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Lars Velten

@larsplus.bsky.social
510 followers 193 following 85 posts

Group leader @crg.eu | blood, single cell, synthetic genomics | Dad | 🇩🇪🇪🇸🇹🇿 | 🚵🧗🏃

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Lars Velten @larsplus.bsky.social · 04/09/2026
Congratulations to the first authors of both studies - @joebowness.bsky.social and Jan Barinka (from @simonhaas.bsky.social lab). I'm very priviliged to work with scientists like you. Data and code is public. (5/5)
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Lars Velten @larsplus.bsky.social · 04/09/2026
The AML story was developed completely independently of that. It dissects clinical outcomes in AML and attributes them to different biological layers - for example: relapse risk rather comes from the immune microenvironment, not the AML itself. Have a look! www.biorxiv.org/content/10.6... (5/n)
biorxiv.org
| bioRxiv
bioRxiv - the preprint server for biology, operated by openRxiv, a nonprofit organization dedicated to advancing scientific communication
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Lars Velten @larsplus.bsky.social · 04/09/2026
But it didn't stop there. We found programs predicting donor age, Venetoclax response, symmetric HSC divisions... All of this suggests that programs of genetic co-regulation - only visible from perturbation experiments - are an important (and highly interpretable) layer of information. (4/n)
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Lars Velten @larsplus.bsky.social · 04/09/2026
We therefore started decomposing RNA-seq datasets into program activity (wrote a small algorithm for that). When we looked at the AML atlas data, we lived a big surprise: One of our Perturb-seq programs predicts long-term survival in AML very well! Independent of genotype. (3/n)
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Lars Velten @larsplus.bsky.social · 04/09/2026
In perturb-seq, Joe identified "gene regulatory programs". These are groups of genes that share common regulators - not co-expression programs. This nicely grouped genes into pathways. So we asked: are these genes sets any useful? (2/n)
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Lars Velten @larsplus.bsky.social · 04/09/2026
It's been preprint week! Joe's great Perturb-seq story "back-to-back" with our single cell AML atlas (led by @simonhaas.bsky.social). 🤒: www.biorxiv.org/content/10.6... 🧬: www.biorxiv.org/content/10.6... These two apparently very different stories were posted back to back because of a surprise 😮🧵:
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Jonathan Pritchard @jkpritch.bsky.social · 29/08/2026
Genome-scale perturb-seq in human T cells. Our fantastic postdocs @ronghuizhu.bsky.social and @emmamarydann.bsky.social have done great work here to show the power and opportunities of perturb-seq in primary cells. This is part of a wonderful long-term collaboration with @marsonlab.bsky.social
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Lars Velten @larsplus.bsky.social · 17/08/2026
Wow! Not sure why this appears in my feed now but what an interesting story! Congrats @gabaldonlab.bsky.social
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Arnaud Krebs @arnaudkr.bsky.social · 12/08/2026
How many TFs to you need to open chromatin at enhancers? Very excited to see this one out! Check out the augmented version with combinatorial motif mutant libraries in Figure 5! Very proud of @guidobarzaghi.bsky.social @valentinabaderna.bsky.social @embl.org
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Lars Velten @larsplus.bsky.social · 01/08/2026
But English is just German that lost both its complexity (grammar, cases) and its simplicity (compounding German words to name new things instead of importing words from other languages: what on earth is a skunk, it is a Stinktier, obviously).
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Lars Velten @larsplus.bsky.social · 16/07/2026
3. And the best: Julia really pulled this project through from start to end. I was *very* hands-off here - makes me look old, but huge congrats to Julia on a great PhD and good luck for your next steps🇨🇭!
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Lars Velten @larsplus.bsky.social · 16/07/2026
2. Biology: Low affinity transcription factor binding sites respond linearly to changes in TF concentration whereas high affinity sites are saturated. Enhancers with high affinity sites are therefore rather regulated by co-factor availability!
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Lars Velten @larsplus.bsky.social · 16/07/2026
1. Technology: The first lentiviral assay to screen enhancer function with single cell resolution in primary cells 🦠. Relevant to developers of gene therapy, gene regulation aficionados and synthetic biologists alike - plasmid is on addgene www.addgene.org/257694/
addgene.org
Addgene: pLS-hu6-EGFP-sc-lentiMPRA
Plasmid pLS-hu6-EGFP-sc-lentiMPRA from Dr. Lars Velten's lab is published in Genome Biol (2026) This plasmid is available through Addgene.
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Lars Velten @larsplus.bsky.social · 16/07/2026
@juruehle.bsky.social's PhD work is now out in Genome Biology 📚🧬 : Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity link.springer.com/article/10.1186/s13059-026-04186-9 Julia achieved three cool things with this work...🧵
link.springer.com
Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity - Genome Biology
Background Cell state-specific gene expression programs emerge from the interplay between cis-regulatory elements (CREs), such as enhancers, and transcription factors (TFs). Massively parallel reporte...
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Annique Claringbould @anniquec.bsky.social · 12/03/2026
🧬 How do immune disease-relevant variants affect gene regulatory networks in CD4+ T cells? 🧪🖥️ We coupled two large-scale CRISPRi screens (>4M cells) to map the downstream cascades of thousands of SNPs More details in the thread below 👇 or in the article 📖 on biorxiv tinyurl.com/CD4screens
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Lars Velten @larsplus.bsky.social · 04/03/2026
Now, synthetic enhancers with single cells - great work by @juruehle.bsky.social : www.biorxiv.org/content/10.6...
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Lars Velten @larsplus.bsky.social · 04/03/2026
