iiinova — where your digital self keeps evolving

Loan Vulliard @lvulliard.bsky.social · 28/09/2026

Check this out for a flexible framework to go from cell-level measurements to interpretable tissue-level descriptors!

Loan Vulliard @lvulliard.bsky.social · 04/08/2026

Thanks to @helloeacr.bsky.social for allowing me to attend their annual congress, last June in Budapest. It was a great opportunity to (re-)connect with colleagues, get a broader sense of where cancers therapies are heading, and remember what's exciting about being a scientist! tinyurl.com/2upz6p5u

magazine.eacr.org

EACR 2026 Congress Travel Grant recipients share their experiences - The Cancer Researcher

We met in Budapest, Hungary for the most recent EACR Congress, and were delighted to award several Travel Grants to help cancer researchers in need of financial assistance to attend.

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Saez-Rodriguez Group @saezlab.bsky.social · 12/03/2026

🧵 See 👇 our new preprint on shared and organ-specific gene expression programs of fibrotic diseases 🧬 📄 Paper: doi.org/10.64898/202... 📊 Explore the data: organfibrosis.saezlab.org

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 24/11/2025

Was lovely to see many of you @ I2K! Despite having major FOMO about missing so much stuff this fall (GloBIAS! CytoData! FoundingGIDE! CBIAS!), conferences ARE usually a great way to find @erinweisbart.bsky.social and I. In Episode 19, we talk through great societies/meetings we think you'll enjoy!

youtu.be

Conferences We've Attended Recently - AskErinDearBeth Episode 19

YouTube video by Ask Erin, Dear Beth

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Alex Kalinin @alxndrkalinin.bsky.social · 31/10/2025

Today is the last chance to register for #CytoData2025. Don’t miss a fantastic program covering the full spectrum of image-based profiling! cytodata25.eu-openscreen.eu

cytodata25.eu-openscreen.eu

Cytodata

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Andre Rendeiro @andre-rendeiro.com · 15/10/2025

New work from Iva Buljan @ivabuljan.bsky.social in our lab! We mapped how human tissue architecture changes with age using ~25k histology slides from 983 donors. This is the first body-wide atlas of human microanatomy. 📄 Preprint: www.biorxiv.org/content/10.1...

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Saez-Rodriguez Group @saezlab.bsky.social · 25/08/2025

We present our MetaProViz #Rpackage for #metabolomics analysis & prior knowledge integration to generate mechanistic hypotheses on how metabolic changes affect metabolite classes, pathways & environment interaction 🔗 www.biorxiv.org/content/10.1... 📦 saezlab.github.io/MetaProViz/ 🧵 Thread ⬇️

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Jess Ewald @ewaldlab.org · 07/08/2025

Check out this opportunity to join my lab as a postdoc! www.ebi.ac.uk/research/pos... Every year, faculty from EMBL-EBI and the Wellcome Sanger Institute co-develop projects that allow fellows to be part of ✨both✨ of these amazing research institutes.

ebi.ac.uk

EMBL-EBI-Sanger postdoctoral fellowships (ESPOD)

The ESPOD fellowship builds on the collaborative relationship between EMBL-EBI and the Wellcome Sanger Institute, offering projects that combine experimental (wet-lab) and computational (dry-lab) appr...

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Martin Garrido-Rodriguez @martingarridorc.bsky.social · 24/07/2025

This project has been in the making for quite some time. CORNETO not only integrates key concepts and methodologies in biological network inference, but also introduces a novel framework for multi-condition analysis. Congrats to the team, and especially to @pablormier.bsky.social for leading this.

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cytodata.bsky.social @cytodata.bsky.social · 21/07/2025

𝗢𝗻𝗲 𝗪𝗲𝗲𝗸 𝗟𝗲𝗳𝘁: Abstract submission for oral presentations 🗣️ and hackathon registration 🧑‍💻 for CytoData 2025 Berlin close July 25! Submit abstracts or register here: 🔗 cytodata25.eu-openscreen.eu/registration/ #Cytodata2025 #Hackathon #ImageBasedProfiling

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Alex Kalinin @alxndrkalinin.bsky.social · 08/07/2025

🔬API-first feature extraction for image-based profiling workflows If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle. 1/6

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cytodata.bsky.social @cytodata.bsky.social · 02/07/2025

Exciting news! We've extended the deadline for oral submissions for Cytodata 2025. You now have until July 25 to submit oral presentations and register for the hackathon. Don't miss this chance! Poster submission closes September 10, and general registration ends October 1

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cytodata.bsky.social @cytodata.bsky.social · 20/06/2025

🌟 𝗥𝗲𝗺𝗶𝗻𝗱𝗲𝗿 🌟 The deadline for abstract submissions for oral presentations at Cytodata 2025 in Berlin is approaching! 👉 𝗦𝘂𝗯𝗺𝗶𝘁 𝘆𝗼𝘂𝗿 𝗮𝗯𝘀𝘁𝗿𝗮𝗰𝘁 𝗯𝘆 𝗝𝘂𝗻𝗲 25! cytodata25.eu-openscreen.eu/registration/ #BerlinConference #Imageanalysis #Microscopy

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cytodata.bsky.social @cytodata.bsky.social · 23/04/2025

Join us in Berlin for CytoData 2025! 👉 Info & registration: cytodata25.eu-openscreen.eu 🔬 Hackathon: Nov 17–19 📢 Symposium: Nov 20–21 Explore advancements in image-based profiling & high-content screening and Tackle real-world challenges using EU-OPENSCREEN data.

