Julio Saez-Rodriguez

Research groups Our world-leading research groups focus on developing and applying computational and mathematical methods to a range of biological questions.

Join our faculty: ebi.ac.uk/research/gro... - our 9-year tenure nurtures our group leaders to go on to do great things: @virginieuhlmann.bsky.social @oliverstegle.bsky.social @moritzgerstung.bsky.social @teichlab.bsky.social @pedrobeltrao.bsky.social John Marioni

we particularly welcome groups with a focus on (AI) methods, especially young female scientists. We evaluate by potential, not just your current track record. @ebi.embl.org is a great place to start a lab - speaking from experience

Do you want to pursue your ideas in computational biology independently, running your group in @embl.org‘s uniquely collaborative environment, beside world’s most comprehensive biomolecular data resources @ebi.embl.org in Genome Campus next to @sangerinstitute.bsky.social?
Apply to join us & share 🙏

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 ⬇️

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! 👇

DREAM Challenges - ISMB/ECCB 2025 - YouTube

Check the talks from @anshulkundaje.bsky.social @juliosaezrod.bsky.social @oldbap.bsky.social @mariabrbic.bsky.social ISMB 2025 special DREAM session on foundation models : youtube.com/playlist?lis...

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

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

Connecting AI to biology: Model Context Protocol Julio Saez-Rodriguez discusses how MCP servers are helping AI connect to life science databases, making AI a more reproducible tool for research.

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...
🧬💻

Postdoctoral fellow - Petsalaki Group - NetworkCommons Your group The Petsalaki, Saez-Rodriguez (EMBL-EBI) and Korcsmáros (Imperial College) groups develop cutting-edge computational and AI approaches to unravel cellular signalling and gene regulation fro...

NEW: Postdoc with @epetsalaki.bsky.social @juliosaezrod.bsky.social and Tamas Korcsmáros

Benchmark and integrate state-of-the-art network contextualisation methods, combining large-scale transcriptomics, proteomics, and single-cell data

Apply by 17 Dec

embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

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

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...

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...

‼️ Deadline extension alert ‼️

The new abstract submission deadline for #EMBLCardioBiology is 10 November 👉 https://s.embl.org/ncb26-01-bl

👉 Join experts pushing the frontiers of heart and vascular science
🫀 Share your work and shape the future of cardiobiology
📜 Submit your abstract today!

Very happy to see this work finally online 🥳

It was really interesting to write a short manuscript mixing method presentation & broader insights on data preprocessing. 📝

Thank you to my co-supervisors @cantinilab.bsky.social & @juliosaezrod.bsky.social for their feedback on this side work! 🫶

5/5

I'm presenting #CIRCE, a Python package to infer co-accessible DNA region networks 🧬

Based on #Cicero 's algorithm (Pliner et al.), it runs ~150x faster, processing an atlas of 700k cells in less than 40 min! ⛷️

Short paper: doi.org/10.1101/2025...
Code: github.com/cantinilab/CIRCE

1/5 ⬇️

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...

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

🥁 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.

🧶⬇️

🚨 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

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

Welcome: Jess Ewald Jess Ewald, Research Group Leader at EMBL-EBI, uses cell profiling and AI to find and characterise chemical hazards to humans and ecosysystems.

Meet our newest Research Group Leader: Jess Ewald @ewaldlab.org ‬🇨🇦

Jess’s group takes a multi-disciplinary approach to identify and characterise chemical hazards to humans and ecosystems, using cell profiling data, machine learning, and integrative data analysis.

www.ebi.ac.uk/about/news/p...

🖥️🧬

Welcome: Tim Coorens EMBL-EBI’s newest Research Group Leader is investigating how somatic mutations reveal the hidden histories of human cells.

Welcome @timcoorens.bsky.social ‪ ‬🇳🇱, our new Research Group Leader.

Find out how Tim’s group is exploring using large-scale single-cell and spatial data to trace cell lineages, understand cancer origins, and uncover how mutations drive disease.

www.ebi.ac.uk/about/news/p...
🖥️🧬

@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 👇

👋 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! 🚀 ✨

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 ⬇️

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!

👀 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 ❗

Diagram showing MCP-enabled research architecture. Part A illustrates the flow between MCP servers (including BioContextAI Knowledgebase MCP and Community-developed MCP servers), Agentic systems connected via Model Context Protocol, and researchers asking research questions. MCP servers connect to knowledgebases and specialized software. Part B details the BioContextAI project components, divided into Registry (Schema.org ontology, Web interface, Open source licensing, MCP-enabled chatbot, Continuous integration) and Community (Documentation, Community forums, MCP server reviews, Shareable collections, Interoperability with tools like BioChatter).

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...

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...