Zev Gartner

🔔 Proud to share the preprint of my PhD work in the Petridou group @nicolettapetridou.bsky.social @embl.org ✨

“A closed feedback between tissue phase transitions and morphogen gradients drives patterning dynamics” 🐟 🔁 📶

🔗 www.biorxiv.org/content/10.1...

#devbio #biophysics

🧵⤵️

Workshop New Technologies for Studying and Reprogramming Development Organisers: Alex Dunn, Zev Gartner, Adrian Jacobo and Matthew Kutys Early-career researchers apply for funded places 16-19 November 2025 Buxted Park, East Sussex, UK

One month left for ECRs to apply for a funded place at our Workshop 'New Technologies for Studying and Reprogramming Development' organised by Alex Dunn,
@zevgartner.bsky.social , @adrianjacobo.bsky.social and Matthew Kutys.
📆Apply by 23 May
biologists.com/workshops/no...
#BiologistsWorkshops

Background of DNA strand with logos of King's College London and the Leverhulme Trust and text Force Talks Mechanics of Life Leverhulme DSP seminar series Dr Jean-Leon Maitre Institut Curie Mechanics of blastocyst morphogenesis Wednesday, 07 May 2025, 15:00-16:00 email:mechanicsoflife@kcl.ac.uk for more information

Join us for our next #ForceTalk on "Mechanics of blastocyst morphogenesis" with Dr Jean-Leon Maitre @maitrejl.bsky.social of Institut Curie:

🗓️ 7 May 2025
🕒 15:00 - 16:00 BST

Online and open to all, link to join 👉 www.kcl.ac.uk/events/force...

#mechanobiology @kingsnmes.bsky.social

Workshop New Technologies for Studying and Reprogramming Development Organisers: Alex Dunn, Zev Gartner, Adrian Jacobo and Matthew Kutys Early-career researchers apply for funded places 16-19 November 2025 Buxted Park, East Sussex, UK

Early-career researchers can apply for a funded place at our Workshop 'New Technologies for Studying and Reprogramming Development' organised by Alex Dunn,
@zevgartner.bsky.social , @adrianjacobo.bsky.social and Matthew Kutys.
📆Apply by 23 May
biologists.com/workshops/no...
#BiologistsWorkshops

Crick PhD student awarded Schmidt Science Fellowship Jake Cornwall Scoones, PhD student in the Developmental Dynamics Laboratory at the Francis Crick Institute, has been awarded a prestigious Schmidt Science Fellowship to support his research into how c...

Many congratulations to @jcornwallscoones.bsky.social on the award of a Schmidt Science Fellowship

Now he just needs to find a lab to host him for his post-doc

www.crick.ac.uk/news/2025-04...

Since I started my PhD in 2013, I have been tantalised by a question: can we measure or evaluate the transcriptional and mechanical states of cells in a tissue at the same time? I pursued this question as a postdoc and then as a PI! A🧵on the answer we have found 👇:

GitHub - Gartner-Lab/Concord Contribute to Gartner-Lab/Concord development by creating an account on GitHub.

9. While we focused on scRNA-seq, early results suggest CONCORD’s applicability to spatial transcriptomics & scATAC-seq. It’s open-source in Python. See galleries: qinzhu.github.io/Concord_docu.... Try it: github.com/Gartner-Lab/....

8. CONCORD integrates datasets based solely on gene co-expression structures—without assuming batch-effect models or shared cellular states. It achieves robust alignment even with minimal dataset overlap, offering faster and scalable analysis from small studies to atlas-scale projects.

neighborhood and dataset aware sampling improves learning

7. The key innovation leading to this performance gain is a probabilistic, dataset- and neighborhood-aware sampling strategy tailored for self-supervised contrastive learning, enabling the generation of coherent, denoised and high-resolution latent cell representations across diverse datasets:

6. CONCORD also provides biologically interpretable encodings representative of context-dependent gene-expression programs.

