Lars Velten

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)

„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)

"A partir de los 50 casi todas las células madre se llaman Rodríguez" (Y eso es malo) Un estudio liderado por dos centros de investigación de Barcelona ha descubierto que, a partir de esa edad, cada vez tenemos menos células madre sanguíneas y las que hay se replican cada vez con más e...

😅: "From age 50 almost all stem cells are called Rodriguez (and that's bad)". All credit for this to @alejofraticelli.bsky.social - family names are a fantastic analogy to explain clonal processes cadenaser.com/nacional/202... (4/n)

Telenotícies - Envelliment de la sang: d'un ecosistema ric i variat a un de dominat per unes poques cèl·lules - 3Cat Una investigació catalana rastreja els "codis de barres" escrits a l'ADN i revela què passa a la sang quan envellim.

❤️: Catalan public TV 3cat nicely covered the science and the emotions when making a cool discovery in their evening news (almost like Sports reporting) www.3cat.cat/3cat/envelli... (3/n)

First of all, here's the science, in case you missed it. bsky.app/profile/lars...
Now come the media highlights (2/n)

"A partir de los 50 casi todas las células madre se llaman Rodríguez" (Y eso es malo) Un estudio liderado por dos centros de investigación de Barcelona ha descubierto que, a partir de esa edad, cada vez tenemos menos células madre sanguíneas y las que hay se replican cada vez con más e...

Thanks to phenomenal work by @crg.eu and @irbbarcelona.org press offices, we got to communicate our findings on 🧬 methylation barcodes and 🩸 blood ageing to a wide audience. A cool experience!

🧵 with highlights in 5 languages and funny moments 😬😅

cadenaser.com/nacional/202... (1/n)

Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics - Nature Methods This work presents SUM-seq, an ultra-high-throughput method for co-profiling chromatin accessibility and gene expression in single nuclei across multiplexed samples, advancing the study of gene regula...

SUM-seq out @natmethods.nature.com !


🚀 Ultra-high-throughput Multiplexed snATAC+RNA

Used to:
⏳ link temporal macrophage GRNs to immune disease genetics
🩸 map T cell regulatory landscapes
🧬✂️ dissect TF function in hiPSC differentiation via CRISPRi/a screens
doi.org/10.1038/s41592-025-02700-8
🧵

Thank you Jorge!

What a year 😅 really really happy that both these projects worked out better that we could ever have planned, and the Barcelona scientific environment was super important for both of them!

It was great to see how this story rapidly developed from a serendipitous discovery on DNA methylation to a project with relevance to blood stem cell ageing and beyond. Big thanks to the funders, especially EHA and AECC.

With help of @leifludwig.bsky.social @caleblareau.bsky.social & colleagues, we compared this to mitochondrial lineage tracing; TL;DR: mitochondrial genetics is complicated (12/n)‬