Connecting AI to biology: Model Context Protocol www.ebi.ac.uk/about/news/p...

Do you know how far phototoxicity can hinder your experiments?🤔 @mariodelr.bsky.social and @gomez-mariscal.bsky.social have just published their work on #PhotoFiTT in @natcomms.nature.com where they explain how to quantitatively measure it in live-cell imaging.⚡🧫🔬 Read more at: shorturl.at/ly9Zn

🚨🔬🤖🚀 #PhotoFiTT is out! With @guijacquemet.bsky.social's & @microbematos.bsky.social's labs, we launched a new phototoxicity measurement for live microscopy using cell clocks⏱️. By rockstars @mariodelr.bsky.social @gomez-mariscal.bsky.social et al! AI-powered + label-free doi.org/10.1038/s414...

It’s FINALLY out! 🎉🚀 We have been working on PhotoFiTT for a long time, and it’s now published, introducing a quantitative framework to measure phototoxicity and optimise live-cell microscopy experiments. So excited to finally share the last version! 🔬✨ #PhotoFiTT doi.org/10.1038/s414...

🚨Amazing news for a cloudy Monday!🌩️😎 I'm extremely happy to share that our last adventure is finally out!🚀🎉Phototoxicity fitness time trial (#PhotoFiTT) - a quantitative framework for assessing phototoxicity in live-cell microscopy experiments 🔬❤️‍🔥⚡️ doi.org/10.1038/s414...

We are hiring! We are looking for a Postdoc to drive our efforts on using tissue clearing for 3D histopathology. @erturklab.bsky.social #Histopathology #TissueClearing #PostDoc www.linkedin.com/feed/update/...

AI holds huge promise for life science research. But unreliable answers currently limit its impact. @juliosaezrod.bsky.social, Head of Research at EMBL-EBI, discusses how Model Context Protocol (MCP) servers are helping to change this. www.ebi.ac.uk/about/news/p... 🧬💻

Doctoral (PhD) Position – Spatial Transcriptomics, Bioinformatics & Mucosal Immunology 📍 Karolinska Institutet, Sweden 🗓️ Deadline: Dec 10, 2025 kidoktorand.varbi.com/what:job/job... #SpatialTranscriptomics #Bioinformatics #MucosalImmunology #SingleCellOmics #IBDResearch #SystemsImmunology

Truly happy to host Victor Puelles in Marburg today, talking about complex tissue analysis across biological scales. Thrilling science and exciting discussions! @puellesv.bsky.social

Really excited for our November issue, and I feel like I'm starting to get into the groove of writing editorials for nBME (with the help of the team of course!). Please check it out!

I won't talk about NMeth @natmethods.nature.com forever (probably), but I do want to brag a bit about the November focus issue on cell segmentation and tracking, which is many ways is my last hurrah (and final editorial) for the journal. I am so proud of these papers!! www.nature.com/nmeth/volume...

BioContextAI is an open-source initiative for creating agentic biomedical research assistants from standardized components go.nature.com/3JmqKux rdcu.be/ePz3v

The Eknoyan Lectureship at #KidneyWk will cover KDIGO Guidelines for CKD on Saturday. Read about the speaker in #ASNKidneyNews kidney.pub/KN1710-55#KidneyWk

At #KidneyWk? Celebrate and listen to the ASN-American Heart Association Donald W. Seldin Young Investigator Award winner, Rafael Kramann, who will speak on “Cell by Cell, Space by Space: Unraveling Fibrosis in the Kidney and Heart” on Friday, November 7. kidney.pub/KN1710-35#KidneyWk?#ASNKidneyNews

BioContextAI is a community hub for agentic biomedical systems - @puellesv.bsky.social @biocontext.ai go.nature.com/3JmqKux

🤖🧬 New biomedical MCP server added to the registry: Skill-To-MCP Server Check it out at https://biocontext.ai/registry/biocontext-ai/skill-to-mcp

Our new review in @natbiomedeng.nature.com is out! RNA-loaded lipid nanoparticles (LNPs) have huge potential—but their strong liver and immune cell uptake has mostly confined them to vaccines and liver therapies. We explore how to move beyond those limits. free to read 🔗 rdcu.be/eLxGs

The #mesoSPIM community just celebrated 10 years of open-source light-sheet microscopy in Zürich! For #3DThursday, we're honoring Martina Schaettin & Fabian Voigt’s iconic 3D chick embryo dataset — a luminous benchmark for open science and shared discovery. #Microscopy #Lightsheet #syGlass

🦠🔬🤖🧑‍💻 #mAIcrobe is out! With @pinholab.bsky.social's lab, we launched an open-source framework for high-throughput bacterial image analysis. By rockstars A. Brito & B. Saraiva et al, making #DeepLearning for phenotyping accessible! Easy to use, plus model training 📜 www.biorxiv.org/content/10.1...

