Julio Saez-Rodriguez
Computational Biologist, Head of research @ebi.embl.org, part-time
Heidelberg University, codirector DREAM challenges. For group's activities, see @saezlab.bsky.social
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-RodriguezNew 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
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-RodriguezNEW: 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...
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- 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
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-RodriguezOur 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...
- 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...
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-RodriguezWe 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
- Reposted by Julio Saez-Rodriguez🥁 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. 🧶⬇️
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-RodriguezIntroducing 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
- Reposted by Julio Saez-RodriguezMeet 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... 🖥️🧬
- Reposted by Julio Saez-RodriguezWelcome @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 👇
- 📢 Recruitment for the EMBL International PhD Programme is officially open! At EMBL, we train young scientists to become skilled and creative future leaders in academia and other sectors. Join us and get a head start on your career in life sciences! bit.ly/47mmiFF
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-RodriguezWe 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 ⬇️
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-RodriguezOur 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...
- Reposted by Julio Saez-Rodriguez🎉 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 👇
- Reposted by Julio Saez-RodriguezThe final version of our multi-omics study on kidney fibrosis is out now (tinyurl.com/kidneyfibMSB). Together w/ Pepperkok + Savitski labs @embl.org, we present a time-resolved #multiomics + computational network modeling approach in combination w/ phenotypic assays to study #kidneyfibrosis
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- I wrote a short piece on how becoming an IgA Nephropathy patient has changed my perspective on biomedical research, developing an appreciation for the challenges in data interpretability & availability and the importance of patient engagement www.nature.com/articles/s41...
- It also reinforced my belief in open science & collaboration. Inspired by @kpmproject.bsky.social we have built the IgAN atlas www.iganatlas.org w J. Barratt, R. Duivenvoorden, L. Gesualdo, M. Kretzler, L. Gerhardt, J. Nystrom, K. Bull, H. Olauson, A. Wernerson and we are open to collaborate
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-RodriguezEver wondered which method to use to infer kinase activities from phosphoproteomics data? 💻💭Our revised comprehensive evaluation of kinase activity inference tools, done in collaboration with the Zhang lab @bcmhouston.bsky.social, is now out @natcomms.nature.com 🔬 tinyurl.com/4twuc6z4
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- join us at ISMB iscb.bsky.social & @dreamchallenges.bsky.social - benchmarking foundation models w. @anshulkundaje.bsky.social @oldbap.bsky.social G. Stolovitzky @bowang87.bsky.social @mariabrbic.bsky.social K. Kalantar, J. Guinney supported by @ebi.embl.org @cziscience.bsky.social Tempus AI
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-Rodriguez📄 Update on our preprint about Gene Regulatory Net (GRN) benchmarking 📄 We have included the original and decoupled version of SCENIC+, added a new metric and two more databases. Dictys and SCENIC+ outperformed others, but still performed poorly in causal mechanistic tasks. doi.org/10.1101/2024... 👇
- We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇 Paper: doi.org/10.1101/2024.12.20.629764 Code: github.com/saezlab/greta
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Reposted by Julio Saez-Rodriguez[Not loaded yet]
- Post-doc opening to join our lab @ebi.embl.org to develop&apply #bioinformatics and #machine-learning methods to study intra-/extra cellular networks to extract disease mechanisms from #single-cell and #spatial multiomic data - please share 🙏 : embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
