Selected publications – Saez-Rodriguez group

Unifying multi-sample network inference from prior knowledge and omics data with CORNETO.

Rodriguez-Mier, P., Garrido-Rodriguez, M., Gabor, A., Saez-Rodriguez J.

Nat Mach Intell, 2025

doi:10.1038/s42256-025-01069-9

Comprehensive evaluation of phosphoproteomic-based kinase activity inference.

Müller-Dott S, Jaehnig EJ, Munchic KP, Jiang W, Yaron-Barir TM, Savage SR, Garrido-Rodriguez M, Johnson JL, Lussana A, Petsalaki E, Lei JT, Dugourd A, Krug K, Cantley LC, Mani DR, Zhang B, Saez-Rodriguez J.

Nat Commun, 2025

doi:10.1038/s41467-025-59779-y.

Learning tissue representation by identification of persistent local patterns in spatial omics data.

Tanevski J, Vulliard L, Ibarra-Arellano MA, Schapiro D, Hartmann FJ, Saez-Rodriguez J.

Nat Commun, 2025

doi:10.1038/s41467-025-59448-0.

A platform for the biomedical application of large language models.

Lobentanzer S, Feng S, Bruderer N, Maier A, BioChatter Consortium, Wang C, Baumbach J, Abreu-Vicente J, Krehl N, Ma Q, Lemberger T, Saez-Rodriguez J.

Nat Biotechnol, 2025

doi:10.1038/s41587-024-02534-3.

Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions.

Lerma-Martin C, Badia-I-Mompel P, Ramirez Flores RO, Sekol P, Schäfer PSL, Riedl CJ, Hofmann A, Thäwel T, Wünnemann F, Ibarra-Arellano MA, Trobisch T, Eisele P, Schapiro D, Haeussler M, Hametner S, Saez-Rodriguez J, Schirmer L.

Nat Neurosci, 2024

doi:10.1038/s41593-024-01796-z.

LIANA+ provides an all-in-one framework for cell-cell communication inference.

Dimitrov D, Schäfer PSL, Farr E, Rodriguez-Mier P, Lobentanzer S, Badia-I-Mompel P, Dugourd A, Tanevski J, Ramirez Flores RO, Saez-Rodriguez J.

Nat Cell Biol, 2024

doi:10.1038/s41556-024-01469-w.

Molecular causality in the advent of foundation models.

Lobentanzer S, Rodriguez-Mier P, Bauer S, Saez-Rodriguez J.

Mol Syst Biol, 2024

doi:10.1038/s44320-024-00041-w.

DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics.

Rahimi A, Vale-Silva LA, Fälth Savitski M, Tanevski J, Saez-Rodriguez J.

Nat Commun, 2024

doi:10.1038/s41467-024-48868-z.

Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition.

Burtscher ML, Gade S, Garrido-Rodriguez M, Rutkowska A, Werner T, Eberl HC, Petretich M, Knopf N, Zirngibl K, Grandi P, Bergamini G, Bantscheff M, Fälth-Savitski M, Saez-Rodriguez J.

Mol Syst Biol, 2024

doi:10.1038/s44320-024-00025-w.

Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease.

Ramirez Flores RO, Lanzer JD, Dimitrov D, Velten B, Saez-Rodriguez J.

Elife, 2023

doi:10.7554/elife.93161.

Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities.

Müller-Dott S, Tsirvouli E, Vazquez M, Ramirez Flores RO, Badia-I-Mompel P, Fallegger R, Türei D, Lægreid A, Saez-Rodriguez J.

Nucleic Acids Res, 2023

doi:10.1093/nar/gkad841.

Democratizing knowledge representation with BioCypher.

Lobentanzer S, Aloy P, Baumbach J, Bohar B, Carey VJ, Charoentong P, Danhauser K, Doğan T, Dreo J, Dunham I, Farr E, Fernandez-Torras A, Gyori BM, Hartung M, Hoyt CT, Klein C, Korcsmaros T, Maier A, Mann M, Ochoa D, Pareja-Lorente E, Popp F, Preusse M, Probul N, Schwikowski B, Sen B, Strauss MT, Turei D, Ulusoy E, Waltemath D, Wodke JAH, Saez-Rodriguez J.

Nat Biotechnol, 2023

doi:10.1038/s41587-023-01848-y.

Gene regulatory network inference in the era of single-cell multi-omics.

Badia-I-Mompel P, Wessels L, Müller-Dott S, Trimbour R, Ramirez Flores RO, Argelaguet R, Saez-Rodriguez J.

Nat Rev Genet, 2023

doi:10.1038/s41576-023-00618-5.