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 👀
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Alejo Rodriguez-Fraticelli @alejofraticelli.bsky.social · 27/02/2026
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
nature.com
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...
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Lars Velten @larsplus.bsky.social · 27/02/2026
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.
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Lars Velten @larsplus.bsky.social · 27/02/2026
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
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Lars Velten @larsplus.bsky.social · 17/02/2026
Early bird registration is closing Feb 28! We will have an AMAZING party!
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Lars Velten @larsplus.bsky.social · 11/01/2026
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?
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Vijay G. Sankaran @bloodgenes.bsky.social · 02/01/2026
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/... 🧵
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Lars Velten @larsplus.bsky.social · 18/12/2025
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).
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Lars Velten @larsplus.bsky.social · 15/12/2025
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.
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Britta Velten @brittavelten.bsky.social · 03/12/2025
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...
cell.com
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...
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Lars Velten @larsplus.bsky.social · 05/12/2025
@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
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Lars Velten @larsplus.bsky.social · 05/12/2025
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
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Lars Velten @larsplus.bsky.social · 20/11/2025
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...
Yes, this is where you would work (the round building, not the boat)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
🗨️ 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)
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Centre de Regulació Genòmica (CRG) @crg.eu · 23/10/2025
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...
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Dan Landau @landau.bsky.social · 14/10/2025
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...
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Max-Planck-Gesellschaft @maxplanck.de · 15/09/2025
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...
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.
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Lars Velten @larsplus.bsky.social · 18/09/2025
This was a lot of fun! Thanks Daylon and @arunsharmaphd.bsky.social for being great hosts!
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Lars Velten @larsplus.bsky.social · 07/09/2025
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
economist.com
Is the decline of reading making politics dumber?
As people read less they think less clearly, scholars fear
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Lars Velten @larsplus.bsky.social · 02/09/2025
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...
nature.com
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.
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Lars Velten @larsplus.bsky.social · 13/08/2025
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!
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 04/08/2025
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! 🧵
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.
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Lars Velten @larsplus.bsky.social · 15/07/2025
Interesting piece on automated enhancer design from the Seelig lab: www.cell.com/cell-systems...
cell.com
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...
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Lars Velten @larsplus.bsky.social · 23/06/2025
Congrats @hoheyn.bsky.social , @lgmartelotto.bsky.social and team!
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Lars Velten @larsplus.bsky.social · 31/05/2025
🇬🇧: 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...
ft.com
Scientists make breakthroughs on blood ageing and limb regrowth
Two new studies could help develop better therapies for rejuvenation and regeneration
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Lars Velten @larsplus.bsky.social · 31/05/2025
😵‍💫: 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...
antena3.com
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...
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Lars Velten @larsplus.bsky.social · 31/05/2025
😬: 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)
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Lars Velten @larsplus.bsky.social · 31/05/2025
🇫🇷: @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)
lemonde.fr
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...
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Lars Velten @larsplus.bsky.social · 31/05/2025
🇦🇹: 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)
science.orf.at
„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 ...
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Lars Velten @larsplus.bsky.social · 31/05/2025
😅: "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)
cadenaser.com
"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...
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Lars Velten @larsplus.bsky.social · 31/05/2025
❤️: 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)
3cat.cat
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.
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Lars Velten @larsplus.bsky.social · 31/05/2025
First of all, here's the science, in case you missed it. bsky.app/profile/lars... Now come the media highlights (2/n)
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Lars Velten @larsplus.bsky.social · 31/05/2025
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)
cadenaser.com
"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...
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