Yoann Gonneau
@yoanngonneau.bsky.social
Exploring Hox genes regulation in Stem Cell-Based Embryo Models at @college-de-france.fr | Duboule Lab | CDSN PhD Fellowship
Reposted by Yoann Gonneau
Happy to present the final version of our Cadherin and gastruloid manuscript, online at @cp-cellreports.bsky.social.
www.cell.com/cell-reports...
Initially in BiorXiv (www.biorxiv.org/content/10.1...) 1/12
www.cell.com/cell-reports...
Initially in BiorXiv (www.biorxiv.org/content/10.1...) 1/12
Cadherins modulate the self-organizing potential of pseudo-embryos
Gastruloids derived from ES cells mimic embryonic patterning through robust self-organization.
Mayran et al. uncover that this competence depends on a cadherin switch regulated
by Snai1-driven E-cadhe...
www.cell.com
November 17, 2025 at 10:37 AM
Happy to present the final version of our Cadherin and gastruloid manuscript, online at @cp-cellreports.bsky.social.
www.cell.com/cell-reports...
Initially in BiorXiv (www.biorxiv.org/content/10.1...) 1/12
www.cell.com/cell-reports...
Initially in BiorXiv (www.biorxiv.org/content/10.1...) 1/12
Reposted by Yoann Gonneau
Transcriptional interferences ensure one olfactory receptor per ant neuron
www.nature.com/articles/s41...
Caviar for RNA-Seq nerds! Check this out
www.nature.com/articles/s41...
Caviar for RNA-Seq nerds! Check this out
October 22, 2025 at 8:40 PM
Transcriptional interferences ensure one olfactory receptor per ant neuron
www.nature.com/articles/s41...
Caviar for RNA-Seq nerds! Check this out
www.nature.com/articles/s41...
Caviar for RNA-Seq nerds! Check this out
Reposted by Yoann Gonneau
🧠 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/...
www.biorxiv.org/cgi/content/...
October 16, 2025 at 6:23 AM
🧠 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/...
www.biorxiv.org/cgi/content/...
Reposted by Yoann Gonneau
Fully-funded 4-year PhD Opportunities available at the @crick.ac.uk , including a project in our lab on human #embryomodels Feel free to share with anyone interested, and apply through the online portal before 5th November! 👏
www.crick.ac.uk/careers-stud...
www.crick.ac.uk/careers-stud...
Moris Lab | Investigating human trunk development using stem cell-based embryo models
www.crick.ac.uk
October 6, 2025 at 12:03 PM
Fully-funded 4-year PhD Opportunities available at the @crick.ac.uk , including a project in our lab on human #embryomodels Feel free to share with anyone interested, and apply through the online portal before 5th November! 👏
www.crick.ac.uk/careers-stud...
www.crick.ac.uk/careers-stud...
Reposted by Yoann Gonneau
🚀 Our new paper is out @natmethods.nature.com!
Kuffer & Marzilli engineered conditionally stable MS2 & PP7 coat proteins (dMCP & dPCP) that degrade unless bound to RNA, enabling ultra–low-background, single-mRNA imaging in live cells.
🔗 www.nature.com/articles/s41...
🧬 www.addgene.org/John_Ngo/
Kuffer & Marzilli engineered conditionally stable MS2 & PP7 coat proteins (dMCP & dPCP) that degrade unless bound to RNA, enabling ultra–low-background, single-mRNA imaging in live cells.
🔗 www.nature.com/articles/s41...
🧬 www.addgene.org/John_Ngo/
September 22, 2025 at 6:27 PM
🚀 Our new paper is out @natmethods.nature.com!
Kuffer & Marzilli engineered conditionally stable MS2 & PP7 coat proteins (dMCP & dPCP) that degrade unless bound to RNA, enabling ultra–low-background, single-mRNA imaging in live cells.
🔗 www.nature.com/articles/s41...
🧬 www.addgene.org/John_Ngo/
Kuffer & Marzilli engineered conditionally stable MS2 & PP7 coat proteins (dMCP & dPCP) that degrade unless bound to RNA, enabling ultra–low-background, single-mRNA imaging in live cells.
