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Noah Bruderer

@noahbruderer.bsky.social
211 followers 639 following 3 posts

PhD candidate @MSarsCentre / Computational biology / Development biology / Image analysis / Data diver

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Reposted by Noah Bruderer
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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Inés Fournon Berodia @inesfournon.bsky.social · 04/08/2026
Very pleased to finally share the main story from my PhD, now published in @natcomms.nature.com ! 🎉 Using a sea anemone we discovered and characterised epithelial cell extrusion as the mechanism underlying starvation-induced cell loss. 🔗 Open-access article: www.nature.com/articles/s41...
nature.com
Epithelial cell extrusion underlies starvation-induced cell loss in a sea anemone - Nature Communications
Epithelial cell extrusion in a sea anemone shares key hallmarks with bilaterians and is dynamically regulated by nutritional status. During starvation-induced body shrinkage, extrusion likely contribu...
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Zebrafish Rock! @zebrafishrock.bsky.social · 26/07/2026
The first 22 hours of #zebrafish development in under one minute. Credit to @zebrafish007.bsky.social in #WeinsteinLab at NIH. #ZebrafishZunday 🧪
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Josh Currie @joshcurrie.bsky.social · 13/07/2026
I love these funky basal epithelial cells in axolotl. Looks just like plant pavement cells
basal squamous epithelial cells in the axolotl expressing a membrane-localized fluorescent protein
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Pawel Burkhardt @pawelburkhardt.bsky.social · 10/07/2026
Our News & Views article “Body-plan organizer in comb jellies hints at animal ancestry” now published in @nature.com 🎉 We discuss fascinating work revealing organizer activity in comb jellies & the evolution of animal development. rdcu.be/fsLWq @ruthstyfhals.bsky.social @msarscentre.bsky.social
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Denis Duboule @denisduboule.bsky.social · 29/06/2026
A sonday in Paris. What a city! From the terrace of @college-de-france.fr Enlightenments in every sense of the word 💡
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Levayer Lab @levayerr.bsky.social · 26/06/2026
Un pétition du collège des sociétés savantes pour mettre en avant le rôle de la recherche dans la campagne politique à venir et rappeler le sous investissement chronique en France depuis 20 ans. N'hésitez pas à faire ciculer recherche-publique-2027.fr
recherche-publique-2027.fr
Recherche Publique 2027 – Appel des scientifiques pour la place de la recherche dans la société
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Manuel Thery @manuelthery.bsky.social · 19/06/2026
Is there a size limit for cells ? How can cells replicate inside the architecture of their environment? Why do cells self-destroy ? This 15-minute movie vimeo.com/1173229237 shows our 2026 edition of the Living Architectures project at the @museeorsay.bsky.social
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eurobioimaging.bsky.social @eurobioimaging.bsky.social · 11/06/2026
Curious about #OMEZarr?Join the Open Bioimaging Practices meet-up (online). #EuroBioImaging's Bugra Ozdemir will present EuBI-Bridge & Lorenzo Cerrone from the BioVisionCenter will present the ome-zarr-converters-tools package. 🗓️ June 30, 4 pm CEST More ⤵️ www.biovisioncenter.uzh.ch/en/events/Up...
biovisioncenter.uzh.ch
Open Bioimaging Practices Meetup June 30th 2026
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Laurie Belcher @lauriebelch.bsky.social · 09/06/2026
The new OrthoFinder paper is out now! In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets www.nature.com/articles/s41... github.com/OrthoFinder/...
nature.com
OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability - Nature Methods
The updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 03/06/2026
Want to build some of the most advanced light-sheet microscopes in the world to watch life assemble itself cell by cell? The Royer Lab @ Biohub is hiring an Optical Engineer (Advanced Light Sheet Microscopy). 🧪🔬💻🔧 #Hardware + #Python + Advanced #Optics job-boards.greenhouse.io/biohub/jobs/...
job-boards.greenhouse.io
Optical Engineer, Advanced Light Sheet Microscopy
San Francisco, CA (Hybrid)
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Lionel Christiaen, PhD (he/him/his) @lionlchristiaen.bsky.social · 19/05/2026
And so it began. The CNRS Jacques Monod Conference 2026 #CJM26 in beautiful Roscoff kick started masterclassfully by Marianne Bronner on the development and evolution of the vertebrate neural crest.
View of Marianne Bronner at the podium and her title slide
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Simon Bullock @simonbullock11.bsky.social · 05/05/2026
Thrilled to see this work published. Thanks to helpful reviewer suggestions, there are some exciting new insights that were not in the preprint (particularly in Figure 4). www.nature.com/articles/s41...
nature.com
Structural basis for recognition of diverse localizing mRNAs by Egl–BicD - Nature Structural & Molecular Biology
Singh et al. combine cryo-electron microscopy and functional studies to reveal how a single protein complex selects diverse mRNAs for subcellular localization using a combination of shape, positional ...