Job opportunity at the University of Zurich! 📢 We are looking for a 𝐋𝐚𝐛𝐨𝐫𝐚𝐭𝐨𝐫𝐲 𝐓𝐞𝐜𝐡𝐧𝐢𝐜𝐢𝐚𝐧 / 𝐑𝐞𝐬𝐞𝐚𝐫𝐜𝐡 𝐀𝐬𝐬𝐢𝐬𝐭𝐚𝐧𝐭 (𝟒𝟎%) to join our Microscopy Innovation Platform (MIP), an open-source initiative focused on advancing and making light-sheet and multiphoton microscopy accessible to researchers. 1/3

✨🥳🎉 Heartfelt congratulations to Humboldtians Susumu Kitagawa and Omar M. Yaghi on winning the #NobelPrize in Chemistry 2025 which they share with Richard Robson for the development of "metal-organic frameworks"! We are truly honoured to have supported a step in their exceptional journey! 💚

✨✨✨ Huge congratulations to the winners of the #NobelPrize in Physics: John Clarke, Michel H. Devoret and John M. Martinis. Clarke and Martinis are both members of the Humboldt Network – as hosts for Feodor Lynen Research Fellows! 💚 Picture: Ill. Niklas Elmehed © Nobel Prize Outreach

In our paper @natimmunol.nature.com we highlight a spatiotemporally conserved progression program into glomerular crescents and sclerosis and indicate new treatment options for autoimmune kidney disease. #UKEHamburg #HCKH_Hamburg #HCTI @uni-hamburg.de www.nature.com/articles/s41...

🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights. 🔗 www.biorxiv.org/content/10.1...

Check out our latest review on Basement Membranes! Including scaled representation of protein & glycan components 😊 @mcrcellmatrix.bsky.social

🥁 Check out our new preprint on OmniPath, the prior knowledge resource for #SystemsBiology, and its brand-new OmniPath Explorer web app! 🥳 📖 Preprint: www.biorxiv.org/content/10.1... 🔍 Explorer: explore.omnipathdb.org OmniPath integrates 160+ resources for multi-omics analysis & modeling. 🧶⬇️

Today 20 years after I started working in a scientific lab while still in 🇨🇱, my lab, the @cellcommlab.bsky.social has its 5th labversary. What a ride ! I'm thankful for the support of my family, friends, & so many great collabs & colleagues. Fig legend 👇🏽 + pending longer thread #PIlife #Science

Definitely the most unexpected @mesospim.bsky.social #lightsheet #microscopy application of the past years: Hunting dark matter with a lightsheet microscope! #astronomy 🔭🔬https://arxiv.org/abs/2503.20732

Want to acquire #ExM images like this and help us understand the true extent of cytoskeletal diversity across the tree of life? This position might be for you! embl.wd103.myworkdayjobs.com/en-US/EMBL/j... With @dudinlab.bsky.social @embl.org @biology-unige.bsky.social @moorefound.bsky.social

Nature research paper: Pathology-oriented multiplexing enables integrative disease mapping go.nature.com/3HdZxZG

Glad to contribute to this collaborative community platform. A case study shows MCP servers working together - combining BioContextAI Knowledgebase with our omnipath omnipathdb.org MCP (work in progress) to showcase interoperability. Looking forward to see how the ecosystem evolves!

Preprint alert 🚨 Do you use chatbots in your work or even build MCP servers and agentic systems yourself? Or would you like to find a way to use biomedical tools using natural language? Then check out biocontext.ai, now out on bioRxiv: www.biorxiv.org/content/10.1...

🚨Scaling multiplexed imaging 📈 We are excited to share Pathology-oriented multiPlexing (PathoPlex). Now out in @nature.com: www.nature.com/articles/s41... 🧵Walk-through thread below ⬇️

@puellesv.bsky.social @n-kaiser.bsky.social @tanevski.bsky.social @juliosaezrod.bsky.social @psl-schaefer.bsky.social @pjsaez.bsky.social @lucaspelkmans.bsky.social @costalab.bsky.social @m-schwerk.bsky.social and many others.

