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 🧠🔬🧬

Amazing! Congratulations Akanksha! Looking forward to all the exciting science in your group 🤩

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...

Thank you so much Filipa!!! ❤️❤️❤️

Thanks Cedric!

Thank you!! 😊

Thanks Chris!! 😄

It was so much fun to work together with @jasperjanssens.bsky.social. Huge thanks to Benedikt, Philipp, @ann-sophiekroell.bsky.social‬, Gosia, Maria, Ryoko, @kkarava.bsky.social‬, @zhisonghe.bsky.social, Marthe, and Manuel for making this possible!

There’s a lot more of our story, including the morphogen dynamics, pre- vs post-patterning, and comparison with primary neurons etc. Find out more in our paper!
www.science.org/doi/10.1126/...

With all the data we have, we put together a summary of in vitro neuronal diversity that is programmed in this study, with the optimal condition to generate corresponding subtypes, the purity, and the enrichment of disease genes and ion channels as a resource for the community.

But are these iN subtypes functional? In collaboration with Hierlemann Lab, we used HD-MEA for electrophysiological measurements and found that patterned iNs are functionally and morphologically distinct! In addition, the morphological complexity is tightly linked with transcriptome maturation.

We experimentally validated the GRNs through TF knock-out or overexpression coupled with scRNA-seq. We found that regulon-hub TFs can be necessary and sufficient for specific neuron subtypes.

How does morphogen combinations contribute to this diversity? We inferred morphogen-centered gene regulatory networks (GRNs), identified combinatorial signaling cues and upregulated TFs underlying neuron subtype specification.

We designed a combinatorial patterning screen on top ot iNs. Using highly multiplexed scRNA-seq enabled by @parse.bsky.social, our screen gives rise to a wide spectrum of neurons, with identities mapped across forebrain, midbrain, hindbrain, spinal cord, sympathetic, and peripheral sensory neurons.

This is actually not surprising because pro-neural TFs such as NGN2 and ASCL1 are widely expressed across the developing nervous system. We started to think about the possibility of guiding iNs into associated lineages using morphogen combinations to program diverse neuron subtypes.

iNs from pro-neural TF overexpression in iPSCs are widely used for disease modeling and drug screens. But as we and Wernig lab previously showed, iNs are heterogeneous with mixing CNS and PNS identities, which can confound results sensitive to neuronal subtypes. www.sciencedirect.com/science/arti...