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larsplus.bsky.social
Lars Velten
@larsplus.bsky.social
440 followers 170 following 62 posts
Group leader @crg.eu | blood, single cell, synthetic genomics
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 8
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...
🧵
Design principles of cell-state-specific enhancers in hematopoiesis
Screen of minimalistic enhancers in blood progenitor cells demonstrates widespread dual activator-repressor function of transcription factors (TFs) and enables the model-guided design of cell-state-sp...
www.cell.com
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Reposted by Lars Velten
maxplanck.de
Max-Planck-Gesellschaft @maxplanck.de · 23d
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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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · 20d
This was a lot of fun! Thanks Daylon and @arunsharmaphd.bsky.social for being great hosts!
stemcellpodcast.com
Stem Cell Podcast @stemcellpodcast.com · 22d
We have a new episode out!

Dr. Lars Velten from the Centre for Genomic Regulation talks about his research on #LineageTracing and #hematopoiesis: https://bit.ly/4gsvo5X
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · Sep 7
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
Is the decline of reading making politics dumber?
As people read less they think less clearly, scholars fear
www.economist.com
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · Sep 2
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...
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.
www.nature.com
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · Aug 13
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!
dom60.bsky.social
Dominik Vonficht @dom60.bsky.social · Aug 13
Excited to share the latest publication from my PhD with @simonhaas.bsky.social at @dkfz.bsky.social, out now in Nature Methods!

A big thanks to all co-authors, especially Lea Jopp-Saile, Schayan Yousefian and @viktoriaflore.bsky.social for all their hard work.
www.nature.com/articles/s41...
Ultra-high-scale cytometry-based cellular interaction mapping - Nature Methods
Interact-omics, a high-throughput cytometry-based framework, resolves the cellular interaction landscape.
www.nature.com
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Reposted by Lars Velten
const-ae.bsky.social
Constantin Ahlmann-Eltze @const-ae.bsky.social · Aug 4
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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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · Jul 15
Interesting piece on automated enhancer design from the Seelig lab: www.cell.com/cell-systems...
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...
www.cell.com
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · Jun 23
Congrats @hoheyn.bsky.social , @lgmartelotto.bsky.social and team!
labwaggoner.bsky.social
Waggoner Lab @labwaggoner.bsky.social · Jun 17
STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging @cellcellpress.bsky.social @lgmartelotto.bsky.social @hoheyn.bsky.social
www.cell.com/cell/fulltex...
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 31
🇬🇧: 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...
Scientists make breakthroughs on blood ageing and limb regrowth
Two new studies could help develop better therapies for rejuvenation and regeneration
www.ft.com
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 31
😵‍💫: 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...
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...
www.antena3.com
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 31
😬: 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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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 31
🇫🇷: @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)
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...
www.lemonde.fr
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 31
🇦🇹: 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
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 31
😅: "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)
"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...
cadenaser.com
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 31
❤️: 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)
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.
www.3cat.cat
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 31
First of all, here's the science, in case you missed it. bsky.app/profile/lars...
Now come the media highlights (2/n)
larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 21
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...
🧵
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
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 31
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)
"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...
cadenaser.com
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Reposted by Lars Velten
mmarttinen.bsky.social
Mikael Marttinen @mmarttinen.bsky.social · May 26
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
🧵
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...
doi.org
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 26
Thank you Jorge!
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 21
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!
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 21
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.
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 21
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)‬
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 21
With help of Lars Steinmetz and Dominik Lindenhofer, Chelsea Szu-Tu added RNA-seq capabilities to the protocol, based on their SDR-seq www.biorxiv.org/content/10.1... (11/n)
Functional phenotyping of genomic variants using multiomic scDNA-scRNA-seq
Genomic variation ranging from single nucleotide polymorphisms to structural variants can impact gene function and expression, contributing to disease mechanisms such as cancer progression. The system...
www.biorxiv.org
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larsplus.bsky.social
Lars Velten @larsplus.bsky.social · May 21
@biotechpedro.bsky.social showed that the same CpGs that work in blood also work on endothelia, suggest a broad applicability to other tissues! (10/n)
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