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Yad Ghavi-Helm @yghavi.bsky.social · 13d

Actually it’s poster 151 and 241!

Yad Ghavi-Helm @yghavi.bsky.social · 14d

In the starting blocks for #EDRC2025!
Come see our work at posters 100 and 155 and during the Gene expression in the 3D nuclear space workshop!

EDRC2025 @edrc2025.bsky.social · 14d

Only a few hours left before our meeting starts! Are you travelling to #EDRC2025 now? Let us know by using the oficial #EDRC2025 hashtag!

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Yad Ghavi-Helm @yghavi.bsky.social · Jul 28

Merci au @cnrsbiologie.bsky.social de mettre en avant notre travail! @baalberti.bsky.social @paulvilloutreix.bsky.social
@igflyon.bsky.social @ensdelyon.bsky.social

CNRS Biologie @cnrsbiologie.bsky.social · Jul 28

Un embryon virtuel pour cartographier l’activité des régions régulatrices du génome

🤝 @yghavi.bsky.social @cnrs-rhoneauvergne.bsky.social

👉 Lire l'article dans @narjournal.bsky.social buff.ly/e41cZQD

Un embryon virtuel pour cartographier l’activité des régions régulatrices du génome

Dans un article publié dans Nucleic Acids Research, des scientifiques décrivent spatial-scERA, une méthode combinant biologie moléculaire, séquençage

buff.ly

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Yad Ghavi-Helm @yghavi.bsky.social · Jul 24

haha me too! Still a long way to go though...

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Yad Ghavi-Helm @yghavi.bsky.social · Jul 24

Yes! We are now cultivating them in the lab since a couple of months thanks to @criscanestro.bsky.social @evodevogenomeub.bsky.social and have started a very exciting project 🤩

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Yad Ghavi-Helm @yghavi.bsky.social · Jul 23

📢 We are recruiting!
Several projects are available and can be tailored to the candidate's profile. Most include confocal imaging/spatial OMICs technologies.
Please share and RT 🙏

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Reposted by Yad Ghavi-Helm

Baptiste Alberti @baalberti.bsky.social · Jul 23

🚨 Our paper is out! 🚨
Check how spatial-scERA can predict enhancer activity in a virtual Drosophila embryo.
Very proud of this first step in the research world published in @narjournal.bsky.social
Thanks to @yghavi.bsky.social, @paulvilloutreix.bsky.social and all the scientists who made it real!

Yad Ghavi-Helm @yghavi.bsky.social · Jul 23

Now available in its final form @narjournal.bsky.social !
doi.org/10.1093/nar/...
Find out how we can reconstruct enhancer activity in vivo in the Drosophila embryo using scRNAseq data and Optimal Transport.

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Yad Ghavi-Helm @yghavi.bsky.social · Jul 23

Thanks Virginia! Hope you like it 😄

Yad Ghavi-Helm @yghavi.bsky.social · Jul 23

Thanks Joaquin!

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Yad Ghavi-Helm @yghavi.bsky.social · Jul 23

This is the work of a talented PhD student @baalberti.bsky.social (on the job market!) together with Séverine Vincent, and a great collaboration with @paulvilloutreix.bsky.social 🙌
@igflyon.bsky.social @cnrsbiologie.bsky.social @ensdelyon.bsky.social

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Yad Ghavi-Helm @yghavi.bsky.social · Jul 23

Now available in its final form @narjournal.bsky.social !
doi.org/10.1093/nar/...
Find out how we can reconstruct enhancer activity in vivo in the Drosophila embryo using scRNAseq data and Optimal Transport.

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Reposted by Yad Ghavi-Helm

Bon Pote @bonpote.com · Jul 19

300 000 signatures dont plus de 200000 en moins de 48h !

L’objectif des 500 000 signatures est possible d’ici dimanche soir, afin d’obtenir un vrai débat à l’Assemblée nationale sur la loi Duplomb.

