Julio Saez-Rodriguez
@juliosaezrod.bsky.social
Computational Biologist, Head of research @ebi.embl.org, part-time Heidelberg University, codirector DREAM challenges. For group's activities, see @saezlab.bsky.social
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
Saez-Rodriguez Group@saezlab.bsky.social · last yr.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 ⬇️
⬇️ Check out this new postdoctoral fellowship to be jointly hosted by Mathew Garnett's lab and our lab! lnkd.in/p/eZUYhWmz
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...
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...
We’re recruiting new Research Group Leaders. We offer: 🔬 World-class IT infrastructure 🧠 Creative freedom for your research 📊 Access to the world’s most comprehensive open biological data Apply by 11 April embl.wd103.myworkdayjobs.com/en-US/EMBL/j... #ResearchCareers @johnlees.bacpop.org @embl.org
🧵 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.
We’re recruiting new Research Group Leaders! Why join? 🌍Work across EMBL’s 6 sites 🎓Participate in @embl.org courses and seminars 🔬Lead discovery-driven research in a collaborative environment Apply by 11 April: embl.wd103.myworkdayjobs.com/en-US/EMBL/j... #ResearchCareers @epetsalaki.bsky.social
🧵 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
doi.org
📢 We want your feedback on our new pilot project for sharing AI models in life science research. Finding, reusing and citing machine learning models remains a major challenge in the life sciences. BioAIrepo is here to help. www.ebi.ac.uk/about/news/t...
BioAIrepo: EMBL-EBI’s hub for life science AI models
New EMBL-EBI repository helps researchers share and reuse machine learning models trained on life science data.
ebi.ac.uk
We’re recruiting new Research Group Leaders! We offer: 🔬 Core funding 💻 Access to world-leading infrastructure 👩🏽🔬A network of world-leading scientists …and much more. Apply by 11 April: embl.wd103.myworkdayjobs.com/en-US/EMBL/j... #ResearchCareers #Bioinformatics @timcoorens.bsky.social @embl.org
As AI is transforming science, robust benchmarks become essential. BEACON is a global initiative advancing standards to evaluate AI using transparent benchmarks and #opendata. #OpenScience #AI #DrugDiscovery @conscience-network.bsky.social @juliosaezrod.bsky.social conscience.ca/news/introdu...
Introducing BEACON: The Benchmarking, Evaluation, and Assessment Consortium for Science - Conscience
We’re pleased to announce the launch of BEACON, a new open benchmarking consortium established through a collaborative effort by its founding partners from five organizations with deep expertise and p...
conscience.ca
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 🙏
EMBL-EBI@ebi.embl.org · 7mo agoWe’re hiring: Research Group Leader in computational biology. Are you generating more research ideas than you can explore? Lead cutting-edge AI & biology research at EMBL-EBI. Apply by 11 April 2026: embl.wd103.myworkdayjobs.com/en-US/EMBL/j... #ScienceCareers @ewaldlab.org @embl.org
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 · 8mo agoWe'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. 🧬🖥️📊
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 · 7mo agoRewiring 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
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...
DREAM Challenges - ISMB/ECCB 2025 - YouTube
youtube.com
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
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
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... 🧬💻
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.
ebi.ac.uk
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...
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...
embl.wd103.myworkdayjobs.com
📍 Latest OmniPath paper is out now! ➡️ academic.oup.com/nar/advance-...
Saez-Rodriguez Group@saezlab.bsky.social · 12mo 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
This link will take you to a page that’s not on LinkedIn
lnkd.in
📄 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 agoWhat 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...
‼️ 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