Alex Hughes Lab

SAVE THE DATE! Stoked to organize the 2026 Santa Cruz Developmental Biology Meeting with @rashmi-priya.bsky.social, @lowelab.bsky.social, and Shelbi Russell. Come learn about Biomedicine, Biomechanics, and the Biosphere, August 24-28, 2026. Registration dates, etc., coming soon! Please RT

So: can a cell hold hands with itself…and do we care? YES and YES! Read on to learn WHY, HOW, and what this has to do with…PARIS (and tree-hugging)? Swansong of Dr. Anamika; Hannah Kim on drums; and fantastic undergrads (Margaret/Lauren) ! 1/n
advanced.onlinelibrary.wiley.com/doi/10.1002/...

Fantastic mechanics in fertility / development story from @katecavanaugh.bsky.social. Hiring committees take note 👀

Now #published @pnas.org: "A model for boundary-driven tissue morphogenesis", a great #biophysics #devbio collaboration led by @danielalber.bsky.social @zhaoshh.bsky.social:

doi.org/10.1073/pnas.2505160122

@mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social @flatironinstitute.org

Cool paper by new Hughes lab postdoc @danielalber.bsky.social

Apply to join our Penn Bioengineering department, featuring friendly, supportive faculty and staff, rigorous science, and top students!
apply.interfolio.com/173716

Great opportunity to work with a very creative PI

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

Pathologists have used nuclear & tissue shapes to diagnose #cancer for decades, but what is the molecular basis for this? In our latest work, we develop a computational pipeline to figure this out in #colorectalcancer! Check out 🧵& preprint #mechanobiology #stemcells www.biorxiv.org/content/10.1...

Multiple autism genes influence GABA neuron remodeling via distinct developmental trajectories Abstract. Variation in over 100 genes are now associated with increased risk for autism and related neurodevelopmental conditions, but how this variation r

Do you like neuronal #plasticity? #genetics? #Celegans? Check out 1st installment of work by Kristi Zoga in the lab. Kristi screened 20 conserved #autism genes for roles in experience-dependent #neuron remodeling and a related behavior.
doi.org/10.1093/genetics/iyaf156

pYtags - our in vivo biosensors for receptor tyrosine kinases - in all their beauty on the cover of Cell Reports! Read more here: www.cell.com/cell-reports...

Super cool project #2

Super cool project @vayyappan.bsky.social

FDA-NIH Workshop: Reducing Animal Testing The FDA is hosting a workshop on reducing animal testing. The workshop is open to current FDA and NIH employees.

Birth defects kill twice as many children as cancer. Animal model are crucial; no stem-cell or computer models can yet recapitulate the embryo's complexity. If you support birth defects research tell NIH that animal models are important! Click & scroll below to comment.

tinyurl.com/mr3he6bx

New preprint out! We show how cellular nematic order can be harnessed to program tissue-wide force fields and guide 3D shape transformations.

The tissue morphogenesis logic, now engineered into living, programmable materials.

www.biorxiv.org/content/10.1...

#ActiveMatter #TissueEngineering

Start of 2025 @mblscience.bsky.social Physiology course! This is the second year of Amy @gladfelterlab.bsky.social and I co-Directing this absolutely amazing and life-changing course: www.mbl.edu/education/ad...

Our own @azyhuang.bsky.social is a student this year representing the kidney fanatics

Guiding Cell Network Assembly using Shape‐Morphing Hydrogels Choreographed movement of cells and extracellular matrix (ECM) is a common, yet under-engineered tissue-building process. Shape-changing metamaterials (“kinomorphs”) made from precisely patterned cel...

We used Hausdorff distance to compare 3D shapes in model:experiment in this paper:
advanced.onlinelibrary.wiley.com/doi/full/10....
Some spatial frequency approach might help you quantify the 'bumpiness' separate from the 'shape'.
Seems like ‪@keenancrane.bsky.social‬ would be helpful

fantastic series of work by @bugajlab.bsky.social and @dennishuang.bsky.social

Geometrically frustrated rose petals Growth and form are deeply interconnected, in a manner often mediated by mechanical instabilities arising from geometric incompatibilities. Although Gauss incompatibility has long been recognized as t...

I'm a big fan of this paper on the shape of rose petals.
www.science.org/doi/10.1126/...

Whoa, fantastic stuff! This may be just the beginning of the somites <--> kidneys connection

Cool thread Rikki, the adhesion and motility correlation makes sense and neat to see the data collapse onto it. cancer invasion / emt would show negative corr right? Also wondering about when global dev rate is faster or slower, local self-organization has to match rate of events happening nearby

I remember that @sshekhr.bsky.social was thinking about this way back at MBL @mblscience.bsky.social Woods Hole Physiology course 2014. Congrats & way cool Shashank!

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

How can an individual protein show adaptation? The light- and temp-sensitive BcLOV4 gives a pulse of translocation during a step input of light. Answer in our preprint: *intra-molecular* feed-forward regulation. bit.ly/3Rg9veD
A @bugajlab.bsky.social collab with @nmrkaygee.bsky.social 🧵

Thrilled to be featured in The New York Times! @nytimes.com

Fantastic piece by @jack-tamisiea.bsky.social on our discovery of the role of physical forces in evolution! With insightful comments from @wcratcliff.bsky.social!

✨congrats! hiring here too 👀

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.

NimbusImage

Super excited to be launching NimbusImage.com! Cloud-based image analysis to democratize machine learning!

Documentation here!
docs.nimbusimage.com

Our paper on 96-well control of temperature is now out @cp-cellsystems.bsky.social. Exceedingly proud of this work led by Will Benman, plus Pavan Iyengar, @trmumford.bsky.social, and much of our lab. Come for DIY hardware, stay for the stress granule dynamics and memory🧵

📝 tinyurl.com/thermoPlate