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Saez-Rodriguez Group

@saezlab.bsky.social

1.8K followers 42 following 130 posts

Account of the Saez-Rodriguez lab at EMBL-EBI and Heidelberg University. We integrate #omics data with mechanistic molecular knowledge into #opensource #ML methods Website: https://saezlab.org/ GitHub: https://github.com/saezlab/

saezlab.org

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Saez-Rodriguez Group @saezlab.bsky.social · Nov 20

We have created a starterpack to make it easier to follow current members and alumni from our lab, check it out 👇 (DM us if we forgot about you)
Also juliosaezrod.bsky.social has recently joined Bluesky
go.bsky.app/5ZtPHPz

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Saez-Rodriguez Group @saezlab.bsky.social · 2d

👋 @veronicalombardi.bsky.social has completed her 6-month visit period with us. She is a PhD student from the University of Rome La Sapienza, and her contribution focused on generating single-cell and patient-specific networks of pancreatic cancer using our tools LIANA+ and CORNETO. All the best! 🍀

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Saez-Rodriguez Group @saezlab.bsky.social · 12d

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

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...

tinyurl.com

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Saez-Rodriguez Group @saezlab.bsky.social · 19d

It was also supported by projects: AI4FOOD-CM (Y2020/TCS6654), FACINGLCOVID-CM (PD2022-004-REACT-EU), INTER-ACTION (PID2021-126521OB-I00 MICINN/FEDER), HumanCAIC (TED2021-131787BI00 MICINN), PowerAI+ (SI4/PJI/2024-00062 Comunidad de Madrid and UAM), and Cátedra ENIA UAM-VERIDAS.

Saez-Rodriguez Group @saezlab.bsky.social · 19d

This work was supported through state funds approved by the State Parliament of Baden-Württemberg for the Innovation Campus Health + Life Science Alliance Heidelberg Mannheim.

Saez-Rodriguez Group @saezlab.bsky.social · 19d

This work was a nice collaboration with Ph.D. student Sergio Romero, supervised by professors Ruben Tolosana and Aythami Morales (UAM, Spain), who was visiting us for 3 months to work on this project with @pablormier.bsky.social and @martingarridorc.bsky.social.

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Saez-Rodriguez Group @saezlab.bsky.social · 19d

🔧 We developed ScAPE using #Keras 3, so you can use #Tensorflow, #JAX or #PyTorch as backends
👉 github.com/scapeML/scape

GitHub - scapeML/scape: Single-cell Analysis of Perturbational Effects using Machine Learning

Single-cell Analysis of Perturbational Effects using Machine Learning - scapeML/scape

github.com

Saez-Rodriguez Group @saezlab.bsky.social · 19d

We benchmarked ScAPE against:
🔹 Other winning challenge methods
🔹 TabPFN, a foundation model for tabular data

➡️ ScAPE matches or outperforms them, showing the value of simple, efficient baselines.

Saez-Rodriguez Group @saezlab.bsky.social · 19d

Despite its simplicity, ScAPE ranked among the top methods in the challenge.
It generalizes across new drug–cell combinations and offers a robust baseline for evaluating novel approaches.

Saez-Rodriguez Group @saezlab.bsky.social · 19d

✨ ScAPE (Single Cell Analysis of Perturbational Effects)

- Lightweight neural network (∼19M params)
- Uses only aggregated gene-level stats (robust + simple)
- Multi-task: predicts both significance (p-values) & effect size (fold-change)

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Saez-Rodriguez Group @saezlab.bsky.social · 19d

Predicting how cells respond to drugs is central to drug discovery & precision medicine. But existing models often struggle to generalize, and don’t always beat simple baselines.

Saez-Rodriguez Group @saezlab.bsky.social · 19d

🚨 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 · 21d

We also gratefully acknowledge our funding support from:
• The Landesinstitut für Bioinformatikinfrastruktur in Baden-Württemberg
• The German Research Foundation (DFG)
• The European Union’s Horizon 2020 Programme
• UKRI Biotechnology and Biological Sciences Research Council (BBSRC)
• TUBITAK ARDEB

Saez-Rodriguez Group @saezlab.bsky.social · 21d

👏 A huge thank you to all 32 authors from @saezlab.bsky.social, @ebi.embl.org and Heidelberg University, Korcsmaros group #ICL, Tunca Dogan’s team at Hacettepe University, Michal Klein @fabiantheis.bsky.social, Francesco Ceccarelli, and everyone else for their fantastic work!