loops, cylinders and filaments in a gut developmental atlas

5. An intestinal development atlas demonstrated CONCORD's ability to resolve complex topologies, including differentiation trajectories intertwined with cell cycle loops (click here for interactive 3D UMAP! qinzhu.github.io/Concord_docu...):

see lineage relationships in C. elegans developmental data sets

4. We validated CONCORD on an embryonic atlas of C. elegans and C. briggsae from @jisaacmurray. CONCORD captured known bifurcations, resolved subtle cell states, and uncovered lineage convergence events missed by other methods (click here for interactive 3D UMAP! qinzhu.github.io/Concord_docu...):

CONCORD outperforms other methods on metrics of geometry and topology

3. We evaluated CONCORD on datasets with topologies such as continuous trajectories, loops, clusters and hierarchical trees. Using scIB metrics, geometric measures, and TDA, we assessed its ability to preserve biological structure. CONCORD outperforms existing methods:

Revealing a coherent cell state landscape across single cell datasets with CONCORD Resolving the intricate structure of the cellular state landscape from single-cell RNA sequencing (scRNAseq) experiments remains an outstanding challenge, compounded by technical noise and systematic ...

2. CONCORD is a simple but powerful ML framework tackling data integration, dimensionality reduction, and denoising in single-cell analysis, developed by @qinzhu1. Read our bioRxiv preprint: doi.org/10.1101/2025...

lineage landscapes and single cell data

1. Struggling to integrate single-cell datasets? Finding it hard to resolve clear differentiation trajectories? Reveal the underlying structure in your data with CONCORD.

Predictable Engineering of Signal-Dependent Cis-Regulatory Elements

Excited to share my latest work with @joadelas.bsky.social and @jamesbriscoe.bsky.social

Predictable Engineering of Signal-Dependent Cis-Regulatory Elements

www.biorxiv.org/content/10.1...
1/11

Congratulations Laura Avinyo! @lauavinyo.bsky.social and Heura Cardona! First paper of your PhD 🎉. doi.org/10.1242/dev.... Beautiful quantified trajectory of how the skeletal pattern of the gene Sox9 emerges during limb development. @embl.org @barcelonacollaboratorium.com

Material-like robotic collectives with spatiotemporal control of strength and shape The vision of robotic materials—cohesive collectives of robotic units that can arrange into virtually any form with any physical properties—has long intrigued both science and fiction. Yet, this visio...

Really excited to present the results of a great collaboration between our group @poldresden.bsky.social and Elliot Hawkes at @ucsantabarbara.bsky.social, which were just published in @science.org. A mix of physics, biology and robotics! 🤖 😀

▶️ www.science.org/doi/10.1126/...

Home - Klein Lab We are interested in understanding how organs form in the embryo and how they renew and regenerate in the adult. We research how development and regeneration

Excited that our new lab website is starting to come together - thanks to the team, particularly Pauline Marangoni and Zhulin Dixon, for assembling this, and stay tuned for additional updates ophirkleinlab.org

Engineering kidney developmental trajectory using culture boundary conditions Kidney explant cultures are traditionally carried out at air-liquid interfaces, which disrupts 3D tissue structure and limits the interpretation of developmental data. To overcome this limitation, we ...

Aria Huang's @azyhuang.bsky.social pre-print just came out on effects of adhesion and stiffness on global kidney explant size, shape and nephron forming efficiency. Along the way, she achieves beautiful 3D cultures that retain proper branching geometry, check it out!

biorxiv.org/cgi/content/...

Co-organizing the GRC Mammary Gland Biology and Neoplasia meeting this coming spring in Maine with Traci Lyons. Submit your abstracts for short talk consideration!

www.grc.org/mammary-glan...

Spectacular

Pre-announcing the EMBO/EMBL symposium "Mechanobiology Across the Tree of Life", Heidelberg, 9-12 June 2026. It is still very very far away, but save the date 🗓️. With Alba Diz-Munoz, @nicolettapetridou.bsky.social , Kirsty Wan @micromotility.bsky.social, Enrique Rojas.
www.embl.org/about/info/c...

My first post on @bsky.app. So happy to announce that our work has been published in Development by @biologists.bsky.social
doi.org/10.1242/dev....

Also a big thanks for "The people behind the papers" article as well! doi.org/10.1242/dev....

Right on the $$$

Hello world!