Publications
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, 43(2): 166-169
2025-02-01
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, 27(12): 2354-2365
Open Access2024-11-05
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, 26(9): 1613-1622
Open Access2024-09-02
Molecular causality in the advent of foundation models.
Lobentanzer S, Rodriguez-Mier P, Bauer S, Saez-Rodriguez J.•Mol Syst Biol, 20(8): 848-858
Open Access2024-06-18
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, 15(1): 4994
2024-06-11
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, 20(4): 458-474
Open Access2024-03-07
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, 12: e93161
Open Access2023-11-22
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, 51(20): 10934-10949
Open Access2023-11-01
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, 41(8): 1056-1059
2023-08-01
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, 24(11): 739-754
2023-06-26
Spatial multi-omic map of human myocardial infarction.
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
Open Access2022-08-10
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data.
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
Open Access2022-06-09
Explainable multiview framework for dissecting spatial relationships from highly multiplexed data.
Tanevski J, Flores ROR, Gabor A, Schapiro D, Saez-Rodriguez J.•Genome Biol, 23(1): 97
Open Access2022-04-14
Integrated intra- and intercellular signaling knowledge for multicellular omics analysis.
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
Open Access2021-03-01
Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses.
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
Open Access2021-01-01
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data.
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
Open Access2020-02-12
Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies.
Eduati F, Jaaks P, Wappler J, Cramer T, Merten CA, Garnett MJ, Saez-Rodriguez J.•Mol Syst Biol, 16(2): e8664
Open Access2020-02-01
Benchmark and integration of resources for the estimation of human transcription factor activities.
Garcia-Alonso L, Holland CH, Ibrahim MM, Turei D, Saez-Rodriguez J.•Genome Res, 29(8): 1363-1375
Open Access2019-07-24
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.
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
Open Access2019-06-17
Perturbation-response genes reveal signaling footprints in cancer gene expression.
Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ, Blüthgen N, Saez-Rodriguez J.•Nat Commun, 9(1): 20
Open Access2018-01-02
OmniPath: guidelines and gateway for literature-curated signaling pathway resources.
Türei D, Korcsmáros T, Saez-Rodriguez J.•Nat Methods, 13(12): 966-967
2016-11-01
A Landscape of Pharmacogenomic Interactions in Cancer.
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
Open Access2016-07-07
Inferring causal molecular networks: empirical assessment through a community-based effort.
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
Open Access2016-02-22