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Shayan Shamipour

@shamipourshayan.bsky.social
215 followers 271 following 31 posts

SNSF Ambizione junior group leader @UZH. Fascinated by how embryos self-organize their shapes and patterns. Postdoc @ Pelkmans lab | PhD @ Heisenberg lab.

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Reposted by Shayan Shamipour
Dagmar Iber & CoBi @iberd.bsky.social · 1h
Two PhD positions open in my group @ethz.ch (Basel): Digital twins of embryonic development. 🧬 Mathematical modelling of biology jobs.ethz.ch/job/view/JOP... 💻 Computing: parameter estimation (incl. PINNs), simulation environments jobs.ethz.ch/job/view/JOP... #PhD #CompBio #Embryology
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Manlio De Domenico @manlius.bsky.social · 28/09/2026
🚨 Tipping elements are large-scale components of the 🌏 system that may undergo abrupt and potentially irreversible transitions once critical thresholds are crossed 🧪🌐 We show here how their connectivity patterns are weakened under high anthropogenic forcing 👇👇👇 journals.aps.org/prresearch/a...
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Levayer Lab @levayerr.bsky.social · 23/09/2026
Not every cell react the same way to caspase activation. In our recent study (led by @tomcumming.bsky.social and initiated by @avillars.bsky.social ), we tried to better understand what explains this difference and outlined a role of past caspase exposure 👇 www.nature.com/articles/s41...
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Reposted by Shayan Shamipour
Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 23/09/2026
What if any dataset, any size, any number of dimensions, opened in a browser tab from a link? 🔬🧪💻 Luxar is out today: write it in Python, share it as a link, explore it in any browser. Open source. 🧵 @biohub.org Preprint: doi.org/10.5281/zen... Code: github.com/royerlab/luxar
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James Briscoe @jamesbriscoe.bsky.social · 22/09/2026
Our latest paper on building models of cell fate decisions -with David Rand, Marine Fontaine & @joadelas.bsky.social- combines developmental biology, dynamical systems theory and bioinformatics. I wrote a short piece to summarise it & explain ideas behind the approach briscoelab.org/blog-quantif...
briscoelab.org
Quantifying Waddington's Landscape | Briscoe Lab
I have written before about how two conceptual frameworks have shaped our thinking about cell fate, Waddington's epigenetic landscape and Davidson's gene...
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Reposted by Shayan Shamipour
Alessandro De Simone @desimonelab.bsky.social · 17/09/2026
How is proliferation modulated in regeneration for tissues to reach their right size? We found that, in zebrafish scales, proliferation is shut down by a moving front of osteoblast maturation. The front's dynamics scale with tissue size, ensuring proper osteoblast amplification. tinyurl.com/5e45twx3
tinyurl.com
A moving front of osteoblast maturation scales regenerating zebrafish bone
Successful regeneration recovers lost tissues to their original form. Here, we investigate how proliferation of bone-forming osteoblasts is timely regulated to control tissue size during zebrafish sca...
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Stefano Di Talia @ditalialab.bsky.social · 25/08/2026
We would like to add one or two postdocs to our lab in the next couple of years. If you are close to finishing your PhD and interested in the science we do, feel free to reach out to discuss opportunities.
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Ben Steventon @bensteventon.bsky.social · 22/09/2026
Super happy to see Carlos’s work highlighted in Development. He figured out how the notochord uses Yap signaling to balance the rate of progenitor entry vs anterior expansion
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Benoit Ladoux @bladoux.bsky.social · 22/08/2026
Happy to share our new paper @natcomms.nature.com on the role of active nematics on myoblast fusion and myotube growth! www.nature.com/articles/s41... Amazinf work from @dubey837.bsky.social, @yoannletoquin.bsky.social and Aleksandra Ardaševa!
