GARRIDO-RODRIGUEZ LAB
Universidad de Córdoba

Translational Systems Biology

We aim to transform large-scale molecular data into actionable biomedical knowledge. We develop experimental and computational approaches to measure and model complex biological systems, studying signal processing from a protein-centric perspective. We focus particularly on how cells process environmental signals, respond to therapeutic perturbations, and communicate with their surroundings. In doing so, we generate testable hypotheses and predictive models to inform translational research and therapeutic decision-making.

Our Research

Proteomics

Studying signal transmission with LC-MS/MS

We develop and apply scalable LC-MS/MS-based proteomics and phosphoproteomics workflows to capture molecular snapshots of biological samples under basal and perturbed conditions, gaining quantitative insight into signaling pathways, cellular states, and treatment-induced molecular responses.

Multi-omics & prior knowledge

Integration with structured biological knowledge

We integrate large-scale molecular readouts, including genomics, transcriptomics, proteomics, phosphoproteomics, and metabolomics, with pathways, regulatory networks, and functional annotations to improve interpretation and prioritize hypotheses for experimental follow-up.

AI & modeling

Predictive modeling of perturbations

Our long-term goal is to build accurate, scalable, and interpretable models that simulate perturbations in biological systems, learning from growing perturbational datasets to predict how cells and tissues respond to drugs, genetic alterations, and environmental change.

Publications

2026

  1. Benchmarking EGF signaling pathway inference using phosphoproteomics and kinase-substrate interactions Garrido-Rodriguez M, Potel CM, Burtscher ML, Becher I, Rodriguez-Mier P, Müller-Dott S, Savitski MM, Saez-Rodriguez J Nature Communications, 17, 2071 (2026) · doi:10.1038/s41467-026-69332-0
  2. Multi-omics and biophysical phosphoproteomics upon BRAF inhibition uncover functional networks of BRAFV600E-driven signaling Burtscher ML, Garrido-Rodriguez M, Mejias PAR, …, Savitski MM bioRxiv (preprint) (2026) · doi:10.64898/2026.02.09.704793

2025

  1. High-throughput peptide-centric local stability assay extends protein–ligand identification to membrane proteins, tissues and bacteria Li K, Potel CM, Becher I, Hüttmann N, Garrido-Rodriguez M, Schwarz J, Burtscher ML, Savitski MM Nature Structural & Molecular Biology, 33, 184–192 (2025) · doi:10.1038/s41594-025-01699-y
  2. Cannabidiol improves metabolic profiles and alleviates liver inflammation and fibrosis in conditions of androgenic obesity and polycystic ovary syndrome Ponce-Díaz FJ, Ruiz-Pino F, Garrido-Rodriguez M, …, Tena-Sempere M Diabetes, Obesity and Metabolism, 27, 6027–6031 (2025) · doi:10.1111/dom.16602
  3. ScAPE: A lightweight multitask learning baseline method to predict transcriptomic responses to perturbations Romero-Tapiador S, Rodriguez-Mier P, Garrido-Rodriguez M, Tolosana R, Morales A, Saez-Rodriguez J bioRxiv (preprint) (2025) · doi:10.1101/2025.09.08.674873
  4. A novel feedback loop between DYRK2 and USP28 regulates cancer homeostasis and DNA damage signaling Suanes-Cobos L, Aguilera-Ventura I, Torres-Ramos M, …, Garrido-Rodriguez M, …, Calzado MA Cell Death & Differentiation, 33, 77–91 (2025) · doi:10.1038/s41418-025-01565-w
  5. Unifying multi-sample network inference from prior knowledge and omics data with CORNETO Rodriguez-Mier P, Garrido-Rodriguez M, Gabor A, Saez-Rodriguez J Nature Machine Intelligence, 7, 1168–1186 (2025) · doi:10.1038/s42256-025-01069-9
  6. Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression Tuechler N, Burtscher ML, Garrido-Rodriguez M, …, Pepperkok R Molecular Systems Biology, 21, 6 (2025) · doi:10.1038/s44320-025-00116-2
  7. Comprehensive evaluation of phosphoproteomic-based kinase activity inference Müller-Dott S, Jaehnig EJ, Munchic KP, …, Garrido-Rodriguez M, …, Saez-Rodriguez J Nature Communications, 16, 4771 (2025) · doi:10.1038/s41467-025-59779-y
  8. What is the current bottleneck in mapping molecular interaction networks? Skinnider MA, Luck K, Mukhtar MS, Garrido-Rodriguez M, …, Krogan NJ Cell Systems, 16, 101295 (2025) · doi:10.1016/j.cels.2025.101295
  9. Uncovering protein glycosylation dynamics and heterogeneity using deep quantitative glycoprofiling (DQGlyco) Potel CM, Burtscher ML, Garrido-Rodriguez M, …, Savitski MM Nature Structural & Molecular Biology, 32, 1111–1126 (2025) · doi:10.1038/s41594-025-01485-w
  10. NetworkCommons: bridging data, knowledge, and methods to build and evaluate context-specific biological networks Paton V, Türei D, Ivanova O, …, Perfetto L, Garrido-Rodriguez M, Saez-Rodriguez J Bioinformatics, 41, btaf048 (2025) · doi:10.1093/bioinformatics/btaf048