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Yad Ghavi-Helm @yghavi.bsky.social · Apr 8

Merci Alexis!

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Yad Ghavi-Helm @yghavi.bsky.social · Apr 2

Honored and extremely grateful to see our project in collaboration with @hilaryashe.bsky.social and @hilsawh.bsky.social awarded an #HFSPReseachGrant @hfspo.bsky.social
Stay tuned for exciting job offers!

Human Frontier Science Program @hfspo.bsky.social · Apr 2

🥳Congratulations to the 104 pioneering scientists from 30 nations awarded 2025 #HFSPResearchGrants! 🎉Your frontier research is shaping the future of #LifeSciences! 🌍🔬🧪
🏆 Meet the awardees & their projects: www.hfsp.org/bookletRG202...
#ScienceDiplomacy #HFSP #FrontierScience #sts

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Yad Ghavi-Helm @yghavi.bsky.social · Jan 23

Thanks @evodevogenomeub.bsky.social @criscanestro.bsky.social for having us and showing us all the secrets of beautiful Oikopleura!! 😍

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Yad Ghavi-Helm @yghavi.bsky.social · Jan 21

Lovely day at @biom-banyuls.bsky.social
So much exciting science on cool marine species!

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Reposted by Yad Ghavi-Helm

Paul Villoutreix @paulvilloutreix.bsky.social · Dec 12

Poster #5 is a collaboration with @yghavi.bsky.social led by Baptiste Alberti where we propose a method for reconstructing of the spatial single-cell enhancer activity in a multicellular organism
www.biorxiv.org/content/10.1...

Spatial reconstruction of single-cell enhancer activity in a multicellular organism

Enhancers play an essential role in developmental processes by orchestrating the spatial and temporal regulation of gene expression. However, mapping the location of these regulatory elements in the g...

www.biorxiv.org

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Yad Ghavi-Helm @yghavi.bsky.social · Nov 20

Thanks!!

Yad Ghavi-Helm @yghavi.bsky.social · Nov 19

Thanks!

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Yad Ghavi-Helm @yghavi.bsky.social · Nov 18

🙋🏽‍♀️

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Yad Ghavi-Helm @yghavi.bsky.social · Nov 18

On my way to Heidelberg @EMBL #EMBLOmics to present our work. Looking forward!!!

Yad Ghavi-Helm @yghavi.bsky.social · Nov 18

🚨Preprint alert!
tinyurl.com/2zkmynsd
Did you ever dream of reconstruction #spatial single-cell #enhancer activity in a multicellular organism using massively parallel enhancer-reporter assays?
Then Spatial-scERA is the method for you!
#spatialOMICs

Spatial reconstruction of single-cell enhancer activity in a multicellular organism

Enhancers play an essential role in developmental processes by orchestrating the spatial and temporal regulation of gene expression. However, mapping the location of these regulatory elements in the g...

tinyurl.com

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Yad Ghavi-Helm @yghavi.bsky.social · Nov 18

This work could not have been possible without the support of @ERC_Research @FRM_officiel @AgenceRecherche especially through the "investissement d'avenir" program that funds the @Spatial_Cell_ID facility @ENSdeLyon @igflyon.bsky.social

Yad Ghavi-Helm @yghavi.bsky.social · Nov 18

While we demonstrate the use of spatial-scERA in Drosophila embryos, this method can be applied to screen the single-cell spatiotemporal activity of hundreds of enhancers in parallel in any multicellular organism amenable to transgenesis.

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Yad Ghavi-Helm @yghavi.bsky.social · Nov 18

Interestingly, our results highlight that chromatin accessibility is often a poor predictor of enhancer activity. Some of the regions we tested overlapped with highly accessible regions. However these regions are not active in reporter assays!

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Yad Ghavi-Helm @yghavi.bsky.social · Nov 18

Just an example to showcase the power of our method:
we could reconstruct the activity pattern of the h_stripe1 enhancer based on the sequencing of our reporter construct in only 9 cells!

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