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epithelial mechanics fan club @epimechfc.bsky.social · 22/03/2026
Hello epithelia enthusiasts! I’m @inesfournon.bsky.social and I study epithelial mechanics in sea anemones 🪼 Did you know epithelial cell extrusion had never been described outside bilaterian animals before? Well… not anymore 👀 Read ⬇️🧵1/9
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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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Michael Sars Centre @msarscentre.bsky.social · 02/02/2026
We are thrilled to announce that registration is now open for the Michael Sars Symposium 2026, co-organized with @cbubergen.bsky.social 🙌 Join us on June 4 in Bergen for a day of fantastic talks, with a focus on living systems in a variable ocean 🌊 🔗 tinyurl.com/joinMSS2026
A poster in tones of blue with white text and pops of pink that reads:
Michael Sars Symposium 2026
Living systems in a variable ocean
In collaboration with the Computational Biology Unit, UiB
June 4, 2026, Media City Bergen

SPEAKERS
Anne-Claude Gavin, Université de Genève
Christian Jørgensen, Dept. of Biological Sciences, UiB
Matthew Rockman, New York University
Isabella Graf, EMBL Heidelberg
Tom Michoel, Computational Biology Unit, UiB
Anthony Mathelier, NCMBM, University of Oslo
Susanna Röblitz, Computational Biology Unit, UiB
Boris Lenhard, Imperial College London
Jonas Brandenburg, Michael Sars Centre, UiB

ORGANIZERS
Lionel Christian, Michael Sars Centre, UiB
Nathalie Reuter, Computational Biology Unit, UiB

Below the text are the logos for the Michael Sars Centre, CBU, University of Bergen, EMBL with the mention 'Partners of', and the hashtag MSS2026
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Patrick Steinmetz @prhsteinmetz.bsky.social · 29/01/2026
Norway’s oil fund yielded NOK 2362 billions in 2025, enough to DOUBLE the current budget of Norwegian Research Council for the next 214 years. 🤷‍♂️ www.nbim.no/no/nyheter-o...
nbim.no
Sterk avkastning i 2025 | Norges Bank Investment Management
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 23/01/2026
📡🧵 Excited to release an updated version of our preprint: Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis 🧪🧬🖥️🐠 doi.org/10.1101/2024... A tour-de-force by @yangjoonkim with an unexpected discovery!
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Thomas Lecuit @thomaslecuit.bsky.social · 03/01/2026
Here is the link to download the PDF of my course#5 on Biological computation. I present & discuss Self-tuning, Adaptation and Learning in biological (non-neuronal) systems, in particular during embryonic development. This course contains various personal ideas/proposals. tinyurl.com/hcpwsbtm
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Nature Methods @natmethods.nature.com · 18/12/2025
In this month's Creature Column, we feature the ascidian tunicate Ciona, a model for marine systems life sciences. www.nature.com/articles/s41...
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Inés Fournon Berodia @inesfournon.bsky.social · 16/12/2025
Thrilled to share the preprint from my PhD! 🥳 Where I characterised epithelial cell extrusion in a sea anemone 🔗 www.biorxiv.org/content/10.6... Big thanks to my supervisor @prhsteinmetz.bsky.social and coauthors @noahbruderer.bsky.social @lionlchristiaen.bsky.social at🇳🇴 @msarscentre.bsky.social ⬇️🧵
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Paul Francois @pfrancois.bsky.social · 10/12/2025
Very happy to share our 'Evoscape' paper, now published in PNAS ! www.pnas.org/doi/10.1073/...
pnas.org
Generative epigenetic landscapes map the topology and topography of cell fates | PNAS
Epigenetic landscapes were proposed by Waddington as the central concept to describe cell fate dynamics in a locally low-dimensional space. In mode...
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Lionel Christiaen, PhD (he/him/his) @lionlchristiaen.bsky.social · 08/12/2025
Very happy to see this piece on the Tunicate Ciona published. Grateful to @alexandrejan.bsky.social and @chiaracastelletti.bsky.social for the Illustrations, and to @natmethods.nature.com for the opportunity to showcase our ever emerging model organism www.nature.com/articles/s41...
nature.com
The tunicate Ciona - Nature Methods
The ascidian tunicate Ciona, one of the closest relatives of the vertebrates, inhabits shallow temperate waters in the worldwide ocean. A unique combination of simple stereotyped embryogenesis, regula...