2024

  1. Etrinabdione (VCE-004.8), a B55α activator, promotes angiogenesis and arteriogenesis in critical limb ischemia García-Martín A, Prados ME, Lastres-Cubillo I, …, Garrido-Rodriguez M, …, Muñoz E Journal of Translational Medicine, 22, 1003 (2024) · doi:10.1186/s12967-024-05748-w
  2. Investigation in the cannabigerol derivative VCE-003.2 as a disease-modifying agent in a mouse model of experimental synucleinopathy Burgaz S, Navarro E, Rodríguez-Carreiro S, …, Garrido-Rodriguez M, …, Fernández-Ruiz J Behavioral and Brain Functions, 20, 28 (2024) · doi:10.1186/s12993-024-00256-9
  3. Pervasive sublethal effects of agrochemicals on insects at environmentally relevant concentrations Gandara L, Jacoby R, Laurent F, …, Garrido-Rodriguez M, …, Crocker J Science, 386, 446–453 (2024) · doi:10.1126/science.ado0251
  4. Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results Paton V, Ramirez Flores RO, Gabor A, Badia-i-Mompel P, Tanevski J, Garrido-Rodriguez M, Saez-Rodriguez J Nucleic Acids Research, 52, 8100–8111 (2024) · doi:10.1093/nar/gkae552
  5. Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition Burtscher ML, Gade S, Garrido-Rodriguez M, …, Saez-Rodriguez J Molecular Systems Biology, 20, 10 (2024) · doi:10.1038/s44320-024-00025-w

2023

  1. FBXW7 tumor suppressor regulation by dualspecificity tyrosine-regulated kinase 2 Jiménez-Izquierdo R, Morrugares R, Suanes-Cobos L, …, Garrido-Rodriguez M, …, Calzado MA Cell Death & Disease, 14, 202 (2023) · doi:10.1038/s41419-023-05724-0

2022

  1. Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks Garrido-Rodriguez M, Zirngibl K, Ivanova O, Lobentanzer S, Saez-Rodriguez J Molecular Systems Biology, 18, e11036 (2022) · doi:10.15252/msb.202211036
  2. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data Dimitrov D, Türei D, Garrido-Rodriguez M, …, Saez-Rodriguez J Nature Communications, 13, 3224 (2022) · doi:10.1038/s41467-022-30755-0
  3. A novel CDC25A/DYRK2 regulatory switch modulates cell cycle and survival Lara-Chica M, Correa-Sáez A, Jiménez-Izquierdo R, Garrido-Rodriguez M, …, Calzado MA Cell Death & Differentiation, 29, 105–117 (2022) · doi:10.1038/s41418-021-00845-5

