Saez-Rodriguez Group
@saezlab.bsky.social
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/
Website: https://saezlab.org/
GitHub: https://github.com/saezlab/
Pinned
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
Also juliosaezrod.bsky.social has recently joined Bluesky
go.bsky.app/5ZtPHPz
📍 Latest OmniPath paper is out now! ➡️ academic.oup.com/nar/advance-...
🥁 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.
🧶⬇️
📖 Preprint: www.biorxiv.org/content/10.1...
🔍 Explorer: explore.omnipathdb.org
OmniPath integrates 160+ resources for multi-omics analysis & modeling.
🧶⬇️
November 20, 2025 at 10:09 AM
📍 Latest OmniPath paper is out now! ➡️ academic.oup.com/nar/advance-...
Reposted by Saez-Rodriguez Group
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
reflecting from my perspective as patient-scientist (www.nature.com/articles/s41...) & sharing work of @saezlab.bsky.social sp. within www.iganatlas.org
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
November 18, 2025 at 3:05 PM
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
reflecting from my perspective as patient-scientist (www.nature.com/articles/s41...) & sharing work of @saezlab.bsky.social sp. within www.iganatlas.org
📄 BioContextAI is now slightly updated and published @natbiotech.nature.com
➡️ www.nature.com/articles/s41...
➡️ www.nature.com/articles/s41...
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!
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!
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...
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...
November 7, 2025 at 1:57 PM
📄 BioContextAI is now slightly updated and published @natbiotech.nature.com
➡️ www.nature.com/articles/s41...
➡️ www.nature.com/articles/s41...
Our 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...
doi.org/10.1101/2024...
November 6, 2025 at 12:10 PM
Our 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...
Reposted by Saez-Rodriguez Group
Bonjour! Masters students in France 🇫🇷, we’ve got an internship for you, in collaboration with the French Embassy in London.
Aimed at students of computer science, statistics or bioinformatics.
Deadline: 7 December 2025
Find out more and apply:
www.ebi.ac.uk/about/jobs/i...
Aimed at students of computer science, statistics or bioinformatics.
Deadline: 7 December 2025
Find out more and apply:
www.ebi.ac.uk/about/jobs/i...
November 3, 2025 at 11:00 AM
Bonjour! Masters students in France 🇫🇷, we’ve got an internship for you, in collaboration with the French Embassy in London.
Aimed at students of computer science, statistics or bioinformatics.
Deadline: 7 December 2025
Find out more and apply:
www.ebi.ac.uk/about/jobs/i...
Aimed at students of computer science, statistics or bioinformatics.
Deadline: 7 December 2025
Find out more and apply:
www.ebi.ac.uk/about/jobs/i...
👋 @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! 🍀
October 6, 2025 at 6:51 AM
👋 @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! 🍀
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
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
September 26, 2025 at 10:16 AM
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
Details & apply by 13/10/25: tinyurl.com/4shdw8dk
🚨 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
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
September 19, 2025 at 7:45 AM
🚨 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
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
🥁 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.
🧶⬇️
📖 Preprint: www.biorxiv.org/content/10.1...
🔍 Explorer: explore.omnipathdb.org
OmniPath integrates 160+ resources for multi-omics analysis & modeling.
🧶⬇️
September 17, 2025 at 1:10 PM
🥁 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.
🧶⬇️
📖 Preprint: www.biorxiv.org/content/10.1...
🔍 Explorer: explore.omnipathdb.org
OmniPath integrates 160+ resources for multi-omics analysis & modeling.
🧶⬇️
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
🔗 Manuscript: www.biorxiv.org/content/10.1...
💻 Code: partipy.readthedocs.io
September 15, 2025 at 8:40 AM
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
🔗 Manuscript: www.biorxiv.org/content/10.1...
💻 Code: partipy.readthedocs.io
Reposted by Saez-Rodriguez Group
@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
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
September 2, 2025 at 6:55 PM
@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 👇
👋 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! 🚀 ✨
September 1, 2025 at 5:35 AM
👋 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! 🚀 ✨
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 ⬇️
🔗
www.biorxiv.org/content/10.1...
📦
saezlab.github.io/MetaProViz/
🧵 Thread ⬇️
August 25, 2025 at 7:07 AM
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 ⬇️
🔗
www.biorxiv.org/content/10.1...
📦
saezlab.github.io/MetaProViz/
🧵 Thread ⬇️
👀 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 ❗
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 ❗
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 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
August 14, 2025 at 9:05 AM
👀 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 ❗
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 ❗
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!
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!
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...
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...
July 31, 2025 at 7:37 AM
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!
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!
🎉 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 👇
🔗 Paper: www.nature.com/articles/s42...
📖 News & Views: www.nature.com/articles/s42...