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Shayan Shamipour @shamipourshayan.bsky.social · 20/09/2026
Excited to share that our **3D-4i multiplexed imaging method** is now out in @natcomms.nature.com 🎉 🔗 www.nature.com/articles/s41... Huge thanks to the reviewers and editor for their constructive feedback and smooth handling of the work!
nature.com
Multiplexed embryo profiling links cellular state to zygotic genome activation in single cells - Nature Communications
The protein landscapes that underlie multicellular self-organization remain challenging to characterize across intact embryos at high spatial resolution. Here, the authors present 3D-4i, a high-throug...
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Development @dev-journal.bsky.social · 16/09/2026
Pathway to Independence – an interview with Nikhil Mishra In this interview, @nikhil-mishra.bsky.social discusses the evolution of his research interests from subcellular beginnings to whole-organism questions, and the importance of scientific security. doi.org/10.1242/dev....
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Dagmar Iber & CoBi @iberd.bsky.social · 13/08/2026
🎉 Our paper is out in Cell Systems @cp-cellsystems.bsky.social ! How does an embryo build an energy-efficient fractal lung before the first breath? 📄 doi.org/10.1016/j.ce... 🧵 bsky.app/profile/iberd.bsky.social/post/3lfrdth6k4c22 @maltemederacke.bsky.social @kevinyamauchi.bsky.social
doi.org
Redirecting
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Marine Biological Laboratory @mblscience.bsky.social · 13/08/2026
What makes the MBL Physiology course a “life-changing experience”? According to one course participant this summer, there’s more than one reason why. Watch the full video and hear what made the experience so meaningful: go.mbl.edu/77pnuj
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David Brückner @davidbrueckner.bsky.social · 20/07/2026
Our paper on nonlocal decoding is now out in @physrevlett.aps.org! See below for a thread about the preprint 🧵 👉 journals.aps.org/prl/abstract...
journals.aps.org
Nonlocal Decoding of Positional and Correlational Information during Development
In many developmental systems, cells differentiate into a tissue by reading out morphogen concentration fields, a process fundamentally limited by noise. How much can the precision of this process be ...
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Reposted by Shayan Shamipour
Mo Ebrahimkhani @moebr.bsky.social · 12/07/2026
The "dead organ" model of the #aging #ovary needs a rethink ? it may be an actively remodeling tissue with the potential in inter-organ signaling during aging? Postmenopausal ovaries aren't just quiescent fibrous tissue.
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Benoit Ladoux @bladoux.bsky.social · 08/07/2026
Thrilled to share our new paper on cell extrusion. A beautiful study with a tremendous amount of data, led by the fantastic @fanny-wodrascka.bsky.social ! www.biorxiv.org/content/10.6...
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Margherita Battistara @mbattistara.bsky.social · 08/07/2026
🪲🪰 Our preprint is out! This was a team effort with @wolframponisch.bsky.social, @matthewabenton.bsky.social and Ewa Paluch. We asked whether Drosophila and Tribolium use the same cell behaviours to fold their embryos during gastrulation. 🧵👇 www.biorxiv.org/content/10.6...
biorxiv.org
Morphospace analysis reveals divergent cellular behaviours driving tissue internalisation during insect gastrulation
During gastrulation, embryonic epithelia undergo large-scale remodelling to internalise the mesoderm. Whether the cellular mechanisms underlying these tissue deformations are conserved across species ...
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Shayan Shamipour @shamipourshayan.bsky.social · 03/07/2026
🚀Excited to share our latest efforts in bringing highly multiplexed whole-mount imaging to intact multicellular systems! Shield-4i: an integrated platform to study multi-scale information flow in 3D embryos and embryo-like systems. Kudos to @rhornb.bsky.social for this major milestone in the lab!🚀
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Cornelia Schwayer @cschwayer.bsky.social · 01/07/2026
Excited to share that our work on ‘How the gut gets patterned during regeneration’ is out now cell.com/cell/fulltext/S0092-8674(26)00696-3 Thanks a lot to @priscaliberali.bsky.social @silviabarbiero.bsky.social @davidbrueckner.bsky.social @ehannezo.bsky.social and all co-authors! 🧵
cell.com
Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning
During regeneration, tissues must translate transient cellular variability into stable spatial organization. Tissue architecture generates a density-dependent window of heterogeneity in the mechanosen...
