iiinova — where your digital self keeps evolving

Saez-Rodriguez Group @saezlab.bsky.social · 29/09/2026

Happy to see the peer-reviewed version of SpaCEy now out: 📄 Published paper: www.nature.com/articles/s41... 💻 Code: github.com/saezlab/SpaCEy

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Saez-Rodriguez Group @saezlab.bsky.social · 28/09/2026

Introducing mc-ASTRA, an open-source Python framework for studying how tissues vary and remodel across patients, perturbations, time points and other biological contexts. Manuscript: www.biorxiv.org/content/10.6... Package: saezlab.github.io/mc-astra/

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Saez-Rodriguez Group @saezlab.bsky.social · 21/09/2026

How do we know whether a biomedical foundation model has learned something biologically meaningful - rather than simply learned to excel on a narrow benchmark? Our new Perspective by @juliosaezrod.bsky.social and @psl-schaefer.bsky.social with Nikolas Kalavros & Gustavo Stolovitzky discusses this 👇

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EMBL-EBI @ebi.embl.org · 17/09/2026

Closing the loop for reproducible science: 🧬 Data ➔ 🤖 Models ➔ 📏 Benchmarks As AI transforms biology, EMBL-EBI is building the infrastructure to ensure models are as rigorous as the data behind them. What’s your biggest challenge when validating AI models? www.embl.org/news/science...

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Saez-Rodriguez Group @saezlab.bsky.social · 07/09/2026

🧵 Introducing Karenina, an open-source framework to evaluate LLMs & agents: doi.org/10.64898/202...

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Saez-Rodriguez Group @saezlab.bsky.social · 20/08/2026

Our tool MetaProViz is now out in Molecular Systems Biology: doi.org/10.1038/s443... Since our preprint we: - advanced our feature processing workflow - added metabolite-sets to MetSigDB - added metabolite-set visualization to aid functional analysis

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Saez-Rodriguez Group @saezlab.bsky.social · 07/08/2026

⬇️ Check out this new postdoctoral fellowship to be jointly hosted by Mathew Garnett's lab and our lab! lnkd.in/p/eZUYhWmz

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Saez-Rodriguez Group @saezlab.bsky.social · 04/08/2026

Check out our recent review ➡️ "Towards Principled Evaluation of Single-Cell Perturbation Prediction Models" More on LinkedIn post: lnkd.in/p/dKuF6f7A

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Saez-Rodriguez Group @saezlab.bsky.social · 09/07/2026

🧵 ParTIpy, our Python package for Pareto Task Inference just got published in Molecular Systems Biology (Peer reviewed at Review Commons) 🔗 Manuscript: link.springer.com/article/10.1... 💻 Code: github.com/saezlab/part... 📚 Docs: partipy.readthedocs.io/en/latest/

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Saez-Rodriguez Group @saezlab.bsky.social · 25/06/2026

🧵 New preprint: Logic models can simulate cancer signalling & screen drug targets in silico, but they need perturbation data & hand-curated networks patients lack. We present FICUS for building dynamic logic models directly from patient omics. 📄 doi.org/10.64898/202...

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EMBL-EBI Training @training.ebi.embl.org · 12/06/2026

Last chance to apply for the EMBO Practical Course 'Causality in biomedicine'. Applications close on 21 June 2026. Funding is available. Join the lineup of phenomenal speakers at @ebi.embl.org. Funded by @embo.org for excellence in the life sciences. www.ebi.ac.uk/training/eve... 🧬🖥️📊🧪🥼💊

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Saez-Rodriguez Group @saezlab.bsky.social · 22/05/2026

Our alumna Sophia Müller-Dott was honored with the MTZ Award for Systems Medicine for her PhD work. Congratulations, Sophia! 🎉 A special thanks to Monika and Thomas Zimmermann from the MTZ Foundation for their enduring support of Systems Medicine. 🙌

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Saez-Rodriguez Group @saezlab.bsky.social · 13/05/2026

1/🧵 New preprint! We built a patient-level map of systemic lupus erythematosus using single-cell blood transcriptomics, linking multicellular immune coordination to patient heterogeneity, future disease activity, and potential tissue pathology. ➡ doi.org/10.64898/202...

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Saez-Rodriguez Group @saezlab.bsky.social · 29/04/2026

This month we welcome Ajita Shree as a postdoctoral researcher, who will be working on computational methods for cell–cell communication 🎉. Ajita has a background in developing deep generative models for single-cell & spatial transcriptomics.