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Saez-Rodriguez Group @saezlab.bsky.social · 21d

🎯 OmnipathR is more than a client—it's a 🛠️ Swiss Army knife for prior knowledge. Access OmniPath and 25+ more databases, translate IDs, and get dedicated support for #metabolomics
➡️ Check it out: r.omnipathdb.org #RStats

Saez-Rodriguez Group @saezlab.bsky.social · 21d

📊 OmniPath was built for #NetworkBiology. Use it for:
• Network analysis directly in Cytoscape (apps.cytoscape.org/apps/omnipath)
• Mechanistic modeling with Corneto (corneto.org) and NetworkCommons

Saez-Rodriguez Group @saezlab.bsky.social · 21d

🔬 Perfect for #singlecell and #spatialomics analysis! The 🐍 #Python client plugs directly into @scverse.bsky.social. Use OmniPath with tools like 🧩 decoupler.readthedocs.io and 🧩 liana-py.readthedocs.io for pathway activity prediction, automated cell annotation, cell-cell communication and more.

Saez-Rodriguez Group @saezlab.bsky.social · 21d

⚙️ Integrate @omnipath.bsky.social directly into your #Bioinformatics workflows. We provide a web service, and powerful clients for R (@bioconductor.bsky.social), Python (@scverse.bsky.social), and Cytoscape. License compliance for companies built-in! ⚖️ 🤑

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Saez-Rodriguez Group @saezlab.bsky.social · 21d

🤖✨ Dive into OmniPath Explorer - Interactively browse millions of annotations & hundreds of thousands of molecular interactions. Our new AI chat agent helps you query the database effortlessly, developed by Jonathan @jonsch.one!

Saez-Rodriguez Group @saezlab.bsky.social · 21d

🧬 What's inside? Literature-curated, mechanistic data is our core:
• Signaling & gene regulatory pathways
• miRNA interactions & enzyme-PTM relationships
• Protein complexes & cell-cell communication
• Functional, localization, & structural annotations
...plus high-throughput & predicted knowledge.

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Saez-Rodriguez Group @saezlab.bsky.social · 21d

🥁 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 · 23d

This work was led by @psl-schaefer.bsky.social, with support from Leoni Zimmermann, Leo Burmedi, @tanevski.bsky.social ‬, Miri Adler and her team (A. Walfisch, N. Goldenberg, S. Yonassi, E. Shaer Tamar). @juliosaezrod.bsky.social ‪‬and @ricoramirez.bsky.social supervised the work.

Saez-Rodriguez Group @saezlab.bsky.social · 23d

Beyond single-cell measurements, ParTI has been applied to cognition, behavior, and morphology. With ParTIpy, these applications become more accessible through a modern, scalable Python implementation. Have a try and share with us your feedback.

Saez-Rodriguez Group @saezlab.bsky.social · 23d

ParTIpy provides tools to assess model fit, explore archetypes, and run downstream analyses. Features like enrichment, cell–cell communication, and spatial mapping support single-cell data, while scverse.bsky.social integration ensures compatibility with other tools.

scverse (@scverse.bsky.social)

Foundational tools for omics data (mostly in python).

scverse.bsky.social

Saez-Rodriguez Group @saezlab.bsky.social · 23d

ParTIpy scales this framework to large-scale datasets by combining advances in initialization, optimization and coreset methods for archetypal analysis, the algorithmic backbone of ParTI.

Saez-Rodriguez Group @saezlab.bsky.social · 23d

Pareto Task Inference (ParTI), pioneered by @urialonlab.bsky.social team, models variability as trade-offs between archetypal functions. Unlike clustering, it captures continuous variation in a principled way. Offering an alternative to cell-state definitions, for example.

Uri Alon (@urialonlab.bsky.social)

The Alon lab explores design principles of biological circuits, focusing on systems medicine, aging, and healthspan.

urialonlab.bsky.social