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Phil Abitua @ohnolog.bsky.social · 30/06/2026
Annual killifish continue to surprise us: they make neutrophils before almost every other cell type, even before gastrulation. Neutrophils usually arise from the lateral plate mesoderm (forming in cyan), but in killifish they are already patrolling around the embryo in gold. tinyurl.com/killiphil
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Dagmar Iber & CoBi @iberd.bsky.social · 08/06/2026
🧰 New tool alert! ⚙️ #MorphoGrad, an open-source toolbox for simulating reaction–diffusion systems in 1D and 2D tissues, with cell-to-cell parameter heterogeneity & graphical user interface. No heavy coding required. Explore complex morphogen gradient models interactively. doi.org/10.1016/j.xp...
cell.com
MorphoGrad: A MATLAB toolbox for simulating steady-state morphogen gradients under cell-to-cell variability
Studying morphogen gradient-based tissue patterning in silico while accounting for biological variability remains challenging. Here, we present a MATLAB-based protocol for simulating steady-state morp...
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Victoria Deneke @vdeneke.bsky.social · 22/05/2026
How do sperm and egg fuse? Surprisingly, we still don’t fully know… Our field has uncovered many pieces of the fertilization puzzle, but not how they fit together. We identify ✨ SPARK ✨ - a conserved sperm complex that couples sperm-egg binding to fusion. tinyurl.com/34cm4xat Read on! 🧵👇
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Mehmet Can Uçar @mehmetcanucar.bsky.social · 08/05/2026
Summer is coming, but how will you maximize your picnic space when everyone else is doing the same? In our new preprint, we show that branched cells may have an elegant solution: As cells grow and repel neighbors, they don't just cover space, but reach a hidden order called hyperuniformity! 🧪⚛️
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James Briscoe @jamesbriscoe.bsky.social · 24/04/2026
Welcome 2026 @dev-journal.bsky.social Pathway to Independence (PI) fellows Maëlle Bellec, @iamzico.bsky.social, @evhealy.bsky.social, @josepmercadal.bsky.social, @nikhil-mishra.bsky.social, Jessica Perochon, Yamini Ravichandran & Margherita Zamboni More info journals.biologists.com/dev/pages/pi...
journals.biologists.com
Dev | PI fellows 2026 | Development | The Company of Biologists
Dev | PI fellows 2026 | Development | The Company of Biologists .pifellow { overflow: hidden; margin: 1rem; } .pifellow img { width: 150px; height: auto; ...
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Daniel MK Lee @dannimklee.bsky.social · 24/04/2026
New Preprint alert!🚨 Super excited to share my postdoc work now on BioRxiv. How does PRC2 loss lead to developmental failures? We combined rapid protein degradation with TLS embryoid models to uncover temporal and lineage-specific dependencies 🧬. Preprint: doi.org/10.64898/2026.04.18.719361
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clementhelsens.bsky.social @clementhelsens.bsky.social · 11/04/2026
We tracked a zebrafish tail tip for 30h of light-sheet imaging. It didn’t exist at t=0. LiLiTTool: CoTracker3 + object detection → real-time microscope steering. 3D, multi-ROI, open source. www.biorxiv.org/content/10.6... #bioimaging #lightsheet thanks @jytinevez.bsky.social
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Alex Schier @schierlab.bsky.social · 12/03/2026
Very happy to see this out. 👏 @yinanwan.bsky.social Bogdan Bintu and team. Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis | free link Science www.science.org/eprint/5MHTM...
science.org
Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis
Gene expression patterns underlie development, but their systematic detection in whole embryos has remained elusive. We introduce a whole-embryo imaging platform using multiplexed error-robust fluores...
