Thrilled to share that our group will be supported by an ERC Starting Grant! 🚀 With the project 'DECIPHER', we will decode and perturb gene regulation to engineer human cell subtypes, niches, and maturation. We’ll soon be recruiting at all levels — stay tuned for opportunities to join us!

Thrilled to share 🎉 I’m starting my lab at University of Zurich, DMLS as Assistant Professor (tenure track) from Jan 2026! The Neural MorphoGenomics & Developmental Dynamics Lab will be exploring how genes + morphogenesis shape brain development with organoids, imaging & spatial genomics 🧠🔬🧬

Final version @science.org "Recent evolution of the developing human intestine affects metabolic and barrier functions". Evolutionary preparation for microbiota, diet, and pathogen exposure is fascinating! Thank you @erc.europa.eu for supporting our vision! www.science.org/doi/10.1126/...

Please RP. We are thrilled to announce that our lab’s first preprint is out! ”Whole-genome single-cell multimodal history tracing to reveal cell identity transition” We report HisTrac-seq, a multiomic single-cell molecular recording platform. www.biorxiv.org/content/10.1...

To all post-docs: The Genome Biology dept ‪@embl.org has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.

🧬🧬🧬 New review from the lab: Evolution of comparative transcriptomics: biological scales, phylogenetic spans, and modeling frameworks authors.elsevier.com/sd/article/S... By @mattezambon.bsky.social & @fedemantica.bsky.social, together with @jonnyfrazer.bsky.social & Mafalda Dias.

Just out in @science.org Silencing mitochondrial gene expression in living cells | Science www.science.org/doi/10.1126/...

🎲 Our paper on the genetics, energetics, and allostery in proteins with randomized cores and surfaces is out today @science.org! 🧬 By charting a protein’s sequence universe, we could rationalize which versions were kept through evolution – and why many stable ones were not.

Our work bridging enhancer-promoter proximity to phenotypic outcomes in vivo is out! Shout out to @olimpiabompadre.bsky.social, to Marie Kmita's lab, and to all the co-authors. www.nature.com/articles/s41...

My postdoc work at Treutlein lab and @graycamplab.bsky.social with @jasperjanssens.bsky.social is out in @science.org ! We screen for neuron subtypes using pro-neural TFs + morphogen combinations + scRNA-seq and profiled over 700,000 cells in 480 conditions. www.science.org/doi/10.1126/...

Neuron programming! Pro-neural TFs + 480 morphogen conditions + scRNA-seq --> Diverse iN subtypes of forebrain, midbrain, hindbrain, spinal cord, and PNS. @hsiuchuanlin.bsky.social‬ @jasperjanssens.bsky.social‬ and Treutlein Lab! @science.org www.science.org/doi/10.1126/... #NGN2 #ASCL1

Excited to be back in Basel to share my work with old and new friends!

Just published, expansion in situ genome sequencing, where you can sequence DNA while still inside the cell, mapping its organization relative to proteins and other markers, with the help of expansion microscopy! Led by @jbuenrostro.bksy.social. www.science.org/doi/10.1126/...

Our latest "Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data" A rigorous mathematical foundation for Waddington's landscape to study cell fate decision making Applied to ventral neural tube development www.biorxiv.org/content/10.1...

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... 🧵

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... 🧵

Registration for Single-cell genomics 2025 is now open! This year we’re back in beautiful Stockholm archipelago. We have a special session on clinical applications, but we also invite abstracts from both PIs and trainees, with plenty of slots for selected talks. conferences.weizmann.ac.il/SCG2025/

Happy to share our resource for blood vessel organoids! @zhisonghe.bsky.social, Makiko Seimiya, Gustav Jonsson, Wuji Cao, Ryo Okuda, Reiner Wimmer, Ryoko Okamoto Barbara Treutlein, @graycamplab.bsky.social, @penningerlab.bsky.social

Yay, we built a thing! With @dominik1klein.bsky.social Daniil, Aviv Regev, Barbara Treutlein @graycamplab.bsky.social @fabiantheis.bsky.social we use flow matching to enable generalised sc phenotype modeling. From cytokine screens to fate programming and organoid engineering tinyurl.com/3xhju7db

New tool 💪 from @steinaerts.bsky.social lab: CREsted, a DL-based approach for predicting cell type-specific reg. elements, applying it to many datasets, incl. mouse cortex, human PBMCs & glioblastoma, demonstrating its ability to identify key TF binding sites: www.biorxiv.org/content/10.1...

