@nrepina
Studying multiscale emergence (cell -> tissue) at FMI Basel complex systems | 3D shape | morphogenesis | self-organization | philosophy of biology | systems evo-devo | image analysis | illustration ✨ always questioning, forever inspired ✨
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...
📢We are excited to announce the Cambridge Morphogenesis Symposium - a full day event at SLCU @slcuplants.bsky.social (and virtually) on 5 June 2026!
🎉Come celebrate the 5th anniversary of the seminar series!
🚩Register & submit abstracts by 3 April! Check out the details: t.ly/YYM3u
Please repost!🙏
Peer Bork died yesterday 💔 which shocked me. In 2003 I did a short-term fellowship in Peer’s lab because I idolized him. I met Martin there & we wrote this paper together. Peer was great at bringing people together; a master collaborator with a rare ability to think up big ideas.
In need of a positive outlook on the future (of developmental biology)? Read our perspectives by my fellow @dev-journal.bsky.social PI fellows and myself. I'm hoping my future will contain much more TE biology and mammalian genome regulation!
journals.biologists.com/dev/article/...
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 🧵 👇
The reality in science is that creativity is not treated as a core skill while hypothesis testing is, and that is the imbalance that we want correct through the Night Science Institute!
www.technologynetworks.com/genomics/art... www.night-science.org
Great commentary, we all need to understand this
Phenotype rescue upon Zic4 and Gata3 double knockdown. (A,B) Maximum projection confocal images of oral (A) and aboral (B) ends of animals after GFP RNAi (control), Zic4 or Gata3 RNAi, and Zic4+Gata3 RNAi. DNA in cyan, peroxidase activity in magenta and Nematocilin in orange. Panels on the right show magnifications of boxed areas on the left. Scale bars: 100μm. Note the ectopic peroxidase staining in tentacle tips upon Zic4 RNAi, and ectopic Nematocilin staining adjacent to the foot upon Gata3 RNAi, as well as rescue of both phenotypes in the double knockdown. (C) Percentage of animals with ectopic peroxidase staining in tentacles upon Zic4 KD and double KD. (D) Percentage of animals with ectopic Nematocilin staining adjacent to the foot in Gata3 KD and double KD. For examples of strong and partial phenotypes refer to Fig. S6. Data in G and H shown for n animals pooled from at least two independent replicates. ***P<0.001 (Fisher's exact test). (E,F) Schematic of proposed model for controlling the choice between basal disk and battery cell fate in Hydra. At the oral pole, Wnt signaling (black dot) activates Zic4 (orange) expression and thus basal disk identity. Without it, Gata3 dominates at the opposite end, leading to basal disk fate establishment (E). Experimentally depleting one of the factors results in ectopic cell fate acquisition at the opposite body end (F).
Hydra body axis balance: a fight between two transcription factors
This Research Highlight showcases the work from Jaroslav Ferenc, Marylène Bonvin, Panagiotis Papasaikas, Jacqueline Ferralli, Clara Nuninger and Charisios D. Tsiairis:
journals.biologists.com/dev/article/...
Out in @science.org! We found that the intestine doesn’t just push out cells when crowded. Instead, cells are in a mechanical tug-of-war, and weaker ones are extruded. A new view of how our gut keeps its balance and stays healthy.
www.science.org/doi/10.1126/...
What a week! A huge thank you to all the students and teachers for the for the engaged discussions, thoughtful questions, and good vibes. Rock on, and stay curious! 🤓 ✨
#VeniceEvoDevo #levels #morphogenesis #sysbio #evodevo
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)
BIG NEWS!! We will be hiring a new professor with 25 years of endowed funding at the @biozentrum.unibas.ch @unibas.ch, focused on using biophysics and structural biology to explore climate-related fundamental science topics. Come start an innovative research cluster with us! 🧪🔬🧶🧬🌾🌍
Visual of segmented human induced pluripotent stem cells with the key workshop dates: Symposium on November 10-11, Hackathon on November 12-14th in Zurich Switzerland
We're happy to announce the 2025 International OME-NGFF workshop 🎉
📅 Dates:
- Symposium: Nov 10–11, 2025
- Hackathon: Nov 12–14, 2025
📍 Location: Zurich, Switzerland
Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...
