¿Te interesa la biología computacional? #JABI2026 reunirá a grupos de investigación computacionales y no computacionales del sur de España y de otras regiones interesados en desarrollar aplicar herramientas bioinformáticas en su investigación. No te lo pierdas, ¡únete!

Jornadas Andaluzas de Bioinformática #JABI2026@jabi-conference.bsky.social · 5mo ago

¿Aún no has enviado tu contribución? Las #JABI2026 amplían el plazo de envío de contribuciones hasta el viernes 27 de marzo. Si estabas ultimando detalles o necesitabas algo más de tiempo, esta es tu oportunidad para participar y compartir tu trabajo con la comunidad.

Is the linear map of cell signaling a myth? New research suggests the reality of cellular networks is more complex. @savitski-lab.bsky.social & @saezlab.bsky.social combined experimental and computational expertise to test how we map kinase–substrate interactions. www.nature.com/articles/s41...

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

nature.com

Phosphorylation-driven signaling plays a central role in how cells communicate. In this study, together with @saezlab.bsky.social , we revisit the EGF signaling pathway and ask: How well does our traditional understanding hold up in the era of modern phosphoproteomics? www.nature.com/articles/s41...

Saez-Rodriguez Group@saezlab.bsky.social · 6mo ago

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...

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

One of the main stories of my postdoc is finally out! It builds on an intuition from my early days in omics data analysis: our signaling pathways are simply too small, underrepresenting cellular complexity after stimulation. Something obvious, yet surprisingly hard to quantify.

Saez-Rodriguez Group@saezlab.bsky.social · 6mo ago

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...

10 years and still standing strong @EMBL 🍾💪 Huge thanks to all members, alumni, supporters & colleagues who made it possible. Here’s to the next decade! 🙏

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 · 6mo ago

Rewiring 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

When I first learned about omics at university, I confidently stopped caring about single proteins. Fast-forward 4 years of a system’s biology PhD, I now have the most amazing favorite single protein which I can’t stop thinking about. Here is the story of how that happened 👀

Savitski Lab@savitski-lab.bsky.social · 6mo ago

Rewiring 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

Rewiring 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

Muy contento de estar de vuelta en casa para las #JABI2026. ¡Gracias por la invitación! ---- Happy to be back home for #JABI2026. Thanks for the invitation!

Jornadas Andaluzas de Bioinformática #JABI2026@jabi-conference.bsky.social · 7mo ago

🔔¡Ponente confirmado!🔔 Del análisis ómico descriptivo a modelos predictivos in silico. No te pierdas la charla plenaria en las #JABI2026 con Martin Garrido-Rodríguez, PhD (@martingarridorc.bsky.social)

Want to learn about the theoretical aspects of proteins/peptides analysis by mass spectrometry? Then join the #EMBLProteomics course where you will get hands-on experience in sample preparation and perform tandem mass tag labelling. Apply by 3 March:https://s.embl.org/sdp26-01-bl 🔬💻

New preprint 🚨 We systematically measured 17 million phospho-specific dose-response curves (133 kinase inhibitors × 5 cell lines) to decrypt the kinases that shape the human phosphoproteome. We show that drug perturbation potency (not effect size) links kinases to substrates while controlling FDR.

Florian P Bayer@flobayer.bsky.social · 9mo ago

Did you ever come across a phosphosite in your proteomics data for which nothing was known? - I bet so! We have developed a new strategy termed "potency coherence analysis" that leverages the drug potency dimension in decryptM to decode the kinases that shape the human phosphoproteome. Read more:

Finally out! 🤩 Check out our HT- PELSA for high throughput screening！

Savitski Lab@savitski-lab.bsky.social · 9mo ago

Happy to see our HT-PELSA paper now published in @natsmb.nature.com 🎊 Big thanks for the constructive review process! 📖Read the manuscript here (www.nature.com/articles/s41...) & check the thread for additional information ⬇️

Happy to see our HT-PELSA paper now published in @natsmb.nature.com 🎊 Big thanks for the constructive review process! 📖Read the manuscript here (www.nature.com/articles/s41...) & check the thread for additional information ⬇️

High-throughput peptide-centric local stability assay extends protein–ligand identification to membrane proteins, tissues and bacteria - Nature Structural & Molecular Biology

Li et al. further develop a high-throughput peptide-centric local stability assay that speeds up sample preparation 100-fold and extends protein–ligand identification to membrane proteins, tissues and...

nature.com

Savitski Lab@savitski-lab.bsky.social · last yr.

