Alexandre Mayran

Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq - Nature Genetics This study introduces single-cell transcription factor (TF) sequencing, a single-cell barcoded and doxycycline-inducible TF overexpression approach that reveals dose-sensitive functional classes of TFs and cellular heterogeneity by mapping TF dose-dependent transcriptomic changes during the reprogramming of mouse embryonic multipotent stromal cells.

🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China

In this beautiful system, we could show uncoupling of gene expression profiles, morphology and patterning… #NotInTheGenes 😉 (also includes a method to do long term 🔬 of elongating gastruloids)
Thank you to all involved @jeromewongng.bsky.social @thomasgregor.bsky.social @alexandremayran.bsky.social

L’art délicat de faire taire les gènes Le développement embryonnaire ne requiert pas uniquement l’activation des gènes, mais également une régulation fine de leur répression.

#ResultatScientifique 🔎| Faire taire les gènes est aussi crucial que les activer : le répresseur Snail révèle son rôle essentiel dans le développement embryonnaire 🧬
✍️ @laghalab.bsky.social et Ovidiu Radulescu
📕 @natcomms.nature.com | buff.ly/pmtzA1t

Fantastic work congrats to you all, it's been great to see this story being build over the years

hoxd13a reporter in a zebrafish larva

Are digits modified fins, or evolutionary innovations? Read how we tackled this old question from a new angle🧪
A story with @chasebolt.bsky.social, @homeobox.bsky.social and myself, coordinated by @denisduboule.bsky.social from @college-de-france.fr and published in @nature.com today!
#InHoxWeTrust

Out today. 🙏 again to everyone for this wonderful piece of work, in particular to Aurelie @aurhin.bsky.social Chase @chasebolt.bsky.social and Brent @homeobox.bsky.social. 🙏 also to the Harris lab @fish4walking.bsky.social and @neilshubin.bsky.social @biology-unige.bsky.social @college-de-france.fr

Bioinformatician / Data Scientist (m/f/d) Bioinformatician / Data scientist position in the Aztekin Lab focusing on Structural Regeneration and support the working group together with the other members

🚀 Looking for a Bioinformatician / Data Scientist to join our crew and explore regeneration through single-cell genomics & evolutionary biology! @mpi-bio-fml.bsky.social
📩 Questions? Contact us ✉️
🔗 Apply here: www.mpg.de/25243280/bio...

Similar huge trend at last round of @erc.europa.eu grant application. @ec.europa.eu must adapt to this trend!

Pleased to announce launching Institut Cochin Foundation, on Sept. 18 at 6 p.m., upon registration, either in the Rosalind Franklin room, 22 rue Méchain, Paris or via video conference: presentation of @institutcochin.bsky.social, meet researchers and call for donations-thanks for your support!

Merci!

Happy to be added too

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...

Looks like private funders, HHMI,CZI etc., are not going to “save” US research. Europe is setting up mechanisms to attract US researchers & it may work. But, common, target junior talent, don’t shower money on superstars who will be flying professors & return to US when the science winter passes.

A complete model of mouse embryogenesis through organogenesis enabled by chemically induced embryo founder cells A small-molecule-only strategy enables reprogramming ESCs into embryo founder cells that give rise to a high-fidelity embryo model directly and efficiently. This embryo model replicates embryogenesis ...

Impressive work from @josesilvalab.bsky.social

www.cell.com/cell/fulltex...

Transgene-free generation of mouse post-gastrulation whole embryo models solely from naive ESCs and iPSCs Hanna and colleagues show that signaling pathway modulation amplifies the inherent flexibility of genetically unmodified mouse naive PSCs to adopt extra-embryonic cell fate potential. This endows them...

1/n Fun journey continues: Our new @cp-cellstemcell.bsky.social paper out on how the Inherent & Dormant Plasticity of Mouse Naive PSCs can be "Exaggerated" to Directly form ~E8.5 Transgene-Free (TF) Mouse SEMs & WITHOUT inducing 8-16-Morula-like "Embryo Founder Cells".

www.cell.com/cell-stem-ce...

Transgene-free generation of mouse post-gastrulation whole embryo models solely from naive ESCs and iPSCs Hanna and colleagues show that signaling pathway modulation amplifies the inherent flexibility of genetically unmodified mouse naive PSCs to adopt extra-embryonic cell fate potential. This endows them with the competence to generate up to E8.5–E8.75 transgene-free stem cell-derived embryo models (TF-SEMs) that complete gastrulation and initiate organogenesis within complex extra-embryonic compartments ex utero.

Online Now! Transgene-free generation of mouse post-gastrulation whole embryo models solely from naive ESCs and iPSCs #stemcells

#jobAlert We are hiring! If you like #imaging ,gene regulation and a dynamic group please apply. We are looking for a research assistant with a master degree and prior experience in academia.

Brain Surfaces of 70 primate species

1
To predict the behaviour of a primate, would you rather base your guess on a closely related species or one with a similar brain shape? We looked at brains & behaviours of 70 species, you’ll be surprised!

🧵Thread on our new preprint with @r3rt0.bsky.social , doi.org/10.1101/2025...

So excited to share my 1st paper !!🌞
Co-authored with @jules-vanaret.bsky.social @dunsingvalentin.bsky.social, we developped an integrated pipeline for imaging, segmenting and analysing cell-scale patterns in gene expression + tissue properties in complex 3D tissues
elifesciences.org/reviewed-pre...

Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes - Nature Genetics Activation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype c...

Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁
Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5

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 ...

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...

A dream come true: my first first-author publication! 🧬 🎉 Working to unravel the mysteries of long-range gene regulation has been an incredible journey. Endless gratitude to Evgeny, the lab, and all of the amazing collaborators who helped make this happen 🙌

Range extender mediates long-distance enhancer activity - Nature The REX element is associated with long-range enhancer–promoter interactions.

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

Congrats Jean Leon!

Congrats! Happy to see it out!

Checkout the full story online now at Dev Cell, the product of a team effort with the help of our fantastic collaborators including @da-bar.bsky.social @borislenhard.bsky.social @mpercharde.bsky.social

Article link:
doi.org/10.1016/j.de...

Sham Tlili, winner of the CNRS 2025 bronze medal - IBDM | Institut de Biologie du Développement de Marseille A distinction that rewards a promising and already fruitful scientific career.

🥇Sham Tlili has been awarded the CNRS 2025 Bronze Medal! She studies how physical forces shape living tissues by using mouse stem cell models known as gastruloids. A unique blend of physics & biology.

🔗 Read more: www.ibdm.univ-amu.fr/sham-tlili-w...

We are looking for a research assistant to join our lab and support ongoing projects with genome engineering in mouse embryonic stem cells! Please get in touch if you are interested.
www.fmi.ch/education-ca...

A major KI initiative to recruit new assistant professors with outstanding proposals in all areas of medicine, biomedicine and public health. We offer an amazing research environment, great colleagues and generous startup packages. Check it out and get working on your applications! (repost please!)

Portrait photo of Dr. Juliane Glaser

We are excited to officially welcome a new group leader at the MPI-IE in #Freiburg. 🎉

Dr Juliane Glaser 🥳 – she studies epigenetic mechanisms of embryonic development, with a focus on transposable elements. 👉 Interview: www.ie-freiburg.mpg.de/6043545/2025...

Welcome, @julianeg.bsky.social!