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

🧵 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/

🧵 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...

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... 🧬🖥️📊🧪🥼💊

EMBL-EBI Training@training.ebi.embl.org · 4mo ago

Gain practical experience using widely adopted tools and resources to apply causal techniques in real-world biomedical contexts. Applications are now open until 21 June. Grants and bursaries are available for this @embo.org Practical Course: www.ebi.ac.uk/training/eve... 🧬🖥️💊📊

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. 🙌

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...

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.

🧵 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.

🧵 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

Interested in kinase-driven signaling interactions? Check out our (now peer-reviewed) paper together with @savitski-lab.bsky.social on reconstructing signaling networks from phosphoproteomics data and prior knowledge: ➡️ doi.org/10.1038/s414...

Benchmarking EGF signaling pathway inference using phosphoproteomics and kinase-substrate interactions - Nature Communications

To what extent can large-scale approaches accurately reconstruct classic signaling pathways? Here, authors revisit the EGF pathway using phosphoproteomics and kinase-substrate interactions

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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

next week 🔜

EMBL-EBI Training@training.ebi.embl.org · 5mo ago

Join us next week for the third free webinar in our spatial transcriptomics series: www.ebi.ac.uk/training/eve... Ricardo Ramirez (EMBL-EBI) presents 'Mapping tissue remodelling using sequencing-based spatial transcriptomics' on 4 March| 14:30 UK time. @saezlab.bsky.social 🧬🖥️

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! 👇

Savitski Lab@savitski-lab.bsky.social · 6mo ago

Rewiring of oncogenic signaling in #DrugResistance is a moving target. In our new study, we used biophysical phosphoproteomics to investigate #BRAF mutant cancer, linking phosphorylation changes to protein function and #MolecularMechanisms through #Multi-Omics integration. tinyurl.com/funsignaling

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 ⬇️

EMBL-EBI Training@training.ebi.embl.org · 6mo ago

We're pleased to announce that our next webinar series is now live. Decoding spatial transcriptomics through sequences, pixels, and bioinformatics will run from 18 February – 8 April 2026: www.ebi.ac.uk/training/eve... Coordinated by: @ajaymishra24.bsky.social, Kristy Ou, and Flaminia Zane. 🧬🖥️📊

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

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 🎉

Congrats! We’re happy to have contributed to the Atlas of Human Inflammation, improving the interpretability of inflammatory signatures through inference of transcription factor activity (Jose Liñares Blanco, @ricoramirez.bsky.social and @juliosaezrod.bsky.social) www.linkedin.com/posts/holger...

#inflammation #diagnostics #precisionmedicine #liquidbiopsy #machinelearning | Holger Heyn | 40 comments

Ladies and gentlemen - Our Atlas of Human Inflammation today out in Nature Medicine 💫 Welcome on stage: The Cell as a Living Biomarker 🩸 We Built an #Inflammation Atlas of Circulating Immune Cells....

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

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

🤗 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.

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

Saez-Rodriguez Group@saezlab.bsky.social · 11mo ago

🥁 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. 🧶⬇️

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

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

Saez-Rodriguez Group@saezlab.bsky.social · last yr.

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!

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...

Saez-Rodriguez Group@saezlab.bsky.social · 2y ago

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...

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...

👋 @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! 🍀

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

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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🚨 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

🥁 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. 🧶⬇️

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