Alex Hughes Lab
@hugheslabpenn.bsky.social
Lab-run account @ Penn Bioengineering. Studying development and tissues using micro-scale engineering, chemical biology, and microscopy. alexhugheslab.com
Pinned
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
rdcu.be/eBSUK
Reposted by Alex Hughes Lab
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/...
advanced.onlinelibrary.wiley.com/doi/10.1002/...
September 30, 2025 at 2:29 PM
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/...
advanced.onlinelibrary.wiley.com/doi/10.1002/...
Fantastic mechanics in fertility / development story from @katecavanaugh.bsky.social. Hiring committees take note 👀
See this? This = implanting mouse embryo. Usually this happens inside its mother and is invisible to us, but we can actually watch implantation ex vivo with the hope of understanding why implantation goes awry in embryos of older women. A 🧵...
October 1, 2025 at 6:28 PM
Fantastic mechanics in fertility / development story from @katecavanaugh.bsky.social. Hiring committees take note 👀
Reposted by Alex Hughes Lab
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
doi.org/10.1073/pnas.2505160122
@mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social @flatironinstitute.org
New #preprint: "A model for boundary-driven tissue morphogenesis" arxiv.org/abs/2503.03688.
A great collaboration with @danielalber.bsky.social @zhaoshh.bsky.social, Alexandre Jacinto, Eric Wieschaus, Stas Shvartsman.
@flatironinstitute.org @mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social
A great collaboration with @danielalber.bsky.social @zhaoshh.bsky.social, Alexandre Jacinto, Eric Wieschaus, Stas Shvartsman.
@flatironinstitute.org @mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social
September 19, 2025 at 7:52 AM
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
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
Peer pressure shapes the gut: latest publication in @pnas.org by @lepuslapis.bsky.social, @zhaoshh.bsky.social from @mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social with colleagues from @flatironinstitute.org and Princeton University. www.mpi-cbg.de/news-outreac...
Peer pressure shapes the gut
International research team develops mechanical model to explain the shaping of the fruit fly hindgut by forces from neighbouring tissues
www.mpi-cbg.de
September 22, 2025 at 5:42 PM
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
apply.interfolio.com/173716
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
September 18, 2025 at 4:51 PM
Apply to join our Penn Bioengineering department, featuring friendly, supportive faculty and staff, rigorous science, and top students!
apply.interfolio.com/173716
apply.interfolio.com/173716
Great opportunity to work with a very creative PI
📢📢Hiring 2 Research Assistants & 2 Postdocs at Emory University in Atlanta to study cytoskeletal biophysics/biochemistry. Please RT.
RAs: great for recent bachelor's/master's in Physics/Bio/Chem/Biochem. Email CV and interests to shekhar@emory.edu.
More info: www.shekharlab.org
RAs: great for recent bachelor's/master's in Physics/Bio/Chem/Biochem. Email CV and interests to shekhar@emory.edu.
More info: www.shekharlab.org
August 29, 2025 at 4:12 AM
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
rdcu.be/eBSUK
August 22, 2025 at 3:46 PM
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
rdcu.be/eBSUK
Reposted by Alex Hughes Lab
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...
August 15, 2025 at 10:50 AM
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...
Reposted by Alex Hughes Lab
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
doi.org/10.1093/genetics/iyaf156
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
doi.org
August 13, 2025 at 10:10 PM
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
doi.org/10.1093/genetics/iyaf156
Reposted by Alex Hughes Lab
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...
July 22, 2025 at 8:52 PM
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
Very excited to share our new work on gastruloids by the incredible Cat Triandafillou! We mapped gene expression across 26 individual gastruloids at single-cell resolution and discovered some pretty amazing patterns about how these "mini-embryos" organize themselves.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Single-cell spatial mapping reveals reproducible cell type organization and spatially-dependent gene expression in gastruloids
Gastruloids are three-dimensional stem-cell-based models that recapitulate key aspects of mammalian gastrulation, including formation of an anterior-posterior (AP) axis. However, we do not have detail...
www.biorxiv.org
July 16, 2025 at 3:05 AM
Super cool project #2
Super cool project @vayyappan.bsky.social
Check out this awesome work from @vayyappan.bsky.social… Embryo Economics! :)
[0/8] Stoked to share our work with @arjunraj.bsky.social on tissue organization in the gastruloid. We use lineage tracing and spatial transcriptomics to show that diversity among stem cell clones promotes, rather than hinders, gastruloid development: www.biorxiv.org/content/10.1...
