and everyone involved!

Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.

Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉

www.nature.com/articles/s41...

We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!

🧵

Iterative deep learning design of human enhancers exploits condensed sequence grammar to achieve cell-type specificity Yin et al. demonstrate the use of iteratively retrained deep learning models to design synthetic enhancers for progressively higher cell-type specificity. They show the feasibility of model training f...

Interesting piece on automated enhancer design from the Seelig lab: www.cell.com/cell-systems...

Congrats @hoheyn.bsky.social , @lgmartelotto.bsky.social and team!

Scientists make breakthroughs on blood ageing and limb regrowth Two new studies could help develop better therapies for rejuvenation and regeneration

🇬🇧: Finally, English-language coverage by Financial Times, a small London-based newspaper 😉. Thanks again @omarjam.bsky.social and Nahia (@irbbarcelona.org) for making all this possible! www.ft.com/content/a1f8...

Científicos españoles descubren cómo envejece la sangre: un gran hallazgo para la lucha contra la leucemia y el envejecimiento Un estudio desarrollado en Barcelona ha dado con la clave para entender cómo envejece la sangre. El hallazgo podría facilitar la detección temprana de enfermedades como la leucemia y abrir nuevas vías...

😵‍💫: Private TV antenna3 hectically shot an interview 1.5h before their 3pm news, got a lot wrong (no we did not rejuvenate mice by ablating old stem cells, Irv Weissman did that) BUT they made us the good news of the day and it's somehow funny www.antena3.com/noticias/cie...

😬: SER Catalunya, most-listened radio around here, interviewed me at 8:40 (instead of 8:50)... they reached me in the elevator, put me live on air and started asking in Catalan. Had to guess what they meant and improvise. The good thing, I was awake after this 😅 (can't upload audio to bsky - 7/n)

Dès l’âge de 50 ans, les cellules de notre sang s’appauvrissent Une équipe espagnole a retracé l’évolution des lignées de cellules du sang chez 13 personnes de 35 à 70 ans. A partir de la cinquantaine, le nombre de cellules souches capables d’engendrer des cellule...

🇫🇷: @scherermich.bsky.social was brave enough to speak to @lemonde.fr in French 💪! Excellent article that definitely sticks out with the accompanying visual.
www.lemonde.fr/sciences/art... (6/n)