🔗 www.nature.com/articles/s41...
🧬 www.addgene.org/John_Ngo/
Reposted by Yoann Gonneau
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
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
September 17, 2025 at 5:26 PM
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
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
Reposted by Yoann Gonneau
Ever wondered how to get a gastruloid to grow a head?
The Bulut-Karslioğlu lab figured out that by growing different stem cell aggregates in high and low oxygen and later assembling them, you can get gastruloids with a fully formed neural tube. Check out our "In preprints": doi.org/10.1242/dev....
The Bulut-Karslioğlu lab figured out that by growing different stem cell aggregates in high and low oxygen and later assembling them, you can get gastruloids with a fully formed neural tube. Check out our "In preprints": doi.org/10.1242/dev....
In preprints: gastruloids get (a)head
A major breakthrough in the field of mammalian embryology is the development of stem-cell based embryo models. Derived from pluripotent stem cells, such as embryonic stem cells or induced pluripotent ...
doi.org
September 16, 2025 at 8:31 AM
Ever wondered how to get a gastruloid to grow a head?
The Bulut-Karslioğlu lab figured out that by growing different stem cell aggregates in high and low oxygen and later assembling them, you can get gastruloids with a fully formed neural tube. Check out our "In preprints": doi.org/10.1242/dev....
The Bulut-Karslioğlu lab figured out that by growing different stem cell aggregates in high and low oxygen and later assembling them, you can get gastruloids with a fully formed neural tube. Check out our "In preprints": doi.org/10.1242/dev....
Reposted by Yoann Gonneau
After nearly twenty years in the making, our attempt at understanding what makes the chaetognath phylum so unique has finally been published! www.nature.com/articles/s41...
with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1
with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1
The genomic origin of the unique chaetognath body plan - Nature
Genomic, single-cell transcriptomic and epigenetic analyses show that chaetognaths, following extensive gene loss in the gnathiferan lineage, relied on newly evolved genes and lineage-specific tandem ...
www.nature.com
August 13, 2025 at 4:38 PM
After nearly twenty years in the making, our attempt at understanding what makes the chaetognath phylum so unique has finally been published! www.nature.com/articles/s41...
with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1
with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1
Reposted by Yoann Gonneau
Hi bsky!
Do embryonic tissues have backup plans🔀? Gastruloids (model of body elongation) can build an axis through different cellular mechanisms when on adherent substrates instead of free floating. A case of developmental plasticity!
w/ A. Delahaye & @bensteventon.bsky.social
shorturl.at/v01DO
Do embryonic tissues have backup plans🔀? Gastruloids (model of body elongation) can build an axis through different cellular mechanisms when on adherent substrates instead of free floating. A case of developmental plasticity!
w/ A. Delahaye & @bensteventon.bsky.social
shorturl.at/v01DO
August 7, 2025 at 3:01 PM
Hi bsky!
Do embryonic tissues have backup plans🔀? Gastruloids (model of body elongation) can build an axis through different cellular mechanisms when on adherent substrates instead of free floating. A case of developmental plasticity!
w/ A. Delahaye & @bensteventon.bsky.social
shorturl.at/v01DO
Do embryonic tissues have backup plans🔀? Gastruloids (model of body elongation) can build an axis through different cellular mechanisms when on adherent substrates instead of free floating. A case of developmental plasticity!
w/ A. Delahaye & @bensteventon.bsky.social
shorturl.at/v01DO
Reposted by Yoann Gonneau
How do enhancer-gene contacts relate to transcription activation? In mouse embryonic stem cells, a combo of STED, oligoFISH & RNA FISH shows that 3% of Dppa3 alleles transcribe. For these, enhancers and promoters come closer (panel E). Stumberger ... Leonhardt & Harz www.biorxiv.org/content/10.1...
July 26, 2025 at 9:36 PM
How do enhancer-gene contacts relate to transcription activation? In mouse embryonic stem cells, a combo of STED, oligoFISH & RNA FISH shows that 3% of Dppa3 alleles transcribe. For these, enhancers and promoters come closer (panel E). Stumberger ... Leonhardt & Harz www.biorxiv.org/content/10.1...
