Zev Gartner

Such an absolute honour 🙏 Thank You @bscb-official.bsky.social Incredibly lucky to be surrounded by the most supportive colleagues and community. This award truly belongs to my wonderful, wonderful lab @crick.ac.uk

🚨Do sign up to our mailing list for this very exciting joint talk by Profs Marino Arroyo and Xavier Trepat on active morphogenesis on Wednesday 21st Jan🚨

8. We thank team member Zuzhi Jiang, collaborators Binyamin Zuckerman, Leor Weinberger, Matt Thomson, funding sources @cancerresearchinst (@CancerResearch) @NIH @czbiohub @czi @UCSF, the thoughtful reviewers from @NatureBiotech, and everyone else who shared data and feedback!

7. Best of all, it's fast (1M cells in <10 mins) and memory-friendly.
💻 Open Source: github.com/Gartner-Lab/... 📖 Docs: qinzhu.github.io/Concord_docu... Try it out and let us know what you think!

modalities

6. It's not just for scRNA-seq. CONCORD seamlessly handles and aligns scATAC-seq and spatial transcriptomics (Xenium, etc.), revealing fine-grained subtypes across technologies

intestinal differentiation

5. CONCORD resolved complex topologies during intestinal development, such as differentiation trajectories linked to cell cycle loops and providing biologically interpretable encodings traced to gene co-expression programs (click here for interactive 3D UMAP! qinzhu.github.io/Concord_docu...):

lineage detail

4. On a whole-organism, multi-species embryonic atlas of C. elegans and briggsae from @jisaacmurray’s lab where lineage annotations provide a ground truth, CONCORD resolved lineage trajectories and bifurcations (see animation and click here for interactive 3D UMAP! qinzhu.github.io/Concord_docu...):

benchmarking

3. With this sampling scheme, we found that even a minimalist single-layer network achieves better-than-SOTA performance. It disentangles biology from batch effects without over-correcting.
We benchmarked it rigorously. Across a diverse set of datasets, CONCORD consistently ranked top:
ben

minibatch sampler overview

2. At the core is a novel mini-batch sampler that changes how the model 'sees' data. Unlike uniform sampling, our approach is two-fold: 🔹 Dataset-aware: Extracts consistent biological structure across batches. 🔹 Hard-negative: Distinguishes differences between closely related cell states.

1. Excited to share CONCORD, out in @NatureBiotech, an ML framework for single-cell analysis addressing integration, dimensionality reduction, and denoising in one go by @qinzhu1.🔗 www.nature.com/articles/s41... Check out this CONCORD model of worm development resolving differentiation trajectories:

Mind blown 🤯

We are all super happy and proud to see our work on the function and evolution of the #cephalic #furrow published in @nature.com. Let me say a few things about the background and history of this work on the #Evolution_of_Morphogenesis (1/12)

Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells - Nature Cell Biology McCreery, Stubb et al. show that mechano-osmotic changes in the nucleus induce general transcriptional repression and prime chromatin for cell fate transitions by relieving repression of specific differentiation genes.

How do #stemcells integrate information to coordinate fate decisions? Delighted to finally see our work showing how growth factors regulate the mechano-osmotic state of the #nucleus and #chromatin to control #pluripotency exit out! www.nature.com/articles/s41... see 🧵 👇

A mechanical origin for implantation defects in embryos from aged females Women over 35 experience a marked reduction in fertility. The origin of these fertility defects appears to reside in the implantation capacity of the embryo itself, but the mechanistic basis of this i...

First, check out my recent bioRxiv preprint w/ @oweinerlab.bsky.social: www.biorxiv.org/content/10.1...
We find contractility shifts the proportion of implantation-competent embryos from young and aged females. Keep reading this for more info!

Very excited to be co-organizing this meeting next February. Fellow collective behavior enthusiasts, this one is for you!

Aria Huang's @azyhuang.bsky.social paper is out on beautiful embryonic kidney 3D cultures that branch properly and enable live defect analysis. She also finds intriguing effects of adhesion and stiffness on explant size, shape, and nephron formation - boundary conditions matter!

rdcu.be/eBSUK

🔔 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...