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Saez-Rodriguez Group @saezlab.bsky.social · 17/03/2026

🧵 What does single-cell transcriptomics reveal about individual patients with acute (AKI) and chronic (CKD) kidney 🫘 disease? Can we use it to find new biomarkers? In our new preprint 👇, we asked this using biopsies from 150+ participants from the Kidney Precision Medicine Project.

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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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Saez-Rodriguez Group @saezlab.bsky.social · 25/02/2026

This month we welcomed Francisca Gaspar Vieira, PhD student from @brittavelten.bsky.social's lab, to visit us at @ebi.embl.org for 6 months 🎉 She will continue to develop probabilistic factor models explicitly incorporating uncertainty in the estimation of perturbation effects in single-cell data

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Saez-Rodriguez Group @saezlab.bsky.social · 12/02/2026

Happy to share new work led by @miraburtscher.bsky.social, together with colleagues from @savitski-lab.bsky.social, @saezlab.bsky.social (shout-out to @martingarridorc.bsky.social), @zimmermannlab.bsky.social and others. Original post + paper below! 👇

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Saez-Rodriguez Group @saezlab.bsky.social · 12/02/2026

On March 4th, our @ricoramirez.bsky.social will share how we can currently study tissue remodelling with spatial transcriptomics data at a webinar from @training.ebi.embl.org. This webinar series includes a great lineup of speakers. For free registration see link below ⬇️

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Laura Cantini @cantinilab.bsky.social · 29/01/2026

New preprint from my team! led by @remitrimbour.bsky.social in collaboration with the @saezlab.bsky.social, we developped ReCoN a new method to model multicellular coordination and its underlying molecular mechanisms. 📜 Paper: lnkd.in/eJ8SfFNH 💻 Code: lnkd.in/e-qx2iNp

lnkd.in

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Saez-Rodriguez Group @saezlab.bsky.social · 20/01/2026

This month we welcome 2 new members and 1 visitor to our lab! 🎉 Veronika Kedlian as a postdoc, Hugo Hakem as a PhD student, and @francescadrummer.bsky.social as a visiting PhD student 🎉

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Saez-Rodriguez Group @saezlab.bsky.social · 15/01/2026

We recently posted a "2025 Publication Countdown" series on LinkedIn. See here ➡️ www.linkedin.com/company/saez...

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Saez-Rodriguez Group @saezlab.bsky.social · 17/12/2025

See 👇 our new manuscript introducing SpaCEy, an explainable method for predicting clinical outcomes from spatial omics data 🧬 📄 Paper: www.biorxiv.org/content/10.6... 💻 Code repo: github.com/saezlab/SpaCEy

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Saez-Rodriguez Group @saezlab.bsky.social · 27/11/2025

🤗 We welcome Jay Chow (Chi Lung), our new Scientific Database Curator. Jay will be joining a collaborative effort between SaezLab, @ebi.embl.org FG team, and GSK for the curation of fibrosis datasets and integration into the Expression Atlases and ArrayExpress collection in BioStudies.

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Saez-Rodriguez Group @saezlab.bsky.social · 20/11/2025

📍 Latest OmniPath paper is out now! ➡️ academic.oup.com/nar/advance-...

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Julio Saez-Rodriguez @juliosaezrod.bsky.social · 18/11/2025

It was an honor to speak about Systems Biology of Kidney Disease at the American Society of Nephrology meeting www.youtube.com/watch?v=YLVs... reflecting from my perspective as patient-scientist (www.nature.com/articles/s41...) & sharing work of @saezlab.bsky.social sp. within www.iganatlas.org

lnkd.in

This link will take you to a page that’s not on LinkedIn

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Saez-Rodriguez Group @saezlab.bsky.social · 07/11/2025

📄 BioContextAI is now slightly updated and published @natbiotech.nature.com ➡️ www.nature.com/articles/s41...

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Saez-Rodriguez Group @saezlab.bsky.social · 06/11/2025

Our revised consensus transcriptional patient map of human heart failure across patient cohorts and single-cell and bulk technologies is now published @natcomms.nature.com www.nature.com/articles/s41...

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EMBL-EBI @ebi.embl.org · 03/11/2025

Bonjour! Masters students in France 🇫🇷, we’ve got an internship for you, in collaboration with the French Embassy in London. Aimed at students of computer science, statistics or bioinformatics. Deadline: 7 December 2025 Find out more and apply: www.ebi.ac.uk/about/jobs/i...