Reposted by Yoann Gonneau
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 ...
www.nature.com
July 9, 2025 at 11:58 AM
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...
Reposted by Yoann Gonneau
Paper alert! I am really pleased to share the final version of the work led by Irène Amblard in the team on a regulatory switch controlling Cdx2 expression during posterior body development! #regulatorylogic #devbio @mrc-lms.bsky.social @imperialmed.bsky.social
June 27, 2025 at 3:07 PM
Paper alert! I am really pleased to share the final version of the work led by Irène Amblard in the team on a regulatory switch controlling Cdx2 expression during posterior body development! #regulatorylogic #devbio @mrc-lms.bsky.social @imperialmed.bsky.social
Reposted by Yoann Gonneau
⚠️ I am really excited to share the work of Anastasios Balaskas, an excellent PhD candidate in the lab, with the wider world. Tasos made a significant advance: generating a stem cell-based embryo model that contains both posterior and anterior neural tissues of the late-stage gastrulating embryo.
June 23, 2025 at 7:51 AM
⚠️ I am really excited to share the work of Anastasios Balaskas, an excellent PhD candidate in the lab, with the wider world. Tasos made a significant advance: generating a stem cell-based embryo model that contains both posterior and anterior neural tissues of the late-stage gastrulating embryo.
Reposted by Yoann Gonneau
If you are interested by epigenetics, early human development in excellent scientific environment in middle of Paris, we are recruiting a postdoc.
app.beetween.com/WeaselWeb/p/...
Don't hesitate to apply or share the post !
app.beetween.com/WeaselWeb/p/...
Don't hesitate to apply or share the post !
Beetween
app.beetween.com
June 13, 2025 at 1:28 PM
If you are interested by epigenetics, early human development in excellent scientific environment in middle of Paris, we are recruiting a postdoc.
app.beetween.com/WeaselWeb/p/...
Don't hesitate to apply or share the post !
app.beetween.com/WeaselWeb/p/...
Don't hesitate to apply or share the post !
Reposted by Yoann Gonneau
Spotiflow, our deep learning based spot detection method for microscopy, is now published in @natmethods.nature.com!
Since the pre-print, we have added many features, notably native 3D detection!
@maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social
Paper: rdcu.be/epIB7
(1/N)
Since the pre-print, we have added many features, notably native 3D detection!
@maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social
Paper: rdcu.be/epIB7
(1/N)
Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression
Nature Methods - Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. The improved accuracy offered by Spotiflow enables improved biological insights in...
rdcu.be
June 6, 2025 at 6:58 PM
Spotiflow, our deep learning based spot detection method for microscopy, is now published in @natmethods.nature.com!
Since the pre-print, we have added many features, notably native 3D detection!
@maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social
Paper: rdcu.be/epIB7
(1/N)
Since the pre-print, we have added many features, notably native 3D detection!
@maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social
Paper: rdcu.be/epIB7
(1/N)
Reposted by Yoann Gonneau
In which we discuss the homologies between amphibian and mammalian organizers from the perspective of #gastruloids with special relevance to recently described A and C gastruloids as containing Spemann/Mangold and Trunk/Tail organizers www.sciencedirect.com/science/arti...
May 23, 2025 at 10:35 AM
In which we discuss the homologies between amphibian and mammalian organizers from the perspective of #gastruloids with special relevance to recently described A and C gastruloids as containing Spemann/Mangold and Trunk/Tail organizers www.sciencedirect.com/science/arti...
Reposted by Yoann Gonneau
Excited to share and be part of this work showing how #Nodal and #Wnt signaling act in distinct time windows to coordinate the mammalian body plan!
We've just updated our manuscript to a more 'publishable' version!
www.biorxiv.org/content/10.1...
New details about the role of Wnt in suppressing neural differentiation and fostering a posterior epiblast state, and the temporal effect of Nodal signalling in driving mesendodermal fates
www.biorxiv.org/content/10.1...
New details about the role of Wnt in suppressing neural differentiation and fostering a posterior epiblast state, and the temporal effect of Nodal signalling in driving mesendodermal fates
May 21, 2025 at 7:38 PM
Reposted by Yoann Gonneau
I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. www.nature.com/articles/s41...
