Martin Garrido-Rodriguez
@martingarridorc.bsky.social
Postdoc Fellow at Saez-Rodriguez and Savitski labs (EMBL). Original from Córdoba, Spain.
Reposted by Martin Garrido-Rodriguez
Finally out! 🤩 Check out our HT- PELSA for high throughput screening！
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 ⬇️
November 5, 2025 at 4:28 PM
Finally out! 🤩 Check out our HT- PELSA for high throughput screening！
Reposted by Martin Garrido-Rodriguez
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 ⬇️
November 5, 2025 at 10:15 AM
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 ⬇️
Reposted by Martin Garrido-Rodriguez
🚨 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
Our 2023 SCP model is now out as a manuscript! Curious about a lightweight baseline for your context generalization task? Check it out 👇
🚨 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 11:02 AM
Our 2023 SCP model is now out as a manuscript! Curious about a lightweight baseline for your context generalization task? Check it out 👇
Reposted by Martin Garrido-Rodriguez
ScAPE: A lightweight multitask learning baseline method to predict transcriptomic responses to perturbations https://www.biorxiv.org/content/10.1101/2025.09.08.674873v1
September 9, 2025 at 7:47 PM
ScAPE: A lightweight multitask learning baseline method to predict transcriptomic responses to perturbations https://www.biorxiv.org/content/10.1101/2025.09.08.674873v1
Reposted by Martin Garrido-Rodriguez
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.
August 20, 2025 at 10:09 AM
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.
Reposted by Martin Garrido-Rodriguez
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!
🧵
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!
🧵
August 4, 2025 at 1:52 PM
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!
🧵
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.
🎉 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 24, 2025 at 7:51 AM
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.
Reposted by Martin Garrido-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 👇
🔗 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 👇
Reposted by Martin Garrido-Rodriguez
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 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.
www.ebi.ac.uk
July 22, 2025 at 9:20 AM
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 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... 🧪
Reposted by Martin Garrido-Rodriguez
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...
Reposted by Martin Garrido-Rodriguez
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
Reposted by Martin Garrido-Rodriguez
Reposted by Martin Garrido-Rodriguez
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
May 30, 2025 at 6:27 AM
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
Reposted by Martin Garrido-Rodriguez
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 🧵👇🏼
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
May 26, 2025 at 6:16 AM
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 🧵👇🏼
Reposted by Martin Garrido-Rodriguez
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
May 23, 2025 at 7:38 AM
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!
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...
www.cell.com
May 22, 2025 at 4:41 PM
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!
www.cell.com/cell-systems...
Big thanks to @juliosaezrod.bsky.social and @cp-cellsystems.bsky.social for the opportunity to contribute!
Reposted by Martin Garrido-Rodriguez
@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...
www.cell.com
May 22, 2025 at 9:25 AM
@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...
Heading back from Boston after attending the Future Developers meeting of the May Institute. Huge thanks to @olgavitek.bsky.social for organizing this meeting, and to all the participants for the great feedback and thoughtful discussions!
Future Developers Meeting – May Institute
computationalproteomics.khoury.northeastern.edu
May 12, 2025 at 6:40 PM
Heading back from Boston after attending the Future Developers meeting of the May Institute. Huge thanks to @olgavitek.bsky.social for organizing this meeting, and to all the participants for the great feedback and thoughtful discussions!
Reposted by Martin Garrido-Rodriguez
Primary article: "Uncovering protein glycosylation dynamics and heterogeneity using deep quantitative glycoprofiling (DQGlyco)" from @savitski-lab.bsky.social et al - equal contribution from @miraburtscher.bsky.social, @martingarridorc.bsky.social, and Clement Potel.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Uncovering protein glycosylation dynamics and heterogeneity using deep quantitative glycoprofiling (DQGlyco) - Nature Structural & Molecular Biology
Here the authors present deep quantitative glycoprofiling (DQGlyco), a method that enables high-throughput analysis of protein glycosylation dynamics. Using DQGlyco, they link gut microbiome compositi...
www.nature.com
May 9, 2025 at 1:43 PM
Primary article: "Uncovering protein glycosylation dynamics and heterogeneity using deep quantitative glycoprofiling (DQGlyco)" from @savitski-lab.bsky.social et al - equal contribution from @miraburtscher.bsky.social, @martingarridorc.bsky.social, and Clement Potel.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Martin Garrido-Rodriguez
Online now - the Spotlight "Accelerating the stride toward functional #glycoproteomics" from @timveth.bsky.social and @nmriley.bsky.social.
#Glycoproteins #Glycoforms #Glycoprofiling #DQGlyco #Glycotime
authors.elsevier.com/a/1l3k53S6Gf...
#Glycoproteins #Glycoforms #Glycoprofiling #DQGlyco #Glycotime
authors.elsevier.com/a/1l3k53S6Gf...
May 9, 2025 at 1:41 PM
Online now - the Spotlight "Accelerating the stride toward functional #glycoproteomics" from @timveth.bsky.social and @nmriley.bsky.social.
#Glycoproteins #Glycoforms #Glycoprofiling #DQGlyco #Glycotime
authors.elsevier.com/a/1l3k53S6Gf...
#Glycoproteins #Glycoforms #Glycoprofiling #DQGlyco #Glycotime
authors.elsevier.com/a/1l3k53S6Gf...
Reposted by Martin Garrido-Rodriguez
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...
High-throughput peptide-centric local stability assay extends protein-ligand identification to membrane proteins, tissues, and bacteria
Systematic mapping of protein-ligand interactions is essential for understanding biological processes and drug mechanisms. Peptide-centric local stability assay (PELSA) is a powerful tool for detectin...
www.biorxiv.org
April 29, 2025 at 6:13 PM
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...
Reposted by Martin Garrido-Rodriguez
🚨 New preprint: Topography Aware Optimal Transport for Alignment of Spatial Omics Data
We present our new alignment framework TOAST www.biorxiv.org/content/10.1...
We present our new alignment framework TOAST www.biorxiv.org/content/10.1...
April 22, 2025 at 9:37 AM
🚨 New preprint: Topography Aware Optimal Transport for Alignment of Spatial Omics Data
We present our new alignment framework TOAST www.biorxiv.org/content/10.1...
We present our new alignment framework TOAST www.biorxiv.org/content/10.1...
Reposted by Martin Garrido-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 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... 👇
March 14, 2025 at 10:34 AM
📄 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 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... 👇
Reposted by Martin Garrido-Rodriguez
Congrats to our @juliosaezrod.bsky.social and all other elected fellows of the International Society for Computational Biology (ISCB) as part of the 2025 Class
🌟 Congrats to the 2025 ISCB Fellows! 🌟 Honoring leaders in #computationalbiology for outstanding research, innovation and service. See this year's Fellows and their contributions here: https://t.ly/VYfLk
March 17, 2025 at 6:03 PM
Congrats to our @juliosaezrod.bsky.social and all other elected fellows of the International Society for Computational Biology (ISCB) as part of the 2025 Class