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Joel Lüthi @joelluethi.bsky.social · 10/03/2026
We’re excited to share our latest preprint on Fractal: our approach towards FAIR bioimage analysis at scale with OME-Zarr-native workflows. Fractal defines interoperable tasks on OME-Zarr and provides a platform for TB-scale image analysis. (1 / 10🧵) www.biorxiv.org/content/10.6...
biorxiv.org
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Diana Pinheiro @dianapinheiro.bsky.social · 24/02/2026
Join us in Vienna for the European 🐠 🐟 meeting👇👇we are excited to welcome researchers working with all fish models in Europe and beyond!We provide travel fellowship opportunities to make the meeting as inclusive as possible 😊
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Ben Steventon @bensteventon.bsky.social · 19/02/2026
Happy to share this work from Carlos Camacho de la Maccora that reveals how rates of posterior progenitor addition and anterior vacuolation are balanced across the notochord. With Alberto Ceccarelli and @osvaldo-chara.bsky.social we present a model of long-range communication to provide robustness.
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Omaya Dudin 𓂆 ¦🍉¦🦠¦🔬¦ @dudinlab.bsky.social · 17/02/2026
A 🆕 #Ichthyosporea story Led by@margaridaaraujo.bsky.social, in Co. @gautamdey.bsky.social & @hiralshah.bsky.social+🔥team across @embl.org & @sciencesunige.bsky.social We finally have a look at what #microtubules are doing during #cellularization in #Sphaeroforma ▶️ tinyurl.com/MTSARC #ProtistsOnSky
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Shayan Shamipour @shamipourshayan.bsky.social · 15/02/2026
it's always fun to look back at phd data in @heisenbergcplab.bsky.social - here a wave of acentrosomal microtubule asters forming in maturing zebrafish oocytes, bringing the cytoplasm into motion...
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Benoit Ladoux @bladoux.bsky.social · 26/01/2026
Happy to highlight our collaborative work from our @ijmonod.bsky.social team with @destriano.bsky.social, B. Goyeau and M. Chabanon. Cytoplasmic crowding acts as a porous medium that hinders macromolecular diffusivity. Plus: a clever way to measure cell volume. www.pnas.org/doi/10.1073/...
pnas.org
Cytoplasmic crowding acts as a porous medium reducing macromolecule diffusion | PNAS
Intracellular transport of macromolecules is crucial for the proper functioning of most cellular processes. Although intracellular crowding is know...
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Institute of Science and Technology Austria (ISTA) @istaresearch.bsky.social · 05/01/2026
In @natphys.nature.com, they demonstrated that the zebrafish embryo “reads” and correctly interprets the zygote’s geometry during the initial few minutes of its existence. They discovered ... 📷 C.-P.Heisenberg, N. Mishra, Y. I. Li (from left to right).
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Yamuna Krishnan @krishnanyamuna.bsky.social · 17/12/2025
Organelles do NOT have a single uniform pH. And if you think they must, because “protons diffuse fast,” this paper is for you. A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
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Alessandro De Simone @desimonelab.bsky.social · 20/11/2025
The lab’s first pre-print! We investigated how growth-inducing Erk activity waves are regulated in regenerating zebrafish scales. We discovered that Erk waves are followed by waves of expression of their own inhibitors, as predicted by excitable waves theory. tinyurl.com/26r2cmpj
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Alexandre Mayran @alexandremayran.bsky.social · 17/11/2025
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
cell.com
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...
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Mostafa Aakhte @aakhte.bsky.social · 14/11/2025
🎉 I am very glad to share that our paper on the rapid isotropic light-sheet microscope has just been published in Nature Biotechnology @natbiotech.nature.com. 🔗 Read the full article: www.nature.com/articles/s41...
nature.com
Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue - Nature Biotechnology
A light-sheet microscope built from off-the-shelf components enables high-resolution clear tissue imaging.
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Eric Topol @erictopol.bsky.social · 15/11/2025
Why do whales and elephants have much lower rates of cancer than expected? "Species with a lower cancer prevalence and mortality risk are those with a higher presence of cooperative and caring habits, while the opposite is found....:" www.science.org/doi/10.1126/...
science.org
Coevolution of cooperative lifestyles and reduced cancer prevalence in mammals
While cooperative mammals evolve reducing cancer prevalence, oncogenes can be maintained by selection in competitive species.