A fun collaboration with @nazbukina.bsky.social @zhisonghe.bsky.social at @Treutleinlab @graycamplab.bsky.social for our posterior brain organoid atlas and morphogen screens!

Awesome summary of the field. An important point is to separate the design method from the oracle model being used. Sometimes, people say they're proposing a new design method but mean a cool new oracle model. Modelling and design of transcriptional enhancers www.nature.com/articles/s44...

Today, we're launching the Arc Virtual Cell Atlas, a growing resource for computation-ready single-cell measurements. arc-website-git-ben-virtual-cell-atlas-tool-arc-institute.vercel.app/news/news/ar...

🚀 Think all white matter (WM) astrocytes are the same? Think again! 🌟 Our latest research reveals striking regional differences that challenge existing views on astrocyte diversity and function. 🧠 www.nature.com/articles/s41...

📣 Hiring, please forward widely!! Two postdoc openings to work on genomics of diabetes 1. Computational regulatory genomics/statistical genetics. 2. Experimental cell-based modeling DM if interested @crg.eu shorturl.at/O3wMi shorturl.at/ieyZy

Our latest: how to generate the notochord "Timely TGFβ signalling inhibition induces notochord" A thread: www.nature.com/articles/s41...

3 reviews on planning, execution, & validation of transcriptomic experiments in neuroscience published in @natureportfolio.bsky.social #NatureNeuroscience. A MUST READ if you're doing transcriptomics. 3 reviews, an amazing editorial, a beautiful cover – this is the issue of the year! (mini thread)

1/🚀 Excited to share RegVelo, our new cell model combining RNA velocity with gene regulatory network (GRN) dynamics to model cellular changes and predict in silico perturbations. Here's how it works and why it matters! 🧵👇 biorxiv.org/content/10.1101/2024.12.11.627935v1

📢 There are 2 open PhD positions in my group at CRG Barcelona! We are looking for candidates interested in cell fate engineering, gene regulation, and single-cell technologies with experience in both wet/dry labs. Please help spread the word 🙌 Apply here ➡️ www.crg.eu/en/content/t...

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. www.nature.com/articles/s41...

"The lives of cells, recorded"--our new review on genomic recording systems and how they can reveal the dynamics of multicellular development. A pleasure to work on this with amazing colleagues from the Allen Discovery Center for Cell Lineage Tracing. www.nature.com/articles/s41...

We have two open PhD positions in my group at @crg.eu. We are seeking candidates with a background in computational and/or molecular biology, and with a broad interest in evolutionary biology, gene regulation, and comparative genomics. 📅Apply before January 12 here: www.crg.eu/en/content/t...

📣 Two ERC-funded positions are available in the lab! If you are interested in exploring the mechanisms underlying mutation, we’d love to hear from you. PhD: shorturl.at/Oc04N Postdoc: shorturl.at/1ShHB RPs and shares would be greatly appreciated! 🧪🧬🖥️ #ScienceJobs #PostdocJobs

Now in Nature! As a highly collaborative team with people from the Treutlein lab, @fabiantheis.bsky.social and @graycamplab.bsky.social, led by me, @le-and-er.bsky.social and @josch1.bsky.social, we generated the so far largest cell atlas of neural #organoid. www.nature.com/articles/s41...

Excited to announce that I will start my group at @crg.eu in Barcelona next April! We will decode and engineer cell fates using stem cell models, perturbation screening and single-cell multiomics. Looking forward to the new chapter ahead!