Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 28/09/2026Introducing 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/ 1115
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 21/09/2026EBI news ➡️ www.embl.org/news/science...embl.orgBenchmarking: the foundation of reliable AI in biomedicine | EMBLEstablishing shared evaluation standards to ensure AI models in biology are rigorous, reliable, and reproducible. 032
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 21/09/2026Perspective ➡️ doi.org/10.1038/s415...doi.orgBenchmarking biomedical foundation models - Nature MethodsFoundation models are becoming increasingly popular across various biological domains, yet rigorous methods to comprehensively evaluate their full potential remain underdeveloped. This Perspective dis... 101
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 21/09/2026How 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 👇 133
Reposted by Julio Saez-RodriguezEMBL-EBI @ebi.embl.org · 17/09/2026Closing 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... 095
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 07/09/2026🧵 Introducing Karenina, an open-source framework to evaluate LLMs & agents: doi.org/10.64898/202... 1176
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 20/08/2026Our 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 092
Reposted by Julio Saez-RodriguezSaez-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 014
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 04/08/2026Check out our recent review ➡️ "Towards Principled Evaluation of Single-Cell Perturbation Prediction Models" More on LinkedIn post: lnkd.in/p/dKuF6f7A 051
Reposted by Julio Saez-RodriguezSaez-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/ 1165
Reposted by Julio Saez-RodriguezSaez-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... 1115
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 22/05/2026Our 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. 🙌 0122
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 13/05/20261/🧵 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... 174
Reposted by Julio Saez-RodriguezEMBL-EBI @ebi.embl.org · 25/03/2026We’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 0129
Reposted by Julio Saez-RodriguezSaez-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. 1155
Reposted by Julio Saez-RodriguezEMBL-EBI @ebi.embl.org · 11/03/2026We’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 01619
Reposted by Julio Saez-RodriguezSaez-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 22411
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 02/03/2026Interested 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.orgBenchmarking EGF signaling pathway inference using phosphoproteomics and kinase-substrate interactions - Nature CommunicationsTo what extent can large-scale approaches accurately reconstruct classic signaling pathways? Here, authors revisit the EGF pathway using phosphoproteomics and kinase-substrate interactions 2187
Reposted by Julio Saez-RodriguezEMBL-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.ukBioAIrepo: EMBL-EBI’s hub for life science AI modelsNew EMBL-EBI repository helps researchers share and reuse machine learning models trained on life science data. 1168
Reposted by Julio Saez-RodriguezEMBL-EBI @ebi.embl.org · 25/02/2026We’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 02121
Reposted by Julio Saez-RodriguezEMBL-EBI @ebi.embl.org · 24/02/2026As 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.caIntroducing BEACON: The Benchmarking, Evaluation, and Assessment Consortium for Science - ConscienceWe’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... 042
Julio Saez-Rodriguez @juliosaezrod.bsky.social · 16/02/2026Do 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 🙏 11415
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 12/02/2026On 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 ⬇️ 072
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 12/02/2026Happy 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! 👇 0104
Reposted by Julio Saez-Rodriguezdreamchallenges.bsky.social @dreamchallenges.bsky.social · 01/02/2026Check 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.comDREAM Challenges - ISMB/ECCB 2025 - YouTube 022
Reposted by Julio Saez-RodriguezLaura Cantini @cantinilab.bsky.social · 29/01/2026New 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-qx2iNplnkd.in 054
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 17/12/2025See 👇 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 11410
Reposted by Julio Saez-RodriguezEMBL-EBI @ebi.embl.org · 02/12/2025AI 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.ukConnecting AI to biology: Model Context ProtocolJulio Saez-Rodriguez discusses how MCP servers are helping AI connect to life science databases, making AI a more reproducible tool for research. 0127
Reposted by Julio Saez-RodriguezOpen Targets @opentargets.org · 26/11/2025NEW: 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.comPostdoctoral fellow - Petsalaki Group - NetworkCommonsYour 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... 046
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 20/11/2025📍 Latest OmniPath paper is out now! ➡️ academic.oup.com/nar/advance-... 0125
Julio Saez-Rodriguez @juliosaezrod.bsky.social · 18/11/2025It 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.orglnkd.inLinkedInThis link will take you to a page that’s not on LinkedIn 071
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 07/11/2025📄 BioContextAI is now slightly updated and published @natbiotech.nature.com ➡️ www.nature.com/articles/s41... 055
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 06/11/2025Our 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... 165
Reposted by Julio Saez-RodriguezEMBL 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! 024
Reposted by Julio Saez-RodriguezRémi Trimbour - MD-PhD student @remitrimbour.bsky.social · 30/09/2025Very 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! 🫶 5/5 033
Reposted by Julio Saez-RodriguezRémi Trimbour - MD-PhD student @remitrimbour.bsky.social · 30/09/2025I'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 ⬇️ 143
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 26/09/2025We 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/4shdw8dktinyurl.comCurrent VacanciesWhether 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... 0910
Reposted by Julio Saez-RodriguezSaez-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. 🧶⬇️ 13921
Reposted by Julio Saez-RodriguezSaez-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 1307
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 15/09/2025Introducing 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 12216
Reposted by Julio Saez-RodriguezEMBL-EBI @ebi.embl.org · 03/09/2025Meet 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.ukWelcome: Jess EwaldJess Ewald, Research Group Leader at EMBL-EBI, uses cell profiling and AI to find and characterise chemical hazards to humans and ecosysystems. 0266
Reposted by Julio Saez-RodriguezEMBL-EBI @ebi.embl.org · 12/08/2025Welcome @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.ukWelcome: Tim CoorensEMBL-EBI’s newest Research Group Leader is investigating how somatic mutations reveal the hidden histories of human cells. 24910
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 👇 062
Reposted by Julio Saez-RodriguezSaez-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! 🚀 ✨ 1363
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 25/08/2025We 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 ⬇️ 22613
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 31/07/2025Glad 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! 0114
Reposted by Julio Saez-RodriguezSaez-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 ❗ 035
Reposted by Julio Saez-RodriguezMalte Kuehl @maltekuehl.com · 29/07/2025Preprint 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... 11410
Reposted by Julio Saez-RodriguezSaez-Rodriguez Group @saezlab.bsky.social · 14/07/2025Our 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.orgARISE2Career Accelerator for Research Infrastructure Scientists 044
Reposted by Julio Saez-RodriguezSaez-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 👇 16129