2021

  1. Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd Gabor A, Tognetti M, Driessen A, …, Garrido-Rodriguez M, …, Lee M Molecular Systems Biology, 17, e10402 (2021) · doi:10.15252/msb.202110402
  2. EHP-101 alleviates angiotensin II-induced fibrosis and inflammation in mice García-Martín A, Navarrete C, Garrido-Rodriguez M, Prados ME, Caprioglio D, Appendino G, Muñoz E Biomedicine & Pharmacotherapy, 142, 112007 (2021) · doi:10.1016/j.biopha.2021.112007
  3. Betulinic Acid Hydroxamate is Neuroprotective and Induces Protein Phosphatase 2A-Dependent HIF-1α Stabilization and Post-transcriptional Dephosphorylation of Prolyl Hydrolase 2 Prados ME, Correa-Sáez A, Unciti-Broceta JD, Garrido-Rodriguez M, …, Muñoz E Neurotherapeutics, 18, 1849–1861 (2021) · doi:10.1007/s13311-021-01089-4
  4. Implementation of CRISPR/Cas9 Genome Editing to Generate Murine Lung Cancer Models That Depict the Mutational Landscape of Human Disease Hartmann O, Reissland M, Maier CR, …, Garrido-Rodriguez M, …, Diefenbacher ME Frontiers in Cell and Developmental Biology, 9, 641618 (2021) · doi:10.3389/fcell.2021.641618
  5. A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways Garrido-Rodriguez M, Lopez-Lopez D, Ortuno FM, Peña-Chilet M, Muñoz E, Calzado MA, Dopazo J PLOS Computational Biology, 17, e1008748 (2021) · doi:10.1371/journal.pcbi.1008748

2020

  1. Updating dual-specificity tyrosine-phosphorylation-regulated kinase 2 (DYRK2): molecular basis, functions and role in diseases Correa-Sáez A, Jiménez-Izquierdo R, Garrido-Rodriguez M, Morrugares R, Muñoz E, Calzado MA Cellular and Molecular Life Sciences, 77, 4747–4763 (2020) · doi:10.1007/s00018-020-03556-1
  2. Δ9 ‐Tetrahydrocannabinolic acid alleviates collagen‐induced arthritis: Role of PPARγ and CB 1 receptors Palomares B, Garrido-Rodriguez M, Gonzalo-Consuegra C, …, Muñoz E British Journal of Pharmacology, 177, 4034–4054 (2020) · doi:10.1111/bph.15155
  3. Effects of EHP-101 on inflammation and remyelination in murine models of Multiple sclerosis Navarrete C, García-Martin A, Garrido-Rodriguez M, Mestre L, Feliú A, Guaza C, Calzado MA, Muñoz E Neurobiology of Disease, 143, 104994 (2020) · doi:10.1016/j.nbd.2020.104994
  4. Phosphorylation-dependent regulation of the NOTCH1 intracellular domain by dual-specificity tyrosine-regulated kinase 2 Morrugares R, Correa-Sáez A, Moreno R, Garrido-Rodriguez M, Muñoz E, de la Vega L, Calzado MA Cellular and Molecular Life Sciences, 77, 2621–2639 (2020) · doi:10.1007/s00018-019-03309-9
  5. Tetrahydrocannabinolic acid A (THCA-A) reduces adiposity and prevents metabolic disease caused by diet-induced obesity Palomares B, Ruiz-Pino F, Garrido-Rodriguez M, …, Muñoz E Biochemical Pharmacology, 171, 113693 (2020) · doi:10.1016/j.bcp.2019.113693
  6. Cannabidiol induces antioxidant pathways in keratinocytes by targeting BACH1 Casares L, García V, Garrido-Rodriguez M, …, Muñoz E Redox Biology, 28, 101321 (2020) · doi:10.1016/j.redox.2019.101321

2019

  1. Cannabinoid derivatives acting as dual PPARγ/CB2 agonists as therapeutic agents for systemic sclerosis García-Martín A, Garrido-Rodriguez M, Navarrete C, …, Muñoz E Biochemical Pharmacology, 163, 321–334 (2019) · doi:10.1016/j.bcp.2019.02.029
  2. SWATH proteomic profiling of prostate cancer cells identifies NUSAP1 as a potential molecular target for Galiellalactone Garrido-Rodriguez M, Ortea I, Calzado MA, Muñoz E, García V Journal of Proteomics, 193, 217–229 (2019) · doi:10.1016/j.jprot.2018.10.012

2018

  1. EHP-101, an oral formulation of the cannabidiol aminoquinone VCE-004.8, alleviates bleomycin-induced skin and lung fibrosis García-Martín A, Garrido-Rodriguez M, Navarrete C, del Río C, Bellido ML, Appendino G, Calzado MA, Muñoz E Biochemical Pharmacology, 157, 304–313 (2018) · doi:10.1016/j.bcp.2018.07.047
  2. Metabolomic profiling of human lung tumor tissues – nucleotide metabolism as a candidate for therapeutic interventions and biomarkers Moreno P, Jiménez-Jiménez C, Garrido-Rodriguez M, …, Calzado MA Molecular Oncology, 12, 1778–1796 (2018) · doi:10.1002/1878-0261.12369