Lars Velten
@larsplus.bsky.social
📤 474
📥 183
📝 67
Group leader
@crg.eu
| blood, single cell, synthetic genomics
pinned post!
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...
🧵
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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...
https://www.cell.com/cell/fulltext/S0092-8674(25)00449-0
8 months ago
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Britta Velten
23 days ago
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...
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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...
https://www.cell.com/cell-genomics/fulltext/S2666-979X%2825%2900332-5
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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
21 days ago
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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...
about 1 month ago
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Lars Velten
Christoph Bock Lab @ CeMM & MedUni Vienna
about 1 month ago
🗨️ 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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Lars Velten
Centre de Regulació Genòmica (CRG)
2 months ago
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
2 months ago
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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Lars Velten
Max-Planck-Gesellschaft
3 months ago
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...
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This was a lot of fun! Thanks Daylon and
@arunsharmaphd.bsky.social
for being great hosts!
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3 months ago
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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
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Is the decline of reading making politics dumber?
As people read less they think less clearly, scholars fear
https://www.economist.com/culture/2025/09/04/is-the-decline-of-reading-making-politics-dumber
4 months ago
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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...
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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.
https://www.nature.com/articles/s41592-025-02805-0
4 months ago
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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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4 months ago
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Lars Velten
Constantin Ahlmann-Eltze
5 months ago
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! 🧵
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Interesting piece on automated enhancer design from the Seelig lab:
www.cell.com/cell-systems...
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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...
https://www.cell.com/cell-systems/fulltext/S2405-4712(25)00135-8
5 months ago
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Congrats
@hoheyn.bsky.social
,
@lgmartelotto.bsky.social
and team!
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6 months ago
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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)
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"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...
https://cadenaser.com/nacional/2025/05/21/descubren-que-a-partir-de-los-50-anos-casi-todas-las-celulas-madre-de-nuestra-sangre-se-llaman-rodriguez-y-eso-es-malo-cadena-ser/
7 months ago
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Lars Velten
Mikael Marttinen
7 months ago
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
🧵
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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...
https://doi.org/10.1038/s41592-025-02700-8
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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...
🧵
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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...
https://doi.org/10.1038/s41586-025-09041-8
7 months ago
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Lars Velten
Oliver Stegle
7 months ago
Super happy and proud of this one. We and others have developed tools for dimensionality reduction for many years. MOFA (linear) and other non-linear generalisations, space/time. scDORI fuses this with GRN inference. It’s a nice and useful piece of software. Here applied to GBM biology.
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Lars Velten
Shalin H. Naik
7 months ago
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...
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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…
https://www.sciencedirect.com/science/article/pii/S0092867425004611?dgcid=author
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Looking forward to hosting ISCO again in Barcelona next year! 📍🗓️ save the date: 28./29. May 2026
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8 months ago
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Very nice press coverage! It was fun working with the
@crg.eu
PR team & explaining synthetic enhancers to journalists in Spanish 😅
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8 months ago
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Lars Velten
Jeff Vierstra
8 months ago
Finally published! We developed an epigenomics to therapeutics screening approach that identifies naturally occurring elements that can titrate expression of transgenes at various levels including single elements stronger than the B-globin LCR.
www.nature.com/articles/s41...
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Large-scale discovery of potent, compact and erythroid specific enhancers for gene therapy vectors - Nature Communications
This study presents a large-scale enhancer screening approach to optimize gene therapy vectors. A compact, potent, erythroid-specific enhancer used in a therapeutic vector, improved viral titers, tran...
https://www.nature.com/articles/s41467-025-59235-x
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Lars Velten
Darío Lupiáñez
8 months ago
🧠 MPRA + AI to decipher rules of enhancer grammar. I wrote some thoughts about the fantastic and inspiring work by Robert Frömel & colleagues from
@larsplus.bsky.social
lab at
@crg.eu
@upf.edu
👏👏👏
sciencemediacentre.es/en/design-dn...