July 16, 2025 at 2:56 AM
Super cool project @vayyappan.bsky.social
Reposted by Alex Hughes Lab
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
tinyurl.com/mr3he6bx
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.
tinyurl.com
July 11, 2025 at 5:22 PM
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
tinyurl.com/mr3he6bx
Reposted by Alex Hughes Lab
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
The tissue morphogenesis logic, now engineered into living, programmable materials.
www.biorxiv.org/content/10.1...
#ActiveMatter #TissueEngineering
June 30, 2025 at 7:53 AM
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
The tissue morphogenesis logic, now engineered into living, programmable materials.
www.biorxiv.org/content/10.1...
#ActiveMatter #TissueEngineering
Reposted by Alex Hughes Lab
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...
June 9, 2025 at 3:03 PM
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
June 3, 2025 at 4:16 AM
Our own @azyhuang.bsky.social is a student this year representing the kidney fanatics
fantastic series of work by @bugajlab.bsky.social and @dennishuang.bsky.social
Proteins often bind targets using avidity, the combined interaction strength of multiple weak binders. Now we’ve harnessed this principle for compact, *single*-component optogenetic tools for translocation. Lead by phenom PhD student @dennishuang.bsky.social #synbiosky🧵
📝 tinyurl.com/aviatar
📝 tinyurl.com/aviatar
May 7, 2025 at 3:05 AM
fantastic series of work by @bugajlab.bsky.social and @dennishuang.bsky.social
Reposted by Alex Hughes Lab
I'm a big fan of this paper on the shape of rose petals.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
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...
www.science.org
May 5, 2025 at 11:00 AM
I'm a big fan of this paper on the shape of rose petals.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Whoa, fantastic stuff! This may be just the beginning of the somites <--> kidneys connection
Check out the latest from Alan Davidson’s lab (of zf kidney regeneration fame) showing somites contribute to making nephrons in zebrafish. GESTALT, Cre lineage tracing, and zf somite transplants 😱. Love a good story that challenges dogma. Great discussions were had!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Somites are a source of nephron progenitors in zebrafish
For over a century it has been believed that the vertebrate kidney arises exclusively from the intermediate mesoderm. Here, we overturn this paradigm by demonstrating that some nephrons, the functiona...
www.biorxiv.org
April 30, 2025 at 3:10 AM
Whoa, fantastic stuff! This may be just the beginning of the somites <--> kidneys connection
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!
📢Excited to share our new paper in Nature Physics
@naturephysics.bsky.social: Cooperative hydrodynamics accompany multicellular-like colonial organization in the unicellular Stentor!
How do single-celled organisms benefit from teamwork? Let’s dive in! #Multicellularity nature.com/articles/s41...?
@naturephysics.bsky.social: Cooperative hydrodynamics accompany multicellular-like colonial organization in the unicellular Stentor!
How do single-celled organisms benefit from teamwork? Let’s dive in! #Multicellularity nature.com/articles/s41...?
April 18, 2025 at 8:01 PM
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!
Reposted by Alex Hughes Lab
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
@zevgartner.bsky.social , @adrianjacobo.bsky.social and Matthew Kutys.
📆Apply by 23 May
biologists.com/workshops/no...
#BiologistsWorkshops
April 11, 2025 at 10:43 AM
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
@zevgartner.bsky.social , @adrianjacobo.bsky.social and Matthew Kutys.
📆Apply by 23 May
biologists.com/workshops/no...
#BiologistsWorkshops
Reposted by Alex Hughes Lab
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 🧵
A @bugajlab.bsky.social collab with @nmrkaygee.bsky.social 🧵
April 15, 2025 at 2:46 PM
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 🧵
A @bugajlab.bsky.social collab with @nmrkaygee.bsky.social 🧵
Reposted by Alex Hughes Lab
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!
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!
April 15, 2025 at 4:55 PM
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!
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!
Reposted by Alex Hughes Lab
1. Struggling to integrate single-cell datasets? Finding it hard to resolve clear differentiation trajectories? Reveal the underlying structure in your data with CONCORD.
March 20, 2025 at 6:08 PM
1. Struggling to integrate single-cell datasets? Finding it hard to resolve clear differentiation trajectories? Reveal the underlying structure in your data with CONCORD.
Reposted by Alex Hughes Lab
Super excited to be launching NimbusImage.com! Cloud-based image analysis to democratize machine learning!
Documentation here!
docs.nimbusimage.com
Documentation here!
docs.nimbusimage.com
NimbusImage
NimbusImage.com
March 17, 2025 at 2:46 PM
Super excited to be launching NimbusImage.com! Cloud-based image analysis to democratize machine learning!
Documentation here!
docs.nimbusimage.com
Documentation here!
docs.nimbusimage.com