Chromatin loops are an ancestral hallmark of the animal regulatory genome - Nature
The physical organization of the genome in non-bilaterian animals and their closest unicellular relatives is characterized; comparative analysis shows chromatin looping is a conserved feature of ...
www.nature.com
May 7, 2025 at 3:23 PM
I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. www.nature.com/articles/s41...
Reposted by Yoann Gonneau
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...
I'm so excited about this!
www.biorxiv.org/content/10.1...
Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data
Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...
www.biorxiv.org
May 9, 2025 at 10:49 AM
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...
I'm so excited about this!
www.biorxiv.org/content/10.1...
Reposted by Yoann Gonneau
Join us in Catalonia to discuss chromatin evolution across the tree of life and from all angles (metabolism, synthetic chromatin, you name it!) meetings.embo.org/event/24-evo...
EvoChromo: Evolutionary approaches to research in chromatin
Chromatin is the complex of DNA, RNA and protein that is found making up the chromosomes in eukaryotic cells. Chromatin is essential for proper genome function and is involved in chromosome segregati…
meetings.embo.org
April 11, 2025 at 1:45 PM
Join us in Catalonia to discuss chromatin evolution across the tree of life and from all angles (metabolism, synthetic chromatin, you name it!) meetings.embo.org/event/24-evo...
Reposted by Yoann Gonneau
A project five years in the making, we've now published complete "T2T" genomes for six additional ape species! It turns out that finishing (and analyzing) six genomes is slightly more work than one... doi.org/10.1038/s415...
April 9, 2025 at 9:31 PM
A project five years in the making, we've now published complete "T2T" genomes for six additional ape species! It turns out that finishing (and analyzing) six genomes is slightly more work than one... doi.org/10.1038/s415...
Reposted by Yoann Gonneau
Just in a week from now! Open symposium @collegedefrance.bsky.social in Paris 😎. The state of the art on enhancer sequences. Import tax-free (for everyone).
April 3, 2025 at 9:53 AM
Just in a week from now! Open symposium @collegedefrance.bsky.social in Paris 😎. The state of the art on enhancer sequences. Import tax-free (for everyone).
Reposted by Yoann Gonneau
Very happy to share that our paper on stem cell culture conditions is now out! doi.org/10.1371/jour... We found that modulating mESC culture conditions influences gastruloid elongation and lineage specification, and helps with making the protocol more reproducible in our hands! more below 🧵⬇️ [1/7]
Stem cell culture conditions affect in vitro differentiation potential and mouse gastruloid formation
Aggregating low numbers of mouse embryonic stem cells (mESCs) and inducing Wnt signalling generates ‘gastruloids’, self-organising complex structures that display an anteroposterior organisation of ce...
doi.org
March 28, 2025 at 3:20 PM
Very happy to share that our paper on stem cell culture conditions is now out! doi.org/10.1371/jour... We found that modulating mESC culture conditions influences gastruloid elongation and lineage specification, and helps with making the protocol more reproducible in our hands! more below 🧵⬇️ [1/7]
Reposted by Yoann Gonneau
I'm really grateful for the large turnout of our Gastruloid meeting in Barcelona. Close to 100 researchers from 9 countries. With the gastruloid field expanding, I hope that the community stays this close and that the meeting becomes an annual tradition! #gastruloids #conference
March 23, 2025 at 5:04 PM
I'm really grateful for the large turnout of our Gastruloid meeting in Barcelona. Close to 100 researchers from 9 countries. With the gastruloid field expanding, I hope that the community stays this close and that the meeting becomes an annual tradition! #gastruloids #conference
Reposted by Yoann Gonneau
Difficult to believe that such a community has emerged @ #gastruloids as a model system to explore many aspects of #DevBio. Great to see a room so full of people, curiosity and good Science @prbb.org @upf.edu Thank you to all that have made this possible & of course to the participants
March 21, 2025 at 6:19 AM
Difficult to believe that such a community has emerged @ #gastruloids as a model system to explore many aspects of #DevBio. Great to see a room so full of people, curiosity and good Science @prbb.org @upf.edu Thank you to all that have made this possible & of course to the participants