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Reposted by Julio Saez-Rodriguez

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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Reposted by Julio Saez-Rodriguez

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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Reposted by Julio Saez-Rodriguez

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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Reposted by Julio Saez-Rodriguez

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

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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Reposted by Julio Saez-Rodriguez

EMBL-EBI @ebi.embl.org · Sep 3

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...

🖥️🧬

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.

www.ebi.ac.uk

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Reposted by Julio Saez-Rodriguez

EMBL-EBI @ebi.embl.org · Aug 12

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...
🖥️🧬

Welcome: Tim Coorens

EMBL-EBI’s newest Research Group Leader is investigating how somatic mutations reveal the hidden histories of human cells.

www.ebi.ac.uk

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Julio Saez-Rodriguez @juliosaezrod.bsky.social · Sep 2

@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 👇

EMBL @embl.org · Sep 1

📢 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

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Reposted by Julio Saez-Rodriguez

Saez-Rodriguez Group @saezlab.bsky.social · Sep 1

👋 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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Reposted by Julio Saez-Rodriguez

Saez-Rodriguez Group @saezlab.bsky.social · Aug 25

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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Reposted by Julio Saez-Rodriguez

Saez-Rodriguez Group @saezlab.bsky.social · Jul 31

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!

Malte Kuehl @maltekuehl.com · Jul 29

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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Reposted by Julio Saez-Rodriguez

Saez-Rodriguez Group @saezlab.bsky.social · Aug 14

👀 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 ❗

EMBL-EBI @ebi.embl.org · Aug 13

Recruitment is now open for the EMBL-EBI–Sanger Postdoctoral Programme.

ESPOD builds on the collaborative relationship between EMBL-EBI and the @sangerinstitute.bsky.social, offering projects that combine experimental and computational approaches.

www.ebi.ac.uk/research/pos...

🧬🖥️🔬#postdocjob

ESPOD, the EMBL-EBI/Sanger postdoctoral fellowship. Applications deadline 30 September. Image credit: Karen Arnott / EMBL-EBI

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Reposted by Julio Saez-Rodriguez

Malte Kuehl @maltekuehl.com · Jul 29

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...

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Reposted by Julio Saez-Rodriguez

Saez-Rodriguez Group @saezlab.bsky.social · Jul 14

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...

ARISE2

Career Accelerator for Research Infrastructure Scientists

www.embl.org

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Reposted by Julio Saez-Rodriguez

Saez-Rodriguez Group @saezlab.bsky.social · Jul 22

🎉 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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Reposted by Julio Saez-Rodriguez

Julio Saez-Rodriguez @juliosaezrod.bsky.social · May 16

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

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Reposted by Julio Saez-Rodriguez

Saez-Rodriguez Group @saezlab.bsky.social · Jun 27

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

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Reposted by Julio Saez-Rodriguez

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

👋 Wishing @paubadiam.bsky.social all the best as he leaves our lab to join the Stanford Department of Genetics in @anshulkundaje.bsky.social lab‬! Looking forward to his future contributions to understanding gene regulation through sequence-to-function deep learning models 💻

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Julio Saez-Rodriguez @juliosaezrod.bsky.social · Jun 23

Thanks to @susanallison.bsky.social for her help editing and many @saezlab.bsky.social members for input on the text

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Julio Saez-Rodriguez @juliosaezrod.bsky.social · Jun 23

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

IgAN Atlas

www.iganatlas.org

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Julio Saez-Rodriguez @juliosaezrod.bsky.social · Jun 23

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...

www.nature.com

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Reposted by Julio Saez-Rodriguez

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

🔧 decoupler 2.0.6 is out thanks to @paubadiam.bsky.social‬, now as a core @scverse.bsky.social package scverse.org

This release includes a streamlined API aligned with scverse standards, updated vignettes, and a new one on pseudotime enrichment analysis 👇
decoupler.readthedocs.io/en/latest/

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Reposted by Julio Saez-Rodriguez

Saez-Rodriguez Group @saezlab.bsky.social · May 30

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...

www.cell.com

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Reposted by Julio Saez-Rodriguez

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

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

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Reposted by Julio Saez-Rodriguez

Saez-Rodriguez Group @saezlab.bsky.social · May 22

Great work by @bayraktarlab.bsky.social , @oliverstegle.bsky.social , and @moritzmall.bsky.social ! Happy that our @ahmetrifaioglu.bsky.social contributed to this study by mapping CCC events between spatially co-localized TME and malignant cells using LIANA+ 🧠 github.com/saezlab/lian...

Omer Ali Bayraktar @bayraktarlab.bsky.social · May 16

Over the past 3 years, we led a fantastic @wellcomeleap.bsky.social collaboration w. @oliverstegle.bsky.social, Behjati, Mall, Mair, @jamesbriscoe.bsky.social & @juliosaezrod.bsky.social labs. We created a massive multiomic atlas & new comp models to discover human GB biology www.gbmspace.org

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Reposted by Julio Saez-Rodriguez

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

Happy Birthday @scverse.bsky.social - Our @juliosaezrod.bsky.social has just joined scverse's Management Committee and we look forward to further using & contributing to the ecosystem github.com/saezlab/deco... github.com/saezlab/lian... & more

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