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Zebrafish Rock! @zebrafishrock.bsky.social · 16/11/2025
#ZebrafishZunday: Cytoplasmic (or ooplasmic) streaming leads to the segregation of embryo from yolk granules. Credit to @shamipourshayan.bsky.social & @heisenbergcplab.bsky.social. 🧪
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Stefano Di Talia @ditalialab.bsky.social · 13/11/2025
@sushantbangru.bsky.social and @rdiegmiller.bsky.social new review on regeneration is out in Nature Reviews Molecular Cell Biology. A fun piece to write and another great collaboration with @kenposs.bsky.social.
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Zebrafish Rock! @zebrafishrock.bsky.social · 13/11/2025
We spy the latest works from the labs of @marymullins.bsky.social, Margot Kossman Williams (x2), @bruceappel.bsky.social, Vladimir Korzh, @ssumanas.bsky.social, @campaslab.bsky.social, @kenposs.bsky.social, @emiliapsantos.bsky.social among others! Do check it out!
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David Brückner @davidbrueckner.bsky.social · 10/11/2025
How can we organize current theoretical approaches for developmental biology - from information to dynamical systems & GRNs - into a common framework? We propose to think along Marr's 3 levels: computational problem, algorithm, implementation Check out our review: arxiv.org/abs/2510.24536
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Yu-Chiun Wang @yuchiunwang.bsky.social · 03/11/2025
Interested in polarity and mechanics during epithelial morphogenesis? Considering joining us! Students to be hired initially as Research Associates. Postdocs encouraged to obtain fellowship, and we help/train you to do that. Apply to tinyurl.com/y6x489t5. Deadline Dec 15. Please repost!
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Rory Cooper @rorylcooper.bsky.social · 30/10/2025
I’ll be speaking about the mechanical development of crocodile and tortoise head scales next Wednesday at 4pm for the @tlmcambridge.bsky.social seminar series. Subscribe to the mailing list to hear more about my work, and that of @maltemederacke.bsky.social! lists.cam.ac.uk/sympa/subscr...
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Shayan Shamipour @shamipourshayan.bsky.social · 29/10/2025
Very happy to share our latest work extending iterative immunofluorescence to in toto imaging of early zebrafish embryos (3D-4i), integrated with a 3D-dedicated image analysis pipeline! 🐟🔬📊 Huge kudos to Max Hess for this PhD milestone! 💪 @lucaspelkmans.bsky.social shorturl.at/cO0u7 Let's zoom in!
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Ceri Weber @ceriweber.bsky.social · 10/10/2025
Vertebral skeletal diversity in mammals is remarkable. How do the differences between vertebral size and shape develop and evolve? See how we tackled this question in our paper published in @natcomms.nature.com today!
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Carl Zimmer @carlzimmer.com · 09/10/2025
Today my @nytimes.com colleagues and I are launching a new series called Lost Science. We interview US scientists who can no longer discover something new about our world, thanks to this year‘s cuts. Here is my first interview with a scientist who studied bees and fires. Gift link: nyti.ms/3IWXbiE
nyti.ms
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Miki Ebisuya @ebisuyamiki.bsky.social · 08/10/2025
New preprint from the lab! We discovered a transient fluidization in the basal region of human forebrains by tracking microdroplets in cerebral organoids.This “basal fluidization”, absent in gorilla and mouse, may contribute to greater surface expansion in human forebrains 1/ doi.org/10.1101/2025...
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Jain_Akanksha_ @akanksha-jain.bsky.social · 07/10/2025
🧠 Join us @uzh-ch.bsky.social ! We are a new lab looking for PhDs, Postdocs & Master’s students interested in studying how human neural systems emerge & go awry using brain organoids, light-sheet imaging & genomics. 🚀 Deadline for LSZGS 1st Nov! www.lifescience-graduateschool.uzh.ch/en.html.
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