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Lionel Christiaen, PhD (he/him/his) @lionlchristiaen.bsky.social · 15/11/2025
Re-upping this with a Bluetorial in a shameless act of self-promotion. 1/n
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Nikolai Slavov @slavov-n.bsky.social · 10/11/2025
Crowding more proteins per cytoplasm unit volume would hamper processes such as diffusion, which is already about ten fold slower inside the cell than in pure water. Source: book.bionumbers.org/what-is-the-...
book.bionumbers.org
» What is the macromolecular composition of the cell?Cell Biology by the Numbers
Vignettes that reveal how numbers serve as a sixth sense to understanding our cells
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Marija Matejčić (mateytch-itch) @marija-matejcic.bsky.social · 07/11/2025
Intestinal villus cells extrude living, following a calcium pulse. Unlike from extruding apoptotic cells, Ca2+ messaging stops at the first neighbors! #FluorescenceFriday Part of our TrepatLab preprint: www.biorxiv.org/content/10.1... Video by @ronjahoutekamer.bsky.social @gloerichlab.bsky.social
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Yelena Bern, Ph.D @yelenab.bsky.social · 04/11/2025
Our latest on how cells get ready for fate transition! @noahbruderer.bsky.social @margauxfailla.bsky.social @lionlchristiaen.bsky.social Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors www.embopress.org/doi/full/10....
embopress.org
Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors | The EMBO Journal
imageimageDuring development, multipotent cardiopharyngeal progenitors express both cardiac and pharyngeal muscle transcriptional programs. This study in the tunicate Ciona shows that cell cycle-regul...
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Alex Kalinin @alxndrkalinin.bsky.social · 23/10/2025
💡Just presented our new paper at the @iccv.bsky.social BioImage Computing workshop: cubic: CUDA-accelerated 3D Bioimage Computing. We introduce a simple way to add GPU acceleration to scikit-image–based bioimage processing pipelines by swapping import statements. 🧵 1/6 #iccv2025
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Levayer Lab @levayerr.bsky.social · 09/10/2025
Happy to share the last version of our story @currentbiology.bsky.social on the role of interfacial tension in mechanical cell competition led by @leovalon.bsky.social and Alexis Matamoro Vidal www.sciencedirect.com/science/arti...
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Thibaut Brunet @thibautbrunet.bsky.social · 05/10/2025
Latest from ours: www.cell.com/cell-reports... This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 25/08/2025
🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods! 📦 Ultrack — robust, scalable nD cell tracking 🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration Let’s dive in! 👇 www.nature.com/articles/s41... www.nature.com/articles/s41...
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John Wallingford @jbwallingford.bsky.social · 02/07/2025
Morphogenesis alert! A unifying physical principle links gastrulation in frogs, fish and flies! Stoked to be part of this new paper with Xin Li in Dave Thirumalai's lab and Robert Huebner in my group and a co-lab with @peiferlabunc.bsky.social and Margot Williams. 1/n www.nature.com/articles/s41...
nature.com
Emergence of cellular nematic order is a conserved feature of gastrulation in animal embryos - Nature Communications
The morphogenetic events that occur during gastrulation involve dramatic cell- and tissue-level changes. Here they show that propagation of nematic order, leading to long-range spatial correlation, is...
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Michael Sars Centre @msarscentre.bsky.social · 26/06/2025
We are thrilled to announce the launch of the Michael Sars Visitors Program! ✨🧪 To spark new connections, we are opening our doors to visiting researchers who wish to conduct a project in #SunnyBergen. Applications are open, help us spread the word!
tinyurl.com
Introducing the Michael Sars Visitors Program
The Michael Sars Centre is launching a Visitors Program designed to foster scientific exchange and collaborations across disciplines.
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Michael Sars Centre @msarscentre.bsky.social · 06/06/2025
What a fantastic morning at #MSS2025 🤩 After an opening by BIO Dept. head @unibergen.bsky.social Ståle Ellingsen, three amazing talks by @lowelab.bsky.social, Georgia Rapti @embl.org and Camila Esguerra @ncmbm.bsky.social on System Evolution 👏
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Marius Pachitariu @marius10p.bsky.social · 03/05/2025
🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸‍♀️. Try it now on 🤗 huggingface.co/spaces/mouse... paper: www.biorxiv.org/content/10.1... w/ @computingnature.bsky.social 1/n
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Michael Sars Centre @msarscentre.bsky.social · 25/04/2025
📣 New article out in @cp-cellreports.bsky.social 🤩 Zonglai Liang and colleagues from the @mchatzigeorgiou.bsky.social group reveal a dual role for Anoctamins in sensory perception & metamorphosis in #Ciona larvae 🧪 Take a peek behind the scenes ⤵️
tinyurl.com
Conserved proteins link sensory input and metamorphosis in a marine chordate
Anoctamins play a key role in sensory perception in mammals. A new article by the Chatzigeorgiou group reveals their dual role in perception and larval metamorphosis in the chordate Ciona.
