@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...🧵

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...

link.springer.com

🧬 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

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

Lars Velten@larsplus.bsky.social · last yr.

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... 🧵

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 👀

Julia Rühle@juruehle.bsky.social · 5mo ago

The main project of my PhD 🧬🔬 is out: we developed single-cell lentiMPRA, a lentivirus-based method to measure enhancer activity and transcriptomes at single-cell resolution. We then applied sc-lentiMPRA to fully synthetic enhancers 🧩... 🔗 doi.org/10.64898/202...

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

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...

nature.com

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.

Centre de Regulació Genòmica (CRG)@crg.eu · 6mo ago

Exactly 25 years ago, @rodericguigo.bsky.social and his PhD student published the first draft of the human genome in Science. The Catalan researchers were the only two from all Spain that took part. Here they are reflecting on the huge scientific feat: www.crg.eu/en/news/25-y...

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

Alejo Rodriguez-Fraticelli@alejofraticelli.bsky.social · 5mo ago

🚨 NEW @FraticelliLab PREPRINT JUST WENT LIVE biorxiv.org/content/10.6... Here, we describe PLSTCs, Soluplus-based expansion cultures of primary mouse *Acute Myeloid Leukemia* Stem Cells. And then we use LARRY barcoding to identify drivers of leukemogenicity and drug resistance!

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

Lars Velten@larsplus.bsky.social · 8mo ago

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

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/... 🧵

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...

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...

cell.com

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

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...

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!

Stem Cell Podcast@stemcellpodcast.com · 11mo ago

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

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

economist.com

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.

nature.com

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!

Dominik Vonficht@dom60.bsky.social · 12mo ago

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...

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! 🧵

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...

cell.com

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

Waggoner Lab@labwaggoner.bsky.social · last yr.

STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging @cellcellpress.bsky.social @lgmartelotto.bsky.social @hoheyn.bsky.social www.cell.com/cell/fulltex...

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

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

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

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.

Manu Saraswat@manusaraswat.bsky.social · last yr.

🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇

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...

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…

sciencedirect.com

Looking forward to hosting ISCO again in Barcelona next year! 📍🗓️ save the date: 28./29. May 2026

Stefanie Grosswendt@stefaniegrosswendt.bsky.social · last yr.

Just wrapped up 2 inspiring days at ISCO – Innovations in Single Cell Omics! A great community came together to share science and fun. A big THANK YOU to all our fantastic speakers and interactive participants