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Julio Saez-Rodriguez

@juliosaezrod.bsky.social
1.4K followers 141 following 10 posts

Computational Biologist, Head of research @ebi.embl.org, part-time Heidelberg University, codirector DREAM challenges. For group's activities, see @saezlab.bsky.social

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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
Saez-Rodriguez Group @saezlab.bsky.social · 21/09/2026
EBI news ➡️ www.embl.org/news/science...
embl.org
Benchmarking: the foundation of reliable AI in biomedicine | EMBL
Establishing shared evaluation standards to ensure AI models in biology are rigorous, reliable, and reproducible.
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Reposted by Julio Saez-Rodriguez
Saez-Rodriguez Group @saezlab.bsky.social · 21/09/2026
Perspective ➡️ doi.org/10.1038/s415...
doi.org
Benchmarking biomedical foundation models - Nature Methods
Foundation models are becoming increasingly popular across various biological domains, yet rigorous methods to comprehensively evaluate their full potential remain underdeveloped. This Perspective dis...
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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
EMBL-EBI @ebi.embl.org · 25/03/2026
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
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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
EMBL-EBI @ebi.embl.org · 11/03/2026
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
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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
Saez-Rodriguez Group @saezlab.bsky.social · 02/03/2026
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...
doi.org
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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EMBL-EBI @ebi.embl.org · 26/02/2026
📢 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...
ebi.ac.uk
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.
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Reposted by Julio Saez-Rodriguez
EMBL-EBI @ebi.embl.org · 25/02/2026
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
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Reposted by Julio Saez-Rodriguez
EMBL-EBI @ebi.embl.org · 24/02/2026
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...
conscience.ca
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...
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Julio Saez-Rodriguez @juliosaezrod.bsky.social · 16/02/2026
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 🙏
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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
dreamchallenges.bsky.social @dreamchallenges.bsky.social · 01/02/2026
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...
youtube.com
DREAM Challenges - ISMB/ECCB 2025 - YouTube
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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
EMBL-EBI @ebi.embl.org · 02/12/2025
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... 🧬💻
ebi.ac.uk
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.
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Reposted by Julio Saez-Rodriguez
Open Targets @opentargets.org · 26/11/2025
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...
embl.wd103.myworkdayjobs.com
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...
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Reposted by Julio Saez-Rodriguez
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
LinkedIn
This link will take you to a page that’s not on LinkedIn
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Reposted by Julio Saez-Rodriguez
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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Reposted by Julio Saez-Rodriguez
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 Events @events.embl.org · 17/10/2025
‼️ Deadline extension alert ‼️ The new abstract submission deadline for #EMBLCardioBiology is 10 November 👉 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!
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Rémi Trimbour - MD-PhD student @remitrimbour.bsky.social · 30/09/2025
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
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Rémi Trimbour - MD-PhD student @remitrimbour.bsky.social · 30/09/2025
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 ⬇️
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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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Reposted by Julio Saez-Rodriguez
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 · 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 · 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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EMBL-EBI @ebi.embl.org · 03/09/2025
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... 🖥️🧬
ebi.ac.uk
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.
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Reposted by Julio Saez-Rodriguez
EMBL-EBI @ebi.embl.org · 12/08/2025
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... 🖥️🧬
ebi.ac.uk
Welcome: Tim Coorens
EMBL-EBI’s newest Research Group Leader is investigating how somatic mutations reveal the hidden histories of human cells.
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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 · 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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Reposted by Julio Saez-Rodriguez
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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Malte Kuehl @maltekuehl.com · 29/07/2025
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...
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).
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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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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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