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 15/04/2025
🧬🔬🧪 We are seeking a Scientist to push the limits of spatial transcriptomics in zebrafish! Come join us! #MolBio #SpatialTranscriptomics #DevelopmentalBiology #ScienceJobs 🧫🐟🔍 job-boards.greenhouse.io/chanzuckerbe...
job-boards.greenhouse.io
Scientist, Spatial Molecular Cartography (Jacobo/Royer Group - Biohub SF)
San Francisco, California, United States
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Michael Sars Centre @msarscentre.bsky.social · 28/03/2025
Loïc Royer @loicaroyer.bsky.social presented today the impressive work of his team @czbiohub.bsky.social in optical engineering and developing analysis tools to explore vertebrate development 🐟🧪 Thank you for an inspiring and visually stunning talk! 🤩
A man in a dark jumper stands similing in front of an audience in a seminar room. On a screen behind him, a slide that says 'optics' and 'biology', with a fluorescent microscopy image of a fish embryo, code, and a piece of equipment.
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Lionel Christiaen, PhD (he/him/his) @lionlchristiaen.bsky.social · 28/03/2025
We are in for a mindblowing treat today at @msarscentre.bsky.social with @loicaroyer.bsky.social from @czbiohub.bsky.social hosted by @noahbruderer.bsky.social for a seminar on “Building a virtual embryo, a single cell at a time”.
Picture of Loic Royer and Boah Bruderer in front of the first slide
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Saez-Rodriguez Group @saezlab.bsky.social · 05/02/2025
Applying LLMs to biomedical research today can go one of two ways: we either use a closed-source web app, or we get coding ourselves. Many researchers lack training for the latter, so their only choice is the former. We want to change that. www.nature.com/articles/s41...
Graphical abstract of BioChatter
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Michael Sars Centre @msarscentre.bsky.social · 29/01/2025
We are excited to announce that registration for the Michael Sars Symposium 2025 is now open! 🤩 Join us on June 6th at Media City Bergen for a day of exceptional talks 🧪 #MSS2025 ✨Learn more and register here: tinyurl.com/yc4jxdvz
A poster in tones of blue and green. At the bottom, the logos of the Michael Sars Centre, University of Bergen, and EMBL with the mention "partner of" above. In the bottom right corner, the hashtag MSS2025. The following text is on the poster:
Michael Sars Symposium 2025
Decoding signals and unveiling architectures, from molecules to organisms
June 6, 2025, Media City Bergen
Speakers:
Georgia Rapti (EMBL Heidelberg)
Ryan Hibbs (University of California San Diego)
Ida Helene Steen (University of Bergen)
Jingwei Xu (ETH Zürich)
Ross Waller (University of Cambridge)
Christopher Lowe (Stanford University)
Yuhong Wang (Michael Sars Centre, University of Bergen)
Ioannis Riziotis (The Francis Crick Institute, London/GSK)
Paola Laurino (Okinawa Institute of Science and Technology)
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Noah Bruderer @noahbruderer.bsky.social · 22/01/2025
Search is changing, using LLMs to reliably query your own data and public data bases will become the norm. Amongst other tools we use @langchain.bsky.social to drastically reduce hallucinations of LLMs.
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Nat Clarke @natclarke.bsky.social · 27/11/2024
I’m delighted to share that I will be starting my lab @univmiami.bsky.social in Spring 2025! We will study cellular and developmental biology in non-bilaterian animals – cnidarians, ctenophores, placozoans, and sponges – to explore early animal evolution.
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Noah Bruderer @noahbruderer.bsky.social · 25/11/2024
Find me at #CBIAS2024 in London! Come to chat about image-to-single-cell morphology and how morphosnaker 🧊🐍🧊 can help. Also come to play around with our virtual embryo. #morphosnaker #singlecell #morphology
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Crick BioImage Analysis Symposium @cbias.bsky.social · 25/11/2024
🚨 Today's the day! #CBIAS2024 is kicking off this morning! buff.ly/4fITsAq #BioImageAnalysis
Crick Bioimage Analysis Symposium logo, with colourful triangles made of tiny coloured numbers
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Emily Claereboudt @emclaereboudt.bsky.social · 21/11/2024
Ciona intestinalis in situ @ 25m around Sotra island,🇳🇴! @msarscentre.bsky.social I am trying to understand how chemical cues lead to these mass aggregations!
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