#bioimaging #openscience #OMENGFF #OMEZarr
(1/x 🧵)
A closed feedback between tissue phase transitions and morphogen gradients drives patterning dynamics https://www.biorxiv.org/content/10.1101/2025.06.06.658228v1
Our latest "Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data"
A rigorous mathematical foundation for Waddington's landscape to study cell fate decision making
Applied to ventral neural tube development
www.biorxiv.org/content/10.1...
🚨📣 New preprint alert!
Excited to share my new postdoc work on direct force and mechanical properties measurements in live embryos!
A great team effort with A. Chamolly (theory), under the supervision of F. Corson and @jeromegros.bsky.social
📄 www.biorxiv.org/content/10.1...
#devbio #mechanics
This is so reasonably wonderful!!!!! 🤩
Mo Pandiarajan, founder of Eden school, shows students a view of a specimen in a Foldscope, which he's attached to his mobile phone. Photo credit: Viraj Nayer for NPR
A.Santhos inserts a slide into the foldscope. He is a former student who lives in the neigbourhood and keeps in touch with the students of his alma mater, often taking them for nature walks to examine the world around them through the foldscope. Viraj Nayer for NPR
Students at Eden School select specimens to examine with their Foldscopes. Viraj Nayer for NPR
Ramana Rajeesh Kumar, 11, Meenakshi, 8, and Magathi Yazhini, 9, with their Foldscopes. Ramana has been fascinated with bugs for a while. "They look even cooler under the Foldscope," he says. "Especially their eyes and hairy feet!" Viraj Nayer for NPR
My favorite NPR story blog - “Goats and Soda” sent a writer and photographer to a rural school in India; an early adopter of Foldscope. A wonderful photo story of kids “reading nature”. In this current challenging climate - the kids show us the way with joy and wonder.
www.npr.org/sections/goa...
Last chance to come join us, don’t forget to apply (by tomorrow March 31st)!!!
Deadline is TOMORROW night (Mar 31).
Not tonight, like wrongly announced at first.
And that's good news: because you get another 24hrs to apply, if you have not yet done so!
What are you waiting for!? 😉
Registration link below:
Our teachers this year:
Mihaela Pavličev
Mihaela co-chairs the Department of Evolutionary Biology at Uni Vienna. She studies mammalian reproduction to understand how organismal organization affects variation.
She will present a model of tissue evolution based on metabolic interdependence.
Our teachers this year:
Thibaut Brunet (@thibautbrunet.bsky.social)
Thibaut studies the evolutionary origin of animal morphogenesis at Institut Pasteur in Paris.
He will be teaching us about this and also how multicellularity first arose in evolution.
Our teachers this year:
Wallace Marshall (@wallaceucsf.bsky.social)
Wallace studies how cells solve engineering problems, how geometry arises within cells, and how it shapes and constrains cellular behavior.
He'll be telling us how cell shape constrains underlying pathways.
Our teachers this year:
Dan Brooks (@dsbrooks.bsky.social)
Dan's research interests span the history & philosophy of the life sciences, concept usage in science & theory in biology.
At our school, he'll have a thing or two to say about levels of organization, what they are & where they come from.
Nature research paper: Topological segregation of stress sensors along the gut crypt–villus axis
https://go.nature.com/4b4jcpC
Our teachers this year:
Nicole Repina (@nrepina.bsky.social)
Nicole is using quantitative imaging to study how complex tissue shape can emerge from cell interactions.
In Venice, she will be speaking about how we can use imaging for multiscale analysis of multicellular systems.
Our teachers this year:
James DiFrisco
James is a philosopher of science and theoretical biologist working @crick.ac.uk on the evolution of gene regulatory networks, modularity and pleiotropy, vertebrate gastrulation, and the developmental basis of morphological homology/tissue organization.
📢‼️ Exciting new preprint from the lab by @nikhil-mishra.bsky.social et al, now out on @biorxivpreprint.bsky.social, reveals that the early embryo geometry spatiotemporally patterns zygotic genome activation (ZGA) in zebrafish. 🐟 tinyurl.com/Biorxiv-nmis...
Read on to learn more... 👇
*** Registration deadline approaching!
Apply to our Summer School in Evolutionary Systems Biology in Venice before
MARCH 31, 2025
Reflect on your science in a beautiful and inspiring environment!
Food & accommodation for the whole week are included in the course fee.
Registration link below.