#HotFromThePress !! What if instead of analyzing 4-6 pathology markers you could check >100 in the *same* sample? @maltekuehl.com & co @puellesv.bsky.social lab introduce #PathoPlex, method that could even predict disease Full www.nature.com/articles/s41... @focalplane.bsky.social @nature.com 🧪🔬

Four more days to apply to our postdoctoral position 👇

🚨Join us! We're soon opening 3 postdoctoral positions in #AIDrivenBiology. Seeking biologists (especially microbiology and infection biology), computer scientists, and microscopy developers. Ideal candidates are those eager to use or develop next-gen tech for cell biology. Get in touch (DM/email)

🧾New paper now on ‪‪‪‪Nature Protocols ‬🎉The #ExSRRF protocol gives you all details on how to merge Expansion Microscopy technique with #eSSRF analysis. Developed by Dominik Kylies, @puellesv.bsky.social and @hannah-superres.bsky.social, @henriqueslab.bsky.social 🔗: www.nature.com/articles/s41...

It's here! ✨ The #ExSRRF protocol paper is out 😍. Full details for merging Expansion Microscopy with our eSRRF analysis. From cells to tissue. A partnership with @puellesv.bsky.social's lab. Lead by Dominik Kylies and @hannah-superres.bsky.social + colleagues. #ExM #eSRRF ➡️ Open link: rdcu.be/euvEw

Postdoc position in our group at @ebi.embl.org about analyzing single cell data sets to better understand and treat neurodegen diseases, in collab with A Bassett, M Lotfollahi, @bayraktarlab.bsky.social, M Strauss and others within Open Targets. Deadline 20/07. Please share tinyurl.com/87wj466m

🔬👨‍💻📰 #SReD is out! Automated structural detection for #ImageJ & #FIJI, from nano to macro ✨🐘. No training data, no bias - texture analysis with GPU acceleration!⚡️ Brainchild of @afonsomendes92.bsky.social and adventure w @christlet.bsky.social lab + friends. Check: www.nature.com/articles/s41...

🧑‍🔬📰🚀 #RxivMaker is here! A framework automating the creation of publication-ready scientific #preprints from simple Markdown. Goodbye manual formatting, and hello gorgeous manuscripts! A great adventure with @guijacquemet.bsky.social's lab 📜: zenodo.org/records/1575... 👨‍💻: github.com/HenriquesLab...

I wrote a short piece on how becoming an IgA Nephropathy patient has changed my perspective on biomedical research, developing an appreciation for the challenges in data interpretability & availability and the importance of patient engagement www.nature.com/articles/s41...

Integrated Organoid Atlas benchmarks new protocols, even more impressive as a Highly Variable Cohort for comparison against perturbation and disease models: nature.com/articles/s41... Lead by @quanxu.bsky.social, in collaboration with Lennard Halle and @fabiantheis.bsky.social

It was fun to learn about blood vessel organoids together with @marinanikolova.bsky.social and Barbara Treutlein! Thanks to Reiner Wimmer and @penningerlab.bsky.social for introducing us to this system! www.cell.com/cell/fulltex... Great support from editors and reviewers @cellpress.bsky.social!

Curious about collagen?? There is an amazing program for the Collagen Gordon in New Hampshire this year. We have ample speaker slots reserved for abstract submissions. Come and join us! www.grc.org/collagen-con... July 6 - 11, 2025 www.grc.org/collagen-grs... July 5 - 6, 2025 Doug,Rachel,Alex

🤩 So many beautiful combinations of #ExM and #SuperResolution 🔬featured in this review!! 👇

🚨🔬💗Whether investigating cell organelles or mapping proteins, together with Victor Puelles's lab we lay a roadmap for selecting optimal #ExM and #SuperResolution #microscopy combinations. Daria Aristova and Dominik Kylies review with amazing co-authors pubs.aip.org/aip/apr/arti...

The self-driving multiscale microscope from @daetwylerstephan.bsky.social is out. It can image an entire zebrafish embryo longitudinally and follow a volume of interest over time with high resolution. We used it to study cancer-immune cell interactions. www.nature.com/articles/s41...

It is indeed my understanding that most research institutions won't survive if this is implemented. I know I will contact my congress and senate members. 5calls.org