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Saez-Rodriguez Group @saezlab.bsky.social · 06/10/2025

👋 @veronicalombardi.bsky.social has completed her 6-month visit period with us. She is a PhD student from the University of Rome La Sapienza, and her contribution focused on generating single-cell and patient-specific networks of pancreatic cancer using our tools LIANA+ and CORNETO. All the best! 🍀

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Saez-Rodriguez Group @saezlab.bsky.social · 26/09/2025

We are hiring a Postdoctoral Fellow in Computational Biology at EMBL-EBI (Cambridge, UK). Focus: methods to study cell–cell communication from sc/spatial omics data (building on LIANA+ and NicheNet), in collab with @yvansaeys.bsky.social VIB/Ghent. Details & apply by 13/10/25: tinyurl.com/4shdw8dk

tinyurl.com

Current Vacancies

Whether you're a scientist, IT specialist, accountant or administrator, you'll help us tackle the challenges of improving human health & biodiversity in the face of climate change on a global scal...

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Saez-Rodriguez Group @saezlab.bsky.social · 19/09/2025

🚨 New preprint We present an extended version of ScAPE, the method that won one of the prizes 🏆 in the @neuripsconf.bsky.social 2023 Single-Cell Perturbation Prediction challenge. 📄 preprint: doi.org/10.1101/2025... 🧬 code: github.com/scapeML/scape

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Saez-Rodriguez Group @saezlab.bsky.social · 17/09/2025

🥁 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. 🧶⬇️

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Saez-Rodriguez Group @saezlab.bsky.social · 15/09/2025

Introducing ParTIpy, a python package for Pareto Task Inference that scales to large-scale datasets, including single-cell and spatial transcriptomics. 🔗 Manuscript: www.biorxiv.org/content/10.1... 💻 Code: partipy.readthedocs.io

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Julio Saez-Rodriguez @juliosaezrod.bsky.social · 02/09/2025

@embl.org PhD programme just open - many interesting projects, including two with us @saezlab.bsky.social @ebi.embl.org - one on #host-microbiome interactions using #spatial omics, and one on #AI in #proteomics 👇

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Saez-Rodriguez Group @saezlab.bsky.social · 01/09/2025

👋 Time to say goodbye to another one of our PhD students, @smuellerdott.bsky.social. She was working on the integration of phosphoproteomics and transcriptomics data and will now join the Computational Oncology Team at Merck. We wish her all the best for this new chapter! 🚀 ✨

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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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Saez-Rodriguez Group @saezlab.bsky.social · 14/08/2025

👀 we are involved in projects 1 & 6 on the list: 1️⃣ Multicellular molecular characterisation of inflammatory bowel disease 6️⃣ Designing Efficient Single-Cell Perturbation Experiments with Lab-in-the-Loop AI Agents 📅 Application deadline is 30th September ❗

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Saez-Rodriguez Group @saezlab.bsky.social · 31/07/2025

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!

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Saez-Rodriguez Group @saezlab.bsky.social · 22/07/2025

🎉 The revised version of CORNETO, our unified Python framework for knowledge-driven network inference from omics data, is published in peer reviewed form 🔗 Paper: www.nature.com/articles/s42... 📖 News & Views: www.nature.com/articles/s42... 💻 Code: corneto.org 🧵 Thread 👇

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Saez-Rodriguez Group @saezlab.bsky.social · 16/07/2025

Four more days to apply to our postdoctoral position 👇

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Saez-Rodriguez Group @saezlab.bsky.social · 16/07/2025

Four more days to apply to our curator position 👇

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EMBL-EBI @ebi.embl.org · 14/07/2025

Don't miss talks in our sponsored Dialogue for Reverse Engineering Assessment and Methods – DREAM – session, kicking off with a talk by our Head of Research, @juliosaezrod.bsky.social on benchmarking foundation models in biology www.iscb.org/ismbeccb2025... #ISMB2025

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Saez-Rodriguez Group @saezlab.bsky.social · 14/07/2025

Our group @ebi.embl.org‬ is a host for the ARISE2 MSCA-funded post-doc fellowship, in collab with @bioimagearchive.bsky.social‬ and ‪@scilifelab.se (esp. A Mezger and S. Giacomello) to support the development of next-gen spatial data infrastructures. Apply by 30/09 www.embl.org/training/ari...

embl.org

ARISE2

Career Accelerator for Research Infrastructure Scientists

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Julio Saez-Rodriguez @juliosaezrod.bsky.social · 23/06/2025

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...

nature.com

Leveraging data as a patient–scientist: frustrations and opportunities - Nature Reviews Nephrology

The transition from data scientist to patient–scientist has given me new perspectives into clinical research and strengthened my commitment to open science. Although limitations on data availability h...

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