Want to know how the ligands interact with proteins beyond model cell lines, e.g., in tissues or bacteria? Interested in membrane targets? Check out our High-Throughput PELSA method which allows you do all these cool screenings for dozens of ligands within two hours! www.biorxiv.org/content/10.1...

🚨 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

Our 2023 SCP model is now out as a manuscript! Curious about a lightweight baseline for your context generalization task? Check it out 👇

Saez-Rodriguez Group@saezlab.bsky.social · 11mo ago

🚨 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

ScAPE: A lightweight multitask learning baseline method to predict transcriptomic responses to perturbations https://www.biorxiv.org/content/10.1101/2025.09.08.674873v1

So grateful and honored to receive the MCP Lectureship Award at the #ASBMBProteomics meeting at the Broad Institute! Huge thanks to the wonderful organizers and to everyone—past and present—who’s been part of our lab.

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉 www.nature.com/articles/s41... We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures! 🧵

This project has been in the making for quite some time. CORNETO not only integrates key concepts and methodologies in biological network inference, but also introduces a novel framework for multi-condition analysis. Congrats to the team, and especially to @pablormier.bsky.social for leading this.

Saez-Rodriguez Group@saezlab.bsky.social · last yr.

🎉 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 👇

🎉 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 👇

How can we find out what’s really going on inside cells when we’re generating so much complex data? CORNETO is an open-source tool that uses machine learning to turn tangled omics datasets into clear maps of how genes, proteins, and signalling pathways interact. www.ebi.ac.uk/about/news/r... 🧪

CORNETO: machine learning to decode complex omics data

New tool combines biological knowledge with machine learning to help researchers extract meaningful insights from complex omics data.

ebi.ac.uk

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...

Leveraging data as a patient–scientist: frustrations and opportunities - Nature Reviews Nephrology

The transition from data scientist to patient–scientist has given me new perspectives into clinical research and strengthened my commitment to open science. Although limitations on data availability h...

nature.com

The 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

In this Voices article, our @martingarridorc.bsky.social & @juliosaezrod.bsky.social discuss key strategies for building context-specific molecular networks: knowledge and data-driven methods, + future directions in the field bridging to structures and perturbations tinyurl.com/z8t6yych

What is the current bottleneck in mapping molecular interaction networks?

Network biologists today have access to a rich assortment of interaction networks produced by assays such as affinity purification-mass spectrometry (AP-MS), yeast two-hybrid (Y2H) screening, co-fract...

cell.com

Very excited that another chapter of my PhD is finally out! 🎉 We compared methods to infer kinase activities from #phosphoproteomics data so check it out if that sounds interesting to you. More details in the thread below 🧵👇🏼

Saez-Rodriguez Group@saezlab.bsky.social · last yr.

Ever 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

Ever 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

We have shared some thoughts on the key challenges in mapping molecular interaction networks in this article. Check it out 👇! www.cell.com/cell-systems... Big thanks to @juliosaezrod.bsky.social and @cp-cellsystems.bsky.social for the opportunity to contribute!

What is the current bottleneck in mapping molecular interaction networks?

Network biologists today have access to a rich assortment of interaction networks produced by assays such as affinity purification-mass spectrometry (AP-MS), yeast two-hybrid (Y2H) screening, co-fract...

cell.com

@cp-cellsystems.bsky.social organized a set of short commentaries on: "What is the current bottleneck in mapping molecular interaction networks?" with contributions from many scientists working on these problems. www.cell.com/cell-systems...

What is the current bottleneck in mapping molecular interaction networks?

Network biologists today have access to a rich assortment of interaction networks produced by assays such as affinity purification-mass spectrometry (AP-MS), yeast two-hybrid (Y2H) screening, co-fract...

cell.com