Excited to share that our paper is out in @natneuro.nature.com, presenting a multi-omic atlas and high-throughput morphogen screen of human organoids modeling the posterior brain! 🧠 nature.com/articles/s41... @zhisonghe.bsky.social @hsiuchuanlin.bsky.social @TreutleinLab @graycamplab.bsky.social

New from the lab: BARseq3! Barcodes + high efficiency spatial transcriptomics and translatomics in the same cells, or just a nice spatial transcriptomics assay. All in a modular, expandable system to enable truly multimodal measurements. Check it out: www.biorxiv.org/content/10.6...

A clear/significant finding derived from the single cell (sc) analysis of biological systems has been the realization that phenotypically homogeneous populations are heterogeneous at the level of gene expression (GE). www.cell.com/fulltext/S00... 🧵

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

Gene expression is a fundamentally stochastic process, with randomness in transcription and translation leading to cell-to-cell variations in mRNA and protein levels. This variation appears in organis...

cell.com

We’re looking for a technician to join our lab in Dresden - help manage the lab and work with us on a cool 'stem cell zoo' comparison projects! 🐁🚶‍♀️🦏🐒 Apply by May 21! tud.link/wbqrwm

Physics of Life Dresden@poldresden.bsky.social · 3mo ago

🚨 #JobAlert: Lab Technician. Please share with your colleagues! 👩‍🔬The Ebisuya lab @ebisuyamiki.bsky.social is looking for an experienced technician in molecular & cell biology to join their interdisciplinary team. Apply now! Learn more here 👉 tud.link/wbqrwm 🗓️Application deadline: May 21.

Latest from Shendure & Qiu labs (@cxqiu.bsky.social) )! We combined a new 4M cell mouse whole embryo scATAC-seq atlas (E10-P0), millions of 'evolutionarily coherent' orthologs from 241 mammalian genomes (Zoonomia), and the CREsted CNN framework (@steinaerts.bsky.social).

🚨 Why can’t mammals regenerate limbs like frog tadpoles or salamanders? In our new paper in @science.org , we show that species-specific oxygen sensing acts as a gatekeeper for initiating limb regeneration 🐭🐸 🔗 www.science.org/doi/10.1126/... #EvoDevo

Today in Nature Neuroscience we have published our exploration of neocortical development leveraging 100's of public datasets. You can interrogate the entire compendium of data at nemoanalytics.org/landing/neoc... and read the paper at www.nature.com/articles/s41....

Excited to share our #preprint showing that #macrophages in the regenerating #zebrafish #heart are shaped by local cardiac-immune microniches, with a fibroblast-to-macrophage signal promoting regeneration over fibrotic repair www.biorxiv.org/content/10.6... @idrm.ox.ac.uk @oxforddpag.bsky.social

New Perspective form Rory Maizels & me: "Gene regulatory networks: from correlative models to causal explanations" Gene regulatory networks are supposed to give us mechanistic explanations of development, so why are we drowning in 'hairballs' of statistical correlations? rdcu.be/e7zx7

Gene regulatory networks: from correlative models to causal explanations

Nature Reviews Genetics - In this Perspective, Maizels and Briscoe discuss the limitations of current models of gene regulatory networks and outline solutions to harness data abundance without...

rdcu.be

Our review “A competition model of multilineage priming and cell-fate decisions” is out: www.cell.com/cell-reports...

A competition model of multilineage priming and cell-fate decisions

In development, cells navigate highly complex gene-regulatory landscapes to make fate choices. Steinschaden et al. synthesize concepts of multilineage priming, microheterogeneity, and collective multi...

cell.com

New preprint on technologies to scale up CRISPR screens. We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells. We also introduce an approach for cloning lentiviral libraries with billions of elements.

Your new batch of cortical organoids resulted in mixed regional identities closer to hindbrain. Why is patterning so hard?😩 ✨Our latest paper might help you✨ tinyurl.com/neorgpat #morphogen #neuralorganoids #patterning #scRNAseq @graycamplab.bsky.social @ethz.ch @nazbukina.bsky.social

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

🧠 The Lipid #Brain Atlas is out now! If you think #lipids are boring and membranes are all the same, prepare to be surprised. Led by @lucafusarbassini.bsky.social with Giovanni D'Angelo's lab, we mapped membrane lipids in the mouse brain at high resolution. www.biorxiv.org/cgi/content/...

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!

Centre de Regulació Genòmica (CRG)@crg.eu · 11mo ago

🎉 Two @erc.europa.eu Starting Grants awarded to CRG researchers! DECODE-PMD @markushopfler.bsky.social explores how half-made proteins can trigger deletion of their own mRNA. DECIPHER @hsiuchuanlin.bsky.social decodes gene networks to program precise, mature human brain cells #ERCStG Read more 👇👇👇

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...

Group Leader - Genome Biology Unit

Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...

embl.wd103.myworkdayjobs.com

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/...

Silencing mitochondrial gene expression in living cells

Mitochondria fulfill central functions in metabolism and energy supply. They express their own genome, which encodes key subunits of the oxidative phosphorylation system. However, the central mechanis...

science.org

🎲 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...

Liebenberg syndrome severity arises from variations in Pitx1 locus topology and proportion of ectopically transcribing cells - Nature Communications

Here the authors show that reducing enhancer-promoter distance at the Pitx1 locus increases proportion of Pitx1 forelimb expressing cells, worsening skeletal defects in Liebenberg syndrome. They also ...

nature.com

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!

BaCell3D@bacell3d.bsky.social · last yr.

New PI highlight talk! By @hsiuchuanlin.bsky.social who just started her group @crg.eu Barcelona. “Profiling and programming in vitro neuronal diversity at single-cell resolution”

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...

Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data

Building a mechanistic understanding of cell fate decisions remains a fundamental goal of developmental biology, with implications for stem cell therapies, regenerative medicine and understanding dise...

biorxiv.org