Publications
Comprehensive evaluation of phosphoproteomic-based kinase activity inference.
2025
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, 16(1): 4771
Learning tissue representation by identification of persistent local patterns in spatial omics data.
2025
Tanevski J, Vulliard L, Ibarra-Arellano MA, Schapiro D, Hartmann FJ, Saez-Rodriguez J.
Nat Commun, 16(1): 4071
A platform for the biomedical application of large language models.
2025
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, 43(2): 166-169
Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions.
2024
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, 27(12): 2354-2365
LIANA+ provides an all-in-one framework for cell-cell communication inference.
2024
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, 26(9): 1613-1622
Molecular causality in the advent of foundation models.
2024Review
Lobentanzer S, Rodriguez-Mier P, Bauer S, Saez-Rodriguez J.
Mol Syst Biol, 20(8): 848-858
DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics.
2024
Rahimi A, Vale-Silva LA, Fälth Savitski M, Tanevski J, Saez-Rodriguez J.
Nat Commun, 15(1): 4994
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition.
2024
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, 20(4): 458-474
Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease.
2023
Ramirez Flores RO, Lanzer JD, Dimitrov D, Velten B, Saez-Rodriguez J.
Elife, 12: e93161
Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities.
2023
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, 51(20): 10934-10949
Democratizing knowledge representation with BioCypher.
2023
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, 41(8): 1056-1059
Gene regulatory network inference in the era of single-cell multi-omics.
2023Review
Badia-I-Mompel P, Wessels L, Müller-Dott S, Trimbour R, Ramirez Flores RO, Argelaguet R, Saez-Rodriguez J.
Nat Rev Genet, 24(11): 739-754
Spatial multi-omic map of human myocardial infarction.
2022
Kuppe C, Ramirez Flores RO, Li Z, Hayat S, Levinson RT, Liao X, Hannani MT, Tanevski J, Wünnemann F, Nagai JS, Halder M, Schumacher D, Menzel S, Schäfer G, Hoeft K, Cheng M, Ziegler S, Zhang X, Peisker F, Kaesler N, Saritas T, Xu Y, Kassner A, Gummert J, Morshuis M, Amrute J, Veltrop RJA, Boor P, Klingel K, Van Laake LW, Vink A, Hoogenboezem RM, Bindels EMJ, Schurgers L, Sattler S, Schapiro D, Schneider RK, Lavine K, Milting H, Costa IG, Saez-Rodriguez J, Kramann R.
Nature, 608(7924): 766-777
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data.
2022
Dimitrov D, Türei D, Garrido-Rodriguez M, Burmedi PL, Nagai JS, Boys C, Ramirez Flores RO, Kim H, Szalai B, Costa IG, Valdeolivas A, Dugourd A, Saez-Rodriguez J.
Nat Commun, 13(1): 3224
Explainable multiview framework for dissecting spatial relationships from highly multiplexed data.
2022
Tanevski J, Flores ROR, Gabor A, Schapiro D, Saez-Rodriguez J.
Genome Biol, 23(1): 97
Integrated intra- and intercellular signaling knowledge for multicellular omics analysis.
2021
Türei D, Valdeolivas A, Gul L, Palacio-Escat N, Klein M, Ivanova O, Ölbei M, Gábor A, Theis F, Módos D, Korcsmáros T, Saez-Rodriguez J.
Mol Syst Biol, 17(3): e9923
Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses.
2021
Dugourd A, Kuppe C, Sciacovelli M, Gjerga E, Gabor A, Emdal KB, Vieira V, Bekker-Jensen DB, Kranz J, Bindels EMJ, Costa ASH, Sousa A, Beltrao P, Rocha M, Olsen JV, Frezza C, Kramann R, Saez-Rodriguez J.
Mol Syst Biol, 17(1): e9730
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data.
2020
Holland CH, Tanevski J, Perales-Patón J, Gleixner J, Kumar MP, Mereu E, Joughin BA, Stegle O, Lauffenburger DA, Heyn H, Szalai B, Saez-Rodriguez J.
Genome Biol, 21(1): 36
Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies.
2020
Eduati F, Jaaks P, Wappler J, Cramer T, Merten CA, Garnett MJ, Saez-Rodriguez J.
Mol Syst Biol, 16(2): e8664
Benchmark and integration of resources for the estimation of human transcription factor activities.
2019
Garcia-Alonso L, Holland CH, Ibrahim MM, Turei D, Saez-Rodriguez J.
Genome Res, 29(8): 1363-1375
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.
2019
Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, AstraZeneca-Sanger Drug Combination DREAM Consortium, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J.
Nat Commun, 10(1): 2674
Perturbation-response genes reveal signaling footprints in cancer gene expression.
2018
Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ, Blüthgen N, Saez-Rodriguez J.
Nat Commun, 9(1): 20
OmniPath: guidelines and gateway for literature-curated signaling pathway resources.
2016
Türei D, Korcsmáros T, Saez-Rodriguez J.
Nat Methods, 13(12): 966-967
A Landscape of Pharmacogenomic Interactions in Cancer.
2016
Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Sayols S, Soleimani M, Tamborero D, Lopez-Bigas N, Ross-Macdonald P, Esteller M, Gray NS, Haber DA, Stratton MR, Benes CH, Wessels LFA, Saez-Rodriguez J, McDermott U, Garnett MJ.
Cell, 166(3): 740-754
Inferring causal molecular networks: empirical assessment through a community-based effort.
2016
Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ, HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S.
Nat Methods, 13(4): 310-318