💻 Code: corneto.org
🧵 Thread 👇
July 22, 2025 at 3:23 PM
🎉 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 👇
🔗 Paper: www.nature.com/articles/s42...
📖 News & Views: www.nature.com/articles/s42...
💻 Code: corneto.org
🧵 Thread 👇
Four more days to apply to our postdoctoral position 👇
Postdoc position in our group at @ebi.embl.org about analyzing single cell data sets to better understand and treat neurodegen diseases, in collab with A Bassett, M Lotfollahi, @bayraktarlab.bsky.social, M Strauss and others within Open Targets. Deadline 20/07.
Please share
tinyurl.com/87wj466m
Please share
tinyurl.com/87wj466m
Postdoctoral Fellow in computational modelling of NeuroImmune Mechanisms of Neurodegeneration (Open Targets)
Your role As a Postdoctoral Fellow on the NeuroImmune Open Targets project, you will develop and apply integrative computational pipelines to dissect immune-cell phenotypes and cell–cell interactions ...
tinyurl.com
July 16, 2025 at 5:32 PM
Four more days to apply to our postdoctoral position 👇
Four more days to apply to our curator position 👇
We have a curator position at @ebi.embl.org to work with GSK within a project to understand fibrotic processes (no PhD required). Deadline 20th July.
Please share 🙏
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Please share 🙏
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Scientific Database Curator – Fibrosis Transcriptomics
We are seeking a technically skilled and biologically literate Scientific Database Curator to join a focused initiative on fibrosis research, hosted at EMBL-EBI in collaboration with the Saez-Rodrigue...
embl.wd103.myworkdayjobs.com
July 16, 2025 at 5:31 PM
Four more days to apply to our curator position 👇
Reposted by Saez-Rodriguez Group
Don't miss talks in our sponsored Dialogue for Reverse Engineering Assessment and Methods – DREAM – session, kicking off with a talk by our Head of Research, @juliosaezrod.bsky.social on benchmarking foundation models in biology
www.iscb.org/ismbeccb2025...
#ISMB2025
www.iscb.org/ismbeccb2025...
#ISMB2025
July 14, 2025 at 9:10 AM
Don't miss talks in our sponsored Dialogue for Reverse Engineering Assessment and Methods – DREAM – session, kicking off with a talk by our Head of Research, @juliosaezrod.bsky.social on benchmarking foundation models in biology
www.iscb.org/ismbeccb2025...
#ISMB2025
www.iscb.org/ismbeccb2025...
#ISMB2025
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...
www.embl.org/training/ari...
ARISE2
Career Accelerator for Research Infrastructure Scientists
www.embl.org
July 14, 2025 at 9:59 AM
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...
www.embl.org/training/ari...
Postdoc position in our group at @ebi.embl.org about analyzing single cell data sets to better understand and treat neurodegen diseases, in collab with A Bassett, M Lotfollahi, @bayraktarlab.bsky.social, M Strauss and others within Open Targets. Deadline 20/07.
Please share
tinyurl.com/87wj466m
Please share
tinyurl.com/87wj466m
Postdoctoral Fellow in computational modelling of NeuroImmune Mechanisms of Neurodegeneration (Open Targets)
Your role As a Postdoctoral Fellow on the NeuroImmune Open Targets project, you will develop and apply integrative computational pipelines to dissect immune-cell phenotypes and cell–cell interactions ...
tinyurl.com
July 2, 2025 at 9:30 AM
Postdoc position in our group at @ebi.embl.org about analyzing single cell data sets to better understand and treat neurodegen diseases, in collab with A Bassett, M Lotfollahi, @bayraktarlab.bsky.social, M Strauss and others within Open Targets. Deadline 20/07.
Please share
tinyurl.com/87wj466m
Please share
tinyurl.com/87wj466m
We have a curator position at @ebi.embl.org to work with GSK within a project to understand fibrotic processes (no PhD required). Deadline 20th July.
Please share 🙏
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Please share 🙏
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Scientific Database Curator – Fibrosis Transcriptomics
We are seeking a technically skilled and biologically literate Scientific Database Curator to join a focused initiative on fibrosis research, hosted at EMBL-EBI in collaboration with the Saez-Rodrigue...
embl.wd103.myworkdayjobs.com
July 2, 2025 at 9:29 AM
We have a curator position at @ebi.embl.org to work with GSK within a project to understand fibrotic processes (no PhD required). Deadline 20th July.
Please share 🙏
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Please share 🙏
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Saez-Rodriguez Group
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
June 23, 2025 at 6:19 AM
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...
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
June 27, 2025 at 1:29 PM
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
👋 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 💻
June 23, 2025 at 11:26 AM
👋 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 💻