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Design DNA fragments that control genes in mammalian cells with AI
A team from the Centre for Genomic Regulation (CRG) and Pompeu Fabra University (UPF) in Barcelona has developed an artificial intelligence tool capable of designing regulatory sequences for genes that do not exist in nature. When introduced into cells, these enhancers can increase or decrease gene activity in a specific way depending on the type of cell targeted. According to the authors, ‘the potential applications are enormous. It's like writing software, but for biology.’ The results are published in the journal Cell.
https://sciencemediacentre.es/en/design-dna-fragments-control-genes-mammalian-cells-ai
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Lars Velten
Cell - a Cell Press journal
8 months ago
Now online! Design principles of cell-state-specific enhancers in hematopoiesis
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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-specific enhancers.
http://dlvr.it/TKdsC6
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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...
🧵
loading . . .
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...
https://www.cell.com/cell/fulltext/S0092-8674(25)00449-0
8 months ago
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This method has already proven super useful to us!
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9 months ago
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I agree, you don’t want to miss it! Technical barriers that have so far impeded most lineage tracing in human are falling and the potential of this field is vast.
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9 months ago
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Very cool study on leukemic stem cells, thank you
@kentsisresearch.bsky.social
for letting us be part of it!
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9 months ago
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Strong! A must read
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9 months ago
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Lars Velten
Itai Yanai
10 months ago
Join us at "Innovations in Single Cell Omics" in Berlin 5.12-13 (+ night science workshop!)
www.isco-conference.eu
Organizers:
@stefaniegrosswendt.bsky.social
,
@simonhaas.bsky.social
@leifludwig.bsky.social
, Ashley Sanders,
@larsplus.bsky.social
,
@elimereu.bsky.social
,
@alejofraticelli.bsky.social
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Lars Velten
Itai Yanai
10 months ago
Single-cell people! Check out the "Innovations in Single Cell Omics" meeting, May 12-13 in Berlin! I'm really looking forward to being a part of this great line-up and also to presenting a Night Science workshop. Join us!
www.isco-conference.eu
Abstract deadline for talks & posters: March 7
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This is big - the effect of cancer mutations on HSCs is determined by pre-existing properties of the stem cell affected! Crazy results on NPM1 🤩
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10 months ago
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Very nice work!
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11 months ago
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Lars Velten
Leif S. Ludwig
11 months ago
Join us to connect with the vibrant
#singlecell
community. 📢Register for the
#ISCO'25
Conference "Innovations in
#SingleCell
#OMICS
" in Berlin! 🗓️ 12-13 May 2025 🎤 Fantastic Keynote and Invited Speakers 🫵🏿 Many slots for talks: submit your abstract 🔗http://isco-conference.eu Please spread the word!
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Just deleted my X account, this has really been overdue.
11 months ago
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Lars Velten
Florian Foos
12 months ago
Just a reminder for Germans abroad that you need to re-register to vote in the Federal Election, even if you didn't move houses since 2021 (yes, I'm a political scientist and had to google this). Here are the docs you need:
www.bundeswahlleiterin.de/bundestagswa...
. (1)
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Deutsche im Ausland - Die Bundeswahlleiterin
Informationen für Deutsche im Ausland zur Teilnahme an der Bundestagswahl 2021.
https://www.bundeswahlleiterin.de/bundestagswahlen/2025/informationen-waehler/deutsche-im-ausland.html#e5e658b0-cc7e-4c5e-9c8c-b5d5f4053b73
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Leopold Parts
11 months ago
We are happy to share our enhancer scramble story, a strategy to create hundreds of stochastic deletions, inversions, and duplications within mammalian gene regulatory regions and associate these new architectures with gene expression levels 🧵
www.biorxiv.org/content/10.1...
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Lars Velten
Britta Velten
12 months ago
My first post here on BlueSky to share our recent work with Claudia Feng and
@leopoldparts.bsky.social
- a large-scale single cell CRISPR screen to chart out gene regulation and the role of genomic background in iPSCs. Check out the data here:
www.sanger.ac.uk/tool/crispri...
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My first post on Bluesky! And I think this one is deserving, good methods to properly DE single cell data between conditions (not cells) have been lacking for way too long
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12 months ago
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you reached the end!!
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