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Andre Rendeiro @andre-rendeiro.com · 12/06/2025

🚨 3 days left to apply! Join us at CeMM (Vienna) to work on AI + computational pathology projects like LazySlide. Amazing team, H100 GPUs, real impact. Apply now: cemm.at/join-cemm/op...

cemm.at

Open Positions

CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences

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Loan Vulliard @lvulliard.bsky.social · 11/06/2025

If you need to compare profiles across many conditions or perturbations, have a look!

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Saez-Rodriguez Group @saezlab.bsky.social · 23/05/2025

Ever wondered which method to use to infer kinase activities from phosphoproteomics data? 💻💭Our revised comprehensive evaluation of kinase activity inference tools, done in collaboration with the Zhang lab @bcmhouston.bsky.social, is now out @natcomms.nature.com 🔬 tinyurl.com/4twuc6z4

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Loan Vulliard @lvulliard.bsky.social · 07/05/2025

If you're interested in finding recurrent spatial patterns in your tissues, now is a good time to check out Kasumi!

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Saez-Rodriguez Group @saezlab.bsky.social · 22/04/2025

We have an opening for a PhD/Postdoc in Spatial Omics for Cardiology in Heidelberg 🫀 #job #academicjob #phd #postdoc #cadiology 👇 jobrxiv.org/job/heidelbe...

jobrxiv.org

PhD/Postdoc in Spatial Omics for Cardiology

Post a job in 3min, or find thousands of job offers like this one at jobRxiv!

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Loan Vulliard @lvulliard.bsky.social · 23/04/2025

Registrations are open for the best scientific event of the year! Source: my very unbiased and authoritative opinion 😂 Join us in Berlin in November to discuss the best ways to go from images to biological insight and new treatments.

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Jovan Tanevski @tanevski.bsky.social · 22/04/2025

🚨 New preprint: Topography Aware Optimal Transport for Alignment of Spatial Omics Data We present our new alignment framework TOAST www.biorxiv.org/content/10.1...

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Saez-Rodriguez Group @saezlab.bsky.social · 09/04/2025

Congrats & Good luck to our @slobentanzer.bsky.social as he starts his group @diabresearch-dzd.bsky.social & @comphealthmunich.bsky.social - he is hiring 👇

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Chris Fell @cfell.bsky.social · 09/04/2025

So excited to share our new paper out today in @nature.com. We repurposed R2 retrotransposons to create STITCHR, a tool that can make virtually any kind of edit in mammalian genomes including the scarless multi-kilobase scale insertions 🧵 www.nature.com/articles/s41...

nature.com

Reprogramming site-specific retrotransposon activity to new DNA sites - Nature

A study of retrotransposon activity repurposes a retroelement called R2Tocc to create a programmable system called STITCHR that enables diverse genome edits including efficient, scarless large pa...

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Loan Vulliard @lvulliard.bsky.social · 09/04/2025

Interested in supporting the advancement of image-based profiling? Want to shape how large cell and tissue image datasets will be analyzed in the future? Please consider hosting CytoData!

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 07/04/2025

Delighted to announce that @erinweisbart.bsky.social and I have teamed up to create a new bioimage analysis video podcast called Ask Erin/Dear Beth - you can check it out at the link below! It will highlight common challenges in #bioimageanalysis, as well as our favorite solutions to them. (1/x)

youtube.com

Ask Erin, Dear Beth

On Ask Erin/Dear Beth, bioimage analysis experts Beth Cimini and Erin Weisbart, of the Imaging Platform at the Broad Institute of MIT and Harvard, answer your image analysis questions! Whether it’s ab...

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Loan Vulliard @lvulliard.bsky.social · 31/03/2025

Big news, you can now follow the CytoData society on BS and get even more image-based profiling in your timeline 🤓

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Leeat Keren @leeat-keren.bsky.social · 26/03/2025

Super excited to finally see this published! Our new method to use combinatorial staining and deep learning to push the multiplexing boundaries of spatial proteomics!

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Galaxy Project @galaxyproject.bsky.social · 17/03/2025

The GBCC2025 Scholarships are here! Thanks to the JXTX Foundation and Galaxy Project, 4 genomics and data science graduate students will receive scholarships to attend GBCC2025 in person. 📅 Apply by April 1, 2025 👉 jxtxfoundation.org/news/2025-2-...

jxtxfoundation.org

JXTX + GBCC 2025 Scholarships

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Saez-Rodriguez Group @saezlab.bsky.social · 20/02/2025

The first version of NetworkCommons is now published in Bioinformatics. Next, we’ll focus on involving more of the network biology community. academic.oup.com/bioinformati... In parallel, we’ll continue expanding benchmarks and developing new applications. Interested in contributing? Reach out! ⬇️

academic.oup.com

NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks

AbstractSummary. We present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage

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Julio Saez-Rodriguez @juliosaezrod.bsky.social · 11/02/2025

Post-doc opening to join our lab @ebi.embl.org to develop&apply #bioinformatics and #machine-learning methods to study intra-/extra cellular networks to extract disease mechanisms from #single-cell and #spatial multiomic data - please share 🙏 : embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

embl.wd103.myworkdayjobs.com

Postdoctoral fellow - Saez-Rodriguez Group

Your group Saez-Rodriguez Research Group Your supervisor Julio Saez-Rodriguez Your role As a postdoctoral fellow in the Saez Rodriguez group, you will develop and apply computational methods and tools...

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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...

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Peter Murphy @peterwmurphy1.bsky.social · 01/01/2025

For Maths fans, 2025 is a square. 45² = 45 x 45 = 2025 Also, 9² x 5² = 2025 40² + 20² + 5² = 2025 My favourite? 1³+2³+3³+4³+5³+6³+7³+8³+9³ = 2025 #Mathematics #teaching #education

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Saez-Rodriguez Group @saezlab.bsky.social · 23/12/2024

We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇 Paper: doi.org/10.1101/2024.12.20.629764 Code: github.com/saezlab/greta

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Rita Strack @ritastrack.bsky.social · 06/12/2024

I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...

nature.com

Method of the Year 2024: spatial proteomics - Nature Methods

Approaches for profiling the spatial proteome in tissues are the basis of atlas-scale projects that are delivering on their promise for understanding biological complexity in health and disease.

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Ferris Jabr @ferrisjabr.bsky.social · 27/11/2024

I was deeply disappointed by the lack of nature/science/climate/enviro on many major end-of-year book lists—so I decided to make my own! Introducing: ✨🎁📚 The 2024 Holiday Gift Guide to Nature & Science Books ✨🎁📚 Please share: Let's make this go viral in time for Black Friday / holiday shopping!

A collage of book covers of new nature & science books. Featured here are Atlas Obscura Wild Life, Dinosaurs at the Dinner Party, Every Living Thing, Alien Earths, Becoming Earth, and Deep Water

A collage of book covers of new nature & science books. Featured here are Frostbite, The Inner Clock, How to Kill an Asteroid, The Great River, The Last Fire Season, and Hoof Beats

A collage of book covers of new nature & science books. Featured here are The Serviceberry, Not the End of the World, Nature's Ghosts, Meet the Neighbors, The Light Eaters, and Our Moon

A collage of book covers of new nature & science books. Featured here are Turning to Stone, The Weight of Nature, What If We Get It Right?, Waves in An Impossible Sea, The Tree Collectors, and Why We Remember

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Saez-Rodriguez Group @saezlab.bsky.social · 26/11/2024

We present NetworkCommons, a unified platform 🪐 for network biology, providing access to omics data, knowledge, and contextualization methods, all with a consistent API 👇🧵 Paper: doi.org/10.1101/2024... Docs: networkcommons.readthedocs.io

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Loan Vulliard @lvulliard.bsky.social · 20/11/2024

One full year to get ready: join us next year in Berlin-Buch if you're into spatial biology, morphology and/or high-content perturbation screens! 🔬💻 #CytoData #Microscopy #ImageBasedProfiling

Poster for the CytoData 2025 event on image-based profiling: Hackathon November 17-19, 2025 and Symposium November 20-21, 2025.

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Saez-Rodriguez Group @saezlab.bsky.social · 11/11/2024

Hi 🦋 This is the saezlab (saezlab.org) bluesky account. We integrate #omics data with mechanistic molecular knowledge into statistical and machine learning #ML methods, and we share our tools as free #opensource packages (github.com/saezlab/) #systemsbiology #biology #compbio

saezlab.org

Saez-Rodriguez GroupSaez-Rodriguez Group – Systems Biomedicine

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Andre Rendeiro @andre-rendeiro.com · 16/11/2024

What if we could look at a human tissue image🔬and quantify its biological age?🧬 And how could we get the same insights without collecting the tissue sample? In our new @biorxivpreprint, we create "tissue clocks" ⏳to do just that! www.biorxiv.org/content/10.1... 📝 #aging #tissue thread below⬇️

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Saez-Rodriguez Group @saezlab.bsky.social · 11/11/2024

What are the key disrupted multicellular processes in heart failure? In our new work we combine 23 years of molecular data with recent single-cell atlases to draw a cross-study patient map doi.org/10.1101/2024...

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